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Sample GSM3729299

Query DataSets for GSM3729299

Status

Public on Apr 19, 2019

Title

D rep3

Sample type

SRA

Source name

Lung

Organism

Gallus gallus

Characteristics

tissue: Lung
strain: Leghorn chicken
age: 13 day old

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.

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).

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.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

BGISEQ-500

Description

E.coli infection

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 ...

Submission date

Apr 18, 2019

Last update date

Apr 19, 2019

Contact name

Zhiyong Wu

E-mail(s)

1033077792@qq.com

Organization name

Northeast Agricultural University

Street address

600 Changjiang Road, Xiangfang District