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| Status |
Public on Dec 16, 2021 |
| Title |
Smad3 binding region in HaCaT cells stimulated with TGF-beta, replicate 2 |
| Sample type |
SRA |
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| Source name |
A human epidermal keratinocyte cell line
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| Organism |
Homo sapiens |
| Characteristics |
ChIP: anti-Smad3 ChIP
stimulation: TGF-beta, 1 ng/ml, 1.5h
cell line: HaCaT
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| Treatment protocol |
Cells were treated with 1 ng/ml of TGF-beta for 1.5 h before fixation.
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| Growth protocol |
HaCaT is a spontaneously immortalized human epidermal keratinocyte cell line that was established previously (Boukamp et al, JCB 1988, 106, 761-771). HaCaT cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP of HaCaT cells were performed using 10 μg of anti-Smad3 antibody (Isogaya et al, Cell Res 2011) or 10 ug of anti-Smad2 antibody (abcam, EP567Y), as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Morikawa et al, Nuc Acids Res 2011). Adaptor-ligated samples were amplified by 15 cycles of PCR.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
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| Description |
anti-Smad3 ChIP-seq data
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| Data processing |
Reference files of the human reference sequence assembly (hg19) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were aligned using Bowtie2 (Langmead et al., 2009).
Smad3 binding reagions were identified using MACS2 software (Model based analysis of ChIP-seq) (Zhang et al, 2008) with the command "callpeak --bdg --SPMR --keep-dup auto" and a q-value threshold of 0.0001 (two sample analysis using input genomic data).
control_HaCaT sample was used as input for peak calling and processed data are not available.
Genome_build: hg19
Supplementary_files_format_and_content: BED and bdg files were generated using MACS2.
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| Submission date |
Nov 22, 2021 |
| Last update date |
Dec 18, 2021 |
| 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) |
| GSE180252 |
ChIP-seq and RNA-seq of Human progenitor epidermal keratinocytes (HPEK) and HaCaT cells |
| GSE189303 |
Smad3 binding regions in human epidermal keratinocytes (HaCaT). |
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| Relations |
| BioSample |
SAMN23382821 |
| SRA |
SRX13190039 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5698660_209_56_50.hg19.q1e4_peaks.bed.gz |
411.5 Kb |
(ftp)(http) |
BED |
| GSM5698660_56_50.hg19.q1e4_treat_pileup.sort.bedgraph.gz |
113.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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