|
| Status |
Public on Nov 13, 2017 |
| Title |
Input DNA from shMSK1 cells |
| Sample type |
SRA |
| |
|
| Source name |
T47D-5516 (DBM)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D-5516 (DBM)
tissue: Breast cancer cell line
|
| Growth protocol |
cultured in standard conditions (37C, 5% CO2) in DMEM 4.5g l–1 D-glucose medium (GIBCO) supplemented with 10% fetal bovine serum (FBS), 50 U ml–1 penicillin, 50 µg ml–1 streptomycin and 5% glutamine;
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DBM shCTRL and shMSK1 cells were trypsinised and crosslinked in 1% formaldehyde for 10 min at RT. rosslinking was quenched with 0.125 M glycine. Pelleted cells were lysed in 1 ml ChIP buffer (150 mM NaCl, 10 mM Tris-HCl, 5 mM EDTA, 1% SDS, 0.5 mM DTT and 1% Triton X-100) and sonicated for 20 min in a Bioruptor Pico (Diagenode).
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following manufacturer's instruction. Antibodies used for ChIP were: H3S10p (Abcam ab5176), H3S28p (Sigma-Aldrich H9908)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
dormant bone metastatic cell subline
MSK1_only_Input_GGCTAC
|
| Data processing |
Quality trimming and removal of artifacts with Trimmomatic version 0.33 and parameters adapters-all.fa:2:30:10 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:25
Alignment with BWA (version 0.7.5a-r405)21 with parameters -n 2 -l 20 and -k 1
Removal of duplicated reads with samtools version 1.3.1
Peak calling with MACS2 version 2.1.1.20160309 and parameters -q 0.01 --broad -B --broad-cutoff 0.01 --nomodel --extsize 300
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files of the signal as generated by Macs2
|
| |
|
| Submission date |
Jun 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Aikaterini Symeonidi |
| E-mail(s) |
ksymeonidh@gmail.com
|
| Organization name |
Institut for Research in Biomedicine (IRB-Barcelona)
|
| Department |
Oncology
|
| Lab |
Stem cells and Cancer Lab
|
| Street address |
Baldiri i Reixac, 10
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE100306 |
MSK1 regulates luminal cell differentiation and metastatic dormancy in breast cancer |
|
| Relations |
| BioSample |
SAMN07260877 |
| SRA |
SRX2941118 |
