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Sample GSM5419833 Query DataSets for GSM5419833
Status Public on Oct 01, 2023
Title Tet1+/- TdgN151A/+ ApcMin/+ .3
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 B3
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 SAMN20079944
SRA SRX11360025

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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