metadata: run_metadata: 21 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation

21 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation_coarse = "Undetermined"

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.growthprotocol	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.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
30662	30662	SRR28125659	SRX23770350	SRS20595835	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …		adult thy untreated	GSM8115869	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy untreated	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115869	GSM8115869: adult thy untreated; Danio rerio; RNA Seq	GSM8115869 r1	GSM8115869	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_untreated_S5_L001_R2_001.fastq.gz adult_thy_untreated_S5_L001_R1_001.fastq.gz adult_thy_untreated_S5_L001_I1_001.fastq.gz	fastq fastq fastq	61867658967.0	487146921.0	GSM8115869 r1	0:8 1:28 2:91	A:12933400034;C:9373762639;G:10188374364;T:11834295354;N:537420	8	28	91	12933400034	9373762639	10188374364	11834295354	537420	SRX23770350	SRS20595835			Oncology/Hematology, Boston Children's Hospital	1	0.90847		0.19603		0.76895		0.56494		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
30663	30663	SRR28125660	SRX23770349	SRS20595836	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …		adult thy liberase 2	GSM8115868	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115868	GSM8115868: adult thy liberase 2; Danio rerio; RNA Seq	GSM8115868 r1	GSM8115868	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_liberase_2_S7_L001_I1_001.fastq.gz adult_thy_liberase_2_S7_L001_R1_001.fastq.gz adult_thy_liberase_2_S7_L001_R2_001.fastq.gz	fastq fastq fastq	64816880653.0	510369139.0	GSM8115868 r1	0:8 1:28 2:91	A:12985717325;C:10400471721;G:10926930853;T:12129907262;N:564488	8	28	91	12985717325	10400471721	10926930853	12129907262	564488	SRX23770349	SRS20595836			Oncology/Hematology, Boston Children's Hospital	1	0.90014		0.13619		0.81103		0.54906		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
30664	30664	SRR28125661	SRX23770348	SRS20595834	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …		adult thy liberase 1	GSM8115867	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115867	GSM8115867: adult thy liberase 1; Danio rerio; RNA Seq	GSM8115867 r1	GSM8115867	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_liberase_1_S6_L001_I1_001.fastq.gz adult_thy_liberase_1_S6_L001_R1_001.fastq.gz adult_thy_liberase_1_S6_L001_R2_001.fastq.gz	fastq fastq fastq	62862684917.0	494981771.0	GSM8115867 r1	0:8 1:28 2:91	A:12631971877;C:10077821577;G:10579831603;T:11753169367;N:546737	8	28	91	12631971877	10077821577	10579831603	11753169367	546737	SRX23770348	SRS20595834			Oncology/Hematology, Boston Children's Hospital	1	0.89921		0.13602		0.814		0.55224		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
33007	33007	SRR29551178	SRX25058395	SRS21755348	SRP516116	PRJNA1128236	The axillary lymphoid organ an external experimentally accessible immune organ in the zebrafish	GSE270797	Other	Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals but the deep internal locations of these organs makes it challenging to study dynamic cellular mechanisms of immune cell interaction with pathogens or other host tissues such as the vasculature in living animals. Here we describe a previously uncharacterized external immune organ located near the base of the zebrafish pectoral fin the pectoral axillary lobe PAL with a variety of features that make it ideally suited for studying immune cell dynamics in vivo. This small transparent organ consists of an outer cortex teeming with immune cells and an inner medulla with a mesh like network of fibroblastic reticular cells along which immune cells migrate and a network of lymphatic vessels draining to a large adjacent lymph sac. Noninvasive high resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals and the PAL is readily accessible to external treatment with antigens or pathogens. This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues including blood and lymphatic vessels. Overall design: Single cell expression profiling by high throughput sequencing	pubmed:39091802	Pectoral axillary lobe scRNA	GSM8352182	source name:Pectoral axillary lobe\|tissue:Pectoral axillary lobe\|geo loc name:missing\|collection date:missing	Pectoral axillary lobe scRNA	cellranger count v7.0.0 Assembly: zv11 Supplementary files format and content: TSV value and matrix files	Pectoral axillary lobe	Cell suspension prepared from 4 pectoral axillary lobes 2 from males 2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pectoral axillary lobe	GSM8352182	GSM8352182: Pectoral axillary lobe scRNA; Danio rerio; RNA Seq	GSM8352182 r1	GSM8352182	1	Cell suspension prepared from 4 pectoral axillary lobes 2 from males 2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516116		LCK1_S3_L001_R1_001.fastq.gz LCK1_S3_L001_R2_001.fastq.gz LCK1_S3_L002_R1_001.fastq.gz LCK1_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	21583802440.0	182913580.0	GSM8352182 r1	0:28 1:90	A:6079984051;C:4913875575;G:5182513698;T:5406578531;N:850585	28	90		6079984051	4913875575	5182513698	5406578531	850585	SRX25058395	SRS21755348	SRA1909244	BG 10 RM 8S261, NICHD, NIH	BG 10 RM 8S261, NICHD, NIH												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-06-25	Adult	Adult	Undetermined	Undetermined
34224	34224	SRR31604147	SRX26968916	SRS23437614	SRP549343	PRJNA1192682	Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells	PRJNA1192682	Other	The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.			CV mCherry negative	strain:EK\|age:6 dpf\|collection date:2021\|geo loc name:USA: Durham NC\|sex:not applicable\|tissue:Sorted cells\|Condition:Conventionalized\|Fluorescence:mCherry negative GFP positive\|BioSampleModel:Model organism or animal								scRNA seq of danio rerio: mCherry positive GFP positive sorted cells from CV larvae	7066 P3	7066 P3	TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM Library & Gel Bead Kit v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549343		CV_IEC_3_S3_L001_I1_001.fastq.gz CV_IEC_3_S3_L001_R1_001.fastq.gz CV_IEC_3_S3_L001_R2_001.fastq.gz CV_IEC_3_S3_L002_I1_001.fastq.gz CV_IEC_3_S3_L002_R1_001.fastq.gz CV_IEC_3_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq	39983364288.0	317328288.0	CV IEC 3 S3 L001 I1 001.fastq.gz	0:8 1:28 2:90	A:7989957184;C:6492876848;G:7106881008;T:6968481488;N:1349392	8	28	90	7989957184	6492876848	7106881008	6968481488	1349392	SRX26968916	SRS23437614	SRA2025080	Duke University\|Cell Biology	Duke University												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-04	Larval	Larval	Undetermined	Undetermined
34225	34225	SRR31604148	SRX26968915	SRS23437613	SRP549343	PRJNA1192682	Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells	PRJNA1192682	Other	The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.			GF mCherry negative	strain:EK\|age:6 dpf\|collection date:2021\|geo loc name:USA: Durham NC\|sex:not applicable\|tissue:Sorted cells\|Condition:Germ free\|Fluorescence:mCherry negative GFP positive\|BioSampleModel:Model organism or animal								scRNA seq of danio rerio: mCherry negative GFP positive sorted cells from GF larvae	7066 P1	7066 P1	TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM Library & Gel Bead Kit v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549343		GF_IEC_1_S1_L001_I1_001.fastq.gz GF_IEC_1_S1_L001_R1_001.fastq.gz GF_IEC_1_S1_L001_R2_001.fastq.gz GF_IEC_1_S1_L002_I1_001.fastq.gz GF_IEC_1_S1_L002_R1_001.fastq.gz GF_IEC_1_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq	40178994030.0	318880905.0	GF IEC 1 S1 L001 I1 001.fastq.gz	0:8 1:28 2:90	A:8197955224;C:6448684398;G:7158064923;T:6893218597;N:1358308	8	28	90	8197955224	6448684398	7158064923	6893218597	1358308	SRX26968915	SRS23437613	SRA2025080	Duke University\|Cell Biology	Duke University												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-04	Larval	Larval	Undetermined	Undetermined
34226	34226	SRR31604149	SRX26968914	SRS23437612	SRP549343	PRJNA1192682	Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells	PRJNA1192682	Other	The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.			CV mCherry positive	strain:EK\|age:6 dpf\|collection date:2021\|geo loc name:USA: Durham NC\|sex:not applicable\|tissue:Sorted cells\|Condition:Conventionalized\|Fluorescence:mCherry positive GFP positive\|BioSampleModel:Model organism or animal								scRNA seq of danio rerio: mCherry positive GFP positive sorted cells from CV larvae	7066 P4	7066 P4	TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM Library & Gel Bead Kit v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549343		CV_LRE_4_S4_L001_I1_001.fastq.gz CV_LRE_4_S4_L001_R1_001.fastq.gz CV_LRE_4_S4_L001_R2_001.fastq.gz CV_LRE_4_S4_L002_I1_001.fastq.gz CV_LRE_4_S4_L002_R1_001.fastq.gz CV_LRE_4_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq	19934299602.0	158208727.0	CV LRE 4 S4 L001 I1 001.fastq.gz	0:8 1:28 2:90	A:4398648037;C:3082182233;G:3214972719;T:3542307593;N:674848	8	28	90	4398648037	3082182233	3214972719	3542307593	674848	SRX26968914	SRS23437612	SRA2025080	Duke University\|Cell Biology	Duke University												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-04	Larval	Larval	Undetermined	Undetermined
34227	34227	SRR31604150	SRX26968913	SRS23437611	SRP549343	PRJNA1192682	Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells	PRJNA1192682	Other	The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.			GF mCherry positive	strain:EK\|age:6 dpf\|collection date:2021\|geo loc name:USA: Durham NC\|sex:not applicable\|tissue:Sorted cells\|Condition:Germ free\|Fluorescence:mCherry positive GFP positive\|BioSampleModel:Model organism or animal								scRNA seq of danio rerio: mCherry positive GFP positive sorted cells from GF larvae	7066 P2	7066 P2	TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM Library & Gel Bead Kit v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549343		GF_LRE_2_S2_L001_I1_001.fastq.gz GF_LRE_2_S2_L001_R1_001.fastq.gz GF_LRE_2_S2_L001_R2_001.fastq.gz GF_LRE_2_S2_L002_I1_001.fastq.gz GF_LRE_2_S2_L002_R1_001.fastq.gz GF_LRE_2_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq	16477189470.0	130771345.0	GF LRE 2 S2 L001 I1 001.fastq.gz	0:8 1:28 2:90	A:3664699916;C:2552676887;G:2506770636;T:3044709641;N:563970	8	28	90	3664699916	2552676887	2506770636	3044709641	563970	SRX26968913	SRS23437611	SRA2025080	Duke University\|Cell Biology	Duke University												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-04	Larval	Larval	Undetermined	Undetermined
69681	69681	SRR19135481	SRX15203073	SRS12941937	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 7 days	GSM6122392	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 7 days	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122392	GSM6122392: sci 7 days; Danio rerio; RNA Seq	GSM6122392 r1	GSM6122392	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_7d_S1_L001_R1_001.fastq.gz 200326B_SCI_7d_S1_L001_R2_001.fastq.gz	fastq fastq	29475258300.0	98250861.0	GSM6122392 r1	0:150 1:150	A:11751410672;C:5165600847;G:5006614388;T:7550835321;N:797072	150	150		11751410672	5165600847	5006614388	7550835321	797072	SRX15203073	SRS12941937	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.84223	0.0	0.39353	1.0	0.74525		0.54601	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69682	69682	SRR19135482	SRX15203073	SRS12941937	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 7 days	GSM6122392	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 7 days	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122392	GSM6122392: sci 7 days; Danio rerio; RNA Seq	GSM6122392 r1	GSM6122392	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_7d_S1_L002_R1_001.fastq.gz 200326B_SCI_7d_S1_L002_R2_001.fastq.gz	fastq fastq	36747988500.0	122493295.0	GSM6122392 r2	0:150 1:150	A:14654774798;C:6464113495;G:6260198771;T:9367916916;N:984520	150	150		14654774798	6464113495	6260198771	9367916916	984520	SRX15203073	SRS12941937	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.84266	0.0	0.38972	1.0	0.74123		0.55802	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69683	69683	SRR19135483	SRX15203073	SRS12941937	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 7 days	GSM6122392	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 7 days	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122392	GSM6122392: sci 7 days; Danio rerio; RNA Seq	GSM6122392 r1	GSM6122392	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_7d_S1_L003_R1_001.fastq.gz 200326B_SCI_7d_S1_L003_R2_001.fastq.gz	fastq fastq	29317600800.0	97725336.0	GSM6122392 r3	0:150 1:150	A:11710887306;C:5127280140;G:4964728517;T:7513923126;N:781711	150	150		11710887306	5127280140	4964728517	7513923126	781711	SRX15203073	SRS12941937	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.84265	0.0	0.3924	1.0	0.74065		0.5513	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69684	69684	SRR19135484	SRX15203073	SRS12941937	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 7 days	GSM6122392	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 7 days	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122392	GSM6122392: sci 7 days; Danio rerio; RNA Seq	GSM6122392 r1	GSM6122392	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_7d_S1_L004_R1_001.fastq.gz 200326B_SCI_7d_S1_L004_R2_001.fastq.gz	fastq fastq	31023693300.0	103412311.0	GSM6122392 r4	0:150 1:150	A:12411824191;C:5462794848;G:5265823465;T:7882413369;N:837427	150	150		12411824191	5462794848	5265823465	7882413369	837427	SRX15203073	SRS12941937	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.84212	0.0	0.38947	1.0	0.74194		0.55424	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69685	69685	SRR19135485	SRX15203072	SRS12941936	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 1 day	GSM6122391	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 1 day	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122391	GSM6122391: sci 1 day; Danio rerio; RNA Seq	GSM6122391 r1	GSM6122391	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_1d_S1_L001_R1_001.fastq.gz 200326B_SCI_1d_S1_L001_R2_001.fastq.gz	fastq fastq	30796719300.0	102655731.0	GSM6122391 r1	0:150 1:150	A:12350014570;C:5356650438;G:5213090421;T:7876134369;N:829502	150	150		12350014570	5356650438	5213090421	7876134369	829502	SRX15203072	SRS12941936	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82474	0.0	0.41531	1.0	0.75676		0.57108	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69686	69686	SRR19135486	SRX15203072	SRS12941936	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 1 day	GSM6122391	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 1 day	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122391	GSM6122391: sci 1 day; Danio rerio; RNA Seq	GSM6122391 r1	GSM6122391	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_1d_S1_L002_R1_001.fastq.gz 200326B_SCI_1d_S1_L002_R2_001.fastq.gz	fastq fastq	50002460700.0	166674869.0	GSM6122391 r2	0:150 1:150	A:20017686965;C:8776481027;G:8531485975;T:12675453459;N:1353274	150	150		20017686965	8776481027	8531485975	12675453459	1353274	SRX15203072	SRS12941936	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82772	0.0	0.41128	1.0	0.75526		0.57912	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69687	69687	SRR19135487	SRX15203072	SRS12941936	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 1 day	GSM6122391	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 1 day	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122391	GSM6122391: sci 1 day; Danio rerio; RNA Seq	GSM6122391 r1	GSM6122391	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_1d_S1_L003_R1_001.fastq.gz 200326B_SCI_1d_S1_L003_R2_001.fastq.gz	fastq fastq	27393087000.0	91310290.0	GSM6122391 r3	0:150 1:150	A:10993720058;C:4767631453;G:4636926918;T:6994070447;N:738124	150	150		10993720058	4767631453	4636926918	6994070447	738124	SRX15203072	SRS12941936	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82551	0.0	0.41348	1.0	0.75463		0.57216	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69688	69688	SRR19135488	SRX15203072	SRS12941936	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		sci 1 day	GSM6122391	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 1 day	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122391	GSM6122391: sci 1 day; Danio rerio; RNA Seq	GSM6122391 r1	GSM6122391	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_SCI_1d_S1_L004_R1_001.fastq.gz 200326B_SCI_1d_S1_L004_R2_001.fastq.gz	fastq fastq	32242489800.0	107474966.0	GSM6122391 r4	0:150 1:150	A:12933266375;C:5621077845;G:5468451507;T:8218829416;N:864657	150	150		12933266375	5621077845	5468451507	8218829416	864657	SRX15203072	SRS12941936	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82532	0.0	0.41398	1.0	0.75605		0.5687	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69689	69689	SRR19135489	SRX15203071	SRS12941935	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		con	GSM6122390	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	con	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122390	GSM6122390: con; Danio rerio; RNA Seq	GSM6122390 r1	GSM6122390	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_ctrl_S1_L001_R1_001.fastq.gz 200326B_ctrl_S1_L001_R2_001.fastq.gz	fastq fastq	29790064800.0	99300216.0	GSM6122390 r1	0:150 1:150	A:11345104518;C:5411837799;G:5387688262;T:7645052714;N:381507	150	150		11345104518	5411837799	5387688262	7645052714	381507	SRX15203071	SRS12941935	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82469	0.0	0.40028	1.0	0.77364		0.56772	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69690	69690	SRR19135490	SRX15203071	SRS12941935	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		con	GSM6122390	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	con	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122390	GSM6122390: con; Danio rerio; RNA Seq	GSM6122390 r1	GSM6122390	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_ctrl_S1_L002_R1_001.fastq.gz 200326B_ctrl_S1_L002_R2_001.fastq.gz	fastq fastq	35497283400.0	118324278.0	GSM6122390 r2	0:150 1:150	A:13499810877;C:6480615844;G:6449186944;T:9067209386;N:460349	150	150		13499810877	6480615844	6449186944	9067209386	460349	SRX15203071	SRS12941935	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82641	0.0	0.39782	1.0	0.7725		0.57807	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69691	69691	SRR19135491	SRX15203071	SRS12941935	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		con	GSM6122390	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	con	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122390	GSM6122390: con; Danio rerio; RNA Seq	GSM6122390 r1	GSM6122390	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_ctrl_S1_L003_R1_001.fastq.gz 200326B_ctrl_S1_L003_R2_001.fastq.gz	fastq fastq	35833932300.0	119446441.0	GSM6122390 r3	0:150 1:150	A:13602986352;C:6579327464;G:6541522676;T:9109635350;N:460458	150	150		13602986352	6579327464	6541522676	9109635350	460458	SRX15203071	SRS12941935	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82721	0.0	0.3953	1.0	0.77165		0.57432	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
69692	69692	SRR19135492	SRX15203071	SRS12941935	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing		con	GSM6122390	tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	con	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish	single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122390	GSM6122390: con; Danio rerio; RNA Seq	GSM6122390 r1	GSM6122390	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP374105		200326B_ctrl_S1_L004_R1_001.fastq.gz 200326B_ctrl_S1_L004_R2_001.fastq.gz	fastq fastq	29912840700.0	99709469.0	GSM6122390 r4	0:150 1:150	A:11383688634;C:5482496317;G:5445959161;T:7600315635;N:380953	150	150		11383688634	5482496317	5445959161	7600315635	380953	SRX15203071	SRS12941935	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82874	0.0	0.39718	1.0	0.77386		0.58106	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-05-07	Adult	Adult	Undetermined	Undetermined
72589	72589	SRR22838795	SRX18797976	SRS16231609	SRP414185	PRJNA914428	Single cell RNA sequencing scRNA seq of GFP+cells isolated from TgBrn3c:mGFP 6 days zebrafish with GFP expression in all hair cells.	GSE221471	Other	Hair cells play key roles in hearing and balance and hair cell loss would result in hearing loss or vestibular dysfunction. Zebrafsh owing to their hair cell enriched organs have been widely applied in hair cell related research worldwide. In this study we analyzed the GFP+cells isolated from TgBrn3c:mGFP larvae with GFP expression in all hair cells using single cell RNA sequencing scRNA seq. Three subtypes of hair cells namely macula hair cell MHC crista hair cell CHC and neuromast hair cell NHC were characterized and validated by whole mount in situ hybridization analysis of marker genes. The hair cell scRNA seq data revealed hair cell specifc genes including hearing loss genes that have been identifed in humans and novel genes potentially involved in hair cell formation and function. Overall design: Zebrafsh were maintained at 28.5 °C. The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform	pubmed:35753015	GFP+ scRNAseq	GSM6873779	tissue:GFP+cells from TgBrn3c:mGFP zebrafish\|cell type:hair cell\|age:6 days	GFP+ scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: FASTQ	GFP+cells from TgBrn3c:mGFP zebrafish	The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		cell type:hair cell\|age:6 days	GSM6873779	GSM6873779: GFP+ scRNAseq; Danio rerio; RNA Seq	GSM6873779 r1	GSM6873779	1	The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP414185		brn3c6dpf_R1.fq.gz brn3c6dpf_R2.fq.gz	fastq fastq	201407352000.0	671357840.0	GSM6873779 r1	0:150 1:150	A:47653455771;C:37496314066;G:61110504409;T:55144480424;N:2597330	150	150		47653455771	37496314066	61110504409	55144480424	2597330	SRX18797976	SRS16231609	SRA1563296	Nantong University	Nantong University	2	0.0	0.90004	0.0	0.18176	1.0	0.76794		0.55523	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-12-20	Larval	Larval	Undetermined	Undetermined

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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");;