|
| Status |
Public on Oct 30, 2015 |
| Title |
22_Control_5hmc_input_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebellar cortex, normal control, input
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cerebellar cortex
diagnosis: control
age: average age 25 yrs
antibody: none
|
| Treatment protocol |
Frozen samples were not treated.
|
| Growth protocol |
Human frozen tissue was obtained from the NICHD Brain and Tissue Bank of Developmental Disorders at the University of Maryland, Baltimore, MD.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with a DNeasy kit from Qiagen, Inc. Immunoprecipitations were performed on sonicated DNA using the Active Motif MeDIP Kit. 5mC MeDIP was performed with Active Motif mAB #39649 and 5hmC MeDIP was performed with Active Motife mAB #39999 antibodies.
Illumina TruSeq DNA Sample kit, run on an Illumina HiSeq 2500 instrument.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Input control.
|
| Data processing |
Basecalls performed using CASAVA version 1.4.
Aligned with hg19 genome using Bowtie.
Enriched regions identified with spp at low confidence levels, yielding tagAlign files.
High-confidence contrasting bed files generated using the IDR procedure (https://sites.google.com/site/anshulkundaje/projects/idr). Resulting bam files, based on thresholds established by IDR, come from pooled replicates.
Overlapping intervals generated using Bedtools.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tagAlign files from spp show low-confidence genomic intervals compared with input control.
Supplementary_files_format_and_content: bed files from IDR show high-confidence contrasting genomic intervals enriched as indicated.
|
| |
|
| Submission date |
Sep 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronald P. Hart |
| E-mail(s) |
rhart@rutgers.edu
|
| Phone |
848-445-1783
|
| Organization name |
Rutgers University
|
| Department |
Cell Biology & Neuroscience
|
| Street address |
604 Allison Rd Rm B430
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE61133 |
MeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum |
| GSE61169 |
Selective loss of 5hmC links to A-T Purkinje cell vulnerability |
|
| Relations |
| BioSample |
SAMN03020209 |
| SRA |
SRX694754 |
