|
Status |
Public on Apr 03, 2013 |
Title |
RNA-seq:KAP1 KD activated |
Sample type |
SRA |
|
|
Source name |
HEL cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: human erythroleukemia cell line, HEL genotype/variation: KAP1 KD 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 |
SRX225204 |
BioSample |
SAMN01911263 |