|
| Status |
Public on Dec 31, 2023 |
| Title |
ATACseq_CTR |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
chip antibody: NA
knockdown: shControl
|
| Treatment protocol |
MDA-MB-231 cells were infected with lentiviral particles for shControl or shRUVBL2 and selected for 48 hr with 2.5 µg/ml puromycin. At 48 hr post-selection ATAC-seq experiment was performed
|
| Growth protocol |
MDA-MB-231 cells (ATCC No.: HTB-26) were cultured in Dulbecco’s modified Eagle’s medium (Biowest; L0106-500) supplemented with 1% penicillin/streptomycin (Gibco; 15140122), 2 mM L-glutamine (Biowest; X0550-100), and 10% FBS (Gibco; 10270106) at 37ºC in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 50,000 cells of each condition were treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina), and DNA was purified using MinElute PCR Purification Kit (Qiagen; 28006). Transposed DNA was amplified by PCR using NEBNextHigh-Fidelity 2 PCR Master Mix (New Englands Labs; M0541S) and primers containing a barcode
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ATAC-seq experiment
|
| Data processing |
ChIP-seq analysis: Alignment: Sequence reads of the samples were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) without the option -m.
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles were normalized by the total number of reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ATAC-seq analysis: Sequence reads of the samples were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000. ChIP-seq genome-wide profiles were normalized by the total number of reads of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)
|
| |
|
| Submission date |
Dec 20, 2019 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
[email protected]
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE142463 |
LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells |
|
| Relations |
| BioSample |
SAMN13660185 |
| SRA |
SRX7423971 |
