run_metadata: 63455
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 63455 | SRR13839920 | SRX10218310 | SRS8362895 | SRP309041 | PRJNA706190 | Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling | GSE168131 | Transcriptome Analysis | The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS. | parent bioproject:PRJNA706402 | pubmed:34936864 | Low Wnt NC cells 1 | GSM5129520 | tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt | Low Wnt NC cells 1 | reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample | FACS sorted NC cells | Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol. | genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt | GSM5129520 | GSM5129520: Low Wnt NC cells 1; Danio rerio; RNA Seq | GSM5129520 | 1 | Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol. | GEO Accession:GSM5129520 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP309041 | loader:fastq load.py | nR032-L4-G1-P013-TCCTGA-READ1-Sequences.txt nR032-L4-G1-P013-TCCTGA-READ2-Sequences.txt | fastq fastq | 3857437450.0 | 19096225.0 | GSM5129520 r1 | 0:101 1:101 | A:929676756;C:1024088841;G:880029487;T:1023570451;N:71915 | 101 | 101 | 929676756 | 1024088841 | 880029487 | 1023570451 | 71915 | SRX10218310 | SRS8362895 | SRA1202348 | GEO | Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine | 2 | 0.93694 | 0.94084 | 0.0529 | 0.05308 | 0.76161 | 0.76079 | 0.51761 | 0.52186 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | United States | 2021-03-03 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |