|
| Status |
Public on Sep 09, 2014 |
| Title |
GRO_CTRL_EGF_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: Nascent RNA was profiled after EGF stimulation in a doxocycline inducible knock-down cell line for INTS11
source: HeLa Tet-inducible INTS11 shRNA cell clone
sample type: GRO-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 |
nuclear RNA |
| Extraction protocol |
GRO-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Nascent RNA was profiled after EGF stimulation in a doxocycline inducible knock-down cell line for 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 |
SAMN02839555 |
| SRA |
SRX573055 |
