|
| Status |
Public on Mar 22, 2016 |
| Title |
CD6_MIGS |
| Sample type |
SRA |
| |
|
| Source name |
human intestinal fibroblasts (HIFs)
|
| Organism |
Homo sapiens |
| Characteristics |
group: Crohn's disease-associated fibrosis
tissue: colon
cell type: intestinal fibroblast
|
| Growth protocol |
Human intestinal fibroblasts (HIFs) were cultured and their purity confirmed by established methods.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified using the Qiagen DNEasy kit.
Genome-wide DNA methylation was mapped using MBD-isolated genome sequencing (MiGS) (Serre, 2010), with the following differences. DNA (10 ug) was sheared on a Covaris S220 to an average fragment size of 120 bp and methylated fragments were purified on PrepEase DNA columns (USB). Methylated DNA sequences were captured with the methyl binding transcriptional repressor protein MBD2 MethylMiner Methylated DNA Enrichment kit #ME10025 (Invitrogen). A sequencing library for each sample was prepared from the immunoprecipitated DNA using Ilumina’s ChIP-seq DNA Sample Prep Kit and the quality of the DNA was assessed on an Agilent Bioanalyser.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For MiGS data, all reads with MAPQ < 10 were filtered. Remaining reads were aligned to hg19 with bowtie2 (options: -N 1 -L 20 -phred33). Average coverage in non-overlapping 50 bp bins were counted genome-wide, and served as input for a differentially methylated region (DMR) detection pipeline in R.
For RNA-seq data, reads were aligned to hg19 using GSNAP. Read counts for RefSeq genes were computed using HTSeq-count.
Genome_build: hg19
Supplementary_files_format_and_content: For MiGS data, rounded average coverage values within 50 bp non-overlapping windows have been provided for each sample as text files. The first column is the chromosome (hg19) followed by start and end coordinates in the second and third columns. The fourth column provides the average coverage within the window, rounded to the nearest integer. Bins with values of zero have been omitted. These were generated in the process of differentially methylated region (DMR) discovery using iDPT (http://idpt.github.io/dptscan/).
Supplementary_files_format_and_content: For RNA-seq data, reads were counted for RefSeq transcription units using HTSeq-count. The tab-delimited text file contains one row for each gene and one column containing the DESeq normalized read counts for each sample.
|
| |
|
| Submission date |
Mar 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Angela H Ting |
| E-mail(s) |
ahting@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Ting
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
Tx |
| ZIP/Postal code |
77054-1901 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE67250 |
Integration of genome-wide DNA methylome and transcriptome of human intestinal fibroblasts reveals novel candidate gene signatures in Crohn’s disease-associated fibrosis |
|
| Relations |
| BioSample |
SAMN03445844 |
| SRA |
SRX967644 |
