|
| Status |
Public on Apr 20, 2022 |
| Title |
MCF7_ERa_Ab2_veh_CR_1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cell line
treatment: Vehicle
|
| Treatment protocol |
Cells were treated with either 20 nM 17-beta-estradiol or vehicle control (0.002% EtOH) for 45 min then harvested using trypsin.
|
| Growth protocol |
Cells were maintained in stripped serum and phenol-red free media for 48 hours prior to treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Takara SMARTer ThruPlex DNA-seq Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
25,000 cells
|
| Data processing |
library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called using MACS2 callpeak (q<0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.
|
| |
|
| Submission date |
Jan 12, 2022 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Melody Wu |
| E-mail(s) |
mwu@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE144716 |
Gene regulation by gonadal hormone receptors defines brain sex differences-[CUT&RUN] |
| GSE144718 |
Gene regulation by gonadal hormone receptors defines brain sex differences |
|
| Relations |
| BioSample |
SAMN24900550 |
| SRA |
SRX13755767 |
