|
Status |
Public on Sep 09, 2014 |
Title |
AFF4_DOX_rep2 |
Sample type |
SRA |
|
|
Source name |
HeLa
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa treatment: AFF4 was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11 antibody: non-commercial rabbit anti-AFF4 Ref PMID 20159561 source: IP with non-commercial rabbit anti-AFF4 Ref PMID 20159561 sample type: ChIP-seq
|
Treatment protocol |
Inducible cell clones were trated with doxycycline 1microgr/ml 72h before collection. EGF stimulation was performed for 20 minutes with 100ng/ml of recombinant EGF. RNA were extracted using QIAGEN Rneasy columns with on column DNAse treatment.
|
Growth protocol |
Wild-type Hela cells were cultivated in DMEM 10% FBS, starvation was performed for 48h in 0.5% FBS before EGF treatment
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP-Seq DNA Sample Prep Kit (Illumina, inc.)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
AFF4 was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11
|
Data processing |
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters) base calling: Bustard (Illumina pipeline 1.9, default parameters) alignment (ChIPseq, RNAseq and GROseq)) bowtie 2.1.0 (end-to-end , sensitive)) tag density files RSeQC package was used to generate BigWiggle files Genome_build: hg 19 Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using RSeqQC package and the wigtobigWig script provided by UCSC. BedGraph were generated using the Bedtools package
|
|
|
Submission date |
Jun 05, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Alessandro Gardini |
E-mail(s) |
agardini@wistar.org
|
Phone |
305-243-7394
|
Organization name |
University of Miami
|
Department |
Sylvester Comprehensive Cancer Center
|
Lab |
Ramin Shiekhattar
|
Street address |
1501 NW 10 Avenue
|
City |
Miami |
State/province |
FL |
ZIP/Postal code |
33136 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE40632 |
Genome-wide analysis of the Integrator complex (HTS) |
GSE58255 |
Genome-wide analysis of the Integrator complex |
|
Relations |
BioSample |
SAMN02839536 |
SRA |
SRX573033 |