|
| Status |
Public on Nov 01, 2016 |
| Title |
MCF_TAM_Input |
| Sample type |
SRA |
| |
|
| Source name |
MCF7L breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
chromatin from approximately 1 × 107 fixed cells was sonicated to a size range of 200-300 bp. Solubilized chromatin was subjected to immunoprecipitation with the FOXA1 antibody bound to protein A and protein G beads. A fraction of the sample was not exposed to antibody to be used as control (input). The samples were reversed crosslinked, treated with proteinase K, and DNA was extracted. DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced using 50-bp reads on the Illumina platform
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics per manual). Libraries were sequenced using Illumina platform
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Parental cells after 45 minutes treatment with 4OH-Tam -input
|
| Data processing |
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to hg19 whole genome using Tophat2 (version 0.6) with parameters -r 300. UCSC known transcripts were supplied in GTF format file.
Peak calling was done using MACS 2
Genome_build: hg19
Supplementary_files_format_and_content: Peaks based on MACS 2 peak calleing
|
| |
|
| Submission date |
Nov 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoyong Fu |
| E-mail(s) |
xiaoyonf@bcm.edu
|
| Phone |
713-798-1626
|
| Organization name |
Baylor College of Medicine
|
| Department |
Breast Center
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
Tx |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE75201 |
CHIP-SEQ of FOXA1 in parental MCF7 cells and tamoxifen resistant MCF7 cells |
| GSE75372 |
FOXA1 overexpression mediates endocrine resistance by increasing IL-8 in oestrogen receptor-positive breast cancer |
|
| Relations |
| BioSample |
SAMN04288922 |
| SRA |
SRX1447318 |
