|
| Status |
Public on Nov 30, 2022 |
| Title |
(Bulk RNA-Seq) 5dpf b9d2 KO Replicate #1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryos
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryos
genotype: b9d2 KO
time point: Day 5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
30-35 2-dpf or 5-dpf zebrafish embryos were pooled to extract RNA with Qiagen Rneasy Plus Mini Kit
The library was prepared with Illumina RNA with PolyA selection package and sequenced with Illumina HiSeq 2x150bp, single index
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq raw reads were trimmed with TrimGalore 0.4.4
Trimmed reads were aligned to Danio rerio GRCz11 with Star 2.7.3a with default setting
Expression counts were calculated with HTSeq-count 0.12.3 with default setting
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each sample
|
| |
|
| Submission date |
Nov 01, 2022 |
| Last update date |
Dec 01, 2022 |
| Contact name |
John M Parant |
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1670 University Blvd
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35233 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE217001 |
Variable phenotypes and penetrance between and within different zebrafish transition zone mutants |
|
| Relations |
| BioSample |
SAMN31557291 |
| SRA |
SRX18108805 |
