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Sample GSM4456008 Query DataSets for GSM4456008
Status Public on Dec 11, 2020
Title RNAseq_45 mir-802fl/fl
Sample type SRA
Source name Enterocytes isolated from upper jejunum
Organism Mus musculus
Characteristics strain: B6.SJL-Tg(Vil-cre)997Gum/J * B6.mir802tm1(fl/fl)MS
genotype: Intestinal miR-802 WT
cell type: Upper jejunum enterocytes
age: 18 weeks (adult)
Sex: Female
Extracted molecule total RNA
Extraction protocol RNA was extracted from jejunum enterocytes isolated from 18-week-old mice using Trizol (Sigma-Aldrich) followed by column purification using the RNeasy column purification kit (Qiagen), with on-column DNase (Qiagen) digestion for all samples. 1ug of total RNA was used for library preparation.
Illumina TruSeq stranded mRNA.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description Total RNA was extracted from samples. PolyA-enrichment.
Data processing bcl2Fastq v2.19 software used for demultiplexing + basecalling.
Reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
Reads mapped and quantified with RSEM 1.2.22.
Differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus/Ensembl/GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text file with the following columns: 1. Identifier (Ensembl TranscriptID), 2. gene_id (= Ensembl GeneID) , 3. gc (=transcript gc-content), 4. width (= transcriptLength in [nt]), 5. transcriptCout (= raw counts), 6.-7. TPM/FPKM (= normalized counts), 8.-10. Applying PosteriorEstimates to previous count information.
Submission date Apr 06, 2020
Last update date Dec 12, 2020
Contact name Algera Goga
Organization name ETH Zurich
Department Biology
Lab Markus Stoffel
Street address Otto-Sttern-Weg 7
City Zurich
State/province Schweiz
ZIP/Postal code Zurich 8093
Country Switzerland
Platform ID GPL21103
Series (1)
GSE148198 MicroRNA-802 regulates the innate immune response through Paneth cell expansion and Wnt signaling
BioSample SAMN14546363
SRA SRX8068456

Supplementary file Size Download File type/resource
GSM4456008_45_female_wt.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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