|
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 |