|
| Status |
Public on May 31, 2018 |
| Title |
siSA2_REP1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Mammary Epithelial Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF10A -Transformed nontumorigenic
experiment: MCF10A cells were arrested in G1 by means of high confluency culture (150,000 cells per cm2). Hi-C was performed as described (Serra et al., 2017) using MboI enzyme. Two library replicates per condition were sequenced (>200 million reads each).
treatment: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG2 siRNAs (Dharmacon L-021351) at seeding in high confluency using DharmaFECT reagent 1.
|
| Growth protocol |
MCF10A cells were 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 |
Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Digested/Ligated genomic DNA
|
| Data processing |
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads. TADbit’s filtering module was used to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks).
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines. Raw counts at 40kb and 100Kb resolution are stored as tab-separated files with bin in first column, second bin as second column, and number of contacts as third column.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw interaction matrices per chromosome are included in the abc format, which has commented lines (start with a “#” character) and the actual interaction counts (one per line) as three column with left-bin, rigth-bin and raw-counts.
|
| |
|
| Submission date |
Apr 24, 2018 |
| Last update date |
May 31, 2018 |
| Contact name |
Ana Losada |
| E-mail(s) |
[email protected]
|
| Phone |
+34 - 917 328 000
|
| Organization name |
Centro Nacional de Investigaciones Oncológicas (CNIO)
|
| Department |
Molecular Oncology Programme
|
| Lab |
Chromosome Dynamics Group
|
| Street address |
C/ Melchor Fernández Almagro, 3.
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE101921 |
Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization |
|
| Relations |
| BioSample |
SAMN08977753 |
| SRA |
SRX3992134 |
