|
| Status |
Public on Oct 01, 2023 |
| Title |
Tet1+/- TdgN151A/+ ApcMin/+ .1 |
| Sample type |
SRA |
| |
|
| Source name |
Colonic adenoma
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Colonic adenoma
genotype: Tet1+/- TdgN151A/+ ApcMin/+
|
| Treatment protocol |
Mice were sacrificed at 150-160 days, and colonic adenomas were dissected for RNA extraction
|
| Growth protocol |
Mutant mice were appropriately crossed to generate experimental mice from four-genotype groups: Tet1-/- Tdg+/+ ApcMin/+; Tet1+/- TdgN151A/+ ApcMin/+ ; Tet1+/+ TdgN151A/+ ApcMin/+; and Tet1+/+ Tdg+/+ ApcMin/+.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen)
The sequencing libraries were constructed from 500 ng of total RNA using the TruSeq RNA Sample pre kit V2 (Illumina), following the manufacturer’s instructions. The fragment size and concentration of RNAseq libraries were determined using a 2100 Bioanalyzer (Agilent) and a Qubit instrument (LifeTech), respectively. The libraries were loaded onto an Illumina HiSeq 2500 at 6-10 pM on the rapid mode for 1x75bp single-end read sequencing. The fastq files were generated on the Illumina’s BaseSpace for further analysis. Sequence reads were aligned to mouse mm10 genome using Tophat2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
B1
|
| Data processing |
Raw sequence reads were aligned to the mouse genome (mm10) using the Tophat algorithm
Cufflinks was implemneted to assemble transcripts and estimate their abundance.
Cuffdiff was used to statistically assess expression changes in quantified genes in different conditions
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Sample ...
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Alfonso Bellacosa |
| E-mail(s) |
alfonso.bellacosa@fccc.edu
|
| Organization name |
Fox Chase Cancer Center
|
| Department |
Cancer Signaling & Epigenetics
|
| Street address |
333 Cottman Avenue
|
| City |
Philadelphia |
| ZIP/Postal code |
19111 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE179526 |
RNA-Seq of adenomas from Apc-Min mice with additional Tet1 and Tdg mutations |
|
| Relations |
| BioSample |
SAMN20079948 |
| SRA |
SRX11360023 |
