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Sample GSM446695 Query DataSets for GSM446695
Status Public on Feb 27, 2010
Title postnatal (day 30)
Sample type SRA
 
Source name at day 30
Organism Sus scrofa
Characteristics developmental stage: postnatal (day 30)
Extracted molecule total RNA
Extraction protocol Ten sample sets used in this experiment that cover six prenatal (entire 114 days of pregnancy) and four postnatal (180 days after birth) developmental stages of Rongchang pigs (a Chinese indigenous breed). Six sows were artificially inseminated with semen from purebred sires and one sow was sacrificed at each of the six prenatal stages (i.e. 30, 45, 60, 75, 90 and 105 days post conception) to obtain three male and three female fetuses. The 30 and 45 days fetuses samples were simply homogenized; other prenatal samples were a mixture of whole body tissues without bones. For four postnatal samples (i.e. birth, 30, 120 and 180 days) the mixture samples were from 60 tissues at equal amounts for each type of tissue. The mixture samples from individual three female and three male fetuses or pigs were kept separately. The low molecular weight RNA was extracted using mirVana miRNA Isolation Kit (Ambion Life Technologies) according to the manufacturer’s protocol. RNA samples were prepared as follows: for each developmental stage, equal quantities (10 µg) of small RNA isolated from six individuals, three female and three male were pooled. Approximately 60 µg of small RNA representing each developmental stage was used for library preparation for sequencing. In brief, the sequencing was performed as follows: small RNA fraction between 18 and 30 nt was isolated by polyacrylamide gel electrophoresis (PAGE), and ligated with proprietary adaptors (Illumina Inc.). The short RNAs were converted to cDNA by RT-PCR and the cDNA was sequenced on the Genome Analyzer GA-I (Illumina Inc.) following the Illumina protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description Mixture of 60 normal tissues
Three female and three male were pooled.
Data processing Sequ-seqs were processed using the Pipeline software from the Genome Analyzer GA-1 instrument (Illumina Inc.) at first, then were subject to a series of data filtration steps to obtain "mappable sequences", which are sequences satisfy the following criteria from the statistics of miRBbase 13.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing no stretches of A7, C8, G6, or T7; (5) been observed more than two times; (6) being longer than 14 nts and shorter than 27 nts; and (7) not originating from mRNA, rRNA, tRNA, snRNA, snoRNA and repetitive sequence elements. Further data analysis of the "mappable sequences" mainly used ACGT101-miR, our own development software for discovering miRNAs from next-generation sequencing (NGS) data (to be published separately), based on the databases of pig genome (Sscrofa9, April 2009) & EST sequences and mammalian konwn miRNA genes in miRBase 13.0 (March 2009).
 
Submission date Aug 31, 2009
Last update date May 15, 2019
Contact name Mingzhou Li
E-mail(s) mingzhou.li@163.com
Phone 86-835-2886000
Organization name Sichuan Agricultural University
Department College of Animal Science and Technology
Lab Institute of Animal Genetics and Breeding
Street address No.46 Xinkang Road
City Ya'an
State/province Sichuan
ZIP/Postal code 625014
Country China
 
Platform ID GPL9126
Series (1)
GSE17885 MicroRNAome of porcine prenatal and postnatal development.
Relations
SRA SRX016799
BioSample SAMN00008942

Data table header descriptions
SEQUENCE read
COUNT count

Data table
SEQUENCE COUNT
TGGAATGTAAAGAAGTATGTATTCGTATGCCGTCTT 1070911
TGGAATGTAAGGAAGTGTGTGATCGTATGCCGTCTT 57100
GGAATGTAAAGAAGTATGTATTCGTATGCCGTCTTC 54297
TGGAATGTAAGGAAGTGTGTGTTCGTATGCCGTCTT 42382
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36725
TGGAATGTAAAGAAGTATGTATTCGTATGCCGTTTT 19074
TGGAATGTAAAGAAGTATGTACTCGTATGCCGTCTT 16480
TGGAATGTAAAGAAGGATGTATTCGTATGCCGTCTT 12197
TGGAATGTAAAGAAGTATGTATTTCGTATGCCGTCT 11151
GGAATGTAAAGAAGTATGTATTCGTATGCCGTCTTT 10384
TGGAATGTAAAGAAGTATGTAATCGTATGCCGTCTT 9424
ACAGTAGTCTGCACATTGGTTTCGTATGCCGTCTTC 8303
ACAGTAGTCTGCACATTGGTTATCGTATGCCGTCTT 8012
TGGAATGTAAAGAAGTATGTATCGTATGCCGTCTTC 7747
TGAGGTAGTAGATTGTATAGTTTCGTATGCCGTCTT 7637
TGAGGTAGTAGGTTGTATAGTTTCGTATGCCGTCTT 7232
TGGAGTGTGACAATGGTGTTTGTCGTATGCCGTCTT 7023
GAATGTAAAGAAGTATGTATTCGTATGCCGTCTTCT 6789
TGGAATGTAAAGAAGTATGTATTCGTATTCCGTCTT 6303
ACGGACTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 6259

Total number of rows: 286508

Table truncated, full table size 10918 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Processed data included within Sample table
Raw data are available in SRA

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