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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 15, 2014 |
| Title |
MB11-H3K4me1 (S00658) |
| Sample type |
SRA |
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| Source name |
midbrain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: midbrain
age: 11 dpc
antibody: H3K4me1 (Abcam ab8895)
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| 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 Illumina HiSeq 1000 following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
ChIP-DNA
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| 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.
These data were normalized by total reads (mapped reads per million reads per kilobase).
Bedgraph files were generated using our in-house program and converted to TDF files using IGVTools version 2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph and TDF files contain identical summary data.
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| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
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| 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 |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE49652 |
Enhancer landscape of mouse developing midbrain at 11.5 dpc embryos |
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| Relations |
| BioSample |
SAMN02313878 |
| SRA |
SRX332681 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1204477_S00658.bedgraph.gz |
57.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1204477_S00658.tdf |
55.6 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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