GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1587428 Query DataSets for GSM1587428
Status Public on Jan 19, 2016
Title LC rep4
Sample type SRA
Source name colorectal biopsy, sigma
Organism Homo sapiens
Characteristics tissue: lymphocytic colitis
medication: none
Extracted molecule total RNA
Extraction protocol 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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing 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
Submission date Jan 20, 2015
Last update date May 15, 2019
Contact name Michal Ruth Schweiger
Organization name Max Planck Institute For Molecular Genetics
Department Lehrach
Lab Schweiger
Street address Ihnestrasse 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
Platform ID GPL16791
Series (1)
GSE65107 Diarrhea in lymphocytic colitis: ERK1/2-dependent ENaC dysregulation and claudin-4-, -5- and -8-related barrier defects
BioSample SAMN03288140
SRA SRX848597

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap