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Sample GSM7904510 Query DataSets for GSM7904510
Status Public on Jan 15, 2024
Title Colon, 9 Months, Rep9 [9M.N9]
Sample type SRA
 
Source name Colon
Organism Mus musculus
Characteristics tissue: Colon
strain: C57BL/6J/Ukj
Sex: Male
age: 9 Months
library batch: Prep 3
Growth protocol All the mice were kept solely for aging in a controlled environment and health status.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using the QIAzol/chloroform extraction method.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 9M.N9
Data processing RNA was isolated using the QIAzol/chloroform extraction method. RNA quality was determined via an Agilent Bioanalyzer 2100 using the RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). An RNA Integrity Number (RIN) value of greater than 7 was considered to be the minimum quality for sequencing.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions. All libraries were sequenced on an NovaSeq 6000 machine (Illumina, San Diego, CA, USA) with an average of 36 million paired-end reads (2x100 bp) at Competence Centre for Genomic Analysis (CCGA, Kiel, Germany) .
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (2.8) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a two-color-chemistry aware, 3’-end quality trimming for a phred-score >= 25 (nextseq-trim=25).
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 from both 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 the tool featureCounts from the subread package (2.0.1) with reverse stranded information, while ignoring chimeric fragments and allowing only properly mapped read pairs with feature sizes in between 50 bp to 600 bp.
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 Nov 16, 2023
Last update date Jan 15, 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 GPL24247
Series (1)
GSE248002 Nonlinear DNA methylation trajectories in aging male mice [RNA-seq]
Relations
SRA SRX22549755
BioSample SAMN38285241

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

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