|
| Status |
Public on Aug 20, 2013 |
| Title |
HCC38, RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC38
cell type: breast cancer
subtype: Claudin-low
|
| Treatment protocol |
None
|
| Growth protocol |
Cells in exponential growth phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy
RNAseq libraries for transcriptome analysis were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system per manufacturers' instructions. Sample prep began with 1 _g of total RNA from each sample. Poly-A RNA was purified from the sample with oligo dT magnetic beads, and the poly(A) RNA was fragmented with divalent cations. Fragmented poly-A RNA was converted into cDNA through reverse transcription and were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3' A-tailing with exo-minus Klenow polymerase was followed by ligation of Illumina paired-end oligo adapters to the cDNA fragment. Ligated DNA was PCR amplified for 15 cycles and purified using AMPure XP beads. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting libraries were analyzed using an Agilent Bioanalyzer High Sensitivity chip.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Process with Alexa-seq software pipeline [PMID: 20835245]
Genome_build: hg18
Supplementary_files_format_and_content: Text file with fpkm-like measurement (see PMID:20835245) for each Ensembl (v53) gene
|
| |
|
| Submission date |
Jun 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura M. Heiser |
| E-mail(s) |
heiserl@ohsu.edu
|
| Organization name |
OHSU
|
| Street address |
3181 SW Sam Jackson Park Rd.
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE48213 |
Transcriptional profiling of a breast cancer cell line panel using RNAseq technology |
| GSE48216 |
Modeling precision treatment of breast cancer |
|
| Relations |
| BioSample |
SAMN02225574 |
| SRA |
SRX317721 |
