run_metadata: 65633
This data as json
| 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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| 65633 | SRR15427704 | SRX11729087 | SRS9757823 | SRP332278 | PRJNA754150 | Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver | GSE181987 | Other | Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 GSM5515733 joint fish human GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt. | pubmed:35315595 | MPI MT 3 | GSM5515736 | source name:Adult zebrafish liver dissection|genotype:mpi+/ mss7|tissue:Liver | MPI MT 3 | FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11 | Adult zebrafish liver dissection | Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium | Adult fish were maintained on a 14:10 light/dark cycle at 28°C. | genotype:mpi+/ mss7|tissue:Liver | GSM5515736 | GSM5515736: MPI MT 3; Danio rerio; RNA Seq | GSM5515736 | 1 | Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium | GEO Accession:GSM5515736 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP332278 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT5 0 G S8 L001 I1 001.fastq.gz read2PairFiles=JACH01 MT5 0 G S8 L001 R1 001.fastq.gz read3PairFiles=JACH01 MT5 0 G S8 L001 R2 001.fastq.gz | JACH01_MT5_0_G_S8_L001_I1_001.fastq.gz JACH01_MT5_0_G_S8_L001_R1_001.fastq.gz JACH01_MT5_0_G_S8_L001_R2_001.fastq.gz | fastq fastq fastq | 12954775700.0 | 129547757.0 | GSM5515736 r1 | 0:8 1:30 2:62 | A:2373305749;C:1813473007;G:1779922398;T:2065049504;N:210276 | 8 | 30 | 62 | 2373305749 | 1813473007 | 1779922398 | 2065049504 | 210276 | SRX11729087 | SRS9757823 | SRA1277309 | GEO | Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai | 1 | 0.94564 | 0.06912 | 0.88712 | 0.74857 | 62 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-12 | Adult | Adult | Liver | Liver and Biliary System |