|
| Status |
Public on Apr 29, 2013 |
| Title |
H1d-Trans-1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
strain: C57BL/6-129/Sv
passages: 10-20
epitope tagged protein: FLAG-H1d Knock-in
chip antibody: FLAG (Sigma, F3165)
|
| Growth protocol |
ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts feeder layers in ESC media consisted of DMEM supplemented with 15% FBS, non-essential amino acids, β-mercaptoethanol, nucleotides and LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Soluble chromatin lysates were extracted from sonicated nuclei and protein-DNA complexes were immunoprecipitated with antibody.
The libraries were prepared from 10 ng of immunoprecipiated DNA or input DNA using Illumina ChIP-seq Sample Preparation Kit and purified with a Qiagen DNA Isolation column.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing was performed with Illumina Genome Analyzer II and Illumina HiSeq 2000 systems. Raw sequence reads containing more than 30% of 'N' were removed and adaptor sequences were trimmed.
Clean sequences were aligned against mouse genome mm9 using Bowtie aligner software
IP-IN signals were calculated by subtraction of tag counts/100bp window/10 million mappable reads of ChIP-seq library (IP) by that of its corresponding input-seq library (IN) using GenPlay software.
aligned.bed files were generated from bowtie alignment. IP-IN.bed and IP-IN.wig files were obtained from Genplay software.
Genome_build: mm9
Supplementary_files_format_and_content: IP-IN.wig files
|
| |
|
| Submission date |
Apr 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuhong Fan |
| Organization name |
Georgia Institute of Technology
|
| Department |
School of Biology and the Petit Institute for Bioengineering and Bioscience
|
| Street address |
IBB 2313, 315 Ferst Drive
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30332 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE46134 |
High Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells |
|
| Relations |
| BioSample |
SAMN02046896 |
| SRA |
SRX266828 |
