run_metadata: 59127
This data as json
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| 59127 | SRR11684036 | SRX8244839 | SRS6592474 | SRP259990 | PRJNA630162 | Zebrafish adult skin mpeg+ cells | GSE149788 | Transcriptome Analysis | We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype | parent bioproject:PRJNA630158 | pubmed:32367800 | GFE4 B Switch.1 | GSM4512728 | tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated | GFE4 B Switch.1 | Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files | skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells | RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix | Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle | developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated | GSM4512728 | GSM4512728: GFE4 B Switch.1; Danio rerio; RNA Seq | GSM4512728 | 1 | RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix | GEO Accession:GSM4512728 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP259990 | so-zf94_GFE4-B-Switch_WT_S4_R2_001.fastq.gz so-zf94_GFE4-B-Switch_WT_S4_R1_001.fastq.gz | fastq fastq | 10963685744.0 | 54275672.0 | GSM4512728 r1 | 0:101 1:101 | A:2843051618;C:2733369632;G:2559200274;T:2827894333;N:169887 | 101 | 101 | 2843051618 | 2733369632 | 2559200274 | 2827894333 | 169887 | SRX8244839 | SRS6592474 | SRA1072141 | GEO | Erasmus MC | 2 | 0.81437 | 0.80007 | 0.30275 | 0.3056 | 0.7933 | 0.79427 | 0.60512 | 0.50903 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Netherlands | 2020-05-04 | Adult | Adult | Skin | Surface Structure |