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Sample GSM4476763 Query DataSets for GSM4476763
Status Public on Oct 05, 2021
Title WT Cecum rep 2
Sample type SRA
 
Source name Intestine epithelium
Organism Mus musculus
Characteristics genotype: wild type
tissue: Cecum
Treatment protocol Epithilal tissues collected by EDTA method 30 days after Tamoxifen injection. Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice
Extracted molecule total RNA
Extraction protocol Qiagen Mini RNA extract kit
The library was constructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction strategy was non-directional eukaryotic mRNA library Sequencing strategy was Pair-end 150 (PE150)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Intestinal_epithelial_normalized_counts.txt
Data processing Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene counts table
 
Submission date Apr 15, 2020
Last update date Oct 05, 2021
Contact name Wei Gu
E-mail(s) wei.gu@beigene.com
Phone 13776921246
Organization name Beigene
Department Beigene Institute
Lab Gu Lab
Street address 51 Rijing Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200135
Country China
 
Platform ID GPL21103
Series (2)
GSE148692 Bulk RNA-seq of Intestine Epithelia (Jejunum, Ileum, Cecum and Colon) from Satb2-deficient and WT mice
GSE148695 SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling
Relations
BioSample SAMN14600379
SRA SRX8118442

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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