run_metadata: 64242
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| 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 |
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| 64242 | SRR14367978 | SRX10720520 | SRS8810970 | SRP317951 | PRJNA726184 | Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine | GSE173570 | Transcriptome Analysis | The purpose of this study was to elucidate potential effects of fxr mutation on the functional specification of intestinal epithelial cells. To do this we sorted GFP positive cells from TgBACcldn15la:GFP transgenics of either fxr+/+ or fxr / fish larvae and subjected them to 10X Genomics single cell RNA seq. Our results uncovered the requirement of fxr in gene expression and differentiation among multiple intestinal epithelial cell types. Overall design: Analysis of sorted cells from 6 dpf zebrafish larvae that were either fxr+/+ WT or fxr / MUT | pubmed:34301599 | fxr +/+ zebrafish intestinal epithelial cells | GSM5270962 | source name:Intestine|transgenic background:TgBACcldn15la:GFP|age:6 dpf|genotype:fxr +/+|tissue:Intestine|cell type:intestinal epithelial cells|sorting fluorescence:GFP+ 7AAD | fxr +/+ zebrafish intestinal epithelial cells | UMIs were demultiplexed and reads were aligned to the reference genome danRer11 following the CellRanger pipeline In Seurat 3.1.0 https://satijalab.org/seurat/ cell barcodes with <3000 detected genes >30 000 UMIs >25% mitochondrial transcripts were removed. Log normalized and integrated datasets based on WT library Scaled data and performed PCA with 100 priciple components Ran UMAP dimensionality reduction with 54 principle components Used FindNeighbors and FindClusters function at resolution of 0.82 Ran UMAP dimensionality reduction with 54 principle components Genome build: danRer11 Supplementary files format and content: count matrix | Intestine | Larvae zebrafish were dissociated using standard protocol post which the fxr+/+; TgBACcldn15la GFP and fxr / ; TgBACcldn15la GFP cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non transgenic and single transgenic controls pools of 50 fish/genotype were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7 AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat inactivated FBS and 10 μM Y 27632 ROCK1 inhibitor and were immediately subjected to the library construction. Each single cell RNA sequencing library was generated from 10 000 FACS sorted TgBACcldn15la GFP IECs of the indicated genotype following the 10x Genomics Single Cell 3’ protocol by the Duke Molecular Genomics Core. The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences a sample index and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell. | Approximately 600 dpf 700 dpf 6 dpf TgBACcldn15la GFP zebrafish larvae of the fxr+/+ and the fxr / genotypes were collected for the FACS experiment respectively. | transgenic background:TgBACcldn15la:GFP|age:6 dpf|genotype:fxr +/+|tissue:Intestine|cell type:intestinal epithelial cells|sorting fluorescence:GFP+ 7AAD | GSM5270962 | GSM5270962: fxr +/+ zebrafish intestinal epithelial cells; Danio rerio; RNA Seq | GSM5270962 | 1 | Larvae zebrafish were dissociated using standard protocol post which the fxr+/+; TgBACcldn15la GFP and fxr / ; TgBACcldn15la GFP cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non transgenic and single transgenic controls pools of 50 fish/genotype were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7 AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat inactivated FBS and 10 μM Y 27632 ROCK1 inhibitor and were immediately subjected to the library construction. Each single cell RNA sequencing library was generated from 10 000 FACS sorted TgBACcldn15la GFP IECs of the indicated genotype following the 10x Genomics Single Cell three prime protocol by the Duke Molecular Genomics Core. The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences a sample index and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell. | GEO Accession:GSM5270962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP317951 | intentional duplicate | WT_bam.bam | 10X Genomics bam file | 41992986763.0 | 461461393.0 | GSM5270962 r1 | 0:91 | A:12152716332;C:8974304021;G:9433492952;T:11389979720;N:42493738 | 91 | 12152716332 | 8974304021 | 9433492952 | 11389979720 | 42493738 | SRX10720520 | SRS8810970 | SRA1225807 | GEO | John Rawls, Molecular Genetics & Microbiology, Duke University | 1 | 0.92473 | 0.17567 | 0.81688 | 0.59128 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc | single_cell_droplet | 10x | United States | 2021-04-29 | Larval | Larval | Gut | Digestive System |