|
| Status |
Public on May 30, 2015 |
| Title |
Methyl miner of cerebellum DNA - LOW methylation capture |
| Sample type |
SRA |
| |
|
| Source name |
Methyl_cereb_WT_LOW
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/C57BL6
genotype/variation: wild type
gender: male
tissue: Cerebellum
chip/rip antibody: MECP2
chip/rip antibody vendor: Sigma
chip/rip antibody cat. #: 9317
|
| Growth protocol |
MeCP2 null and wild type brain tissue was used
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP and Methylminer libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.
RNA expression libraries were prepared according to Illumina's instructions accompanying the mRNA Sample Kit.
RNA immunoprecipitated libraries were prepared according to NEBnext intructions accompanying the mRNA library prep mix set kit.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Methylminer-seq (MBD-seq), LOW METHYLATION DENSITY
processed_data: TSSCOUNT_METHYL_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt
|
| Data processing |
Illumina Genome Analyzer
Illimina Pipeline 1.6
Alignment with bwa 0.5.7 against the MM9 genome
Feature analysis with Seqmonk version 0.20.0
Description of the processed data files format and contents are included in the 'readme.txt' file linked to Series records.
Genome_build: MM9
Supplementary_files_format_and_content: Tab delimited txt files containing genomic feature counts of various sequence reads and enrichment, fold change values [available on Series records]
|
| |
|
| Submission date |
May 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Assam El-Osta |
| Organization name |
Baker Heart and Diabetes Institute
|
| Lab |
Human Epigenetics
|
| Street address |
75 Commercial Road
|
| City |
Melbourne |
| ZIP/Postal code |
3004 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE38324 |
Chromatin context and ncRNA highlight physiological targets of MECP2 in brain. |
|
| Relations |
| SRA |
SRX150275 |
| BioSample |
SAMN01000735 |
