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| Status |
Public on Jan 11, 2018 |
| Title |
ATF6+/+ hMSC tunicamycin-1 H3K4me3 ChIP-seq |
| Sample type |
SRA |
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| Source name |
MSC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: MSC
treatment: tunicamycin
passages: p5
chip antibody: H3K4me3
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| Treatment protocol |
Cell were treated with vehicle or Tunicamycin for 12 hours.
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| Growth protocol |
hESCs were maintained on Matrigel-coated plates with mTeSR medium. hMSCs were cultured in aMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 0.1 mM non-essential amino acids, and 1 ng/ml bFGF. hWAPCs were cultured in DMEM medium with 7.5% KOSR, 7.5% BSA, 0.5% non-essential amino acids, 0.5% penicillin/streptomycin, 0.1 mM dexamethasone, 10 mg/ml insulin and 0.5 mM Rosiglitazone.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was extracted with Trizol reagent. To obtain the genomic DNA fragments of interest, the cells were crosslinked and lysed, and then the chromatin was sheared into fragments using sonication. Then samples were incubated with anti-H3K4me3 antibody(Abcam, ab8580) or anti-FLAG(Sigma, F1804) antibody overnight. The DNA was de-crosslinked and extracted on the next day.
1.5 μg of total RNA was used to construct RNA sequencing libraries by TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s recommended protocol. After the DNA was de-crosslinked and extracted, the ChIP-sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) according to the manufacturer’s instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ab-WT-TM-1
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| Data processing |
QC: For RNA Seq, the whole pipeline were availuable in https://github.com/huboqiang/RNA_v2 for details.
RNA-seq: Tophat(v2.0.9) mapping
RNA-seq: Cufflinks(v2.2.11) quantification
QC: For ChIP Seq, the whole pipeline were availuable in https://github.com/huboqiang/ChIP
ChIP-seq: bwa mapping(0.7.5a)
ChIP-seq: macs2(v2.1.0.20150731) calling peaks with IDR pipeline
Genome_build: hg19
Supplementary_files_format_and_content: processed data of RNA seq were FPKM values in csv format. ChIP-Seq data were narrowPeaks results of MACSs2
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| Submission date |
Jul 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Boqiang John Hu |
| E-mail(s) |
huboqiang@gmail.com
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| Organization name |
Peking university
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| Department |
bio-dynamic imaging center
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| Street address |
5th Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
10086 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE102004 |
ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells |
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| Relations |
| BioSample |
SAMN07422068 |
| SRA |
SRX3045429 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2720365_Ab-WT-TM-1.bw |
39.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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