|
| Status |
Public on Apr 30, 2024 |
| Title |
NonSil.Bmp4_26 |
| Sample type |
SRA |
| |
|
| Source name |
NB26
|
| Organism |
Homo sapiens |
| Characteristics |
smad4_status: Expressing
bmp4_status: Enforced
metastatic_propensity: Low
|
| Growth protocol |
TurboGFP-tagged MDA-MB-231-HM cells (one million in 1:1 Cultrex:PBS) with modified expression of BMP4 and/or SMAD4 were injected into the fourth mammary fat pad of NSG mice. Tumours were resected when they reached 400 mm3 in volume.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from TurboGFP-positive MDA-MB-231-HM cells (recovered by FACS) was extracted using the RNeasy micro kit with on-column DNase treatment. Samples from four different tumours with an RNA integrity number (RIN) above 9.9 and the highest RNA concentration, as determined by the Tapestation RNA ScreenTape, were included for each tumour type in downstream analysis.
cDNA library from purified mRNA was synthesised according to the Illumina TruSeq RNA sample preparation workflow. The pooled library containing 16 indexed samples was sequenced in four lanes using the NextSeq 500/550 high output kit (75 cycles) at the La Trobe Genomics Platform (Bundoora, Victoria, Australia).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The quality of the sequencing output was checked with the FastQC quality control tool.
Sequence alignment and feature counting were completed in R using the Rsubread package and the genome reference consortium human build 38 (hg38) assembly available at http://asia.ensembl.org/info/data/ftp/index.html.
Lowly expressed genes with counts per million (CPM) values lower than 0.5 (equivalent to approximately less than 10 counts) in more than 12 samples were removed to avoid interference with downstream statistical analysis.
Gene expression was then normalised and analysed using the edgeR and limma packages. Interactive volcano and MD plots were generated using the Glimma package. Additional plots were generated using gplots, ggplot2, ggrepel and ggpubr packages.
Gene set testing was completed using the camera function in limma and curated molecular signature databases available at http://bioinf.wehi.edu.au/software/MSigDB/.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Mar 28, 2022 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Lap Hing Chi |
| Organization name |
Olivia Newton-John Cancer Research Institute
|
| Department |
Translational Breast Cancer Program
|
| Lab |
Metastasis Research Lab
|
| Street address |
145 Studley Road
|
| City |
Heidelberg |
| State/province |
Victoria |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE199628 |
Loss of tumor-derived SMAD4 enhances primary tumor growth but not metastasis following BMP4 signalling |
|
| Relations |
| BioSample |
SAMN27025090 |
| SRA |
SRX14639512 |
