run_metadata: 62906
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 62906 | SRR13429039 | SRX9843971 | SRS8025680 | SRP301615 | PRJNA691919 | A single cell transcriptomic atlas identifies synapse associated microglia in the developing zebrafish single cells | GSE164772 | Transcriptome Analysis | This study profiles developing and adult zebrafish macrophages and defines regional and functional microglial subtypes. Overall design: Macrophages Mpeg+ and CD45+ cells were sorted and sequenced from 28 dpf and 6 mpf zebrafish | pubmed:34625548 | Juvenile A | GSM5018534 | tissue:Brain and Spinal Cord Mpeg+ and CD45+|age:28 dpf A|cell type:Mpeg+ myeloid cells and CD45+ immune cells | Juvenile A | Cell Ranger 3.1.0 STAR alignment with Danio rerio zebrafish transcriptome z11 Quality control to select cells with <10% mitochondrial RNA 500 3 000 unique genes and 1 200 15 000 unique mRNA counts [scaledata only] Log normalization Seurat v3.2 with scale factor 10 000 [scaledata only] most variable genes scaled with "vst" algorithm and #genes/cell regressed out Seurat v3.2 Genome build: z11 Supplementary files format and content: Counts: unnormalized count data for all cells included in the manuscript Supplementary files format and content: Metadata: file containing age individual and cluster assignment for each cell Supplementary files format and content: sc dr Silva2021Counts.txt: All cells in paper Supplementary files format and content: sc dr Silva2021 metadata.csv: All cells in paper Supplementary files format and content: sc dr Silva2021 JMscaledata.txt: Juvenile Mpeg+ cells Supplementary files format and content: sc dr Silva2021 Jscaledata.txt: All Juvenile cells Supplementary files format and content: sc dr Silva2021 Ascaledata.txt: Adult and Juvenile Mpeg+ cells | Brain and Spinal Cord Mpeg+ and CD45+ | Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA | age:28 dpf A|cell type:Mpeg+ myeloid cells and CD45+ immune cells | GSM5018534 | GSM5018534: Juvenile A; Danio rerio; RNA Seq | GSM5018534 | 1 | Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA | GEO Accession:GSM5018534 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP301615 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Sample1 L1 S1 L001 I1 001.fastq.gz read2PairFiles=Sample1 L1 S1 L001 R1 001.fastq.gz read3PairFiles=Sample1 L1 S1 L001 R2 001.fastq.gz | Sample1-_L1__S1_L001_I1_001.fastq.gz Sample1-_L1__S1_L001_R1_001.fastq.gz Sample1-_L1__S1_L001_R2_001.fastq.gz | fastq fastq fastq | 12770179370.0 | 98232149.0 | GSM5018534 r1 | 0:8 1:28 2:94 | A:3657439948;C:2724528296;G:2851650695;T:3529904486;N:6655945 | 8 | 28 | 94 | 3657439948 | 2724528296 | 2851650695 | 3529904486 | 6655945 | SRX9843971 | SRS8025680 | SRA1183553 | GEO | Anna Molofsky Lab, Psychiatry, UCSF | 1 | 0.89472 | 0.26792 | 0.78837 | 0.55341 | 94 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2021-01-13 | Larval | Larval | Multi-tissue | Multi-system |