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Sample GSM1642984 Query DataSets for GSM1642984
Status Public on Mar 22, 2016
Title NL3_MIGS
Sample type SRA
Source name human intestinal fibroblasts (HIFs)
Organism Homo sapiens
Characteristics group: control
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 (
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
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
BioSample SAMN03445835
SRA SRX967639

Supplementary file Size Download File type/resource
GSM1642984_binnedProfile.NL3.txt.gz 170.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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