|
| Status |
Public on Oct 01, 2020 |
| Title |
D3 - CcK #13 [9-13CT] |
| Sample type |
SRA |
| |
|
| Source name |
CcK colonized_Day 3_CT
|
| Organism |
Meleagris gallopavo |
| Characteristics |
status: Treated; CcK colonized
day: Day 3
tissue: Cecal tonsils (CT)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was preserved in RNALAter, flash frozen on in liquid notrogen, and total RNA was harvested using mirVana and Trizol reagents. Illumina HiSeq3000 RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
9-13CT_S15_L002
|
| Data processing |
STAR v2.5.2b used for mapping and read qualtification
Reads were normalised using VST approach from DESeq2 package in R
Differential gene expression was calculated using DESeq2 in R
Genome_build: Meleagris gallopavo Turkey_5.1
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized (DESeq2) values for each Sample.
|
| |
|
| Submission date |
Sep 28, 2020 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Sathesh K Sivasankaran |
| E-mail(s) |
sathesh@iastate.edu
|
| Organization name |
University of Missouri
|
| Lab |
Bioinformatics and Analytics Core
|
| Street address |
Bond Life Sciences Center Suite 106, 1201 Rollins Street
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL29195 |
| Series (1) |
| GSE158639 |
The acute host-response of turkeys colonized with Campylobacter coli |
|
| Relations |
| BioSample |
SAMN16278501 |
| SRA |
SRX9201172 |
