|
| Status |
Public on Aug 10, 2020 |
| Title |
Small intestine, Erk1/2-KO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Small intestine
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Small intestine
age: post natal day 14
genotype: Erk1/2 -/-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Small intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.1.0.
Raw counts of all genes were estimated by the program “htseq-count” in HTSeq software (version 0.6.0). The number of reads were normalized by R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count for each Sample
|
| |
|
| Submission date |
Jul 15, 2019 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Jiwei Chen |
| E-mail(s) |
chenjiwei@bio.ecnu.edu.cn
|
| Organization name |
East China Normal University
|
| Street address |
500 Dongchuan Rd.
|
| City |
Shanghai |
| ZIP/Postal code |
200241 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE134249 |
Erk1/2 mediated negative feedback regulation is essential for postnatal intestinal development and homeostasis |
|
| Relations |
| BioSample |
SAMN12273883 |
| SRA |
SRX6441451 |
