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| Status |
Public on Jul 16, 2014 |
| Title |
SVZ Total H3 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
neural progenitors cells, total H3 ChIP
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| Organism |
Papio anubis |
| Characteristics |
tissue: brain
region: subventricular zone
developmental stage: adult
chip antibody: anti-histone H3
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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 H3K4me3 antibody-conjugated Protein A Dynabeads (Millipore #07-473, lot# 2289139, 1:1000; Active Motif #39160, 1:500; 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 (unmodified H3 antibody, Millipore #05-499; 1:1000). Subsequently, enriched chromatin fragments were eluted, subjected to de-crosslink.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina TruSeq v2.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
SVZ Total H3
Subventricular zone primary cells.
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| Data processing |
Basecalls were performed with Illumina RTA version 1.12.4.2.
Reads were aligned to the Rhesus Macaque reference rheMac2 with Bowtie version 0.12.7 using the following parameters: bowtie -p 8 --mm -n 2 -m 1 --best --phred33-quals.
FDR 1% Peaks were called with the HotSpot program: http://www.uwencode.org/proj/hotspot/ using the default configuration.
Genome_build: Mmul_051212 (rheMac2)
Supplementary_files_format_and_content: Bed file containing ChIP-Seq peak calls generated from HotSpot, with FDR = 0.01.
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| Submission date |
Jun 16, 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 (2) |
| GSE58530 |
Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche [ChIP-seq] |
| GSE58531 |
Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche |
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| Relations |
| BioSample |
SAMN02863388 |
| SRA |
SRX603399 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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