|
| Status |
Public on Jun 05, 2018 |
| Title |
Tumor from ApcMin/+/Macrod2-/- mouse_3 |
| Sample type |
SRA |
| |
|
| Source name |
epithelial tumor from large intestine
|
| Organism |
Mus musculus |
| Characteristics |
genotype: ApcMin/+/Macrod2-/-
Sex: Male
strain: C57BL/6
tissue: intestinal tumor
|
| Treatment protocol |
N/A
|
| Growth protocol |
ApcMin/+/Macrod2+/+, ApcMin/+/Macrod2-/+, ApcMin/+/Macrod2-/- mice were maintained in colonies at the WEHI animal facility.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
On autopsy of knock-out mice, the intestinal tract was removed and tumors resected. Total RNA was extracted using the AllPrep DNA/RNA Mini kit (Qiagen).
TruSeq Stranded Total RNA Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
T3_Macrod2_hom
|
| Data processing |
trimmed adaptors using Trimmomatic, reads <50 bp removed (v0.22)
tophat -g 1 -library-type fr-firststrand mm10 <fastq.gz> (v2.0.8)
featureCounts -a mm10_ucsc.gtf -t exon -g gene_name -s 2 (subread-1.4.5-p1-Linux-x86_64)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts and rpkms for each Sample
|
| |
|
| Submission date |
Jan 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Oliver Sieber |
| Organization name |
Walter and Eliza Hall Insitute of Medical Reseach
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE93514 |
MACROD2 haploinsufficiency promotes chromosome instability and growth of intestinal tumors |
|
| Relations |
| BioSample |
SAMN06217926 |
| SRA |
SRX2485203 |
