|
| Status |
Public on Dec 12, 2021 |
| Title |
HCI005 Vehicle 3_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HCI005 Vehicle tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer PDX model HCI005
treatment: Vehicle
replicate: 3
|
| Treatment protocol |
Mice were randomly assigned to treatment groups and treated with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).
|
| Growth protocol |
A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from snap-frozen tumour PDX tissue samples using the RNeasy Mini Kit (QIAGEN)
RNA was prepared for sequencing using the TruSeq Stranded mRNA Library Prep kit (Illumina) and libraries were sequenced on Illumina NovaSeq S4 in paired-end mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Veh.vs.Dec_HCI005.cntTable
HCI005_Veh_3
|
| Data processing |
Sequence adaptors were trimmed using Trim Galore (v.0.11.2), reads were processed with Xenome v.10.1. (Conway et al., 2012) to remove mouse sequences and remaining reads were mapped with STAR (v.2.7.7a) (Dobin et al., 2013) to the hg38/GRCh38 human genome build with GENCODE v33 used as a reference transcriptome (parameter settings: –quantMode TranscriptomeSAM–outFilterMatchNmin 101 –outFilterMultimapNmax 20).
TPM counts for each sample were obtained from DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: normalized transcript abundance measurment
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Dec 12, 2021 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
[email protected]
|
| Organization name |
South Australian Immunogenomics Cancer Institute
|
| Street address |
AHMS Building, North Terrace
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE171073 |
Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [RNA-seq] |
| GSE171074 |
The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer |
|
| Relations |
| BioSample |
SAMN18527958 |
| SRA |
SRX10469166 |
