{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"10x\" and tissue_curation_coarse = \"Endocrine System\"", "rows": [[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.", null, "pubmed:29644996", null, "Pancreas 3 endo scar", "GSM3032170", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Primary pancreatic islet", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult", "GSM3032170", "GSM3032170: Pancreas 3 endo scar; Danio rerio; OTHER", "GSM3032170", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032170", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 741745261, 801599713, 561531527, 431666561, 1238334, "SRX3768867", "SRS3023384", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Adult", "Adult", "Pancreas", "Endocrine System"], [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.", null, "pubmed:29644996", null, "Pancreas 3 endo mRNA", "GSM3032164", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult", "GSM3032164", "GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq", "GSM3032164", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032164", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 11833690021, 9547054378, 9724089290, 10470148302, 18799909, "SRX3768861", "SRS3023378", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Adult", "Adult", "Pancreas", "Endocrine System"], [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 \u2013attribute=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.", null, "pubmed:32694805", null, "2mpf Pancreas", "GSM3509161", null, "tissue:pancreatic cells|age:2mpf|strain:Tgins:BB1.0L|disease state:Normal", "2mpf Pancreas", "The raw sequencing data was then processed with the \u2018count\u2019 command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option \u2018  expect cells\u2019 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018  attribute=gene biotype:protein coding   attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense\u2019. Genome sequence and filtered annotation were then used as input to the \u2018mkref\u2019 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", null, "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\u2019s 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 \u2013 was performed based on the manufacturer\u2019s protocol.", null, "age:2mpf|strain:Tgins:BB1.0L|disease state:Normal", "GSM3509161", "GSM3509161: 2mpf Pancreas; Danio rerio; RNA Seq", "GSM3509161", null, "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 \u2013 was performed based on the manufacturer's protocol.", "GEO Accession:GSM3509161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP173304", null, null, "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, null, null, 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", null, "Belgium", "2018-12-11", "Juvenile", "Juvenile", "Pancreas", "Endocrine System"], [50860, "SRR8315379", "SRX5128211", "SRS4141333", "SRP173374", "PRJNA509801", "Single cell sequencing analysis of the zebrafish pineal gland", "GSE123778", "Transcriptome Analysis", "The purpose of this study was to genetically describe the different pineal cell types  and in particular the type of cells expressing the gene agrp2.  The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells  and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample  twenty adult pineal glands were dissected and processed together.", null, "pubmed:31178320", null, "scSeq2", "GSM3511193", null, "source name:pineal glands|tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month", "scSeq2", "Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10  Ensembl release 91 annotations  and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally  reads were aligned  UMIs processed  and transcripts counted to generate gene/barcode matrices  which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files.", "pineal glands", null, "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3\u2019 Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", null, "tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month", "GSM3511193", "GSM3511193: scSeq2; Danio rerio; RNA Seq", "GSM3511193", null, "1", "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", "GEO Accession:GSM3511193", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP173374", null, null, "scSeq2_L001_R1_001.fastq.gz scSeq2_L001_R2_001.fastq.gz", "fastq fastq", 29063395032.0, 234382218.0, "GSM3511193 r1", "0:26 1:98", "A:8483803116;C:5981698341;G:6389916823;T:8203926541;N:4050211", 26, 98, null, null, 8483803116, 5981698341, 6389916823, 8203926541, 4050211, "SRX5128211", "SRS4141333", "SRA823034", "GEO", "Tel Aviv University", 2, 0.00394, 0.91121, 0.00091, 0.19356, 0.99389, 0.80984, 0.23443, 0.48501, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Israel", "2018-12-13", "Adult", "Adult", "Pineal Gland", "Endocrine System"], [50861, "SRR8315380", "SRX5128211", "SRS4141333", "SRP173374", "PRJNA509801", "Single cell sequencing analysis of the zebrafish pineal gland", "GSE123778", "Transcriptome Analysis", "The purpose of this study was to genetically describe the different pineal cell types  and in particular the type of cells expressing the gene agrp2.  The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells  and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample  twenty adult pineal glands were dissected and processed together.", null, "pubmed:31178320", null, "scSeq2", "GSM3511193", null, "source name:pineal glands|tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month", "scSeq2", "Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10  Ensembl release 91 annotations  and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally  reads were aligned  UMIs processed  and transcripts counted to generate gene/barcode matrices  which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files.", "pineal glands", null, "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3\u2019 Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", null, "tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month", "GSM3511193", "GSM3511193: scSeq2; Danio rerio; RNA Seq", "GSM3511193", null, "1", "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", "GEO Accession:GSM3511193", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP173374", null, null, "scSeq2_L002_R1_001.fastq.gz scSeq2_L002_R2_001.fastq.gz", "fastq fastq", 29003313560.0, 233897690.0, "GSM3511193 r2", "0:26 1:98", "A:8453400725;C:5974567982;G:6382782124;T:8189587364;N:2975365", 26, 98, null, null, 8453400725, 5974567982, 6382782124, 8189587364, 2975365, "SRX5128211", "SRS4141333", "SRA823034", "GEO", "Tel Aviv University", 2, 0.00378, 0.91135, 0.00087, 0.19518, 0.99413, 0.80937, 0.20454, 0.48353, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Israel", "2018-12-13", "Adult", "Adult", "Pineal Gland", "Endocrine System"], [50862, "SRR8315377", "SRX5128210", "SRS4141331", "SRP173374", "PRJNA509801", "Single cell sequencing analysis of the zebrafish pineal gland", "GSE123778", "Transcriptome Analysis", "The purpose of this study was to genetically describe the different pineal cell types  and in particular the type of cells expressing the gene agrp2.  The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells  and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample  twenty adult pineal glands were dissected and processed together.", null, "pubmed:31178320", null, "scSeq1", "GSM3511192", null, "source name:pineal glands|tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month", "scSeq1", "Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10  Ensembl release 91 annotations  and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally  reads were aligned  UMIs processed  and transcripts counted to generate gene/barcode matrices  which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files.", "pineal glands", null, "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3\u2019 Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", null, "tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month", "GSM3511192", "GSM3511192: scSeq1; Danio rerio; RNA Seq", "GSM3511192", null, "1", "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", "GEO Accession:GSM3511192", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP173374", null, null, "scSeq1_L001_R1_001.fastq.gz scSeq1_L001_R2_001.fastq.gz", "fastq fastq", 15101906060.0, 121789565.0, "GSM3511192 r1", "0:26 1:98", "A:4389085504;C:3222094251;G:3483928123;T:3991523000;N:15275182", 26, 98, null, null, 4389085504, 3222094251, 3483928123, 3991523000, 15275182, "SRX5128210", "SRS4141331", "SRA823034", "GEO", "Tel Aviv University", 2, 0.00534, 0.86489, 0.00171, 0.14238, 0.99204, 0.85263, 0.2798, 0.50024, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Israel", "2018-12-13", "Adult", "Adult", "Pineal Gland", "Endocrine System"], [50863, "SRR8315378", "SRX5128210", "SRS4141331", "SRP173374", "PRJNA509801", "Single cell sequencing analysis of the zebrafish pineal gland", "GSE123778", "Transcriptome Analysis", "The purpose of this study was to genetically describe the different pineal cell types  and in particular the type of cells expressing the gene agrp2.  The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells  and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample  twenty adult pineal glands were dissected and processed together.", null, "pubmed:31178320", null, "scSeq1", "GSM3511192", null, "source name:pineal glands|tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month", "scSeq1", "Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10  Ensembl release 91 annotations  and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally  reads were aligned  UMIs processed  and transcripts counted to generate gene/barcode matrices  which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files.", "pineal glands", null, "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3\u2019 Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", null, "tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month", "GSM3511192", "GSM3511192: scSeq1; Danio rerio; RNA Seq", "GSM3511192", null, "1", "Pineal glands were dissected and enzymatically dissociated Papain Dissociation System  Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry.", "GEO Accession:GSM3511192", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP173374", null, null, "scSeq1_L002_R1_001.fastq.gz scSeq1_L002_R2_001.fastq.gz", "fastq fastq", 12784244380.0, 103098745.0, "GSM3511192 r2", "0:26 1:98", "A:3711546705;C:2726963744;G:2944583108;T:3391689087;N:9461736", 26, 98, null, null, 3711546705, 2726963744, 2944583108, 3391689087, 9461736, "SRX5128210", "SRS4141331", "SRA823034", "GEO", "Tel Aviv University", 2, 0.00543, 0.85703, 0.00187, 0.14217, 0.99222, 0.85665, 0.27512, 0.51728, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Israel", "2018-12-13", "Adult", "Adult", "Pineal Gland", "Endocrine System"], [52953, "SRR9609654", "SRX6373048", "SRS5034105", "SRP212225", "PRJNA551501", "Single cell RNA sequencing of zebrafish thyroid cells", "GSE133466", "Transcriptome Analysis", "The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production  storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes  surrounded by thyroid follicular epithelial cells  or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established  it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words  the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes  we performed droplet based next generation sequencing of individual thyrod gland cells. Using unsupervised clustering  we could identify all the major cell types present in the thyroid gland. 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 thyroid cells from zebrafish. Thyroid gland was enzymatically 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 6000 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 \u2013attribute=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.", null, null, null, "8mpf Thyroid", "GSM3909772", null, "tissue:thyroid gland|treatment:8mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal", "8mpf Thyroid", "The raw sequencing data was then processed with the \u2018count\u2019 command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option \u2018  expect cells\u2019 set to 6000 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018  attribute=gene biotype:protein coding   attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense\u2019. Genome sequence and filtered annotation were then used as input to the \u2018mkref\u2019 command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells.", "thyroid gland", null, "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\u2019s instructions to yield 12000 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 \u2013 was performed based on the manufacturer\u2019s protocol.", null, "treatment:8mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal", "GSM3909772", "GSM3909772: 8mpf Thyroid; Danio rerio; RNA Seq", "GSM3909772", null, "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 12000 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 \u2013 was performed based on the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP212225", null, null, "L38696_Track-76232_R1.fastq.gz L38696_Track-76232_R2.fastq.gz", "fastq fastq", 9752526168.0, 116101502.0, "GSM3909772 r1", "0:28 1:56", "A:2760523285;C:2129359977;G:2225570954;T:2632796182;N:4275770", 28, 56, null, null, 2760523285, 2129359977, 2225570954, 2632796182, 4275770, "SRX6373048", "SRS5034105", "SRA914541", "GEO", "Singh Lab, IRIBHM", 2, 0.00831, 0.90972, 0.00332, 0.2088, 0.99157, 0.80182, 0.40796, 0.56239, 28, 56, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2019-06-27", "Adult", "Adult", "Thyroid", "Endocrine System"], [52954, "SRR9609653", "SRX6373047", "SRS5034104", "SRP212225", "PRJNA551501", "Single cell RNA sequencing of zebrafish thyroid cells", "GSE133466", "Transcriptome Analysis", "The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production  storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes  surrounded by thyroid follicular epithelial cells  or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established  it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words  the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes  we performed droplet based next generation sequencing of individual thyrod gland cells. Using unsupervised clustering  we could identify all the major cell types present in the thyroid gland. 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 thyroid cells from zebrafish. Thyroid gland was enzymatically 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 6000 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 \u2013attribute=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.", null, null, null, "2mpf Thyroid", "GSM3909771", null, "tissue:thyroid gland|treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal", "2mpf Thyroid", "The raw sequencing data was then processed with the \u2018count\u2019 command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option \u2018  expect cells\u2019 set to 6000 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018  attribute=gene biotype:protein coding   attribute=gene biotype:lincRNA \u2013attribute=gene biotype:antisense\u2019. Genome sequence and filtered annotation were then used as input to the \u2018mkref\u2019 command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells.", "thyroid gland", null, "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\u2019s instructions to yield 12000 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 \u2013 was performed based on the manufacturer\u2019s protocol.", null, "treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal", "GSM3909771", "GSM3909771: 2mpf Thyroid; Danio rerio; RNA Seq", "GSM3909771", null, "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 12000 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 \u2013 was performed based on the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP212225", null, null, "L38695_Track-76231_R2.fastq.gz L38695_Track-76231_R1.fastq.gz", "fastq fastq", 9092057268.0, 108238777.0, "GSM3909771 r1", "0:28 1:56", "A:2584354341;C:1956113829;G:2086486284;T:2461142498;N:3960316", 28, 56, null, null, 2584354341, 1956113829, 2086486284, 2461142498, 3960316, "SRX6373047", "SRS5034104", "SRA914541", "GEO", "Singh Lab, IRIBHM", 2, 0.01005, 0.87575, 0.00435, 0.23392, 0.99192, 0.80344, 0.39812, 0.53402, 28, 56, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2019-06-27", "Juvenile", "Juvenile", "Thyroid", "Endocrine System"], [58918, "SRR11540947", "SRX8111243", "SRS6476317", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "Transplant", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "GSM4474605", "GSM4474605: Transplant; Danio rerio; RNA Seq", "GSM4474605", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474605", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "ubieGFP_Pit-Endo-transp_3mpf-m-1_S25_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-1_S25_L001_R1_001.fastq.gz", "fastq fastq", 32025333121.0, 217126081.0, "GSM4474605 r1", "0:27 1:120.50", "A:9314654962;C:6522735572;G:6826173512;T:9343095148;N:18673927", 27, 120, null, null, 9314654962, 6522735572, 6826173512, 9343095148, 18673927, "SRX8111243", "SRS6476317", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00161, 0.90845, 0.00057, 0.11751, 0.99687, 0.82771, 0.47738, 0.59877, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58919, "SRR11540948", "SRX8111243", "SRS6476317", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "Transplant", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "GSM4474605", "GSM4474605: Transplant; Danio rerio; RNA Seq", "GSM4474605", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474605", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "ubieGFP_Pit-Endo-transp_3mpf-m-2_S26_L001_R1_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-2_S26_L001_R2_001.fastq.gz", "fastq fastq", 37830323844.0, 256490571.0, "GSM4474605 r2", "0:27 1:120.49", "A:11021068490;C:7699701868;G:8072819621;T:11014855601;N:21878264", 27, 120, null, null, 11021068490, 7699701868, 8072819621, 11014855601, 21878264, "SRX8111243", "SRS6476317", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00167, 0.90711, 0.00066, 0.11917, 0.99663, 0.83, 0.53886, 0.59796, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58920, "SRR11540949", "SRX8111243", "SRS6476317", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "Transplant", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "GSM4474605", "GSM4474605: Transplant; Danio rerio; RNA Seq", "GSM4474605", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474605", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "ubieGFP_Pit-Endo-transp_3mpf-m-3_S27_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-3_S27_L001_R1_001.fastq.gz", "fastq fastq", 28249532732.0, 191530324.0, "GSM4474605 r3", "0:27 1:120.49", "A:8193419181;C:5751619572;G:6039589822;T:8248615264;N:16288893", 27, 120, null, null, 8193419181, 5751619572, 6039589822, 8248615264, 16288893, "SRX8111243", "SRS6476317", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.0017, 0.90552, 0.0006, 0.11697, 0.99667, 0.82576, 0.54976, 0.60065, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58921, "SRR11540950", "SRX8111243", "SRS6476317", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "Transplant", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month", "GSM4474605", "GSM4474605: Transplant; Danio rerio; RNA Seq", "GSM4474605", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474605", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "ubieGFP_Pit-Endo-transp_3mpf-m-4_S28_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-4_S28_L001_R1_001.fastq.gz", "fastq fastq", 28226688209.0, 191373742.0, "GSM4474605 r4", "0:27 1:120.50", "A:8176659734;C:5765390596;G:6034905304;T:8233376515;N:16356060", 27, 120, null, null, 8176659734, 5765390596, 6034905304, 8233376515, 16356060, "SRX8111243", "SRS6476317", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00163, 0.90646, 0.00056, 0.11667, 0.99667, 0.82603, 0.57, 0.59607, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58922, "SRR11540943", "SRX8111242", "SRS6476316", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Male1", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474604", "GSM4474604: Male1; Danio rerio; RNA Seq", "GSM4474604", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474604", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M1_Pituitary_Sox17creERUbiGtR-1_S13_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-1_S13_L001_R1_001.fastq.gz", "fastq fastq", 31605717037.0, 214359798.0, "GSM4474604 r1", "0:27 1:120.44", "A:9104842871;C:6521304311;G:6857625119;T:9101526427;N:20418309", 27, 120, null, null, 9104842871, 6521304311, 6857625119, 9101526427, 20418309, "SRX8111242", "SRS6476316", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00259, 0.88483, 0.00097, 0.20321, 0.995, 0.80079, 0.52597, 0.56862, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58923, "SRR11540944", "SRX8111242", "SRS6476316", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Male1", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474604", "GSM4474604: Male1; Danio rerio; RNA Seq", "GSM4474604", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474604", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M1_Pituitary_Sox17creERUbiGtR-2_S14_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-2_S14_L001_R1_001.fastq.gz", "fastq fastq", 27674233334.0, 187694200.0, "GSM4474604 r2", "0:27 1:120.44", "A:7958817473;C:5737419593;G:6003046001;T:7957045184;N:17905083", 27, 120, null, null, 7958817473, 5737419593, 6003046001, 7957045184, 17905083, "SRX8111242", "SRS6476316", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00275, 0.88312, 0.00108, 0.20427, 0.99478, 0.80608, 0.47634, 0.56166, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58924, "SRR11540945", "SRX8111242", "SRS6476316", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Male1", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474604", "GSM4474604: Male1; Danio rerio; RNA Seq", "GSM4474604", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474604", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M1_Pituitary_Sox17creERUbiGtR-3_S15_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-3_S15_L001_R1_001.fastq.gz", "fastq fastq", 35522886586.0, 240929767.0, "GSM4474604 r3", "0:27 1:120.44", "A:10224992422;C:7358725736;G:7719740991;T:10196515119;N:22912318", 27, 120, null, null, 10224992422, 7358725736, 7719740991, 10196515119, 22912318, "SRX8111242", "SRS6476316", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.0028, 0.88842, 0.00103, 0.20371, 0.99468, 0.80127, 0.46449, 0.4682, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58925, "SRR11540946", "SRX8111242", "SRS6476316", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Male1", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474604", "GSM4474604: Male1; Danio rerio; RNA Seq", "GSM4474604", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474604", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M1_Pituitary_Sox17creERUbiGtR-4_S16_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-4_S16_L001_R1_001.fastq.gz", "fastq fastq", 22322824317.0, 151402860.0, "GSM4474604 r4", "0:27 1:120.44", "A:6438472506;C:4603208282;G:4838569546;T:6428191408;N:14382575", 27, 120, null, null, 6438472506, 4603208282, 4838569546, 6428191408, 14382575, "SRX8111242", "SRS6476316", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00247, 0.88259, 0.00091, 0.20556, 0.99521, 0.80395, 0.47651, 0.55966, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58926, "SRR11540939", "SRX8111241", "SRS6476315", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Males", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474603", "GSM4474603: Males; Danio rerio; RNA Seq", "GSM4474603", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474603", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M_Pituitary_Sox17creERUbiGtR-1_S9_L001_R1_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-1_S9_L001_R2_001.fastq.gz", "fastq fastq", 47824931084.0, 324315726.0, "GSM4474603 r1", "0:27 1:120.46", "A:13805207199;C:9886339394;G:10399128349;T:13703273256;N:30982886", 27, 120, null, null, 13805207199, 9886339394, 10399128349, 13703273256, 30982886, "SRX8111241", "SRS6476315", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00277, 0.89029, 0.00096, 0.16996, 0.99462, 0.81481, 0.49279, 0.59136, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58927, "SRR11540940", "SRX8111241", "SRS6476315", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Males", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474603", "GSM4474603: Males; Danio rerio; RNA Seq", "GSM4474603", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474603", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M_Pituitary_Sox17creERUbiGtR-2_S10_L001_R2_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-2_S10_L001_R1_001.fastq.gz", "fastq fastq", 32243370700.0, 218650680.0, "GSM4474603 r2", "0:27 1:120.47", "A:9305381092;C:6663053359;G:7018746988;T:9235440820;N:20748441", 27, 120, null, null, 9305381092, 6663053359, 7018746988, 9235440820, 20748441, "SRX8111241", "SRS6476315", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00277, 0.8884, 0.00091, 0.1672, 0.99458, 0.81533, 0.51123, 0.58754, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58928, "SRR11540941", "SRX8111241", "SRS6476315", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Males", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474603", "GSM4474603: Males; Danio rerio; RNA Seq", "GSM4474603", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474603", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M_Pituitary_Sox17creERUbiGtR-3_S11_L001_R1_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-3_S11_L001_R2_001.fastq.gz", "fastq fastq", 28915149568.0, 196083542.0, "GSM4474603 r3", "0:27 1:120.46", "A:8347281799;C:5984386507;G:6301924708;T:8262927533;N:18629021", 27, 120, null, null, 8347281799, 5984386507, 6301924708, 8262927533, 18629021, "SRX8111241", "SRS6476315", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00281, 0.88705, 0.00088, 0.16827, 0.99454, 0.81233, 0.49184, 0.58837, 27, 118, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [58929, "SRR11540942", "SRX8111241", "SRS6476315", "SRP256300", "PRJNA625098", "Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary", "GSE148591", "Transcriptome Analysis", "Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2  which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "Males", "10X Genomic Cellranger v3.0.0 was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP  mCherry  and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies  we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned  CCA space  we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information  tab delimited file with gene names  sparse matrix file with raw count associated with previous two files", "Pituitary", null, "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "6mpf animals Males and Male1 and 3mpf animal for transplant", "genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month", "GSM4474603", "GSM4474603: Males; Danio rerio; RNA Seq", "GSM4474603", null, "1", "Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA  the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively.", "GEO Accession:GSM4474603", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP256300", null, null, "M_Pituitary_Sox17creERUbiGtR-4_S12_L001_R2_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-4_S12_L001_R1_001.fastq.gz", "fastq fastq", 33158543550.0, 224853573.0, "GSM4474603 r4", "0:27 1:120.47", "A:9576940269;C:6855014912;G:7203590871;T:9501520990;N:21476508", 27, 120, null, null, 9576940269, 6855014912, 7203590871, 9501520990, 21476508, "SRX8111241", "SRS6476315", "SRA1065111", "GEO", "Crump Lab, Stem Cell, USC", 2, 0.00273, 0.8878, 0.00089, 0.16918, 0.99494, 0.81801, 0.51694, 0.58973, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:35088828", null, "Pancreas 14dpa", "GSM5060849", null, "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", null, "Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.", null, "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", null, "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", null, "SRP304424", null, null, "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, null, null, 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", null, "Germany", "2021-02-02", "Adult", "Adult", "Pancreas", "Endocrine System"], [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.", null, "pubmed:35088828", null, "Pancreas 7dpa", "GSM5060848", null, "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", null, "Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.", null, "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", null, "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", null, "SRP304424", null, null, "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, null, null, 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", null, "Germany", "2021-02-02", "Adult", "Adult", "Pancreas", "Endocrine System"], [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.", null, "pubmed:35088828", null, "Pancreas 2dpa", "GSM5060847", null, "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", null, "Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.", null, "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", null, "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", null, "SRP304424", null, null, "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, null, null, 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", null, "Germany", "2021-02-02", "Adult", "Adult", "Pancreas", "Endocrine System"], [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.", null, "pubmed:35088828", null, "Pancreas 0dpa", "GSM5060846", null, "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", null, "Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.", null, "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", null, "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", null, "SRP304424", null, null, "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, null, null, 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", null, "Germany", "2021-02-02", "Adult", "Adult", "Pancreas", "Endocrine System"], [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.", null, "pubmed:35088828", null, "Pancreas Control", "GSM5060845", null, "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", null, "Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.", null, "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", null, "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", null, "SRP304424", null, null, "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, null, null, 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", null, "Germany", "2021-02-02", "Adult", "Adult", "Pancreas", "Endocrine System"]], "truncated": false, "filtered_table_rows_count": 26, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", 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prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "10x", "p2": "Endocrine System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=10x&tissue_curation_coarse=Endocrine+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 25, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=10x&tissue_curation_coarse=Endocrine+System&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": 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