run_metadata: 63458
This data as json
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| 63458 | SRR13839917 | SRX10218307 | SRS8362893 | 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 | High Wnt NC cells 1 | GSM5129517 | tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt | High 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:High Wnt | GSM5129517 | GSM5129517: High Wnt NC cells 1; Danio rerio; RNA Seq | GSM5129517 | 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:GSM5129517 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP309041 | loader:fastq load.py | nR032-L4-G1-P010-TAAGGC-READ1-Sequences.txt nR032-L4-G1-P010-TAAGGC-READ2-Sequences.txt | fastq fastq | 3745434914.0 | 18541757.0 | GSM5129517 r1 | 0:101 1:101 | A:936339102;C:939766668;G:898475105;T:970783756;N:70283 | 101 | 101 | 936339102 | 939766668 | 898475105 | 970783756 | 70283 | SRX10218307 | SRS8362893 | SRA1202348 | GEO | Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine | 2 | 0.91218 | 0.92961 | 0.05044 | 0.05165 | 0.75463 | 0.75373 | 0.52717 | 0.52628 | 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 |