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Sample GSM1419176 Query DataSets for GSM1419176
Status Public on Jul 25, 2016
Title Infected cecum repeat 2
Sample type SRA
Source name cecum
Organism Gallus gallus
Characteristics breed: SPF leghorn
tissue: cecum
infectious agent: Campylobacter jejuni
Treatment protocol The chickens in treated group were inoculated with 10^8 cfu C. jejuni per chicken
Growth protocol The infeced and non-infected SPF Leghorn chickens were raised in separate incubator
Extracted molecule total RNA
Extraction protocol Cecum was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent
The smaller RNA fraction (<100KDa) was further fractioned on a 15% tris-borate-EDTA (TBE) urea polyacrylamide gel and the 18-38 nt fraction was obtained. Subsequently, 5′ and 3′ RNA adapters were ligated to the small RNA by T4 RNA ligase (Promega), followed by reverse transcription and PCR product purification. Purified products were quantified on the Qubit® 2.0 fluorometer (Invitrogen) using QubitTM dsDNA HS array kit(Invitrogen), then were diluted to 2 nM to finish cluster generation
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer IIx
Data processing The raw reads were obtained using the Solexa deep-sequencing analyzer, then removing the low-quality reads and eliminating reads with5’ primer contaminants, without 3’ primer and insert tag, reads with poly(A) and shorter than 18nt, the clean reads were obtained and were used for further analysis.
The small RNA sequence reads were pre-processed using FASTX-Toolkit, excluding low-quality reads (ambiguous N, quality<10 nt, and length<18 nt) as well as 3′ adapter, 5′ adapter and poly(A) sequences.
Further annotation analyses were performed using the commercial software CLC Genomic Workbench 5.5
Genome_build: galGal4
Supplementary_files_format_and_content: Sequence and Count
Submission date Jun 24, 2014
Last update date May 15, 2019
Contact name XIANYAO LI
Organization name Shandong Agricultural University
Department Department of Animal Science
Street address No. 61 Daizong Street,
City Tian'an
ZIP/Postal code 271018
Country China
Platform ID GPL13797
Series (1)
GSE58767 MicroRNA expression in chicken cecum following Campylobacter jejuni infection
BioSample SAMN02870497
SRA SRX621393

Supplementary file Size Download File type/resource
GSM1419176_Processed_T2.txt.gz 251.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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