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Status |
Public on Apr 19, 2019 |
Title |
A rep1 |
Sample type |
SRA |
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Source name |
Lung
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Organism |
Gallus gallus |
Characteristics |
tissue: Lung strain: Leghorn chicken age: 13 day old
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Treatment protocol |
Control group (A): No treatment control, fed with the same environment, keeping up with the end of the experiment.Co-infection group (B): The infectious dose was diluted into 0.2ml MG medium in left caudal thoracic air sac at the 7th day, and injected intraperitoneally with 0.1 ml of E.coli bacteria at day 10. MG group (C): The MG infection model was constructed one time by left caudal thoracic air sac inoculation with MG Rlow strain 0.2mL at the 7th day. E.coli group (D): The infectious dose was injected intraperitoneally with 0.1 ml of E.coli bacteria at day 10.
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Growth protocol |
Eighty (1 day old) commercial Leghorn chickens were obtained from Chia Chau Chicken Farm (Harbin, Heilongjiang, China) and were assigned randomly to four groups namely control group, co-infection group, MG group, E.coli group. The chickens were in healthy conditions, MG and E.coli-free and did not undergo vaccination and raised to the 10th day in four separate environmentally controlled chambers (named A, B, C and D).
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Extracted molecule |
total RNA |
Extraction protocol |
Lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen) BGISEQ-500 RNA-Seq Library. Library was validated on the Agilent Technologies 2100 bioanalyzer.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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Description |
Control
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Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters v1.5.2, then mapped to Gallus_gallus-5.0 genome using bowtie2 v2. 2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Gallus_gallus-5.0 Supplementary_files_format_and_content: csv files include RPKM values for each Sample ...
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Submission date |
Apr 18, 2019 |
Last update date |
Apr 19, 2019 |
Contact name |
Zhiyong Wu |
E-mail(s) |
1033077792@qq.com
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Organization name |
Northeast Agricultural University
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Street address |
600 Changjiang Road, Xiangfang District
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City |
Harbin |
ZIP/Postal code |
150030 |
Country |
China |
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Platform ID |
GPL24996 |
Series (1) |
GSE130015 |
Transcriptomic analyses of co-infection of Mycoplasma gallisepticum and Escherichia coli in chicken lungs |
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Relations |
BioSample |
SAMN11461710 |
SRA |
SRX5708060 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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