|
| Status |
Public on Oct 26, 2020 |
| Title |
SKBR3_siNT_DMSO_24h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SKBR-3 HER2+ breast carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKBR-3 HER2+
treatment: non-targeting (NT) siRNA control pool for 48h, then treated with DMSO for 24h
library preparation kit: Illumina TruSeq RNA library kit v2
|
| Treatment protocol |
RPMI supplemented with 10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy Plus kit.
4 ug total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
For DESeq differential expression analysis comparing pre-treatment and post-treatment patient tumors: RSEM gene-level expected read counts were imported into R version 3.2.2. and were analyzed using DESeq2 v1.12.3 to detect genes that were differentially expressed between pre-treatment and post-treatment conditions. Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.
|
| |
|
| Submission date |
Oct 23, 2020 |
| Last update date |
Oct 27, 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) |
| GSE160001 |
FOXA1-dependent responses of the HER2+ SKBR-3 cell line to lapatinib |
| GSE160670 |
Adaptive responses to HER2-directed therapy in breast cancer cell line models |
|
| Relations |
| BioSample |
SAMN16539456 |
| SRA |
SRX9353404 |
