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Status |
Public on Jan 19, 2016 |
Title |
LC rep3 |
Sample type |
SRA |
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Source name |
colorectal biopsy, sigma
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Organism |
Homo sapiens |
Characteristics |
tissue: lymphocytic colitis medication: none
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
Jan 20, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Michal Ruth Schweiger |
E-mail(s) |
mschweig@molgen.mpg.de
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Organization name |
Max Planck Institute For Molecular Genetics
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Department |
Lehrach
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Lab |
Schweiger
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Street address |
Ihnestrasse 63-73
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City |
Berlin |
ZIP/Postal code |
14195 |
Country |
Germany |
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Platform ID |
GPL16791 |
Series (1) |
GSE65107 |
Diarrhea in lymphocytic colitis: ERK1/2-dependent ENaC dysregulation and claudin-4-, -5- and -8-related barrier defects |
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Relations |
BioSample |
SAMN03288134 |
SRA |
SRX848596 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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