|
| Status |
Public on Aug 20, 2020 |
| Title |
TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To better understand the transcriptional regulators involved in the development of lung cancer, we used H3K27ac and open chromatin data to define enhancer regions which may be affected by differential transcriptional regulator activity. Additionally, we performed siRNA knockdown of key transcriptional regulators identified by our study followed by RNA-seq to identify potential downstream target genes of these regulators
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| |
|
| Overall design |
ChIP-seq for active H3K27ac histone marks and ATAC-seq for regions of open chromatin in alveolar epithelial cells, along with RNA-seq in A549 lung adenocarcinoma cells after siRNA knockdown of transcriptional regulators FOXM1 and MYBL2
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| |
|
| Contributor(s) |
Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK |
| Citation(s) |
32925947 |
| Submission date |
Jan 06, 2020 |
| Last update date |
Nov 19, 2020 |
| Contact name |
Daniel James Mullen |
| E-mail(s) |
dmullen@usc.edu
|
| Organization name |
University of Southern California
|
| Department |
Biochemistry and Molecular Medicine, Surgery
|
| Lab |
Offringa
|
| Street address |
1441 Eastlake Ave., Room NTT 6420
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (22)
|
| GSM4250944 |
Donor 2 D0 ATAC-seq |
| GSM4250945 |
A549 siControl rep1 RNA-seq |
| GSM4250946 |
A549 siControl rep2 RNA-seq |
| GSM4250947 |
A549 siControl rep3 RNA-seq |
| GSM4250948 |
A549 siControl rep4 RNA-seq |
| GSM4250949 |
A549 siMYBL2 rep1 RNA-seq |
| GSM4250950 |
A549 siMYBL2 rep2 RNA-seq |
| GSM4250951 |
A549 siMYBL2 rep3 RNA-seq |
| GSM4250952 |
A549 siMYBL2 rep4 RNA-seq |
| GSM4250953 |
A549 siFOXM1 rep1 RNA-seq |
| GSM4250954 |
A549 siFOXM1 rep2 RNA-seq |
| GSM4250955 |
A549 siFOXM1 rep3 RNA-seq |
| GSM4250956 |
A549 siFOXM1 rep4 RNA-seq |
| GSM4704964 |
RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep1 |
| GSM4704965 |
RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep2 |
| GSM4704966 |
RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep3 |
| GSM4704967 |
RNA-seq in A549 cells after FOXM1 and MYBL2 siRNA double knockdown treatment rep1 |
| GSM4704968 |
RNA-seq in A549 cells after FOXM1 and MYBL2 siRNA double knockdown treatment rep2 |
| GSM4704969 |
RNA-seq in A549 cells after FOXM1 and MYBL2 siRNA double knockdown treatment rep3 |
|
| Relations |
| BioProject |
PRJNA599095 |
| SRA |
SRP239534 |
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