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| Status |
Public on Oct 23, 2018 |
| Title |
Hs578T, SMAD2 binding region after ActA stimulation rep2 |
| Sample type |
SRA |
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| Source name |
A human breast cancer cell line, Hs578T
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| Organism |
Homo sapiens |
| Characteristics |
breast cancer subtype: triple negative breast cancer
treatment: ActA, 50 ng/ml, 1.5h, replicate 2
antibody: anti-SMAD2 antibody (EP567Y, ab207451, Abcam)
cell line: Hs578T
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| Treatment protocol |
Recombinant human Activin A (R&D Systems), Palbociclib/PD0332991 (Sigma-Aldrich)
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| Growth protocol |
Hs578T was obtained from ATCC, and maintained as reccomended. Briefly, cells were cultured at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Thermo Fisher Scientific) supplemented with 10% FBS, 10 μg/ml insulin and 100 U/ml penicillin-streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation, sonication and immunoprecipitation using anti-SMAD2 antibody (EP567Y, ab207451, Abcam) was performed essentially as described (Isogaya K et al., Cell Res, 2014; Morikawa M et al., Stem Cell Rep, 2016).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Reference files of the human reference sequence assembly (NCBI Build 37/hg19, February 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie (version 1.1.0) (Langmead et al., 2009) with the command “-S -a --best --strata -v 1 -m 1”.
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
SMAD2 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.0.9) (Zhang et al, 2008) with a default q-value threshold of 0.05.
WIG to bigWig conversion was performed using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED and WIG files were generated using MACS2 (version 2.0.9).
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| Submission date |
Jul 23, 2018 |
| Last update date |
Oct 23, 2018 |
| Contact name |
Daizo Koinuma |
| E-mail(s) |
d-koinuma@umin.ac.jp
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| Organization name |
University of Tokyo
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| Department |
Pathology
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| Street address |
Hongo 7-3-1, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
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| Platform ID |
GPL17303 |
| Series (2) |
| GSE117496 |
SMAD2 binding regions in triple negative breast cancer cell line, Hs578T |
| GSE117502 |
SMAD2 binding regions in breast cancer cell line and RNA-seq transcriptome analyses in T47D |
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| Relations |
| BioSample |
SAMN09703437 |
| SRA |
SRX4417030 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3301954_Hs578T-SMAD2-ActA.rep2.50.hg19.bw |
23.3 Mb |
(ftp)(http) |
BW |
| GSM3301954_Hs578T-SMAD2-ActA.rep2.50.hg19.q5e2_summits.bed.gz |
86.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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