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|Public on Jan 19, 2016
|colorectal biopsy, sigma
|tissue: lymphocytic colitis
|Biopsies were taken and RNA was immediately harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|Illumina HiSeq 2500
|Illumina bcl2fastq 1.8.4 software was used for basecalling.
Sequenced reads were mapped to hg19/GRCh37 whole genome using bwa 0.5.9-r16 with default parameters
Mapped reads where counted for each mRNA of the Ensembl v73 database if a read overlapped the Exon coordinates by at least one base
Raw counts were processed in R using functions of the edgeR library to normalize (calcNormFactors), and calculate logratios and significance using a robust trended dispersion estimate. Counts per Million were calculated using the function cpm from edgeR
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: tab-delimited text file including raw counts and CPM values for each sample as well as the logratios and pValues calculated compairing all LC vs all benign samples
|Jan 20, 2015
|Last update date
|May 15, 2019
|Michal Ruth Schweiger
|Max Planck Institute For Molecular Genetics
|Diarrhea in lymphocytic colitis: ERK1/2-dependent ENaC dysregulation and claudin-4-, -5- and -8-related barrier defects