|
| Status |
Public on Jan 27, 2018 |
| Title |
St2-/- => St2-/- biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
St2-/- => St2-/-
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Balb/c
gender: Male
origin: Colon tumor
protocol: 6xAOM treated
time last after aom injection: 14 weeks
|
| Treatment protocol |
The tumor was excised from the colon of bone marrow chimeras treated for 6 consecutive weeks with azoxymethane (AOM) 13 to 14 weeks after last AOM injection.
|
| Growth protocol |
Mice were euthanised with Co2 prior to excision of the tumors from the colon that were then immediately snap-frozen in dry-ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from snap-frozen tumors collected from the colon of bone marrow chimeras using Trizol®Reagent (Life Technologies). Extracted RNA was then further purified using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were generated using the Illumina Truseq RNA sample preparation kit according to the manufacturer’s instructions. Three biological replicates were generated and sequenced for each group of BM chimeras by subjecting 1μg of RNA to single-end (50 pb) sequencing on an Illumina HiSeq 2500 instrument at the Australian Genome Research Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
109_top
109_C81U4ANXX_ACAGTG_L001
|
| Data processing |
FASTQ files were output using standard Illumina protocols and software.
Untrimmed reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the TopHat aligner with Bowtie2
Genewise counts were obtained using HTseqCount. Genes were discarded for further downstream analysis if they failed to achieve at least 0.5 counts per million in at least two samples.
Genome_build: GRCm38/mm10 build of the Mus musculus genome
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene
|
| |
|
| Submission date |
Jan 26, 2018 |
| Last update date |
Jan 29, 2018 |
| Contact name |
Moritz Falk Eissmann |
| E-mail(s) |
moritz.eissmann@onjcri.org.au
|
| Organization name |
Olivia Newotn-John Cancer Research Institute
|
| Lab |
Cancer and Inflammation
|
| Street address |
145 Studley Road
|
| City |
Heidelberg |
| State/province |
Victoria |
| ZIP/Postal code |
3081 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE109694 |
RNA-seq analysis of colon tumors collected from St2-/- and WT reciprocal bone marrow chimeric mice treated with azoxymethane. |
|
| Relations |
| BioSample |
SAMN08399284 |
| SRA |
SRX3601955 |
