|
| Status |
Public on May 23, 2023 |
| Title |
colon, KO-8 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
genotype: Nrg4 KO
cage: A
age: adult (11-12 wks-old)
|
| Growth protocol |
Mutant (Nrg4-/-) and wildtype (WT) mice were co-housed to mix genotypes at 9 weeks of age. Animals were dissected at 11-12 weeks of age. Both male and female mice were included in the experiment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were euthanized and their colons dissected. Full-thickness distal colonic tissue was homogenized and lysed. RNA was prepared using OMEGA Bio-tek EZNA on-column isolation kit.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on NextSeq High Output Runs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Differential expression calls (p values) were made in sleuth using a full linear model (genotype + cage) against a reduced model (cage only), to account for cage-to-cage variability.
Displayed differential expression ratios take into account only the global gene expression values and do not normalize per cage.
Assembly: mm10
Supplementary files format and content: Comma-separated file includes tpm levels of individual principal transcripts for each sample and results of differential expression testing.
|
| |
|
| Submission date |
Jun 26, 2022 |
| Last update date |
May 23, 2023 |
| Contact name |
Cambrian Yangshao Liu |
| E-mail(s) |
cambrian@uchicago.edu
|
| Organization name |
The University of Chicago
|
| Department |
Department of Medicine
|
| Street address |
5841 S Maryland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE206965 |
Differential gene expression in the colons of mice lacking neuregulin-4 |
|
| Relations |
| BioSample |
SAMN29358892 |
| SRA |
SRX15898546 |
