|
| Status |
Public on Jun 20, 2024 |
| Title |
Colon_LN_PP_Citro_infected_CD4_D4_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
genotype: LN/PP CD4(dILC3)
treatment: Citro infected
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total mRNA was isolated from 0.5 cm pieces of terminal ileum or distal colon, sorted CD4 T cells, or IECs from ileal scrapings after homogenization in Trizol using standard protocols.
RNA-seq libraries were constructed using Illumina Stranded mRNA Prep Ligation kit following manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Element AVITI |
| |
|
| Data processing |
Raw reads were processed by Cutadapt v2.1 to remove low-quality bases and TruSeq adapters
Remaining reads passing quality filtering were then analyzed by Kallisto v0.46.1 with default setting to quantify gene expression
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample
Supplementary files format and content: tab-delimited text file includes estimated reads count from pseudo-alignment for each Sample
|
| |
|
| Submission date |
Jun 20, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Yiming Huang |
| E-mail(s) |
yiminghuang0405@gmail.com
|
| Organization name |
Columbia University
|
| Department |
Department of Systems Biology
|
| Street address |
3960 Broadway
|
| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL34475 |
| Series (1) |
| GSE270398 |
Context-dependent role of type 3 innate lymphoid cells in mucosal protection |
|
| Relations |
| BioSample |
SAMN41050802 |
| SRA |
SRX24341241 |
