|
Status |
Public on Nov 13, 2017 |
Title |
ChIP-seq_S28P of 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)
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
dormant bone metastatic cell subline MSK1_only_S28P_CAGATC
|
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
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|
|
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 |
SAMN07260875 |
SRA |
SRX2941120 |