|
| Status |
Public on Mar 12, 2015 |
| Title |
MeCP2IP_MeCP2_ChIP_Forebrain1 |
| Sample type |
SRA |
| |
|
| Source name |
Forebrain
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
strain: C57BL/6
chip antibody: Total MeCP2 antibody (Chen et al. 2003)
age: 8 weeks
|
| Growth protocol |
Brain tissue was taken from wild-type mice maintained under standard housing conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as described in Cohen et al. Neuron 2012, Ebert et al Nature 2013
Single-end short read sequencing libraires were prepared using standard protocols, following the manufacturers instructions. 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 2000 |
| |
|
| Data processing |
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq files were aligned to mouse mm9 reference genome with bwa 0.6.2. Uniquely mapped reads were extended in silico to reflect average fragment size of the input DNA(~250bp).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of unnormalized histograms for mapped, in silico extended reads
|
| |
|
| Submission date |
Aug 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Harrison Wren Gabel |
| E-mail(s) |
gabelh@pcg.wustl.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Neurbiology
|
| Lab |
Michael Greenberg
|
| Street address |
220 longwood avenue
|
| City |
brookline |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE60071 |
Length-dependent gene misregulation in Rett syndrome (ChIP-seq) |
| GSE60077 |
Length-dependent gene misregulation in Rett syndrome |
|
| Relations |
| BioSample |
SAMN02951529 |
| SRA |
SRX669235 |
