|
| Status |
Public on Mar 26, 2015 |
| Title |
MeCP2IP_MeCP2_ChIP_FC1.fastq.gz |
| Sample type |
SRA |
| |
|
| Source name |
Frontal Cortex
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
strain: C57BL/6
chip antibody: Total MeCP2 antibody (Chen et al. 2003)
age: 6 weeks
|
| Growth protocol |
Brain tissue was taken from wild-type mice maintained under standard housing conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
total MeCP2 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. Libraries were sequenced on the HiSeq 2500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq.gz 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 |
Mar 25, 2015 |
| 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 |
GPL17021 |
| Series (2) |
| GSE60077 |
Length-dependent gene misregulation in Rett syndrome |
| GSE67293 |
Length-dependent gene misregulation in Rett syndrome (ChIP-Seq 2) |
|
| Relations |
| BioSample |
SAMN03447208 |
| SRA |
SRX968949 |
