|
| Status |
Public on Apr 12, 2024 |
| Title |
BT474, DTEP, Month 6, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
BT474
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT474
cell type: HER2+ breast cancer cell line
genotype: WT
treatment: Lapatinib, 1 uM
time: Month 6
|
| Treatment protocol |
The cells were treated with 1 uM of lapatinib every 3 days for 9 months
|
| Growth protocol |
BT474 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using the NucleoSpin RNA purification kit (Macherey‐Nagel). 300 ng of total RNA was used for the construction of sequencing libraries.
TruSeq® Stranded mRNA Sample Preparation, Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
DTEP_3
|
| Data processing |
Reads were called using the manufacturer's bcl2fastq2 base calling software.
Reads were then aligned the reference genome (hg38) using Star version 2.5.2b, with the reference genome along with annotations downloaded from Illumina iGenomes web site.
Reads were then associated with known genes and the number of reads associated with each gene was counted using the subreads-package v1.5.1.
Gene-wise read counts were normalised using the TMM normalization method of the edgeR R/Bioconductor package with log(x+1) transformation for downstream applications.
The data processing pipeline was run using default parameters when possible.
Assembly: hg38
Supplementary files format and content: Tab-separated gene-wise expression (rows) per samples (columns) normalized using TMM.
|
| |
|
| Submission date |
May 02, 2023 |
| Last update date |
Apr 12, 2024 |
| Contact name |
Teemu Daniel Laajala |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Turku
|
| Department |
Department of Mathematics and Statistics
|
| Street address |
Turun yliopisto
|
| City |
Turku |
| ZIP/Postal code |
20014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE231525 |
DUSP6 inhibition overcomes Neuregulin/HER3-driven therapy resistance in HER2+ breast cancer [BT474] |
| GSE231526 |
DUSP6 inhibition overcomes neuregulin/HER3-driven therapy tolerance in HER2+ breast cancer |
|
| Relations |
| BioSample |
SAMN34539757 |
| SRA |
SRX20200555 |
