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Sample GSM3629956 Query DataSets for GSM3629956
Status Public on Nov 01, 2019
Title EAE107 Co dist B2-2
Sample type SRA
 
Source name distal colon tissue
Organism Mus musculus
Characteristics tissue: distal colon tissue
condition: Trp-def
strain: C57BL/6
gender: female
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen colon whole tissues of the mice using the RNeasy mini kit from Qiagen using standard protocol. The frozen tissue samples were homogenized using Tissue Lyser II for the RNA extraction.
Individual strand-specific single-end sequencing libraries were constructed from the total RNA isolated from the samples using TruSeq Stranded mRNA kit (Illumina Inc.). Sequencing was performed on the Illumina HiSeq3000 (1 x 50 bp) using standard protocols.  
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description colonic tissue from mouse under Tryptophan-deficient diet
H01579
Data processing Sequence reads from were trimmed for adapters using the software Trimgalore (version 0.4.4)
All filtered reads were mapped to the GRCm38 reference using the software STAR (version 2.5.2b)
Expression counts of genes were estimated using featureCounts (version 1.5.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with expression counts for each sample
 
Submission date Feb 26, 2019
Last update date Nov 02, 2019
Contact name Neha Mishra
E-mail(s) n.mishra@ikmb.uni-kiel.de
Organization name Institute of Clinical Molecular Biology
Lab Cell biology Lab
Street address Rosalind-Franklin-Str. 12
City Kiel
ZIP/Postal code 24105
Country Germany
 
Platform ID GPL21493
Series (1)
GSE127190 RNA-sequencing analysis of colon tissue in a murine EAE model after dietary tryptophan deprivation.
Relations
BioSample SAMN11022250
SRA SRX5431572

Supplementary file Size Download File type/resource
GSM3629956_H01579-L1_S69_L007Aligned.sortedByCoord.out_gene.featureCounts.txt.gz 2.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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