run_metadata: 61988
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 61988 | SRR13089283 | SRX9535221 | SRS7741720 | SRP293304 | PRJNA679624 | A Cell Atlas of Microbe Responsive Processes in the Zebrafish Intestine | GSE161855 | Transcriptome Analysis | To understand intestinal cell specific responses to host commensal bacteria we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single cell RNA seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue and describe distinct microbial responses in each cell type. Overall design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single cell suspension for sequencing on the 10X Genomics platform. | pubmed:35108531 | Germ free Sample 2 | GSM4916094 | tissue:Dissociated intestines from germ free fish|genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:germ free | Germ free Sample 2 | Cell Ranger v3.0 10X Genomics was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome Genome build: Ensembl GRCz11.96 Supplementary files format and content: TSV/MTX files | Dissociated intestines from germ free fish | Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3 | genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:germ free | GSM4916094 | GSM4916094: Germ free; Danio rerio; RNA Seq | GSM4916094 | 1 | Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3 | GEO Accession:GSM4916094 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP293304 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=GF S2 L003 I1 001.fastq.gz read2PairFiles=GF S2 L003 R1 001.fastq.gz read3PairFiles=GF S2 L003 R2 001.fastq.gz | GF_S2_L003_I1_001.fastq.gz GF_S2_L003_R1_001.fastq.gz GF_S2_L003_R2_001.fastq.gz | fastq fastq fastq | 67406082128.0 | 218850916.0 | GSM4916094 r1 | 0:8 1:150 2:150 | A:16033538561;C:12891030760;G:13419497134;T:25045893164;N:16122509 | 8 | 150 | 150 | 16033538561 | 12891030760 | 13419497134 | 25045893164 | 16122509 | SRX9535221 | SRS7741720 | SRA1161597 | GEO | 6-59 HMRC, Medical Microbiology and Immunology, University of Alberta | 1 | 0.92012 | 0.08227 | 0.87988 | 0.70616 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Canada | 2020-11-19 | Larval | Larval | Gut | Digestive System |