|
Status |
Public on May 01, 2016 |
Title |
M1 mRNA |
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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
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
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|
|
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 |
SAMN04217731 |
SRA |
SRX1387663 |