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Sample GSM5351022 Query DataSets for GSM5351022
Status Public on May 29, 2024
Title KO2a_2
Sample type SRA
 
Source name small intestine
Organism Mus musculus
Characteristics cell type: small intestine epithelial cells
strain: HIF2[alpha][delta]IEC
treatment: naïve mice
Extracted molecule total RNA
Extraction protocol small intestine were dissected and small intestine epithelial cells was isolated from collagen induced arthritis model, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Nanodrop: Preliminary quantitation
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Agarose Gel Electrophoresis: tests RNA degradation and potential contamination
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Paired-end sequencing libraries are sequenced by Illumina high-throughput sequencer.
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Jun 01, 2021
Last update date May 29, 2024
Contact name Pang Lyu
E-mail(s) 15538398590lv@gmail.com
Phone 0152 2677 4319
Organization name University Hospital Erlangen
Department Department of Internal Medicine 3
Street address Glückstr. 6
City Erlangen
ZIP/Postal code 91054
Country Germany
 
Platform ID GPL21103
Series (1)
GSE175907 HIFα-regulated genes in small intestine epithelial cells from naïve mice
Relations
BioSample SAMN19487947
SRA SRX11039312

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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