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| Status |
Public on Dec 04, 2012 |
| Title |
rat_ts_h3k27ac |
| Sample type |
SRA |
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| Source name |
Trophoblast stem cells
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: HSD
chip antibody: H3K27ac (Abcam, ab4729, lot 730178)
cell type: Trophoblast stem cells
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| Growth protocol |
Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004). Rat TSCs were cultured as previously (Asanoma et al, Developmental Biology 2011)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). 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 (3' to 5' 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 200~400 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 Genome Analyzer II or HiSeq following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ChIP DNA
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| Data processing |
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using BWA 0.9.6 (-q 10 -I), and filtered using samtools view (-q 1) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.9 with default settings, using --broad setting for histone marks.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-Seq bed files contain peaks called by MACS v2.0.9
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| Submission date |
Nov 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Edward Chuong |
| E-mail(s) |
edward.chuong@colorado.edu
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| Organization name |
University of Colorado Boulder
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| Department |
BioFrontiers
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| Lab |
Chuong
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| Street address |
596 UCB
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| City |
Boulder |
| ZIP/Postal code |
80304 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
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| Relations |
| SRA |
SRX204149 |
| BioSample |
SAMN01805502 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1035395_r_ts_h3k27ac_broad_peaks.bed.gz |
107.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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