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Sample GSM8162656 Query DataSets for GSM8162656
Status Public on Mar 27, 2024
Title Colon, 9 Months, Rep4
Sample type SRA
 
Source name Colon
Organism Mus musculus
Characteristics tissue: Colon
strain: C57BL/6J/Ukj
Sex: Male
age: 9 Months
library batch: Run 3
Growth protocol All the mice were kept solely for aging in a controlled environment and a controlled health status.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from tissue samples of liver, colon and left brain hemisphere with the phenol-chloroform extraction method using for each tissue 1ml Qiazol Lysis Reagent (Qiagen, Hilden, Germany).
RNA was reverse transcripted into Illumina shotgun sequencing libraries at Competence Centre for Genomic Analysis (CCGA, Kiel Germany) with TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions and sequenced for 2x75 cycles (2x100 for colon) in paired end mode with ~13 samples per lane on a HiSeq4000 machine. Demultiplexing was done with zero mismatches allowed in the barcodes.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 9M.N4
Colon_9M_N4
colon_RNA_gene_counts.tsv.gz
Data processing Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (1.12) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a 3’-end quality trimming for a phred-score >=30.
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim also from the 5’-end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using HTSeq count (0.6.1) with reverse stranded information in union mode.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Tabular delimited matrix text files of read counts per GRCm38 gene (rows) and sample (columns).
 
Submission date Mar 22, 2024
Last update date Mar 27, 2024
Contact name Lena Best
E-mail(s) l.best@iem.uni-kiel.de
Organization name Christian-Albrechts-University Kiel
Department Institute of Experimental Medicine
Lab Kaleta Lab
Street address Michaelis-Straße 5
City Kiel
ZIP/Postal code 24105
Country Germany
 
Platform ID GPL21103
Series (1)
GSE262290 Metabolic modeling reveals the aging-associated decline of host–microbiome metabolic interactions in mice
Relations
BioSample SAMN40584124
SRA SRX24028125

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

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