|
| Status |
Public on Jan 14, 2014 |
| Title |
MB11-RING1B |
| Sample type |
SRA |
| |
|
| Source name |
midbrain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: midbrain
age: 11 dpc
chip antibody: anti-RING1B antibody
chip antibody info: PMID: 11289226
|
| Growth protocol |
ES cells were cultured in standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and RING1B-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 |
midbrain from mouse 11dpc embryos, antibody: RING1B
|
| 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.
Processed files in wiggle format were generated using in-house program.
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: wiggle
|
| |
|
| Submission date |
Jul 01, 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) |
| GSE48464 |
RING1B binding in the 11 dpc embryonic tissues |
|
| Relations |
| BioSample |
SAMN02222204 |
| SRA |
SRX317037 |
