metadata: run_metadata: 9 rows where experiment.library_strategy = "OTHER", experiment.platform = "ILLUMINA" and tissue_curation

9 rows where experiment.library_strategy = "OTHER", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	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.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	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
32781	32781	SRR29411985	SRX24925451	SRS21630866	SRP513930	PRJNA1124008	Cell state transitions are decoupled from cell division during early embryo development [II]	GSE269848	Other	Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…		pubmed:37546736	24 38 hpf and 48 hpf tails	GSM8328864	source name:embryo tail\|tissue:embryo tail\|geo loc name:missing\|collection date:missing	24 38 hpf and 48 hpf tails	Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f…	embryo tail		Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		tissue:embryo tail	GSM8328864	GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER	GSM8328864 r1	GSM8328864	1	Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP513930	Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz	fastq fastq fastq fastq	58603546956.0	505202991.0	GSM8328864 r1	0:86 1:8 2:8 3:14	A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340	86	8	8	14	13191204330	9162028793	9431065581	11662090182	1068340	SRX24925451	SRS21630866	SRA1899240	Harvard University	Harvard University												B		usable mapping rate	illumina	novaseq_era	unknown	other	trueseq	sc	single_cell_droplet	indrops	United States	2024-06-14	Multi-stage	Embryo	Tail	Multi-system
32782	32782	SRR29411986	SRX24925451	SRS21630866	SRP513930	PRJNA1124008	Cell state transitions are decoupled from cell division during early embryo development [II]	GSE269848	Other	Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…		pubmed:37546736	24 38 hpf and 48 hpf tails	GSM8328864	source name:embryo tail\|tissue:embryo tail\|geo loc name:missing\|collection date:missing	24 38 hpf and 48 hpf tails	Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f…	embryo tail		Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		tissue:embryo tail	GSM8328864	GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER	GSM8328864 r1	GSM8328864	1	Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP513930	Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz	fastq fastq fastq fastq	44072422880.0	379934680.0	GSM8328864 r2	0:86 1:8 2:8 3:14	A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152	86	8	8	14	9919784228	6894965731	7094749745	8764100624	782152	SRX24925451	SRS21630866	SRA1899240	Harvard University	Harvard University												B		usable mapping rate	illumina	novaseq_era	unknown	other	trueseq	sc	single_cell_droplet	indrops	United States	2024-06-14	Multi-stage	Embryo	Tail	Multi-system
43987	43987	SRR6811828	SRX3768868	SRS3023414	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Pancreas 3 exo scar	GSM3032171	source name:Pancreas except primary islet liver\|strain/background:Zebrabow M\|tissue:Pancreas except primary islet liver\|developmental stage:Adult	Pancreas 3 exo scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Pancreas except primary islet liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas except primary islet liver\|developmental stage:Adult	GSM3032171	GSM3032171: Pancreas 3 exo scar; Danio rerio; OTHER	GSM3032171		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032171	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	P7exo_scar_R1.fastq.gz P7exo_scar_R2.fastq.gz	fastq fastq	4291410352.0	34608148.0	GSM3032171 r1	0:26 1:98	A:1266869162;C:1345773385;G:950601988;T:726078376;N:2087441	26	98			1266869162	1345773385	950601988	726078376	2087441	SRX3768868	SRS3023414	SRA623333	GEO	Max Delbrück Center	2	0.00014	0.00241	0.00012	0.00024	0.99995	0.99691	0.0	0.65306	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Multi-tissue	Multi-system
43989	43989	SRR6811826	SRX3768866	SRS3023382	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Heart 3 scar	GSM3032169	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 3 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM3032169	GSM3032169: Heart 3 scar; Danio rerio; OTHER	GSM3032169		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032169	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	H7_scar_R1.fastq.gz H7_scar_R2.fastq.gz	fastq fastq	3999397296.0	32253204.0	GSM3032169 r1	0:26 1:98	A:1170970784;C:1255843391;G:881154893;T:689473188;N:1955040	26	98			1170970784	1255843391	881154893	689473188	1955040	SRX3768866	SRS3023382	SRA623333	GEO	Max Delbrück Center	2	0.00018	0.00228	0.00015	0.00019	0.99991	0.99659	0.8	0.67235	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Multi-tissue	Multi-system
44008	44008	SRR6211484	SRX3320759	SRS2626332	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Heart 2 scar	GSM2830055	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 2 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM2830055	GSM2830055: Heart 2 scar; Danio rerio; OTHER	GSM2830055		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830055	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	H6_scar_R1.fastq.gz H6_scar_R2.fastq.gz	fastq fastq	2079107172.0	15065994.0	GSM2830055 r1	0:28 1:110	A:580640871;C:641740953;G:501505035;T:355092832;N:127481	28	110			580640871	641740953	501505035	355092832	127481	SRX3320759	SRS2626332	SRA623333	GEO	Max Delbrück Center	2	5e-05	0.00253	4e-05	0.00023	1.0	0.99778		0.58419	28	110	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44009	44009	SRR6211483	SRX3320758	SRS2626348	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Pancreas 2 scar	GSM2830054	source name:Pancreas and liver\|strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	Pancreas 2 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Pancreas and liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	GSM2830054	GSM2830054: Pancreas 2 scar; Danio rerio; OTHER	GSM2830054		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830054	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	P6_scar_R1.fastq.gz P6_scar_R2.fastq.gz	fastq fastq	1026715860.0	7439970.0	GSM2830054 r1	0:28 1:110	A:287816843;C:320879355;G:243598630;T:174359452;N:61580	28	110			287816843	320879355	243598630	174359452	61580	SRX3320758	SRS2626348	SRA623333	GEO	Max Delbrück Center	2	0.00029	0.00123	0.00028	6e-05	1.0	0.99914		0.25714	28	110	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44010	44010	SRR6211482	SRX3320757	SRS2626331	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Heart 1 scar	GSM2830053	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 1 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM2830053	GSM2830053: Heart 1 scar; Danio rerio; OTHER	GSM2830053		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830053	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	H5_scar_R1.fastq.gz H5_scar_R2.fastq.gz	fastq fastq	1287546624.0	10218624.0	GSM2830053 r1	0:26 1:100	A:365272675;C:413037677;G:296495693;T:212570153;N:170426	26	100			365272675	413037677	296495693	212570153	170426	SRX3320757	SRS2626331	SRA623333	GEO	Max Delbrück Center	2	0.00023	0.00044	0.00022	3e-05	1.0	0.99955		0.32653	26	100	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44012	44012	SRR6211480	SRX3320755	SRS2626329	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Pancreas 1 scar	GSM2830051	source name:Pancreas and liver\|strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	Pancreas 1 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Pancreas and liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	GSM2830051	GSM2830051: Pancreas 1 scar; Danio rerio; OTHER	GSM2830051		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830051	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	P5_scar_R1.fastq.gz P5_scar_R2.fastq.gz	fastq fastq	1192602600.0	9465100.0	GSM2830051 r1	0:26 1:100	A:346841760;C:383266222;G:268916933;T:193424756;N:152929	26	100			346841760	383266222	268916933	193424756	152929	SRX3320755	SRS2626329	SRA623333	GEO	Max Delbrück Center	2	0.00021	0.00091	0.00014	2e-05	0.99997	0.99892	0.0	0.23931	26	100	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
50874	50874	SRR8356798	SRX5167561	SRS4175446	SRP173971	PRJNA510841	Transcription factor induction of vascular blood stem cell niches in vivo [TOMO Seq]	GSE124150	Other	We report RNA tomography tomo seq gene expression data for the tail region of a 72 hpf zebrafish embryo. The portion of the tail containing the caudal hematopoietic tissue CHT was isolated by manual dissection snap froze and then cryosections 40 in total 8 µm thick were collected along the dorsal ventral axis. Each cryosection was placed into a tube and the RNA was exctracted and barcoded during a reverse trancription step prior to library synthesis and sequencing. Overall design: The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice. The RNA from individual cryosections was extracted using Trizol reagent and then barcoded during a reverse transcription step prior to library synthesis according to the previously published method Junker et al. 2014.	parent bioproject:PRJNA510836		Tomo seq zebrafish tail at 72 hpf	GSM3521717	source name:mpx:GFP transgenic zebrafish embryo wild type Casper background\|tissue:tail\|developmental stage:72 hpf	Tomo seq zebrafish tail at 72 hpf	Library strategy: RNA tomography tomo seq Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the Junker et al. 2014. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Mapping and demultiplexing were done as described in Grün et al. Validation of noise models for single cell transcriptomics Nature Methods 2014. The script needed to process the data is available in https://www.dropbox.com/sh/7s59vvocwtn2ct4/AAAR6pWte8xOzObCYONAFPvIa?dl=0 where script tomo.sh is an example for how to run the mapping scripts. Genome build: zv9	mpx:GFP transgenic zebrafish embryo wild type Casper background	No treatment	The total RNA from individual cryosections 40 in total each 8 µm thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014.	mpx:GFP transgenic zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then euthanized by tricaine overdose. The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice.	tissue:tail\|developmental stage:72 hpf	GSM3521717	GSM3521717: Tomo seq zebrafish tail at 72 hpf; Danio rerio; OTHER	GSM3521717		1	The total RNA from individual cryosections 40 in total each 8 µm thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014.	GEO Accession:GSM3521717	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP173971			3762222874.0	24959737.0	GSM3521717 r1	0:75.36 1:75.37	A:1160852277;C:485683733;G:556965887;T:1558649449;N:71528	75	75			1160852277	485683733	556965887	1558649449	71528	SRX5167561	SRS4175446	SRA825234	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.20644	0.76788	0.14917	0.11551	0.98169	0.8382	0.50072	0.52728	76	76	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	other	unknown	sc	single_cell_plate	celseq	United States	2018-12-19	Larval	Larval	Tail	Multi-system

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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");;