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| Status |
Public on Oct 01, 2014 |
| Title |
SVZ H3K9me3 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
neural progenitors cells
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| Organism |
Papio anubis |
| Characteristics |
tissue: brain
region: subventricular zone
cell type: neural progenitors cells
chip antibody: H3K9me3 antibody
chip antibody info: Millipore #07-442, Lot 2383148
chip antibody info: Upstate #07-442, Lot DAM1411287
chip antibody info: Active Motif #39162, Lot 13509002
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We manually conjugated antibody against cell type markers, such as GFAP, Nestin, Vimentin, PSA-NCAM, or Doublecortin to Dynabeads. We then used the Dynabeads-conjugated antibody to purify cells dissociated from SVZ microdissection. Briefly, cells from fresh dissected baboon SVZ were immediately dissociated with Accutase, equilibrated in binding buffer containing phosphate-buffered saline (PBS), 0.05% TritonX-100 (or saponin, detergent choice depends upon antibody), and subsequently subjected to Dynabeads-conjugated antibody purification. After elution with high salt and pH-gradient buffer, the purified populations were crosslinked in 1.1% formaldehyde before chromatin shearing by Diagenode Bioruptor. The resulting sheared chromatin fragments in a size range between 200 to 500 base pairs were incubated with H3K9me3 antibody-conjugated Protein A Dynabeads (Millipore #07-473, Upstate #07-442; Active Motif #39162; Life Technology Dynabeads protein A) overnight. For normalization, the aliquot of sheared chromatin fragments were incubated with antibody against total histone 3-conjugated Protein A Dynabeads (unmodifiedH3 antibody, Millipore #05- 499; 1:1000). Subsequently, enriched chromatin fragments were eluted, subjected to de-crosslink, purified for library preparation (Illumina Library Kit) and sequenced with 200millinon tags through Illumina HiSeq2000 sequencer.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina TruSeq v2. Total H3 reads are maintained in GEO Sample GSM1413005.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to the Rhesus Macaque reference rheMac with Bowtie version 0.12.7 using the following parameters: bowtie -p 8 --mm -n 2 -m 1 --best --phred33-quals
FDR 5% Peaks were called with the MACS2 program, using -q 0.05
Genome_build: rheMac2
Supplementary_files_format_and_content: xls file containing ChIP-Seq peak calls generated from MACS2, with FDR = 0.05
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| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chin-Hsing Annie Lin |
| Organization name |
University of Texas at San Antonio
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| Department |
Biology
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| Lab |
BSB2.03.24
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| Street address |
One UTSA Circle
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| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78249 |
| Country |
USA |
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| Platform ID |
GPL18808 |
| Series (1) |
| GSE59074 |
H3K9me3 ChIP-Seq of baboon SVZ primary cells |
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| Relations |
| BioSample |
SAMN02902446 |
| SRA |
SRX645379 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1426209_7BV9.fdr0.05.formatted-header.spreadsheet.xls.gz |
295.6 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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