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Sample GSM1919484 Query DataSets for GSM1919484
Status Public on May 01, 2016
Title M5 microRNA
Sample type SRA
 
Source name MAP-infected ileal tissue
Organism Bos taurus
Characteristics tissue: MAP-infected ileal tissue
infection: MAP-Infected
Extracted molecule total RNA
Extraction protocol The tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of small RNA sequencing libraries. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of RNA sequencing libraries.
RNA-seq libraries and small RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Data processing All the RNA-seq reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) bovine gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
All the small RNA reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
The small RNAs sequencing reads with good quality were subjected to 3’ adaptor sequence trimming by miRDeep2
The miRNA expression (CPM) were identified by miRDeep2, while piRNA expression (CPM) were identified by costumised Perl program based on method descibed by other studies (Liu et al., 2012.PLoS ONE 7(4): e34770).
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample
 
Submission date Oct 27, 2015
Last update date May 15, 2019
Contact name Guanxiang Liang
E-mail(s) liangguanxiang@gmail.com
Organization name University of Alberta
Street address 410 Agriculture/Forestry Centre
City Edmonton
State/province Alberta
ZIP/Postal code T6G 2P5
Country Canada
 
Platform ID GPL15749
Series (1)
GSE74394 Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection
Relations
BioSample SAMN04217725
SRA SRX1387657

Supplementary file Size Download File type/resource
GSM1919484_M5_miRNA.txt.gz 3.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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