metadata: run_metadata: 8 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue

8 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Pancreas"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.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.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
43988	43988	SRR6811827	SRX3768867	SRS3023384	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.	pubmed:29644996	Pancreas 3 endo scar	GSM3032170	source name:Primary pancreatic islet\|strain/background:Zebrabow M\|tissue:Primary pancreatic islet\|developmental stage:Adult	Pancreas 3 endo scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Primary pancreatic islet	Single cell dissociation. 10X Genomics Chromium	strain/background:Zebrabow M\|tissue:Primary pancreatic islet\|developmental stage:Adult	GSM3032170	GSM3032170: Pancreas 3 endo scar; Danio rerio; OTHER	GSM3032170	1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032170	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	P7endo_scar_R1.fastq.gz P7endo_scar_R2.fastq.gz	fastq fastq	2537781396.0	20465979.0	GSM3032170 r1	0:26 1:98	A:741745261;C:801599713;G:561531527;T:431666561;N:1238334	26	98	741745261	801599713	561531527	431666561	1238334	SRX3768867	SRS3023384	SRA623333	GEO	Max Delbrück Center	2	0.00014	0.00289	0.00012	0.00028	0.99995	0.99602	1.0	0.68478	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Pancreas	Endocrine System
43994	43994	SRR6811821	SRX3768861	SRS3023378	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.	pubmed:29644996	Pancreas 3 endo mRNA	GSM3032164	source name:Primary pancreatic islet\|strain/background:Zebrabow M\|tissue:Primary pancreatic islet\|developmental stage:Adult	Pancreas 3 endo mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Primary pancreatic islet	Single cell dissociation. 10X Genomics Chromium	strain/background:Zebrabow M\|tissue:Primary pancreatic islet\|developmental stage:Adult	GSM3032164	GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq	GSM3032164	1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032164	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343	P7endo_wt_R1.fastq.gz P7endo_wt_R2.fastq.gz	fastq fastq	41593781900.0	335433725.0	GSM3032164 r1	0:26 1:98	A:11833690021;C:9547054378;G:9724089290;T:10470148302;N:18799909	26	98	11833690021	9547054378	9724089290	10470148302	18799909	SRX3768861	SRS3023378	SRA623333	GEO	Max Delbrück Center	2	0.00308	0.92936	0.00192	0.05695	0.9973	0.8686	0.45945	0.58814	26	98	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Pancreas	Endocrine System
50847	50847	SRR8312900	SRX5126276	SRS4139398	SRP173304	PRJNA509469	Single cell RNA sequencing of zebrafish pancreatic cells	GSE123662	Other	The pancreatic beta cells regulate blood glucose levels by secreting the hormone insulin in response to increasing glucose levels. Recent work has identified molecular and functional heterogeneity among the beta cell community. To ontain an unbiased picture into the molecular heterogeneity present in zebrafish pancreatic cells we performed droplet based next generation sequencing of individual pancreatic cells. Using unsupervised clustering we could identify all the major cell types present in the pancreas. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile pancreatic cells from zebrafish. Pancreatic islets from six animals were dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense'. Genome sequence and filtered annotation were then used as input to the 'mkref' command of Cell Ranger to build the appropriate Cellranger Reference.	pubmed:32694805	2mpf Pancreas	GSM3509161	tissue:pancreatic cells\|age:2mpf\|strain:Tgins:BB1.0L\|disease state:Normal	2mpf Pancreas	The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ‘ expect cells’ set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger options: ‘ attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: csv format with rows as genes and columns as cells	pancreatic cells	Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol.	age:2mpf\|strain:Tgins:BB1.0L\|disease state:Normal	GSM3509161	GSM3509161: 2mpf Pancreas; Danio rerio; RNA Seq	GSM3509161	1	Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer's protocol.	GEO Accession:GSM3509161	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP173304	s2mpf_R1.fastq.gz s2mpf_R2.fastq.gz	fastq fastq	3682641276.0	44369172.0	GSM3509161 r1	0:26 1:57	A:950388419;C:876060179;G:944476013;T:911635661;N:81004	26	57	950388419	876060179	944476013	911635661	81004	SRX5126276	SRS4139398	SRA822849	GEO	Single Cell Endocrinology, IRIBHM	2	0.00373	0.9564	0.0008	0.03195	0.99508	0.9024	0.38273	0.59374	26	57	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2018-12-11	Juvenile	Juvenile	Pancreas	Endocrine System
63128	63128	SRR13616487	SRX10009741	SRS8178664	SRP304424	PRJNA699078	Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration	GSE166052	Transcriptome Analysis	To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.	pubmed:35088828	Pancreas 14dpa	GSM5060849	tissue:Zebrafish pancreas\|strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 14 days post MTZ	Pancreas 14dpa	bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices	Zebrafish pancreas	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:Pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 14 days post MTZ	GSM5060849	GSM5060849: Pancreas 14dpa; Danio rerio; RNA Seq	GSM5060849	1	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	GEO Accession:GSM5060849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP304424	L59491_Track-100378_R1.fastq.gz L59491_Track-100378_R2.fastq.gz	fastq fastq	21882647280.0	168328056.0	GSM5060849 r1	0:29 1:101	A:5304415368;C:5193690448;G:5721535951;T:5662241808;N:763705	29	101	5304415368	5193690448	5721535951	5662241808	763705	SRX10009741	SRS8178664	SRA1190924	GEO	Ninov Lab, CRTD, TU Dresden	2	0.0137	0.94318	0.00185	0.03707	0.99263	0.91078	0.60061	0.58256	29	101	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-02	Adult	Adult	Pancreas	Endocrine System
63129	63129	SRR13616486	SRX10009740	SRS8178663	SRP304424	PRJNA699078	Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration	GSE166052	Transcriptome Analysis	To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.	pubmed:35088828	Pancreas 7dpa	GSM5060848	tissue:Zebrafish pancreas\|strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 7 days post MTZ	Pancreas 7dpa	bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices	Zebrafish pancreas	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:Pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 7 days post MTZ	GSM5060848	GSM5060848: Pancreas 7dpa; Danio rerio; RNA Seq	GSM5060848	1	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	GEO Accession:GSM5060848	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP304424	L47897_Track-91889_R1.fastq.gz L47897_Track-91889_R2.fastq.gz	fastq fastq	11982402020.0	98216410.0	GSM5060848 r1	0:29 1:93	A:3162707284;C:2774571882;G:2736678637;T:3307378654;N:1065563	29	93	3162707284	2774571882	2736678637	3307378654	1065563	SRX10009740	SRS8178663	SRA1190924	GEO	Ninov Lab, CRTD, TU Dresden	2	0.01025	0.93044	0.00221	0.066	0.98938	0.85823	0.52941	0.62147	29	93	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-02	Adult	Adult	Pancreas	Endocrine System
63130	63130	SRR13616485	SRX10009739	SRS8178662	SRP304424	PRJNA699078	Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration	GSE166052	Transcriptome Analysis	To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.	pubmed:35088828	Pancreas 2dpa	GSM5060847	tissue:Zebrafish pancreas\|strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 2 days post MTZ	Pancreas 2dpa	bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices	Zebrafish pancreas	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:Pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 2 days post MTZ	GSM5060847	GSM5060847: Pancreas 2dpa; Danio rerio; RNA Seq	GSM5060847	1	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	GEO Accession:GSM5060847	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP304424	L47899_Track-88823_R1.fastq.gz L47899_Track-88823_R2.fastq.gz	fastq fastq	12079250378.0	99010249.0	GSM5060847 r1	0:29 1:93	A:3187642396;C:2755358695;G:2795295173;T:3340653508;N:300606	29	93	3187642396	2755358695	2795295173	3340653508	300606	SRX10009739	SRS8178662	SRA1190924	GEO	Ninov Lab, CRTD, TU Dresden	2	0.00631	0.94202	0.00135	0.0615	0.99123	0.84307	0.55742	0.56593	29	93	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-02	Adult	Adult	Pancreas	Endocrine System
63131	63131	SRR13616484	SRX10009738	SRS8178661	SRP304424	PRJNA699078	Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration	GSE166052	Transcriptome Analysis	To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.	pubmed:35088828	Pancreas 0dpa	GSM5060846	tissue:Zebrafish pancreas\|strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 0 days post MTZ	Pancreas 0dpa	bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices	Zebrafish pancreas	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:Pooled male and female\|age:Adult\|treatment:MTZ treatment for 24 hours\|time point:Dissection at 0 days post MTZ	GSM5060846	GSM5060846: Pancreas 0dpa; Danio rerio; RNA Seq	GSM5060846	1	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	GEO Accession:GSM5060846	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP304424	L59306_Track-100369_R1.fastq.gz L59306_Track-100369_R2.fastq.gz	fastq fastq	19138165410.0	147216657.0	GSM5060846 r1	0:29 1:101	A:4905247743;C:4584481588;G:4969548524;T:4678220753;N:666802	29	101	4905247743	4584481588	4969548524	4678220753	666802	SRX10009738	SRS8178661	SRA1190924	GEO	Ninov Lab, CRTD, TU Dresden	2	0.02866	0.88637	0.00798	0.14499	0.99105	0.87251	0.51922	0.57508	29	101	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-02	Adult	Adult	Pancreas	Endocrine System
63132	63132	SRR13616483	SRX10009737	SRS8178660	SRP304424	PRJNA699078	Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration	GSE166052	Transcriptome Analysis	To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.	pubmed:35088828	Pancreas Control	GSM5060845	tissue:Zebrafish pancreas\|strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:pooled male and female\|age:Adult\|treatment:Untreated\|time point:Untreated	Pancreas Control	bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices	Zebrafish pancreas	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	strain/background:AB\|genotype/variation:Wildtype expressing NTR gene under the insulin promoter\|cell type:Pancreatic cells\|Sex:Pooled male and female\|age:Adult\|treatment:Untreated\|time point:Untreated	GSM5060845	GSM5060845: Pancreas Control; Danio rerio; RNA Seq	GSM5060845	1	Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.	GEO Accession:GSM5060845	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP304424	L47898_Track-88822_R1.fastq.gz L47898_Track-88822_R2.fastq.gz	fastq fastq	8952747472.0	73383176.0	GSM5060845 r1	0:29 1:93	A:2223721886;C:2087634305;G:2235052745;T:2406116444;N:222092	29	93	2223721886	2087634305	2235052745	2406116444	222092	SRX10009737	SRS8178660	SRA1190924	GEO	Ninov Lab, CRTD, TU Dresden	2	0.00837	0.9475	0.00144	0.0366	0.99263	0.88759	0.58964	0.57851	29	93	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-02	Adult	Adult	Pancreas	Endocrine System

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