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| Status |
Public on Sep 12, 2018 |
| Title |
iOL_Seh1_ChIP-Seq |
| Sample type |
SRA |
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| Source name |
oligodendrocyte
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: forebrain
antibody: Seh1
age: post natal day 1-2
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| Growth protocol |
OPCs were trypsinized and plated onto poly-D-lysine-coated plates. Cells were grown in DMEM/F-12 (GIBCO) with addition of 2% B-27 (GIBCO), 1% N2 (GIBCO), 20 ng/ml PDGF-AA (Peprotech, 100-13A), 10 ng/ml CNTF (Peprotech, 450-02), 20 ng/ml bFGF (Sino Biological, 10014-HNAE), and 1 ng/ml NT3 (Peprotech, 450-03). For OPCs differentiation, triiodothyronine (T3) (60 nM) added to the media and PDGF-AA, bFGF and NT3 were removed.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, for ChIP-Seq, approximately 5 x10^6 cells were cross-linked with 1% formaldehyde for 10 min at room temperature and then were quenched with 125 mM glycine for 5min. Sonicated chromatin was used for immunoprecipitation by incubation with appropriate antibodies (4 g) overnight at 4°C. Immunoprecipitated complexes were collected using protein 40l A/G plus agarose beads (Millipore). SubSequently, beads were washed Sequentially with low-salt buffer, high-salt buffer, LiCl buffer and twice with TE and elution in 500 l of elution buffer (1% SDS, 0.1M NaHCO3). The elutes were heated at 42°C for 2h and treatment with proteinaseK followed by 65°C 10 h to reverse the cross-linking and were treated with RNaseA for 30 min before DNA was extracted and purified.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie2 alignment programs in two ways: only uniquely aligned reads were kept or both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).
The multiple reads were collapsed in order to reduce the PCR biases. The aligned reads were used for peak finding with HOMER
Peaks were identified by searching locations of high read density using a 200-bp sliding window. Regions of maximal density exceeding a given threshold were called as peaks, and we required adjacent peaks to be at least 500 bp away to avoid redundant detection
Peaks from separate experiments were considered equivalent/co-bound if their peak centers were located within 200 bp of each other. Read density heat maps were created by first using HOMER to generate read densities and then visualized using Java TreeView
Genome_build: Rat rn6
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| Submission date |
Sep 11, 2018 |
| Last update date |
Sep 12, 2018 |
| Contact name |
Liu Zhixiong |
| E-mail(s) |
2452503371@qq.com
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| Phone |
8615160067720
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| Organization name |
Xiamen University
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| Department |
School of Life Sciences
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| Lab |
State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network
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| Street address |
Xiangan Nanlu 4221-120
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| City |
xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361102 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE119814 |
Seh1 Interacts with Olig2 and Brd7 to Promote Oligodendrocyte Differentiation and Myelination (ChIP-Seq) |
| GSE119816 |
Seh1 Interacts with Olig2 and Brd7 to Promote Oligodendrocyte Differentiation and Myelination |
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| Relations |
| BioSample |
SAMN10034165 |
| SRA |
SRX4670972 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3384416_iOL_Seh1_ChIP-Seq_peaks.txt.gz |
611.5 Kb |
(ftp)(http) |
TXT |
| GSM3384416_iOL_Seh1_ChIP-seq_peaks.bed.gz |
60.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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