|
| Status |
Public on Aug 03, 2023 |
| Title |
colonic epithelial cells, Tvp23b_KO2 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
cell type: colonic epithelial cells
genotype: Tvp23b homozygous mutant
treatment: No
|
| Treatment protocol |
No
|
| Growth protocol |
No
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colons were isolated from mice and stool removed from the lumen. Colons were then cut to 5-10 mm pieces and incubated at room temperature for 30 minutes in PBS containing 5 mM EDTA with rotation on a platform shaker. The epithelial cells were collected by passing through a 100-μm cell strainer. RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters were trimmed from fastq.gz files using cutadapt v1.9.dev4
Trimmed fastq.gz were aligned to the mm10 reference genome using tophat-2.0.10
BAM files resulting from alignments were run through cuffdiff (cufflinks v2.1.1) for differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw gene counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample
Supplementary files format and content: excel file include differential gene expression between WT and KO
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
Aug 03, 2023 |
| Contact name |
Jin Huk Choi |
| E-mail(s) |
Jin.Choi@UTSouthwestern.edu, Xue.Zhong@UTSouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE224516 |
Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation |
|
| Relations |
| BioSample |
SAMN33059541 |
| SRA |
SRX19279774 |
