|
| Status |
Public on Jul 28, 2017 |
| Title |
Control 3 |
| Sample type |
SRA |
| |
|
| Source name |
Rectal wall
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Control
gender: male
tissue: Rectal wall
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from frozen whole rectal wall samples with the RNAeasy Mini Plus Kit (Qiagen, Hilden, Germany) and checked for quality and quantity with Agilent’s 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, USA).
cDNA libraries were prepared using Illumina’s TruSeqTM RNA Sample Preparation v2 protocol. Sequencing was performed using an Illumina HiSeqTM 2500. Quality and quantity was checked with Agilent's 2100 Bioanalyzer using DNA 1000 Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
lind_90_br3
|
| Data processing |
Basecalls and demultiplexing were performed using CASAVA for HiSeq2500 sequencing. Each sample was previously splitted into four samples indicated by name affix 'gp 1-4'
Mapping was performed with TopHat2 (v2.0.5, default settings) against the human reference genome assembly "hg19" with the annotation from Gencode "v17".
Gene quantification was calculated with a python script, “rpkmforgenes.py” from the Sandberg Laboratory (http://sandberg.cmb.ki.se/rnaseq/) at readcount and RPKM level (=reads per kilobase of exon model per million mapped reads) according to Mortazavi et al. using uniquely mapped reads.
Differential gene expression profiling was carried out exclusively based on readcount quantification via the DESeq2 package developed for RNA sequencing data.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Jul 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Corinna Rosenbaum |
| Organization name |
University Hospital Wuerzburg
|
| Department |
Department of Tissue Engineering and Regenerative Medicine
|
| Street address |
Röntgenring 11
|
| City |
Würzburg |
| ZIP/Postal code |
97082 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE101968 |
Obstructed defecation – an enteric neuropathy? An exploratory study of patient samples |
|
| Relations |
| BioSample |
SAMN07419567 |
| SRA |
SRX3043728 |
