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| Status |
Public on Jul 01, 2020 |
| Title |
Signal-Specific Genomic Regulation of NF-κB by EGFR and IL-1R |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To study how NF-κB-dependent transcription is regulated differentially by EGFR, compared to the Interleukin-1 receptor (IL-1R), a classical NF-κB activator, we integrated transcriptional analyses by profiling by RNA-seq) and DNA binding by ChIP-seq analyses in human mammary epithelial cells (HMECs).
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| Overall design |
Signal-specific NF-κB-dependent genes activated or repressed by EGF or IL-1 were identified by differential gene expression analysis of RNA-seq data of treated versus untreated samples with or without knockdown of the RELA (p65) subunit of NF-κB. Signal-specific NF-κB binding sites were identified by ChIP-seq using an antibody against p65 followed by differential binding analysis of p65 peaks in treated versus untreated samples.
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| Contributor(s) |
Dermawan JK, Stark GR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jul 17, 2015 |
| Last update date |
Jul 02, 2020 |
| Contact name |
George Stark |
| E-mail(s) |
starkg@ccf.org
|
| Organization name |
Cleveland Clinic Lerner Research Institute
|
| Department |
Cancer Biology
|
| Street address |
9500 Euclid Avenue
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA290218 |
| SRA |
SRP061289 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE71069_EGF-1_peaks.narrowPeak.gz |
21.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_EGF-2_peaks.narrowPeak.gz |
10.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_EGF_merge_BigWig.bw |
304.0 Mb |
(ftp)(http) |
BW |
| GSE71069_EGF_merge_peaks.narrowPeak.gz |
41.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_EGF_merge_peaks.subpeaks.narrowPeak.SortedUniq.bedgraph.gz |
567.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE71069_EGF_merge_peaks.subpeaks.narrowPeak.bed.gz |
37.7 Kb |
(ftp)(http) |
BED |
| GSE71069_EGF_merge_peaks.subpeaks.narrowPeak.bw |
857.6 Kb |
(ftp)(http) |
BW |
| GSE71069_IL1-1_peaks.narrowPeak.gz |
194.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_IL1-2_peaks.narrowPeak.gz |
9.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_IL1_merge_BigWig.bw |
257.9 Mb |
(ftp)(http) |
BW |
| GSE71069_IL1_merge_peaks.narrowPeak.gz |
125.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_IL1_merge_peaks.subpeaks.narrowPeak.SortedUniq.bedgraph.gz |
1.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE71069_IL1_merge_peaks.subpeaks.narrowPeak.bed.txt.gz |
121.5 Kb |
(ftp)(http) |
TXT |
| GSE71069_IL1_merge_peaks.subpeaks.narrowPeak.bw |
1.9 Mb |
(ftp)(http) |
BW |
| GSE71069_RAW.tar |
1.2 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE71069_UT-1_peaks.narrowPeak.gz |
14.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_UT-2_peaks.narrowPeak.gz |
6.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_UT_merge_BigWig.bw |
125.1 Mb |
(ftp)(http) |
BW |
| GSE71069_UT_merge_peaks.narrowPeak.gz |
36.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE71069_UT_merge_peaks.subpeaks.narrowPeak.SortedUniq.bedgraph.gz |
510.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE71069_UT_merge_peaks.subpeaks.narrowPeak.bed.txt.gz |
27.3 Kb |
(ftp)(http) |
TXT |
| GSE71069_UT_merge_peaks.subpeaks.narrowPeak.bw |
677.1 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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