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Sample GSM1642994 Query DataSets for GSM1642994
Status Public on Mar 22, 2016
Title CD8_RNASEQ
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 polyA RNA
Extraction protocol RNA was extracted using the Qiagen RNEasy mini kit.
A sequencing library for each sample (1ug RNA) was prepared using the Illumina TruSeq RNA Sample Prep Kit v2 (polyA selection).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file: RnaSeqCounts.txt
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 GPL16791
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 SAMN03445840
SRA SRX967649

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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