|
| Status |
Public on Sep 14, 2022 |
| Title |
Chemo_tumour_3 [B335] |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 tumour in mouse_chemo treated
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: MDA-MB-231
host strain: Balb/c nude mice
drug: Docetaxel (4 mg/kg)
|
| Treatment protocol |
Chemotherapy (docetaxel) was administered intraperitoneally weekly for 3 weeks and PKC-θ peptide inhibitor was administered interaperitoneally daily for 5 weeks.
|
| Growth protocol |
MDA-MB-231 Cells 2 x 10^6 in 50µl (50:50 PBS:Matrigel) were transplanted subcutaneously into the mammary fat pads of balb/c nude mice and 50 days later the tumour was excised from the sacrificed mouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tumor tissues were collected in Allprotect tissue reagent kit and then processed using the Rneasy Microarray Tissue Mini Kit according to manufacturer’s protocol (tissues were lysed mechanically using the Tissue Lyser II)
Libraries were constructed with theTruSeq mRNA Paired-End kit per manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B335_S8
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of docetaxel weekly for 3 weeks
|
| Data processing |
Reads were cleaned with trimmomatic (v0.36) and tagdust (v2.33)
before separately mapping to the human (Hg38) and mouse (mm10) genomes (HISAT2 v2.04, no--discordant -- nomixed).
reads that mapped to both genomes were discarded (Picard).
Gene counts were obtained using Stringtie and Ballgown
TMM and library size normalized in EdgeR.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: normalised counts for Human and Mouse (gene_count_matrix_m) reads.
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
Sep 14, 2022 |
| Contact name |
Kristine Hardy |
| E-mail(s) |
kristine.hardy@anu.edu.au
|
| Organization name |
University of Canberra
|
| Lab |
Cytokine Gene Expression
|
| Street address |
University of Canberra
|
| City |
Bruce |
| State/province |
ACT |
| ZIP/Postal code |
0200 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE137467 |
Investigating the effects on the tumour and tumour environment transcriptome, of inhibiting PKC in conjunction with Docetaxel treatment [RNA-seq] |
|
| Relations |
| BioSample |
SAMN12758332 |
| SRA |
SRX6852905 |
