|
| Status |
Public on May 30, 2023 |
| Title |
surface_d9_cKO4 |
| Sample type |
SRA |
| |
|
| Source name |
EpCAM1+ CEACAM1hi CD45- L/D dye- FSChi SSChi
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Surface IEC
time: Post_Citrobacter_rodentium_infection_day_9
genotype: IL22 fl/fl CD4-Cre +
|
| Treatment protocol |
Citrobacter rodentium i.g. 2 x 10^9
|
| Growth protocol |
All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
IECs were directly sorted into Qiazol LS and RNA was isolated the SAME DAY with chloroform extract followed by Qiagen miRNAeasy kit
Nugen Universal Plus mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
IECs from middle/distal colon regions (pooled from 2-4 mice per sample) were isolated with DTT, followed by EDTA, and then sorted into three populations (All were CD45-LD-EpCAM1+): CEACAM1Hi Surface, CEACAM1Int/lo SSCHi Large Crypt, and CEACAM1- FSClo SSClo Small Crypt cells
|
| Data processing |
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build GRCm38 using STAR (version2.5.3) (Dobin et al.2013). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample
|
| |
|
| Submission date |
May 11, 2018 |
| Last update date |
May 30, 2023 |
| Contact name |
Min Gao |
| E-mail(s) |
mgao@uabmc.edu
|
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1900 University Blvd, THT Building Suite #130G
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE114338 |
IL-22+ T cells protect intestinal crypts from bacterial invasion and epithelial damage. |
|
| Relations |
| BioSample |
SAMN09197318 |
| SRA |
SRX4072171 |
