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| Status |
Public on Feb 02, 2016 |
| Title |
hNPC SOX2 ChIP-seq |
| Sample type |
SRA |
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| Source name |
H9 derived NPCs
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC
chip antibody: SOX2 (R&D 2018)
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| Growth protocol |
H9 cells were maintained in mTeSR1 in BD hESC qualified matrigel coated dishes. Culture was daily changed, and hESCs were passaged using Accutase or 1mg/ml dispase. hNPCs were differentiated from H9 cells using established protocol (Chambers SM, Nat Biotechnol, 2009; 27: 275–280). Briefly, we used Noggin (500ng/ml), SB431542 (10mM) and Compound C (10mM) to induce neural differentiaiton.Neural rosettes were picked up and replated onto matrigel coated dishes, and then dissociated into single NPCs and maintained in N2B27 medium supplemented with 10ng/ml bFGF. hNPCs were then passaged using 0.05% trypsin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and SOX2-DNA complexes and POI II-DNA complexes were immunoprecipitated with SOX2 antibody (R&D AF2018) or POI II antibody (Covance MMS-126R). Protein A and G Magenetic Dynabeads were used to capture antibody bound protein-DNA complexes.
ChIP-seq libraries preparation: The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding ‘‘A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq2500 platforms.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
CASAVA1.8.2 convert per-cycle *.bcl files into FASTQ files
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.0.10 with the following setting: shift-size (73), q-value (0.01)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by MACS2, the score represents number of bp fall into the single base pair region.
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| Submission date |
Jun 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ying Jin |
| E-mail(s) |
yjin@sibs.ac.cn
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| Organization name |
Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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| Street address |
225 South Chongqing Road
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| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE69479 |
Genome-wide map of SOX2 occupancy in human ES cells (hESCs) and hESC derived neural progenitor cells (hNPCs) |
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| Relations |
| BioSample |
SAMN03759641 |
| SRA |
SRX1047416 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1701828_NPC_SOX2.bed.gz |
535.1 Kb |
(ftp)(http) |
BED |
| GSM1701828_NPC_SOX2.bw |
282.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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