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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jul 20, 2012 |
Title |
H2A.Z_hES_ChIPSeq |
Sample type |
SRA |
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Source name |
H2A.Z_hES_ChIPSeq
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Organism |
Homo sapiens |
Characteristics |
cell type: H1 human embryonic stem cells passage: passage 30-40 chip antibody: H2A.Z (Millipore 07-594)
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Growth protocol |
Mouse v6.5 ES cells were cultured on fibroblast feeders in DMEM (Sigma) with 15% fetal bovine serum (Hyclone), GlutaMax (Invitrogen), MEM non-essential amino acids (Invitrogen), pen/strep (Invitrogen), ESGRO (Chemicon) and 2-mercaptoethanol (Sigma), incubating at 37oC, 5% CO2 [16]. Prior to harvest, these cells were passaged 2-3 times on feeder-free gelatinized tissue culture plates. Mouse NP cells were generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium). Human H1 ES cells were cultured in TeSR media on Matrigel by Cellular Dynamics International. Cells were split with dispase and harvested at a passage number between 30 and 40. Prior to harvest, cells were karyotyped and stained for Oct4 to confirm pluripotency.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA or protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Genome Analyzer or HiSeq following the manufacturer's protocols.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
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Description |
H1-human embryonic stem cells
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Data processing |
ChIP-Seq reads for mouse and human were aligned to reference assemblies mm8 and hg18, respectively. Bowtie version 0.12.8 was used with the default parameters, with reads discarded if they aligned to more than 10 places. To create density files, the reads were extended to 200 bp and converted to BigWig using BedTools and UCSC wigToBigWig. Supplementary_files_format_and_content: BigWig files containing the read densities for all regions.
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Submission date |
Jul 10, 2012 |
Last update date |
Nov 19, 2022 |
Contact name |
Kevin Dong |
Organization name |
Dana-Farber Cancer Institute
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Street address |
360 Longwood Ave
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City |
Boston |
State/province |
MASSACHUSETTS |
ZIP/Postal code |
02215 |
Country |
USA |
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Platform ID |
GPL9052 |
Series (1) |
GSE39237 |
H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions |
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Relations |
SRA |
SRX159088 |
BioSample |
SAMN01086973 |
Supplementary file |
Size |
Download |
File type/resource |
GSM958507_hESH1_H2AZ_hg18.sorted.bw |
216.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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