|
| Status |
Public on Dec 13, 2022 |
| Title |
Mut3 |
| Sample type |
SRA |
| |
|
| Source name |
endothelial cells
|
| Organism |
Danio rerio |
| Characteristics |
time: 28 hours post fertilization
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
kdrl-positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep (Zymo). Ribosomal RNA was depleted with Ribogone (Clontech).
Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA-Seq Kit (Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
rRNA-depleted
|
| Data processing |
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM, Cufflinks (version 2.2.1) was used.
Assembly: GRcz10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Jun 13, 2022 |
| Last update date |
Dec 13, 2022 |
| Contact name |
Teresa Bowman |
| E-mail(s) |
teresa.bowman@einsteinmed.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL21741 |
| Series (2) |
| GSE206017 |
RNA-seq of endothelial cells from 28 hours post fertilization sf3b1 mutant and sibling zebrafish |
| GSE206021 |
SF3B1 |
|
| Relations |
| BioSample |
SAMN29012028 |
| SRA |
SRX15688383 |
