|
| Status |
Public on Dec 09, 2015 |
| Title |
hMe-Seal combined patient input |
| Sample type |
SRA |
| |
|
| Source name |
Input from samples 8-11
|
| Organism |
Homo sapiens |
| Characteristics |
day of differentiation: N/A
normal/tumor: N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep RNA/DNA/miRNA Universal Kit (Qiagen)
RNA libraries were built following polyA selection using Illumina kits; DNA libraries were constructed using Illumina kits. All library construction and sequencing was performed by the University of Chicago NGS core
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Input for Samples 8-11
|
| Data processing |
alignment with BWA-backtrack to hg19; peak calling with MACS 1.4
Genome_build: hg19
Supplementary_files_format_and_content: wig outputs from MACS 1.4 for hMe-Seal data; RNA-seq FPKM values outputted by Cufflinks 2.2.1 provided as supplemental information as Excel spreadsheet
|
| |
|
| Submission date |
May 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Mariani |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Street address |
900 E 57 St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE69333 |
TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer |
|
| Relations |
| BioSample |
SAMN03742293 |
| SRA |
SRX1041887 |
