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Sample GSM446690 Query DataSets for GSM446690
Status Public on Feb 27, 2010
Title prenatal, fetus at day 60
Sample type SRA
 
Source name E60d (fetus at day 60)
Organism Sus scrofa
Characteristics developmental stage: prenatal, fetus at day 60
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 all tissues, only discard the bones
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 SRX016794
BioSample SAMN00008937

Data table header descriptions
SEQUENCE read
COUNT count

Data table
SEQUENCE COUNT
TGGAGTGTGACAATGGTGTTTGTCGTATGCCGTCTT 456866
TGAGGTAGTAGGTTGTATAGTTTCGTATGCCGTCTT 147583
TGGAATGTAAAGAAGTATGTATTCGTATGCCGTCTT 127981
TGGAGTGTGACAATGGTGTTTTCGTATGCCGTCTTC 123151
TGGAGTGTGACAATGGTGTTTGATCGTATGCCGTCT 97251
TGAGGTAGTAGGTTGTATGGTTTCGTATGCCGTCTT 92813
TGAGGTAGTAGATTGTATAGTTTCGTATGCCGTCTT 82994
TGGAATGTAAGGAAGTGTGTGATCGTATGCCGTCTT 47020
TGAGGTAGTAGGTTGTGTGGTTTCGTATGCCGTCTT 37699
ACAGTAGTCTGCACATTGGTTATCGTATGCCGTCTT 36662
TGGAGTGTGACAATGGTGTTTGTTCGTATGCCGTCT 32333
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31324
TGAGGTAGTAGTTTGTACAGTTTCGTATGCCGTCTT 31162
ACAGTAGTCTGCACATTGGTTTCGTATGCCGTCTTC 26777
GGAGTGTGACAATGGTGTTTGTCGTATGCCGTCTTC 24008
TGGAGTGTGACAATGGTGTTTTCGTATGCCGTCTTT 23800
TTCAGAGTTCTACAGTCCGACGATCTCGTATGCCGT 22406
TGGAGTGTGACAATGGTGTTTGTCGTATGCCGGCTT 14335
TGGAGTGTGACAATGGTGTTTCGTATGCCGTCTTCT 13323
AGCAGCATTGTACAGGGCTATTCGTATGCCGTCTTC 13253

Total number of rows: 587856

Table truncated, full table size 22404 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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