metadata: run_metadata: 7 rows where devstage_curation = "Blastula" and experiment.library

7 rows where devstage_curation = "Blastula" and experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL"

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.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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.r2_length	run.r3_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
60662	60662	SRR12474621	SRX8968761	SRS7224498	SRP278034	PRJNA657343	Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development	PRJNA657343	Other	Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.			scRNAseq FLAG SATB2	scRNAseq FLAG SATB2 dome	strain:TU\|isolate:Satb2 OE\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:4.5 hpf\|dev stage:Dome\|sex:not applicable\|tissue:whole embryo\|Replicate:replicate=FLAG SATB2 dome\|BioSampleModel:Model organism or animal								scRNAseq FLAG SATB2	scRNAseq FLAG SATB2 dome	scRNAseq FLAG SATB2 dome	10x chromium 3 mRNA		OTHER	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP278034	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=scRNAseq FLAG SATB2 dome I1 sorted.fastq read2PairFiles=scRNAseq FLAG SATB2 dome R1 sorted.fastq read3PairFiles=scRNAseq FLAG SATB2 dome R2 sorted.fastq	scRNAseq_FLAG_SATB2_dome_I1_sorted.fastq scRNAseq_FLAG_SATB2_dome_R1_sorted.fastq scRNAseq_FLAG_SATB2_dome_R2_sorted.fastq	fastq fastq fastq	47518418346.0	340198768.0	scRNAseq FLAG SATB2 dome I1.fastq.gz	0:8 1:30.68 2:101	A:13016292601;C:10075463201;G:10532642161;T:13868229463;N:25790920	8	30	101	13016292601	10075463201	10532642161	13868229463	25790920	SRX8968761	SRS7224498	SRA1114017	IISER-PUNE\|biology	IISER-PUNE	1	0.92339	0.12479	0.81485	0.52987	101	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2020-09-01	Blastula	Embryo	Whole Organism	All anatomical structures
74109	74109	SRR23380804	SRX19321395	SRS16719694	SRP422528	PRJNA934545	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]	GSE224918	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo zfs:0000015 NT replicate B scRNAseq	GSM7035740	source name:zebrafish embryo\|tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:NT\|geo loc name:missing\|collection date:missing	zebrafish embryo zfs:0000015 NT replicate B scRNAseq	Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo	20mM 4sUTP injection at 1 cell stage	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:NT	GSM7035740	GSM7035740: zebrafish embryo zfs:0000015 NT replicate B scRNAseq; Danio rerio; RNA Seq	GSM7035740 r1	GSM7035740	1	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	loader:fastq load.py	B07_S7_I1_001.fastq.gz B07_S7_R1_001.fastq.gz B07_S7_R2_001.fastq.gz	fastq fastq fastq	5107507608.0	30401831.0	GSM7035740 r1	0:8 1:20 2:140	A:1271612661;C:768251429;G:1315055363;T:901018360;N:318527	8	20	140	1271612661	768251429	1315055363	901018360	318527	SRX19321395	SRS16719694	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.6633	0.0322	0.86898	0.73112	140	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74110	74110	SRR23380805	SRX19321394	SRS16719693	SRP422528	PRJNA934545	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]	GSE224918	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo zfs:0000015 IAA replicate B scRNAseq	GSM7035739	source name:zebrafish embryo\|tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:IAA\|geo loc name:missing\|collection date:missing	zebrafish embryo zfs:0000015 IAA replicate B scRNAseq	Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo	20mM 4sUTP injection at 1 cell stage	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:IAA	GSM7035739	GSM7035739: zebrafish embryo zfs:0000015 IAA replicate B scRNAseq; Danio rerio; RNA Seq	GSM7035739 r1	GSM7035739	1	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	loader:fastq load.py	B08_S8_R2_001.fastq.gz B08_S8_R1_001.fastq.gz B08_S8_I1_001.fastq.gz	fastq fastq fastq	6618266424.0	39394443.0	GSM7035739 r1	0:8 1:20 2:140	A:1772472371;C:1058335373;G:1382074511;T:1301941080;N:398685	8	20	140	1772472371	1058335373	1382074511	1301941080	398685	SRX19321394	SRS16719693	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.66052	0.03428	0.84902	0.4999	140	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74111	74111	SRR23380806	SRX19321393	SRS16719692	SRP422528	PRJNA934545	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]	GSE224918	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo zfs:0000015 NT replicate A scRNAseq	GSM7035738	source name:zebrafish embryo\|tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:NT\|geo loc name:missing\|collection date:missing	zebrafish embryo zfs:0000015 NT replicate A scRNAseq	Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo	20mM 4sUTP injection at 1 cell stage	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:NT	GSM7035738	GSM7035738: zebrafish embryo zfs:0000015 NT replicate A scRNAseq; Danio rerio; RNA Seq	GSM7035738 r1	GSM7035738	1	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	loader:fastq load.py	B01_S1_I1_001.fastq.gz B01_S1_R1_001.fastq.gz B01_S1_R2_001.fastq.gz	fastq fastq fastq	2465114064.0	14673298.0	GSM7035738 r1	0:8 1:20 2:140	A:682033408;C:384987859;G:496372763;T:490717526;N:150164	8	20	140	682033408	384987859	496372763	490717526	150164	SRX19321393	SRS16719692	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.83566	0.03718	0.85021	0.68773	140	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74112	74112	SRR23380807	SRX19321392	SRS16719691	SRP422528	PRJNA934545	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]	GSE224918	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo zfs:0000015 IAA replicate A scRNAseq	GSM7035737	source name:zebrafish embryo\|tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:IAA\|geo loc name:missing\|collection date:missing	zebrafish embryo zfs:0000015 IAA replicate A scRNAseq	Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo	20mM 4sUTP injection at 1 cell stage	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	tissue:zebrafish embryo\|developmental stage:zfs:0000015\|strain:AB/TL\|treatment:IAA	GSM7035737	GSM7035737: zebrafish embryo zfs:0000015 IAA replicate A scRNAseq; Danio rerio; RNA Seq	GSM7035737 r1	GSM7035737	1	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	loader:fastq load.py	B02_S2_I1_001.fastq.gz B02_S2_R1_001.fastq.gz B02_S2_R2_001.fastq.gz	fastq fastq fastq	12337001376.0	73434532.0	GSM7035737 r1	0:8 1:20 2:140	A:3313181087;C:1943751072;G:2424458605;T:2598692748;N:750968	8	20	140	3313181087	1943751072	2424458605	2598692748	750968	SRX19321392	SRS16719691	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.73328	0.03858	0.84045	0.49156	140	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74113	74113	SRR23380808	SRX19321391	SRS16719689	SRP422528	PRJNA934545	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]	GSE224918	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo Dome NT replicate B scRNAseq	GSM7035736	source name:zebrafish embryo\|tissue:zebrafish embryo\|developmental stage:Dome\|strain:AB/TL\|treatment:NT\|geo loc name:missing\|collection date:missing	zebrafish embryo Dome NT replicate B scRNAseq	Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo	20mM 4sUTP injection at 1 cell stage	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	tissue:zebrafish embryo\|developmental stage:Dome\|strain:AB/TL\|treatment:NT	GSM7035736	GSM7035736: zebrafish embryo Dome NT replicate B scRNAseq; Danio rerio; RNA Seq	GSM7035736 r1	GSM7035736	1	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	loader:fastq load.py	B05_S5_I1_001.fastq.gz B05_S5_R1_001.fastq.gz B05_S5_R2_001.fastq.gz	fastq fastq fastq	8803995984.0	52404738.0	GSM7035736 r1	0:8 1:20 2:140	A:2610393348;C:1221729748;G:1971221134;T:1532772530;N:546560	8	20	140	2610393348	1221729748	1971221134	1532772530	546560	SRX19321391	SRS16719689	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.6884	0.03585	0.86423	0.72819	140	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74114	74114	SRR23380809	SRX19321390	SRS16719690	SRP422528	PRJNA934545	A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]	GSE224918	Other	During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates	parent bioproject:PRJNA933118	pubmed:37131717;pubmed:38600066	zebrafish embryo Dome IAA replicate B scRNAseq	GSM7035735	source name:zebrafish embryo\|tissue:zebrafish embryo\|developmental stage:Dome\|strain:AB/TL\|treatment:IAA\|geo loc name:missing\|collection date:missing	zebrafish embryo Dome IAA replicate B scRNAseq	Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files	zebrafish embryo	20mM 4sUTP injection at 1 cell stage	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	tissue:zebrafish embryo\|developmental stage:Dome\|strain:AB/TL\|treatment:IAA	GSM7035735	GSM7035735: zebrafish embryo Dome IAA replicate B scRNAseq; Danio rerio; RNA Seq	GSM7035735 r1	GSM7035735	1	Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	loader:fastq load.py	B06_S6_I1_001.fastq.gz B06_S6_R1_001.fastq.gz B06_S6_R2_001.fastq.gz	fastq fastq fastq	21140863800.0	125838475.0	GSM7035735 r1	0:8 1:20 2:140	A:6033328114;C:2907546987;G:4997520100;T:3677695966;N:1295333	8	20	140	6033328114	2907546987	4997520100	3677695966	1295333	SRX19321390	SRS16719690	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.54964	0.01991	0.86539	0.48683	140	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	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");;