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| Status |
Public on Feb 28, 2024 |
| Title |
ileum, 35C, infection (HSi)-Rep 4 |
| Sample type |
SRA |
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| Source name |
ileum
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| Organism |
Gallus gallus |
| Characteristics |
tissue: ileum
genotype: Ross708
treatment: HSi
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the trizol-chloroform method and purified with Rneasy Mini kit
4 µg total RNA using the TruSeq RNA Sample Preparation Kit to acquire cDNA fragments with an average size of 229 bp, or 355 bp inclusive of the adapter sequences.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequence reads were trimmed using Trimmomatic v.0.36.
Reads were aligned to the chicken reference genome using STAR aligner
Expressed genes and transcripts were detected using Cufflinks v 2.2.1
Frangements per kilobase of exon per million mapped fragments for each sample was determined using Cuffdiff v 2.11
Orthogonal differences of differentially expressed genes among the treatments were tested using DESeq2
Assembly: Gallus gallus 5.0.90, Ensembl
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| Submission date |
Aug 28, 2023 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Samuel E Aggrey |
| E-mail(s) |
saggrey@uga.edu
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| Phone |
+1-706-542-1354
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| Organization name |
University of Georgia
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| Department |
Poultry Science
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| Lab |
NutriGenomics
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| Street address |
110 Cedar Street
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL16133 |
| Series (1) |
| GSE241777 |
Host transcriptome response to heat stress and Eimeria maxima infection in meat-type chickens |
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| Relations |
| BioSample |
SAMN37168674 |
| SRA |
SRX21487339 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7743468_458.counts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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