run_metadata: 68666
This data as json
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| 68666 | SRR18124526 | SRX14274933 | SRS12093624 | SRP361285 | PRJNA809951 | A lysosomal regulatory circuit essential for the development and function of microglia | GSE197349 | Transcriptome Analysis | We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS RNA was extracted and sequencing was performed. | parent bioproject:PRJNA809950 | pubmed:36044568 | rraga mutant macrophage sample biological replicate 4 | GSM5914975 | tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages | rraga mutant macrophage sample biological replicate 4 | Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data Q20 Q30 and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts normalized FPKM reads for genes identified by gene name and ENSEMBL ID | Macrophages | Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS. | RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit | Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU | genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages | GSM5914975 | GSM5914975: rraga mutant macrophage sample biological replicate 4; Danio rerio; RNA Seq | GSM5914975 r1 | GSM5914975 | 1 | RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP361285 | loader:fastq load.py | RRGA5_S63_1.fq.gz RRGA5_S63_2.fq.gz | fastq fastq | 16056097500.0 | 53520325.0 | GSM5914975 r1 | 0:150 1:150 | A:4294601650;C:3737735522;G:3760015896;T:4263588285;N:156147 | 150 | 150 | 4294601650 | 3737735522 | 3760015896 | 4263588285 | 156147 | SRX14274933 | SRS12093624 | SRA1377812 | Talbot, Developmental Biology, Stanford University | Talbot, Developmental Biology, Stanford University | 2 | 0.94205 | 0.93992 | 0.04764 | 0.04795 | 0.76278 | 0.76512 | 0.48852 | 0.48702 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | United States | 2022-02-24 | Larval | Larval | Blood | Hematopoietic System |