|
Status |
Public on Aug 25, 2015 |
Title |
DOX_EGF_NELFA_rep1 |
Sample type |
SRA |
|
|
Source name |
HeLa cell line
|
Organism |
Homo sapiens |
Characteristics |
cell type: Hela cell line treatment: doxycyclin EGF antibody: IP with goat antibody sc-23599 (Santa Cruz)
|
Treatment protocol |
Inducible cell clones were treated 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: NEBNext ChIP-seq library kit (new England Biolabs)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
molecule: genomic DNA NELFA 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): bowtie 2.1.0 (end-to-end , sensitive)) alignment (RNAseq): tophat 2 (default parameters) tag density files: RSeQC package was used to generate BigWiggle files Genome_build: hg19 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.
|
|
|
Submission date |
Apr 29, 2015 |
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 |
GPL18573 |
Series (1) |
GSE68401 |
Enhancer activation during EGF response |
|
Relations |
BioSample |
SAMN03573688 |
SRA |
SRX1013968 |