 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 21, 2020 |
| Title |
DIEC_naΪve 2 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8 weeks
genotype: ko
treatment: water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colons were dissected and cleaned, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing by using Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ExpressionTable.xlsx
|
| Data processing |
Base calling was performed using bcl2fastq (Illumina, v2.17.1.14).
RNA-seq reads were aligned to the mouse (mm10) genome with STAR (v2.2.0c) with default parameters
Only uniquely alignable reads were used for downstream analysis.
Gene expression values were calculated using HOMER (v4.9, http://homer.ucsd.edu/homer/) by quantifying strand-specific reads across annotated gene exons (RefSeq) and reported as FPKM (fragments per kilobase of exon per million mapped reads FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: microsoft excel
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
May 21, 2020 |
| Contact name |
Shujuan Chen |
| E-mail(s) |
s18chen@ucsd.edu
|
| Phone |
8588221351
|
| Organization name |
University of California, San Diego
|
| Department |
Pharmacology
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE136153 |
RNA-sequencing study on DSS-induced ulcerative colitis in mice of wild type and intestinal epithelial cell-sepific NCoR1 deletion. |
|
| Relations |
| BioSample |
SAMN12617257 |
| SRA |
SRX6749222 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
