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  • Endocrine System · 26 ✖

technology 1

  • 10x · 26 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 26 ✖

experiment.library_layout 1

Link 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 run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
43988 43988 SRR6811827 SRX3768867 SRS3023384 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 3 endo scar GSM3032170   source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult Pancreas 3 endo scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Primary pancreatic islet   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult GSM3032170 GSM3032170: Pancreas 3 endo scar; Danio rerio; OTHER GSM3032170   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032170 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     P7endo_scar_R1.fastq.gz P7endo_scar_R2.fastq.gz fastq fastq 2537781396.0 20465979.0 GSM3032170 r1 0:26 1:98 A:741745261;C:801599713;G:561531527;T:431666561;N:1238334 26 98     741745261 801599713 561531527 431666561 1238334 SRX3768867 SRS3023384 SRA623333 GEO Max Delbrück Center 2 0.00014 0.00289 0.00012 0.00028 0.99995 0.99602 1.0 0.68478 26 98 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Pancreas Endocrine System
43994 43994 SRR6811821 SRX3768861 SRS3023378 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 3 endo mRNA GSM3032164   source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult Pancreas 3 endo mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Primary pancreatic islet   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult GSM3032164 GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq GSM3032164   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     P7endo_wt_R1.fastq.gz P7endo_wt_R2.fastq.gz fastq fastq 41593781900.0 335433725.0 GSM3032164 r1 0:26 1:98 A:11833690021;C:9547054378;G:9724089290;T:10470148302;N:18799909 26 98     11833690021 9547054378 9724089290 10470148302 18799909 SRX3768861 SRS3023378 SRA623333 GEO Max Delbrück Center 2 0.00308 0.92936 0.00192 0.05695 0.9973 0.8686 0.45945 0.58814 26 98 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Pancreas Endocrine System
50847 50847 SRR8312900 SRX5126276 SRS4139398 SRP173304 PRJNA509469 Single cell RNA sequencing of zebrafish pancreatic cells GSE123662 Other The pancreatic beta cells regulate blood glucose levels by secreting the hormone insulin in response to increasing glucose levels. Recent work has identified molecular and functional heterogeneity among the beta cell community. To ontain an unbiased picture into the molecular heterogeneity present in zebrafish pancreatic cells we performed droplet based next generation sequencing of individual pancreatic cells. Using unsupervised clustering we could identify all the major cell types present in the pancreas. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile pancreatic cells from zebrafish. Pancreatic islets from six animals were dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense'. Genome sequence and filtered annotation were then used as input to the 'mkref' command of Cell Ranger to build the appropriate Cellranger Reference.   pubmed:32694805   2mpf Pancreas GSM3509161   tissue:pancreatic cells|age:2mpf|strain:Tgins:BB1.0L|disease state:Normal 2mpf Pancreas The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ‘ expect cells’ set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger options: ‘ attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: csv format with rows as genes and columns as cells pancreatic cells   Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol.   age:2mpf|strain:Tgins:BB1.0L|disease state:Normal GSM3509161 GSM3509161: 2mpf Pancreas; Danio rerio; RNA Seq GSM3509161   1 Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer's protocol. GEO Accession:GSM3509161 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP173304     s2mpf_R1.fastq.gz s2mpf_R2.fastq.gz fastq fastq 3682641276.0 44369172.0 GSM3509161 r1 0:26 1:57 A:950388419;C:876060179;G:944476013;T:911635661;N:81004 26 57     950388419 876060179 944476013 911635661 81004 SRX5126276 SRS4139398 SRA822849 GEO Single Cell Endocrinology, IRIBHM 2 0.00373 0.9564 0.0008 0.03195 0.99508 0.9024 0.38273 0.59374 26 57 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2018-12-11 Juvenile Juvenile Pancreas Endocrine System
50860 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.   pubmed:31178320   scSeq2 GSM3511193   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   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’ 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.   tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month GSM3511193 GSM3511193: scSeq2; Danio rerio; RNA Seq GSM3511193   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   SRP173374     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     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   Israel 2018-12-13 Adult Adult Pineal Gland Endocrine System
50861 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.   pubmed:31178320   scSeq2 GSM3511193   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   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’ 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.   tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month GSM3511193 GSM3511193: scSeq2; Danio rerio; RNA Seq GSM3511193   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   SRP173374     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     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   Israel 2018-12-13 Adult Adult Pineal Gland Endocrine System
50862 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.   pubmed:31178320   scSeq1 GSM3511192   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   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’ 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.   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   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   SRP173374     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     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   Israel 2018-12-13 Adult Adult Pineal Gland Endocrine System
50863 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.   pubmed:31178320   scSeq1 GSM3511192   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   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’ 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.   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   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   SRP173374     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     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   Israel 2018-12-13 Adult Adult Pineal Gland Endocrine System
52953 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: ' …       8mpf Thyroid GSM3909772   tissue:thyroid gland|treatment:8mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal 8mpf Thyroid 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 –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells. thyroid gland   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 – was performed based on the manufacturer’s protocol.   treatment:8mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal GSM3909772 GSM3909772: 8mpf Thyroid; Danio rerio; RNA Seq GSM3909772   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 – was performed based on the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP212225     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     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   Belgium 2019-06-27 Adult Adult Thyroid Endocrine System
52954 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: ' …       2mpf Thyroid GSM3909771   tissue:thyroid gland|treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal 2mpf Thyroid 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 –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells. thyroid gland   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 – was performed based on the manufacturer’s protocol.   treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal GSM3909771 GSM3909771: 2mpf Thyroid; Danio rerio; RNA Seq GSM3909771   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 – was performed based on the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP212225     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     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   Belgium 2019-06-27 Juvenile Juvenile Thyroid Endocrine System
58918 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.   pubmed:33093109   Transplant GSM4474605   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58919 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.   pubmed:33093109   Transplant GSM4474605   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58920 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.   pubmed:33093109   Transplant GSM4474605   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58921 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.   pubmed:33093109   Transplant GSM4474605   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58922 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.   pubmed:33093109   Male1 GSM4474604   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58923 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.   pubmed:33093109   Male1 GSM4474604   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58924 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.   pubmed:33093109   Male1 GSM4474604   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58925 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.   pubmed:33093109   Male1 GSM4474604   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58926 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.   pubmed:33093109   Males GSM4474603   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58927 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.   pubmed:33093109   Males GSM4474603   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58928 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.   pubmed:33093109   Males GSM4474603   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
58929 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.   pubmed:33093109   Males GSM4474603   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   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   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   SRP256300     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     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   United States 2020-04-13 Adult Adult Pituitary Gland Endocrine System
63128 63128 SRR13616487 SRX10009741 SRS8178664 SRP304424 PRJNA699078 Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration GSE166052 Transcriptome Analysis To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.   pubmed:35088828   Pancreas 14dpa GSM5060849   tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 14 days post MTZ Pancreas 14dpa bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices Zebrafish pancreas   Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.   strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 14 days post MTZ GSM5060849 GSM5060849: Pancreas 14dpa; Danio rerio; RNA Seq GSM5060849   1 Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. GEO Accession:GSM5060849 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP304424     L59491_Track-100378_R1.fastq.gz L59491_Track-100378_R2.fastq.gz fastq fastq 21882647280.0 168328056.0 GSM5060849 r1 0:29 1:101 A:5304415368;C:5193690448;G:5721535951;T:5662241808;N:763705 29 101     5304415368 5193690448 5721535951 5662241808 763705 SRX10009741 SRS8178664 SRA1190924 GEO Ninov Lab, CRTD, TU Dresden 2 0.0137 0.94318 0.00185 0.03707 0.99263 0.91078 0.60061 0.58256 29 101 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-02 Adult Adult Pancreas Endocrine System
63129 63129 SRR13616486 SRX10009740 SRS8178663 SRP304424 PRJNA699078 Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration GSE166052 Transcriptome Analysis To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.   pubmed:35088828   Pancreas 7dpa GSM5060848   tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 7 days post MTZ Pancreas 7dpa bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices Zebrafish pancreas   Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.   strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 7 days post MTZ GSM5060848 GSM5060848: Pancreas 7dpa; Danio rerio; RNA Seq GSM5060848   1 Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. GEO Accession:GSM5060848 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP304424     L47897_Track-91889_R1.fastq.gz L47897_Track-91889_R2.fastq.gz fastq fastq 11982402020.0 98216410.0 GSM5060848 r1 0:29 1:93 A:3162707284;C:2774571882;G:2736678637;T:3307378654;N:1065563 29 93     3162707284 2774571882 2736678637 3307378654 1065563 SRX10009740 SRS8178663 SRA1190924 GEO Ninov Lab, CRTD, TU Dresden 2 0.01025 0.93044 0.00221 0.066 0.98938 0.85823 0.52941 0.62147 29 93 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-02 Adult Adult Pancreas Endocrine System
63130 63130 SRR13616485 SRX10009739 SRS8178662 SRP304424 PRJNA699078 Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration GSE166052 Transcriptome Analysis To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.   pubmed:35088828   Pancreas 2dpa GSM5060847   tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 2 days post MTZ Pancreas 2dpa bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices Zebrafish pancreas   Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.   strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 2 days post MTZ GSM5060847 GSM5060847: Pancreas 2dpa; Danio rerio; RNA Seq GSM5060847   1 Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. GEO Accession:GSM5060847 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP304424     L47899_Track-88823_R1.fastq.gz L47899_Track-88823_R2.fastq.gz fastq fastq 12079250378.0 99010249.0 GSM5060847 r1 0:29 1:93 A:3187642396;C:2755358695;G:2795295173;T:3340653508;N:300606 29 93     3187642396 2755358695 2795295173 3340653508 300606 SRX10009739 SRS8178662 SRA1190924 GEO Ninov Lab, CRTD, TU Dresden 2 0.00631 0.94202 0.00135 0.0615 0.99123 0.84307 0.55742 0.56593 29 93 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-02 Adult Adult Pancreas Endocrine System
63131 63131 SRR13616484 SRX10009738 SRS8178661 SRP304424 PRJNA699078 Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration GSE166052 Transcriptome Analysis To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.   pubmed:35088828   Pancreas 0dpa GSM5060846   tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 0 days post MTZ Pancreas 0dpa bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices Zebrafish pancreas   Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.   strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 0 days post MTZ GSM5060846 GSM5060846: Pancreas 0dpa; Danio rerio; RNA Seq GSM5060846   1 Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. GEO Accession:GSM5060846 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP304424     L59306_Track-100369_R1.fastq.gz L59306_Track-100369_R2.fastq.gz fastq fastq 19138165410.0 147216657.0 GSM5060846 r1 0:29 1:101 A:4905247743;C:4584481588;G:4969548524;T:4678220753;N:666802 29 101     4905247743 4584481588 4969548524 4678220753 666802 SRX10009738 SRS8178661 SRA1190924 GEO Ninov Lab, CRTD, TU Dresden 2 0.02866 0.88637 0.00798 0.14499 0.99105 0.87251 0.51922 0.57508 29 101 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-02 Adult Adult Pancreas Endocrine System
63132 63132 SRR13616483 SRX10009737 SRS8178660 SRP304424 PRJNA699078 Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration GSE166052 Transcriptome Analysis To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics.   pubmed:35088828   Pancreas Control GSM5060845   tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:Untreated|time point:Untreated Pancreas Control bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices Zebrafish pancreas   Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol.   strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:Untreated|time point:Untreated GSM5060845 GSM5060845: Pancreas Control; Danio rerio; RNA Seq GSM5060845   1 Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. GEO Accession:GSM5060845 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP304424     L47898_Track-88822_R1.fastq.gz L47898_Track-88822_R2.fastq.gz fastq fastq 8952747472.0 73383176.0 GSM5060845 r1 0:29 1:93 A:2223721886;C:2087634305;G:2235052745;T:2406116444;N:222092 29 93     2223721886 2087634305 2235052745 2406116444 222092 SRX10009737 SRS8178660 SRA1190924 GEO Ninov Lab, CRTD, TU Dresden 2 0.00837 0.9475 0.00144 0.0366 0.99263 0.88759 0.58964 0.57851 29 93 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2021-02-02 Adult Adult Pancreas Endocrine System

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