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Sample GSM4079831 Query DataSets for GSM4079831
Status Public on Sep 14, 2022
Title Combination_tumour_2 [H362]
Sample type SRA
 
Source name MDA-MB-231 tumour in mouse_combination treated
Organisms Homo sapiens; Mus musculus
Characteristics cell line: MDA-MB-231
host strain: Balb/c nude mice
drug: Docetaxel (4mg/kg) + PKC-θ peptide inhibitor (40mg/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 H362_S14
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 and PKC-θ peptide inhibitor daily for 5 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 SAMN12758327
SRA SRX6852910

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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