|
| Status |
Public on Jan 30, 2023 |
| Title |
MCF10A_Control_R2_HiC |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
cell line: MCF10A
cell type: epithelial
treatment: mock transfection
|
| Treatment protocol |
MCF10A cells were transfected with 50 nM siRNAs using DharmaFECT reagent 1 and Gibco Opti-MEM I Reduced Serum Media and harvested 72h later.
|
| Growth protocol |
MCF10A cells are grown in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MCF10A cells (3 mill cells per condition) were fixed with 2% formaldehyde (Sigma, #252549) in PBS with 10% FBS for 10 min. Formaldehyde was quenched with 300 mM of glycine at RT for 5 minutes. Hi-C experiments were performed with Arima-HiC Kit (A510008) following manufacturer’s instructions.
Libraries were prepared with Swift Biosciences Accel-NGS 2S Library Kit (Cat# 21024) and amplified with KAPA Library Amplification Kit (KAPA Cat# KK2620). For all the libraries, 8-9 PCR cycles were used for amplification and they were then sequenced on an Illumina NextSeq550 (82x43 bp).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Alignment of sequences to the reference human genome (hg19) was performed using ‘Bowtie2′ with --local --reorder flags.
To assess the reproducibility of the replicates, 5-kb raw matrices were summed to obtain 40-kb matrices and these were normalized first by coverage and then by KR algorithm.
Given the high correlation of the distribution of contacts as a function of genomic distance among replicates for each condition (control or KD), replicates were merged and analyzed at 5-kb resolution
Assembly: hg19
Supplementary files format and content: mcool
|
| |
|
| Submission date |
Jun 28, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Daniel Gimenez |
| E-mail(s) |
dgimenezl@cnio.es
|
| Organization name |
CNIO
|
| Street address |
Calle de Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE207115 |
Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [Hi-C] |
| GSE207116 |
Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels |
|
| Relations |
| BioSample |
SAMN29402671 |
| SRA |
SRX15930068 |
