|
| Status |
Public on Jan 14, 2022 |
| Title |
runx1-/- kidney1 |
| Sample type |
SRA |
| |
|
| Source name |
adult kidney
|
| Organism |
Danio rerio |
| Characteristics |
strain: EK
genotype/variation: runx1-/- (del25, hg97)
age: 2.5 months
tissue: kidney
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from ~2.5 months old fish (n= 3 for each genotype, pool of 3 kidneys/replicate) and immediately collected in Trizol (#15596018, Invitrogen). Samples were then put in a heatblock at 52oC for 10 min and then overnight in -80oC. RNA was extracted following the manufacturer protocol using Direct-zolTM RNA MiniPrep Kit (Zymo Research #R2051).
Sequencing libraries were prepared using paired-end library preparation (TruSeq RNA Library Prep Kit v2).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
runx1_del25_null_4
|
| Data processing |
RNA-seq reads were aligned to the zebrafish genome reference (GRCz10) and transcript reference (GRCz10.87) using STAR (v2.5.26).
We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix.
Genome_build: GRCz10
Supplementary_files_format_and_content: *.count.txt: Gene expression count matrix.
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Jan 15, 2022 |
| Contact name |
Kai Yu |
| E-mail(s) |
kai.yu@nih.gov
|
| Organization name |
NHGRI
|
| Street address |
50 South Drive, Bldg 50, Room 5151
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE158098 |
Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development |
| GSE158101 |
Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development |
|
| Relations |
| BioSample |
SAMN16191102 |
| SRA |
SRX9139720 |
