Comment[ArrayExpressAccession]	E-GEOD-35646
MAGE-TAB Version	1.1			
Public Release Date	2013-04-22
Investigation Title	MicroRNA discovery and analysis of Dirofilaria immitis by deep sequencing.			
Comment[Submitted Name]	MicroRNA discovery and analysis of Dirofilaria immitis by deep sequencing.
Experiment Description	To understand how microRNA are involved in the complex biology of this zoonotic parasite, we describe our initial attempts to characterize small RNA in adult Dirofilaria immitis by using Illumina/Solexa deep-sequencing technology. Examination of 4 different adult Dirofilaria immitis (pooled)			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Yang	Fu	Yang	
Person First Name	Guangyou	Yan	Guangyou	
Person Email	sicau_parasitology_lab@hotmail.com			
Person Affiliation	Sichuan Agricultural University			
Person Address	Department of Parasitology , Sichuan Agricultural University, Xinkang Road 46*, Ya'an, China			
Person Roles	submitter			
Protocol Name	P-GSE35646-1	P-GSE35646-4	P-GSE35646-3	P-GSE35646-2
Protocol Description	Firstly, the data is processed by the following steps: (1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table). (2) Getting rid of reads with 5' primer contaminants. (3) Getting rid of reads without 3' primer. (4) Getting rid of reads without the insert tag. (5) Getting rid of reads with poly A. (6) Getting rid of reads shorter than 18nt. (7) Summarize the length distribution of the clean reads. Secondly, map the small RNA tags to the Brugia malayi genome by SOAP to analyze their expression and distribution on the genome. Thirdly, align small RNA tags to the miRNA precursor/mature miRNA of all animals in miRBase17.0. Show the sequence and count of miRNA families(no specific species) which can be found in the samples. Align small RNA tags to repeat associated RNA to find matched tags in the sample. Then annotate the small RNA tags with sequences from Rfam and get rid of matched tags from unannotated tags. Finally, summarize all alignments and annotation before. Di_unique counts.txt contains the length of the sequence (nt) information along with SEQUENCE, COUNT. SEQUENCE =  COUNT = COUNT	Firstly, the data is processed by the following steps: (1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table). (2) Getting rid of reads with 5' primer contaminants. (3) Getting rid of reads without 3' primer. (4) Getting rid of reads without the insert tag. (5) Getting rid of reads with poly A. (6) Getting rid of reads shorter than 18nt. (7) Summarize the length distribution of the clean reads. Secondly, map the small RNA tags to the Brugia malayi genome by SOAP to analyze their expression and distribution on the genome. Thirdly, align small RNA tags to the miRNA precursor/mature miRNA of all animals in miRBase17.0. Show the sequence and count of miRNA families(no specific species) which can be found in the samples. Align small RNA tags to repeat associated RNA to find matched tags in the sample. Then annotate the small RNA tags with sequences from Rfam and get rid of matched tags from unannotated tags. Finally, summarize all alignments and annotation before. Di_unique counts.txt contains the length of the sequence (nt) information along with SEQUENCE, COUNT.	RNA fragments of 18-44 bases long were isolated and purified from 10 μg total RNA using a Novex 15% TBE-Urea gel. The 5’ and 3’ adaptors (Illumina) were added to the ends of fragments. Reverse transcription PCR (RT-PCR) was performed using a RT-PCR kit (Invitrogen). The fragments were purified using a 6% TBE PAGE gel and used for high-throughput sequencing with a Solexa sequencer.	Dirofilaria immitis resided in the heart of an adult dog.
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol
Publication Title	Identification of Dirofilaria immitis miRNA using illumina deep sequencing.			
Publication Author List	Fu Y, Lan J, Wu X, Yang D, Zhang Z, Nie H, Hou R, Zhang R, Zheng W, Xie Y, Yan N, Yang Z, Wang C, Luo L, Liu L, Gu X, Wang S, Peng X, Yang G			
PubMed ID	23331513			
Publication DOI	10.1186/1297-9716-44-3			
Comment[SecondaryAccession]	GSE35646			
Comment[GEOReleaseDate]	2013-04-22			
Comment[ArrayExpressSubmissionDate]	2012-02-09			
Comment[GEOLastUpdateDate]	2013-04-22			
Comment[AEExperimentType]	RNA-seq of non coding RNA			
Comment[SecondaryAccession]	SRP010846			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR407367-SRR407367			
SDRF File	E-GEOD-35646.sdrf.txt