|
| Status |
Public on May 18, 2020 |
| Title |
TamR_ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
growth protocol: TamR
|
| Growth protocol |
MCF7 parental cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S). The TamR cells were kept in phenol-red free RPMI/1640 medium supplemented with 10% heat-inactivated charcoal-stripped-FBS and 1% P/S with the addition of 100 nM 4-hydroxytamoxifen (4-OHT, H7904, Sigma). All cells were kept at 37 °C in a humified incubator with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were harvested for each condition. After purification of nuclei, transposition was performed with Tn5 transposase from Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030). ATAC-seq library prep was performed as in Buenrostro et al, 2015. Libraries were sequenced with Mid 75bp PE on Illumina NextSeq 500 (4 samples in one lane).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TamR_full media_ATAC-seq
|
| Data processing |
Basecalls performed using Illuminal CASAVA software.
The adaptor was removed by using cutadapt v1.11 with parameters "-m 20 -e 0.1". The clean reads were aligned to the hg19 genome assembly using bowtie2 v2.2.9 with parameters "-mm --very-sensitive --no-discordant -X 2000", and only primary alignments were retained. The alignments were shifted with +4 for plus strand and -5 for minus strand.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
May 19, 2020 |
| Contact name |
Zhijie Jason Liu |
| E-mail(s) |
liuz7@uthscsa.edu
|
| Organization name |
Universality of Texas Health Science Center at San Antonio
|
| Department |
Department of Molecular Medicine
|
| Lab |
Liu lab
|
| Street address |
7703 Floyd Curl Drive
|
| City |
San Antonio |
| State/province |
TEXAS |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE128444 |
Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance [ATAC-Seq] |
| GSE128460 |
Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance |
|
| Relations |
| BioSample |
SAMN11159102 |
| SRA |
SRX5534693 |
