|
| Status |
Public on Jan 14, 2022 |
| Title |
WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal Epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Intestinal epithelium was isolated by EDTA-DTT separation method. The total RNA from the intestinal epithelium of 4-month-old WT and Faci-/- mice (n = 3 per group) was extracted by RNAiso Plus reagent (Takara)
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequenced libraries were evaluated with FastQC
Software SOAPnuke was used to filter reads
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) software was used for RNA-seq reads alignment to reference genome
We detect DEGs with DEseq2. Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt files include read counts for each sample
|
| |
|
| Submission date |
Jan 14, 2022 |
| Last update date |
Jan 14, 2022 |
| Contact name |
Yun Cheng |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Hong Kong
|
| Street address |
21 Sassoon Road, Pokfulam
|
| City |
Hong Kong |
| State/province |
Hong Kong |
| ZIP/Postal code |
852 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE193731 |
Comparison of intestinal epithelial transcriptomes of WT and FACI-/- mice |
|
| Relations |
| BioSample |
SAMN25002856 |
| SRA |
SRX13790707 |
