|
| Status |
Public on Apr 03, 2013 |
| Title |
RNA-seq:KAP1 WT activated |
| Sample type |
SRA |
| |
|
| Source name |
HEL cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human erythroleukemia cell line, HEL
genotype/variation: KAP1 WT
activation: hemin
|
| Treatment protocol |
HEL were activated in presence of hemin at a final concentration of 50 micromolar during five days
|
| Growth protocol |
no growth protocol for CD71+Ter119+ cells. HEL are cultured in RPMI 10%
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TZrizol according to Manufacturer protocol.
The library was generated from 250 ng total RNA using the TruSeq RNA Sample Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Cells were activated (or not) in presence of hemin at a final concentration of 50 micromolar during five days. RNA was extracted using TZrizol according to Manufacturer protocol.
Processed data file: HELKAP1KDvsCtrl_RNAseq.txt
|
| Data processing |
Raw reads were mapped to the mouse genome and human transcriptome using Bowtie
Peaks were called using MACS
RPKM values were calculated using R/Bioconductor
Genome_build: hg19 (human)
Supplementary_files_format_and_content: .txt file include RPKM values for each Sample (linked as supplementary file on Series record)
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Adamandia Kapopoulou |
| E-mail(s) |
adamandia.kapopoulou@epfl.ch
|
| Phone |
0041216930940
|
| Organization name |
EPFL
|
| Department |
Sciences de la Vie
|
| Lab |
Trono
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE44061 |
KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy [Seq] |
| GSE44065 |
KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy |
|
| Relations |
| SRA |
SRX225206 |
| BioSample |
SAMN01911265 |
