|
| Status |
Public on Sep 08, 2011 |
| Title |
0hrKCl-MeCP2IP-sampleB2 |
| Sample type |
SRA |
| |
|
| Source name |
cultured cortical neurons E16+7DIV
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
sample: B2
ip antibody: Custom Anti-MeCP2 c-terminal antibody
condition: Unstimulated
fragmentation method: sonication
|
| Treatment protocol |
neuronal cultures were pre-treated with 1 µM tetrodotoxin (TTX) and 100 µM D-APV (Tocris Bioscience) overnight to reduce endogenous neuronal activity prior to stimulation and then left unstimulated or membrane depolarized for 2hrs with 55 mM extracellular KCl by addition of 0.5 volumes of prewarmed depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES pH7.5)
|
| Growth protocol |
Dissociated cortical cultures (E16+7DIV) grown in neurobasal media supplemented with B27, glutamine, and pen/strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were crosslinked, chromatin was fragmented and immunoprecipitation was performed using the indicated antibodies. IP'd DNA was decrosslinked and purified. qPCR was used to validate successful IP before proceeding with library preparation. Input samples were taken after fragmentation, but before IP. Sequencing libraries were constructed by cloning fragments of ~125-175bp using the SOLiD Fragment Library Adaptor kit Module 1-16 (PN4444836)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
Reads were mapped to mm9 using the large genomes matching pipeline from Life Technolofies with parameters -e 3 -t 35 -z 10. BigWig files were generated for uniquely mapped reads of IP samples; reads were extended to 150 bps, corresponding to the estimated fragmen length of the DNA. If multiple reads were mapped to the same starting base and strand, only one of those reads was retained.
|
| |
|
| Submission date |
Sep 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Harrison Wren Gabel |
| E-mail(s) |
harrison_gabel@hms.harvard.edu
|
| Phone |
617-512-0289
|
| Organization name |
Harvard Medical School
|
| Department |
Neurobiology
|
| Lab |
Michael Greenberg
|
| Street address |
7 Linden St Apt 3
|
| City |
Brookline |
| State/province |
MA |
| ZIP/Postal code |
02445 |
| Country |
USA |
| |
|
| Platform ID |
GPL14602 |
| Series (2) |
| GSE31851 |
Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function |
| GSE31951 |
Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [ChIP-Seq] |
|
| Relations |
| SRA |
SRX096338 |
| BioSample |
SAMN00716114 |
| Named Annotation |
GSM791714_MeCP2_MeCP2_0hrKClIPSonicated_B2_E150.bigWig |
