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Sample GSM8408159 Query DataSets for GSM8408159
Status Public on Jul 19, 2024
Title SI Apc Pik3ca/+ Rep4
Sample type SRA
 
Source name Small Intestine
Organism Mus musculus
Characteristics tissue: Small Intestine
Sex: Male
time point: Day 4
genotype: vilCreER Apcfl/fl Pik3caH1047R/+
Treatment protocol Induction of genetic recombination was performed by 2 x 80mg/kg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues were harvested after 3 or 4 days, as noted.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (either 2x36 cycles, paired end (Apc, Apc Kras/+, Apc Kras/+ Pik3ca/+, Apc Kras/+ Pten, Apc Pik3ca/+, Apc Pten) or 2x74bp paired end (Apc Pik3ca, Apc Kras/+ Pik3ca, Apc Pik3ca Slc7a5, Apc Kras/+ Pik3ca Slc7a5)).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description WT_Apc_KRas_LZR18181128_S18
Data processing Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts
 
Submission date Jul 19, 2024
Last update date Jul 19, 2024
Contact name Kathryn Gilroy
E-mail(s) K.gilroy@beatson.gla.ac.uk
Organization name Beatson Institute for Cancer Research
Street address Garscube
City Glasgow
ZIP/Postal code G611BD
Country United Kingdom
 
Platform ID GPL19057
Series (1)
GSE272639 Transcriptional profiling of intestinal tissue from mice with Apc and additional mutations.
Relations
BioSample SAMN42649539
SRA SRX25387562

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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