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| Status |
Public on Jan 19, 2016 |
| Title |
Ctrl rep3 |
| Sample type |
SRA |
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| Source name |
colorectal biopsy, sigma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: benign
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 |
SAMN03288131 |
| SRA |
SRX848592 |
| 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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