|
| Status |
Public on Apr 13, 2018 |
| Title |
TAMR_4OHT_FOXA1_KC119_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
TAMR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TAMR
treatment: 4OHT
treatment time: 45min
factor: FOXA1
chip antibody: Abcam, ab23738
replicate: Rep2
|
| Treatment protocol |
3 days in media, 45min hormone treatment. ETOH, 10-8 E2, 10^-7 4OHT.
|
| Growth protocol |
Phenol red free DMEM/F12 with 8% charcoal stripped FBS, supplemented with NaPyr and NEAA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell pellets were thawed on ice, and then resuspended in Lysis Buffer containing 1% SDS, 0.25mM EDTA, 2.5mM Tris-HCl, pH 8.0, protease inhibitor cocktail. Cell lysates were sonicated using the Covaris.
KAPA HTP
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MCF7-derived 4-OHT resistant.
|
| Data processing |
FASTQ files were clipped using Skewer and aligned with BWA mem.
Peak calling was performed using Homer.
Differential peak calling was performed using PePr.
BigWig files (bw) are normalized using deeptools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bed: Bed files include peak calls from Homer.
Supplementary_files_format_and_content: *.bw: bigWig files include peak calls from PePr.
|
| |
|
| Submission date |
Apr 12, 2018 |
| Last update date |
Apr 13, 2018 |
| Contact name |
Jeff Jasper |
| Organization name |
Duke University
|
| Department |
Pharmacology and Cancer Biology
|
| Lab |
McDonnell
|
| Street address |
Box 3813
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE106695 |
GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer |
| GSE113092 |
GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN08924064 |
| SRA |
SRX3931031 |
