|
| Status |
Public on Jul 14, 2017 |
| Title |
Chix 43_Infected_Day 5 |
| Sample type |
SRA |
| |
|
| Source name |
Infected White Leghorn Chicken
|
| Organism |
Gallus gallus |
| Characteristics |
host breed: White Leghorn
infection: Infected
infectious agent: M. gallisepticum Rlow
time: Day 5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of tracheal cells/content of tracheal lumen
Total RNA was collected in TRIzol, extracted using the zymo direct-zol mini prep, and enriched using Illumina PolyA selection per product instructions
rRNA depleted RNA
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA library prep kit HT)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cuffdiff_Day5ci.txt
|
| Data processing |
Illumina RTA v2 was used for base-calling
Fastq data from individual chickens were mapped using the TopHat package (version 2.0.1) utilizing the Bowtie2 engine (version 2.2.5) to align reads to the Gallus gallus reference genome
BAM files were processed using Cuffdiff to calculate FPKM expression values and differential expression
Genome_build: Gallus gallus genome (WASHUC2)
Supplementary_files_format_and_content: tab-delimited text files including FPKM values, fold change, and significance. Each cuffdiff .txt file contains the tophat output from each chicken used to determine FPKMs and differential expression of genes between birds/within groups (Controls v. infected for each time point).
|
| |
|
| Submission date |
Jul 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Edan Tulman |
| E-mail(s) |
edan.tulman@uconn.edu
|
| Phone |
860-486-0836
|
| Organization name |
University of Connecticut
|
| Street address |
61 North Eagleville Rd
|
| City |
Storrs |
| State/province |
CT |
| ZIP/Postal code |
06269 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE101403 |
Transcriptional Profiling of the Chicken Tracheal Response to Virulent Mycoplasma gallisepticum Strain Rlow |
|
| Relations |
| BioSample |
SAMN07349313 |
| SRA |
SRX3001048 |
