|
Status |
Public on May 08, 2015 |
Title |
cFB_N_02 |
Sample type |
SRA |
|
|
Source name |
Colon Normal Fibroblasts
|
Organism |
Homo sapiens |
Characteristics |
tissue source: normal colon cell type: Fibroblast passage: p4-7 cell subtype: Colon Normal Fibroblasts
|
Treatment protocol |
Medium was removed, cells were washed with ice cold PBS and harvested on ice in lysis buffer
|
Growth protocol |
After sample dissociation, cells were grown for 4-7 passages (to confluency) on plastic dishes from NUNC in corresponding medium (DMEM for fibroblasts, M199 for HUVECs)
|
Extracted molecule |
total RNA |
Extraction protocol |
Machery-Nagel mRNA NucleoSpin was used following manufacturer's instructions RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Sequencing data was processed using the Illumina Pipeline Software version 1.82. Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8). Reads were aligned against Homo sapiens.GRCh38.76 genome using STAR (v. 2.4.0f1, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Homo sapiens.GRCh38.76 gene annotation. Genome_build: Homo sapiens.GRCh38 Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.
|
|
|
Submission date |
Apr 16, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Rüegg Curzio |
E-mail(s) |
curzio.ruegg@unifr.ch
|
Organization name |
Université de Fribourg
|
Department |
Département de Médecine 3
|
Lab |
Pathology
|
Street address |
Albert-Gockel 1
|
City |
Fribourg |
ZIP/Postal code |
1700 |
Country |
Switzerland |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE67945 |
Investigation about fibroblasts of different origins in culture |
|
Relations |
BioSample |
SAMN03487289 |
SRA |
SRX997398 |