RNA-Seq of chicken cecal tonsil samples treated with chronic heat stress
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ABSTRACT:
PROVIDER: PRJEB32134 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To study the effect of chronic heat stress on mature laying type hens, RNA-Seq was performed on cecal tonsil samples during a 4-week heat stress experiment. RNA-Seq samples were collected 3-hour, 2-weeks, and 4-weeks post heat from both control (unheated) and treatment (heated) birds. RNA was extracted from the tissues with RNAqueous Total RNA Isolation Kit, treated with DNase, and mRNA cDNA libary were prepared with Illumina TrueSeq Stranded mRNA Library Prep Kit. Sequencing was done on 2 lanes with 12 libraries per lane on Illumina HiSeq 3000 platform.
2019-05-01 | E-MTAB-7865 | biostudies-arrayexpress
Project description:Chicken 60-mer oligonucleotide microarray, including 39854 cDNA and ESTs, entire Marek’s disease virus and avian influenza virus genomes, and 150 chicken microRNAs, was developed. Cecal tonsil, ileum, liver and spleen from 6 chickens were selected for hybridization to validate the microarray performance. There are 2886, 2886, 2660, 358, 3208 3355, and 3710 genes significantly expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum at the P<10-7. Number of tissue specific genes for cecal tonsil, ileum, liver and spleen was 95, 71, 535, and 108, respectively with p < 10-7. More than 95% of spots had high SNR (>10). Keywords: characteristics of newly developed microarray using different normal tissue
2008-02-29 | GSE7452 | GEO
Project description:Chicken 60-mer oligonucleotide microarray, including 39854 cDNA and ESTs, entire Marek’s disease virus and avian influenza virus genomes, and 150 chicken microRNAs, was developed. Cecal tonsil, ileum, liver and spleen from 6 chickens were selected for hybridization to validate the microarray performance. There are 2886, 2886, 2660, 358, 3208 3355, and 3710 genes significantly expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum at the P<10-7. Number of tissue specific genes for cecal tonsil, ileum, liver and spleen was 95, 71, 535, and 108, respectively with p < 10-7. More than 95% of spots had high SNR (>10). Keywords: characteristics of newly developed microarray using different normal tissue Loop design was carried on for all of tissue samples from the six chickens. Samples of four tissues from a chicken were used in each loop. The order of the tissues in each loop was changed so that all pairs of tissues were combined on an array with an equal number of times. Dye swap was used so that each tissue was measured an equal number of times with each dye. Data from 12 measurements for each tissue were collected, in total, 48 measurements from 24 arrays.
2008-02-28 | E-GEOD-7452 | biostudies-arrayexpress
Project description:It is essential to understand host response to Campylobacter jejuni infection in order to genetically improve resistance to its colonization in chickens. A custom Agilent chicken 44K array was used to examine gene expression profiles after Campylobacter jejuni infection of two broiler lines (A and B). Day-old chicks were orally inoculated with C. jejuni. After day 7 post-infection, the cecal tonsil was collected for total RNA isolation and cecal content for bacteria burden quantification. Twenty highest and lowest bacterial burden birds and non-infected birds within each line were used to pool four biological replicates for each group. The pair comparisons among high, low bacterial burden, and non-infected group were used. The signal intensity of each gene was normalized by LOWESS method. A mixed model including the fixed effects of dye, line, treatment and line × treatment interaction, and random effects of slide and array was used to identify differentially expressed genes at P < 0.001 by SAS program. Within line A, there were 61, 163, and 90 genes significantly differentially expressed between high and low bacterial burden, high bacterial burden and non-infected group, and low bacterial burden and non-infected group, respectively; 2637, 1684, 561 genes within line B, respectively. The results suggested that genetics, treatment and genetics × treatment interaction played important role in gene regulation of C. jejuni infection. The findings in the current study will lead the identification of potential candidate genes for genetic resistance to C. jejuni infection in chickens. Keywords: diease state analysis
2010-08-03 | GSE10257 | GEO
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Project description:RNA-Seq of chicken breast samples treated with chronic heat stress
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