|
| Status |
Public on May 08, 2015 |
| Title |
cFB_T_03 |
| Sample type |
SRA |
| |
|
| Source name |
Colon Tumor Fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: colon tumor
cell type: Fibroblast
passage: p4-7
cell subtype: Colon Tumor 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 |
SAMN03487293 |
| SRA |
SRX997402 |
