|
| Status |
Public on Feb 09, 2017 |
| Title |
Cancer Patient 37 |
| Sample type |
SRA |
| |
|
| Source name |
metastatic breast cancer patient
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: metastatic breast cancer
cell type: CD11b+ myelomonocytic cells
|
| Treatment protocol |
CD11b+ cells were isolated from 8ml total blood within 24h after venous puncture using Miltenyi MACS separation magnetic beads, and cells were lysed in Qiagen RLT buffer.
|
| Growth protocol |
-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Plus Mini Kit 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. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Homo sapiens.GRCh38.76 genome using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using Homo sapiens.GRCh38.76 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.
|
| |
|
| Submission date |
Jun 30, 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) |
| GSE70404 |
Investigation about Monocytes in metastatic breast cancer patients under chemotherapy +/- Avastin |
|
| Relations |
| BioSample |
SAMN03801575 |
| SRA |
SRX1077245 |
