|
| Status |
Public on Jul 16, 2012 |
| Title |
bulk chromatin |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
shearing protocol: Mnase
affinity tag: none
|
| Treatment protocol |
Nuclei were isolated and chromatin was prepared as described in Foltz et al. (Nature Cell Biology 8:458, 2006)
|
| Growth protocol |
HeLa cells were grown in DMEM with 10% calf serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were digested with Mnase and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
bulk chromatin before immunoprecipitation
|
| Data processing |
Sequenced reads were mapped to the human genome (hg18) using Bowtie aligner. Only uniquely mapped tags with no more than two mismatches in the first 28 base pairs of the read were retained.
Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous, potentially resulting from amplification bias, and the tags mapped to those positions were discarded.
The tag frequency at each genome position was calculated separately for DNA positive and negative strands.
Genome_build: hg18
Supplementary_files_format_and_content: Processed files list the 5'-end coordinates of Solexa reads retained for all replicates of the corresponding sample, after data filtering for possible library preparation artifacts. These are tab delimited text files.
|
| |
|
| Submission date |
May 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE38284 |
Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [ChIP-Seq] |
| GSE38771 |
Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells |
|
| Relations |
| SRA |
SRX149732 |
| BioSample |
SAMN00998631 |
