|
| Status |
Public on Nov 18, 2020 |
| Title |
117-O |
| Sample type |
SRA |
| |
|
| Source name |
Patient 117
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor specimen
disease state: HER2-positive
time point: post-treatment
treatment: trastuzumab
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy Plus Mini with DNase treatment
KAPA Stranded mRNAseq Kit, 1 ug total RNA input, 10 cycles PCR amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the human reference genome (hg38) using STAR 2.4.2a
reads were translated to transcriptome coordinates using Salmon 0.60
Isoform data were collated to single gene IDs using the R package biomaRt, and abundance estimates were upper quartile normalized using R
Genome_build: hg38
Supplementary_files_format_and_content: Processed files (.xlsx) contain transcript abundance estimates, organized by official gene symbol--both pre-normalization (...genes.xlsx) and post upper quartile normalization (...genes.norm.xlsx)
|
| |
|
| Submission date |
Nov 18, 2020 |
| Last update date |
Nov 18, 2020 |
| Contact name |
Steven P Angus |
| E-mail(s) |
[email protected]
|
| Phone |
317-274-8911
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Pediatrics
|
| Street address |
1044 W Walnut St
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE160670 |
Adaptive responses to HER2-directed therapy in breast cancer cell line models |
| GSE161743 |
Adaptive responses to targeted therapy in HER2-positive breast cancer (RNAseq) - TBCRC 036 / LCCC1214 / ClinicalTrials.gov Identifier: NCT01875666 |
|
| Relations |
| BioSample |
SAMN16828391 |
