|
| Status |
Public on Jul 08, 2021 |
| Title |
Sftpd_KO_Proximal_small_intestine_3 |
| Sample type |
SRA |
| |
|
| Source name |
Proximal small intestine
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Sftpd_KO
treatment: Vibrio cholerae infection
tissue: Proximal small intestine
age: P3
|
| Treatment protocol |
Infected with V. cholerae.
|
| Growth protocol |
Infant P3 day old C57BL/6 mouse WT and Sftpd KO.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Proximal and distal small intestine tissues were harvested and preserved using Trizol reagent. Total RNA was extracted using the RNeasy mini kit (Qiagen).
mRNA libraries were prepared using KAPA mRNA HyperPrep kit (Roche).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
TRA00210817
GSE_Raw_Counts_Proximal_Small_intestine.txt
|
| Data processing |
Reads were trimmed using Trim Galore with automatic adapter sequence detection.
Trimmed reads were mapped to the mouse reference genome and annotation using RNA STAR.
Feature Counts was used to build a count matrix from mapped reads using the Ensembl annotation as a guide.
Genome_build: GRCm38
Supplementary_files_format_and_content: GSE_Raw_Counts_Proximal_Small_intestine.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: GSE_Raw_Counts_Distal_Small_intestine.txt: Tab-delimited text file includes raw counts.
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Matthew K Waldor |
| Organization name |
Harvard Medical School
|
| Department |
Microbiology
|
| Lab |
Waldor Lab
|
| Street address |
181 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE179528 |
Proteomic analysis of the pathogen surface in cholera identifies host proteins involved in defense and microbiota recognition [I] |
| GSE179530 |
Proteomic analysis of the pathogen surface in cholera identifies host proteins involved in defense and microbiota recognition |
|
| Relations |
| BioSample |
SAMN20079994 |
| SRA |
SRX11360080 |
