|
| Status |
Public on Nov 12, 2014 |
| Title |
H3K4me1 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
11 dpc embryonic forebrain_H3K4me1 ChIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 11 dpc embryo
tissue: forebrain
chip antibody: H3K4me1
chip antibody vendor: Abcam
chip antibody cat. #: ab8895
chip antibody lot #: GR46388-1
|
| 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 NEB's instructions accompanying the DNA Sample Kit (NEB# E6240L). 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 |
| |
|
| Description |
H3K4me1
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2.1.0 with default parameters.
Reads of control experiment were normalized using total reads of the experiment (read per million reads per kilobase genome) and those of treated cells were normalized using internal control (5 positions from Rpl13a).
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated using our in-house program and converted to TDF files using IGVTools version 2.2.1.
|
| |
|
| Submission date |
Nov 12, 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) |
| GSE52280 |
Enhancer landscape of mouse developing forebrain at 11.5 dpc embryos [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN02401335 |
| SRA |
SRX376590 |
