|
| Status |
Public on Nov 20, 2013 |
| Title |
WT_Undifferentiated_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype/variation: Wild type
treatment: Undifferentiated
drb treatment: no
antibody: in house antibody
|
| Treatment protocol |
DRB is used last 16 hours before harvesting the cells if necessary.
|
| Growth protocol |
Differentiating embryonic stem cells are cultured on a gelatin-coated 100-mm dish with 10% serum for 2 days in the presence of 10 nM retinoic acid. Undifferentiated embryonic stem cells are maintained in the presence of KSR (15%), LIF (1,000U), serum (1%).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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 (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. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Botwie2 (version 2.0.5) with default parameters.
peaks were called using MACS2 (version 2.0.10) with default parameters
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: Wiggle
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Integrative Genomics
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE48421 |
Genome-wide analyses of the DRB response of the histone H3 Lys36 methylation state, as well as Ash1l occupancy in mouse embryonic stem cells. |
|
| Relations |
| BioSample |
SAMN02216992 |
| SRA |
SRX316694 |
