metadata: run_metadata: 51 rows where devstage_curation = "Pharyngula" and technology = "indrops"

51 rows where devstage_curation = "Pharyngula" and technology = "indrops"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
47776	47776	SRR6890896	SRX3841329	SRS3087489	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 5	GSM3067200	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 5	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067200	GSM3067200: TracerSeq Embryo 5; Danio rerio; RNA Seq	GSM3067200	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW167.fastq.gz	fastq	811220746.0	14099347.0	GSM3067200 r1	0:57.54	A:226775040;C:163877565;G:173170450;T:247395403;N:2288	57	226775040	163877565	173170450	247395403	2288	SRX3841329	SRS3087489	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88233	0.12759	0.79082	0.51035	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47777	47777	SRR6890897	SRX3841329	SRS3087489	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 5	GSM3067200	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 5	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067200	GSM3067200: TracerSeq Embryo 5; Danio rerio; RNA Seq	GSM3067200	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW168.fastq.gz	fastq	824982674.0	14331143.0	GSM3067200 r2	0:57.57	A:231177547;C:167432521;G:176426897;T:249943460;N:2249	57	231177547	167432521	176426897	249943460	2249	SRX3841329	SRS3087489	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88583	0.12411	0.79277	0.52031	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47778	47778	SRR6890898	SRX3841329	SRS3087489	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 5	GSM3067200	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 5	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067200	GSM3067200: TracerSeq Embryo 5; Danio rerio; RNA Seq	GSM3067200	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW169.fastq.gz	fastq	693186309.0	12065222.0	GSM3067200 r3	0:57.45	A:197516210;C:138205483;G:144601216;T:212861628;N:1772	57	197516210	138205483	144601216	212861628	1772	SRX3841329	SRS3087489	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.86621	0.12722	0.78823	0.51859	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47779	47779	SRR11699740	SRX3841329	SRS3087489	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 5	GSM3067200	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 5	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067200	GSM3067200: TracerSeq Embryo 5; Danio rerio; RNA Seq	GSM3067200	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW167.gfp.fastq.gz	fastq	637401493.0	11247658.0	GSM3067200 r11	0:56.67	A:211763567;C:130934906;G:157778746;T:136920350;N:3924	56	211763567	130934906	157778746	136920350	3924	SRX3841329	SRS3087489	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00818	0.0001	0.99902	0.79816	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47780	47780	SRR11699741	SRX3841329	SRS3087489	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 5	GSM3067200	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 5	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067200	GSM3067200: TracerSeq Embryo 5; Danio rerio; RNA Seq	GSM3067200	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW168.gfp.fastq.gz	fastq	648934432.0	11464121.0	GSM3067200 r12	0:56.61	A:211915696;C:134836103;G:161336635;T:140841785;N:4213	56	211915696	134836103	161336635	140841785	4213	SRX3841329	SRS3087489	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.0103	0.00018	0.99853	0.78199	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47781	47781	SRR11699742	SRX3841329	SRS3087489	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 5	GSM3067200	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 5	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067200	GSM3067200: TracerSeq Embryo 5; Danio rerio; RNA Seq	GSM3067200	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW169.gfp.fastq.gz	fastq	555982541.0	9807444.0	GSM3067200 r13	0:56.69	A:182949392;C:115632932;G:137856329;T:119540249;N:3639	56	182949392	115632932	137856329	119540249	3639	SRX3841329	SRS3087489	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.01235	0.00032	0.99868	0.81431	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47782	47782	SRR6890891	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW162.fastq.gz	fastq	884280521.0	15352773.0	GSM3067199 r1	0:57.60	A:248995548;C:176713956;G:184425201;T:274143441;N:2375	57	248995548	176713956	184425201	274143441	2375	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.87729	0.1278	0.77904	0.51481	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47783	47783	SRR6890892	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW163.fastq.gz	fastq	952171001.0	16579450.0	GSM3067199 r2	0:57.43	A:269068875;C:192967485;G:199258236;T:290873928;N:2477	57	269068875	192967485	199258236	290873928	2477	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.86963	0.12299	0.78261	0.51621	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47784	47784	SRR6890893	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW164.fastq.gz	fastq	1133026695.0	19698928.0	GSM3067199 r3	0:57.52	A:320544827;C:227286162;G:235085716;T:350106942;N:3048	57	320544827	227286162	235085716	350106942	3048	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.87678	0.12527	0.78169	0.50623	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47785	47785	SRR6890894	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW165.fastq.gz	fastq	793581204.0	13818281.0	GSM3067199 r4	0:57.43	A:223975396;C:158365631;G:165125978;T:246112109;N:2090	57	223975396	158365631	165125978	246112109	2090	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.87803	0.12874	0.78374	0.50983	44	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47786	47786	SRR6890895	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW166.fastq.gz	fastq	792728001.0	13800321.0	GSM3067199 r5	0:57.44	A:225238995;C:161675115;G:167314732;T:238497072;N:2087	57	225238995	161675115	167314732	238497072	2087	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.87776	0.11531	0.79458	0.53005	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47787	47787	SRR11699735	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW162.gfp.fastq.gz	fastq	725258705.0	12804354.0	GSM3067199 r11	0:56.64	A:244821707;C:144850405;G:178149916;T:157432024;N:4653	56	244821707	144850405	178149916	157432024	4653	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00953	0.00045	0.99874	0.84025	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47788	47788	SRR11699736	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW163.gfp.fastq.gz	fastq	709146800.0	12584798.0	GSM3067199 r12	0:56.35	A:239870182;C:143213119;G:172165989;T:153892922;N:4588	56	239870182	143213119	172165989	153892922	4588	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00541	0.00022	0.99888	0.84231	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47789	47789	SRR11699737	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW164.gfp.fastq.gz	fastq	648001757.0	11476883.0	GSM3067199 r13	0:56.46	A:220229172;C:129764679;G:155857424;T:142146491;N:3991	56	220229172	129764679	155857424	142146491	3991	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00638	0.00028	0.999	0.82363	53	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47790	47790	SRR11699738	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW165.gfp.fastq.gz	fastq	596792506.0	10531209.0	GSM3067199 r14	0:56.67	A:200618246;C:122094142;G:144891967;T:129184490;N:3661	56	200618246	122094142	144891967	129184490	3661	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00789	0.00046	0.99888	0.84071	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47791	47791	SRR11699739	SRX3841328	SRS3087488	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 4	GSM3067199	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 4	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067199	GSM3067199: TracerSeq Embryo 4; Danio rerio; RNA Seq	GSM3067199	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW166.gfp.fastq.gz	fastq	566854985.0	10065909.0	GSM3067199 r15	0:56.31	A:192383179;C:111486159;G:139172733;T:123809364;N:3550	56	192383179	111486159	139172733	123809364	3550	SRX3841328	SRS3087488	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00671	0.00038	0.99886	0.85738	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47792	47792	SRR6890887	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW158.fastq.gz	fastq	965976032.0	16779564.0	GSM3067198 r1	0:57.57	A:270793370;C:196343924;G:207973938;T:290862136;N:2664	57	270793370	196343924	207973938	290862136	2664	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88031	0.11243	0.7919	0.51366	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47793	47793	SRR6890888	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW159.fastq.gz	fastq	1015306225.0	17632016.0	GSM3067198 r2	0:57.58	A:282554762;C:206663548;G:220061729;T:306023342;N:2844	57	282554762	206663548	220061729	306023342	2844	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88781	0.11491	0.79251	0.51135	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47794	47794	SRR6890889	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW160.fastq.gz	fastq	958415543.0	16704238.0	GSM3067198 r3	0:57.38	A:267638469;C:191936701;G:204743895;T:294094008;N:2470	57	267638469	191936701	204743895	294094008	2470	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.87973	0.12017	0.78922	0.48734	34	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47795	47795	SRR6890890	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW161.fastq.gz	fastq	911486560.0	15853985.0	GSM3067198 r4	0:57.49	A:254067794;C:182351617;G:196560408;T:278504296;N:2445	57	254067794	182351617	196560408	278504296	2445	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88691	0.12363	0.78435	0.50693	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47796	47796	SRR11699731	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW158.gfp.fastq.gz	fastq	714356770.0	12690001.0	GSM3067198 r11	0:56.29	A:238801241;C:146515701;G:173416188;T:155618953;N:4687	56	238801241	146515701	173416188	155618953	4687	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00355	0.00025	0.99902	0.70542	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47797	47797	SRR11699732	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW159.gfp.fastq.gz	fastq	692190367.0	12308538.0	GSM3067198 r12	0:56.24	A:231865817;C:139854334;G:169105319;T:151360408;N:4489	56	231865817	139854334	169105319	151360408	4489	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00277	0.00018	0.99931	0.70414	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47798	47798	SRR11699733	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW160.gfp.fastq.gz	fastq	713049432.0	12694194.0	GSM3067198 r13	0:56.17	A:239502412;C:145346774;G:172186875;T:156008904;N:4467	56	239502412	145346774	172186875	156008904	4467	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00331	0.00023	0.9991	0.70743	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47799	47799	SRR11699734	SRX3841327	SRS3087487	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 3	GSM3067198	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 3	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067198	GSM3067198: TracerSeq Embryo 3; Danio rerio; RNA Seq	GSM3067198	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW161.gfp.fastq.gz	fastq	753741455.0	13357439.0	GSM3067198 r14	0:56.43	A:251557444;C:154340741;G:181807551;T:166030917;N:4802	56	251557444	154340741	181807551	166030917	4802	SRX3841327	SRS3087487	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.0034	0.00026	0.99924	0.74673	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47800	47800	SRR6890881	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW105.fastq.gz	fastq	2236392658.0	38613668.0	GSM3067197 r1	0:57.92	A:632525539;C:430906734;G:458150451;T:714800928;N:9006	57	632525539	430906734	458150451	714800928	9006	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88225	0.11769	0.77895	0.49448	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47801	47801	SRR6890882	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW106.fastq.gz	fastq	2231823587.0	38523508.0	GSM3067197 r2	0:57.93	A:630838902;C:434227222;G:457362069;T:709386360;N:9034	57	630838902	434227222	457362069	709386360	9034	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88583	0.11501	0.78171	0.51228	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47802	47802	SRR6890883	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW107.fastq.gz	fastq	2017895917.0	34862336.0	GSM3067197 r3	0:57.88	A:571926612;C:389743099;G:413210412;T:643007658;N:8136	57	571926612	389743099	413210412	643007658	8136	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88214	0.11984	0.78234	0.5107	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47803	47803	SRR6890884	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW108.fastq.gz	fastq	2137179290.0	36984331.0	GSM3067197 r4									SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47804	47804	SRR6890885	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW109.fastq.gz	fastq	1732824461.0	29964040.0	GSM3067197 r5	0:57.83	A:488970094;C:337910710;G:363385259;T:542551597;N:6801	57	488970094	337910710	363385259	542551597	6801	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88484	0.11274	0.78782	0.52053	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47805	47805	SRR6890886	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW110.fastq.gz	fastq	1869184778.0	32270092.0	GSM3067197 r6	0:57.92	A:523455278;C:363490974;G:393498418;T:588732594;N:7514	57	523455278	363490974	393498418	588732594	7514	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.89075	0.11527	0.78435	0.516	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47806	47806	SRR11699725	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW105.gfp.fastq.gz	fastq	864508154.0	15268405.0	GSM3067197 r11	0:56.62	A:280405131;C:177118247;G:209076103;T:197907076;N:1597	56	280405131	177118247	209076103	197907076	1597	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00246	0.00014	0.99945	0.57366	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47807	47807	SRR11699726	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW106.gfp.fastq.gz	fastq	1836795274.0	32436891.0	GSM3067197 r12	0:56.63	A:598413910;C:375443322;G:442230080;T:420704508;N:3454	56	598413910	375443322	442230080	420704508	3454	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00339	0.00022	0.99904	0.81609	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47808	47808	SRR11699727	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW107.gfp.fastq.gz	fastq	1098090093.0	19584542.0	GSM3067197 r13	0:56.07	A:358936332;C:225531082;G:265165807;T:248454887;N:1985	56	358936332	225531082	265165807	248454887	1985	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00394	0.00027	0.99924	0.79207	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47809	47809	SRR11699728	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW108.gfp.fastq.gz	fastq	973690024.0	17208640.0	GSM3067197 r14	0:56.58	A:315592395;C:202218220;G:234572367;T:221305217;N:1825	56	315592395	202218220	234572367	221305217	1825	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00289	0.00018	0.99943	0.77946	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47810	47810	SRR11699729	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW109.gfp.fastq.gz	fastq	860964317.0	15239252.0	GSM3067197 r15	0:56.50	A:280154617;C:178242732;G:206646971;T:195918375;N:1622	56	280154617	178242732	206646971	195918375	1622	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.0029	0.00016	0.9992	0.8034	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47811	47811	SRR11699730	SRX3841326	SRS3087486	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 2	GSM3067197	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 2	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067197	GSM3067197: TracerSeq Embryo 2; Danio rerio; RNA Seq	GSM3067197	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW110.gfp.fastq.gz	fastq	353310699.0	6684362.0	GSM3067197 r16	0:52.86	A:116163854;C:71721845;G:85203701;T:80220874;N:425	52	116163854	71721845	85203701	80220874	425	SRX3841326	SRS3087486	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00187	0.00013	0.99959	0.84967	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47812	47812	SRR6890877	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW101.fastq.gz	fastq	2986488041.0	51575075.0	GSM3067196 r1	0:57.91	A:848651747;C:586829293;G:609184887;T:941810264;N:11850	57	848651747	586829293	609184887	941810264	11850	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88677	0.11046	0.7905	0.53466	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47813	47813	SRR6890878	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW102.fastq.gz	fastq	2367681335.0	40881016.0	GSM3067196 r2	0:57.92	A:671355626;C:465619829;G:484744401;T:745951960;N:9519	57	671355626	465619829	484744401	745951960	9519	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.8812	0.10473	0.78884	0.51963	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47814	47814	SRR6890879	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW103.fastq.gz	fastq	2331578063.0	40348694.0	GSM3067196 r3	0:57.79	A:661550584;C:462384104;G:479423343;T:728210706;N:9326	57	661550584	462384104	479423343	728210706	9326	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88193	0.10461	0.78839	0.52362	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47815	47815	SRR6890880	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW104.fastq.gz	fastq	2049500633.0	35395333.0	GSM3067196 r4	0:57.90	A:579583630;C:404370534;G:423144188;T:642394171;N:8110	57	579583630	404370534	423144188	642394171	8110	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.88736	0.10152	0.78727	0.49826	61	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47816	47816	SRR11699721	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW101.gfp.fastq.gz	fastq	770401542.0	13588300.0	GSM3067196 r11	0:56.70	A:252451711;C:161581601;G:188319243;T:168047500;N:1487	56	252451711	161581601	188319243	168047500	1487	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00572	0.00021	0.99912	0.78671	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47817	47817	SRR11699722	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW102.gfp.fastq.gz	fastq	930082189.0	16450240.0	GSM3067196 r12	0:56.54	A:307009540;C:193290503;G:225634898;T:204145591;N:1657	56	307009540	193290503	225634898	204145591	1657	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00499	0.00023	0.99908	0.82519	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47818	47818	SRR11699723	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW103.gfp.fastq.gz	fastq	1127167312.0	19917784.0	GSM3067196 r13	0:56.59	A:373217299;C:236443835;G:273368582;T:244135449;N:2147	56	373217299	236443835	273368582	244135449	2147	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.00429	0.00014	0.99922	0.82	60	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47819	47819	SRR11699724	SRX3841325	SRS3087485	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	TracerSeq Embryo 1	GSM3067196	tissue:Zebrafish Embryo Dissociated Cells\|strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	TracerSeq Embryo 1	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:AB\|developmental stage:24hpf\|treatment:embryos injected with TracerSeq library and Tol2 transposase mRNA at xxx cell stage\|genotype:wild type	GSM3067196	GSM3067196: TracerSeq Embryo 1; Danio rerio; RNA Seq	GSM3067196	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName	DEW104.gfp.fastq.gz	fastq	975575896.0	17282185.0	GSM3067196 r14	0:56.45	A:321010798;C:205573092;G:237075384;T:211914717;N:1905	56	321010798	205573092	237075384	211914717	1905	SRX3841325	SRS3087485	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.0035	8e-05	0.99924	0.83208	61	T	under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47820	47820	SRR6890870	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW021.fastq.gz	fastq	2019482704.0	60636489.0	GSM3067195 r1	0:33.30	A:493417632;C:419033159;G:432871824;T:674158736;N:1353	33	493417632	419033159	432871824	674158736	1353	SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.82488	0.11082	0.78522	0.51753	34	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47821	47821	SRR6890871	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW052.fastq.gz	fastq	1757215612.0	52765096.0	GSM3067195 r2	0:33.30	A:441169837;C:344094059;G:363706881;T:608242069;N:2766	33	441169837	344094059	363706881	608242069	2766	SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.83362	0.12368	0.78553	0.52928	33	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47822	47822	SRR6890872	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW053.fastq.gz	fastq	1821864281.0	54670237.0	GSM3067195 r3									SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.82644	0.12187	0.78784	0.52385	33	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47823	47823	SRR6890873	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW054.fastq.gz	fastq	1678567945.0	50389624.0	GSM3067195 r4	0:33.31	A:409485468;C:338736084;G:352566121;T:577777533;N:2739	33	409485468	338736084	352566121	577777533	2739	SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.84082	0.12109	0.78744	0.5204	33	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47824	47824	SRR6890874	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW055.fastq.gz	fastq	1767167982.0	53040354.0	GSM3067195 r5	0:33.32	A:434649073;C:352847211;G:367753051;T:611915672;N:2975	33	434649073	352847211	367753051	611915672	2975	SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.83659	0.12547	0.78626	0.51721	31	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47825	47825	SRR6890875	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW056.fastq.gz	fastq	1848811670.0	55500253.0	GSM3067195 r6	0:33.31	A:454979688;C:370746083;G:384432449;T:638650390;N:3060	33	454979688	370746083	384432449	638650390	3060	SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.83588	0.12238	0.78723	0.51497	34	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
47826	47826	SRR6890876	SRX3841324	SRS3087484	SRP136369	PRJNA445487	Systematic mapping of cell state trajectories cell lineage and perturbations in the zebrafish embryo using single cell transcriptomics	GSE112294	Transcriptome Analysis	High throughput mapping of cellular differentiation hierarchies from single cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single cell RNA sequencing to >92 000 cells from zebrafish embryos during the first day of development. Using a graph based approach we mapped a cell state landscape that describes axis patterning germ layer formation and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon based barcoding approach “TracerSeq” for reconstructing single cell lineage histories. Clonally related cells were often restricted by the state landscape including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin deficient embryos. We provide web based resources for further analysis of the single cell data. Overall design: Single cell mRNA sequencing of zebrafish embryonic cells. Samples1 7: Single cell libraries from untreated embryos 4 hpf 24 hpf Samples8 12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1 cell stage. Samples13 18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1 cell stage.	pubmed:29700229	Zebrafish Embryos 24hpf	GSM3067195	tissue:Zebrafish Embryo Dissociated Cells\|strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	Zebrafish Embryos 24hpf	inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Each sequencing spot is associated with a single biological read and 1 3 technical reads depending on the specific inDrops library preparation chemistry used. FASTQs DEW001 DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read. DEW010 DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read. DEW101 208 used V3 chemistry in which read1 is the biological read read2 carries the first half of the cell barcode read3 carries the library index and read4 carries the second half of the cell barcode and the UMI. Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 "Identify abundant barcodes" see https://github.com/indrops/. Each cDNA read was trimmed using Trimomatic version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16. Cell specific barcodes for each cDNA read were then matched against a set of pre determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded. cDNA reads were then aligned to a zebrafish transcriptome using Bowtie version 1.1.1 parameters: n 1 l 15 e 200 m 200 best strata a. The reference transcriptome was built from the zebrafish GRCz10 genome assembly Accesion: GCF 000002035.5.Mapped reads were then processed into counts of UMI filtered transcripts per gene. UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode and thresholding only the top 95% of the largest and oft…	Zebrafish Embryo Dissociated Cells	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	strain:TU\|developmental stage:24hpf\|treatment:untreated embryos\|genotype:wild type	GSM3067195	GSM3067195: Zebrafish Embryos 24hpf; Danio rerio; RNA Seq	GSM3067195	1	Zebrafish embryos were incubated to the indicated times post fertilization and chorions were removed by incubating in 1mg/mL Pronase Sigma P5147 1G for 3 4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl 2.1 mM KCl 1.2 mM MgSO4 1.8 mM CaNO32 15 mM HEPES pH 7.6]. Dissociation of embryonic tissues was performed similarly as previously described Manoli & Driever Cold Spring Harbor Protocols 2012 with the following specifications. Wild type and CRISPR targeted samples were each prepared from 20 100 embryos. Embryo tissues were triturated to homogeneity in 1 5mL FACSmax cell dissociation solution Genlantis T200100 and incubated for 4 5 minutes at room temperature. Cells were then filtered through a 40μm cell strainer mesh Fisher 352340 and centrifuged in a swinging bucket rotor at 310g for 5 minutes. Cell pellets were resuspended in 1X DPBS no Ca/Mg Life Technologies 14190 144 containing 1% BSA Sigma A3311 100G and subjected to 2 3 additional rounds of centrifugation and resuspension. post washing cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium Sigma D1556 250ML. Cell density was quantified manually using INCYTO™ C Chip™ Disposable Hemacytometers Fisher 22 600 100 and adjusted to 100 000 cells per mL. For single embryo dissociations all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes Eppendorf 022431005 that had been pre coated with 10% BSA/DPBS for 15 minutes at room temperature. Single cell transcriptomes were then barcoded using the inDrops platform as previously described Zilionis et al. Nature Protocols 2017. Following the within droplet reverse transcription step emulsions were split into batches of approximately 1 000 2 000 cells frozen at 80C and subsequently processed as individual RNA seq libraries. Single cell RNA Seq libraries were prepared using a protocol customized for the inDrops platform see Zilionis et al. Nature Protocols 2017	GEO Accession:GSM3067195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP136369	loader:fastq load.py\|options: appendBCtoName platform=Illumina	DEW057.fastq.gz	fastq	1748505537.0	52490191.0	GSM3067195 r7	0:33.31	A:445047455;C:338487369;G:357051616;T:607916307;N:2790	33	445047455	338487369	357051616	607916307	2790	SRX3841324	SRS3087484	SRA672434	GEO	Systems Biology, Harvard Medical School	1	0.82436	0.11709	0.79192	0.50453	33	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2018-03-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;