run_metadata: 71453
This data as json
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| 71453 | SRR21631156 | SRX17631564 | SRS15166367 | SRP398129 | PRJNA882122 | Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish | GSE213728 | Transcriptome Analysis | Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2. | tNCCs treated 100uM cyclopamine Sample4 | GSM6592894 | source name:neural crest cells|tissue:neural crest cells|genotype:wildtype|treatment:100uM Cyclopamine 50%epiboly to 24hpf|geo loc name:missing|collection date:missing | tNCCs treated 100uM cyclopamine Sample4 | Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file | neural crest cells | For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf | standard Illumina Kit for stranded RNAseq | Embryos reared at 28C until 24hpf. | tissue:neural crest cells|genotype:wildtype|treatment:100uM Cyclopamine 50%epiboly to 24hpf | GSM6592894 | GSM6592894: tNCCs treated 100uM cyclopamine Sample4; Danio rerio; RNA Seq | GSM6592894 r1 | GSM6592894 | 1 | standard Illumina Kit for stranded RNAseq | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP398129 | loader:fastq load.py | S1_100uM_RFP_S41_L001_R1_001.fastq.gz S1_100uM_RFP_S41_L001_R2_001.fastq.gz | fastq fastq | 13002170590.0 | 43053545.0 | GSM6592894 r1 | 0:151 1:151 | A:3161816467;C:2810101954;G:4085613729;T:2944516445;N:121995 | 151 | 151 | 3161816467 | 2810101954 | 4085613729 | 2944516445 | 121995 | SRX17631564 | SRS15166367 | SRA1501497 | Lencer Laboratory, Department of Biology, Lafayette College | Lencer Laboratory, Department of Biology, Lafayette College | 2 | 0.87647 | 0.86789 | 0.10005 | 0.09935 | 0.77439 | 0.77646 | 0.48741 | 0.49136 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2022-09-19 | Multi-stage | Embryo | Brain | Nervous System |