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Sample GSM1974444 Query DataSets for GSM1974444
Status Public on Dec 18, 2015
Title IS3
Sample type SRA
 
Source name Uterine tissues from the implantation site (IS) on day 7.25 of pregancy
Organism Oryctolagus cuniculus
Characteristics tissue: uterus
group: implantation site
Growth protocol Adult New Zealand White rabbits, aged 3~4 mo and weighted 2.5~3.1 kg, were used for this study. Female rabbits were mated with males and the time of mating was designated as day 0 of pregnancy. Animals (n=3) were euthanased on day 7.25 (6 h after day 7) of pregnancy by injecting 20 ml air into the auricular veins. Uterine tissues from the implantation site (IS) and the inter-implantation site (IIS) were collected separately. All samples were flash-frozen in liquid nitrogen and stored at -80 °C for further analysis. All animal procedures were approved by the Institutional Animal Care and Use Committee of South China Agricultural University.
Extracted molecule total RNA
Extraction protocol Total RNA from uterine samples was extracted using TRIzol reagent (invitrogen). RNA purity was assessed using the ND-1000 Nanodrop and RNA integrity was evaluated using the Agilent 2200 TapeStation. The following RNA quality control parameters were used: A260/A280 ratio ≥ 1.8, A260/A230 ratio ≥ 2.0 and RIN value ≥ 7.0. The mRNA-Seq sample preparation kit (Illumina) was used for the preparation of RNA-Seq libraries. Briefly, poly-(A)+ mRNA was purified with oligo-(dT) magnetic beads and fragmented to approximately 200 bp in fragmentation buffer. The obtained cleaved RNA fragments were reverse transcribed to first-strand cDNA, followed by second-strand cDNA synthesis. The double-stranded cDNA fragments were purified, end-repaired and then ligated to sequencing adapters. After purification, suitable fragments were amplified through 15 cycles of PCR to generate the final sequencing libraries. Finally, PCR products were purified and quantified for high-throughput sequencing using the Illumina HiSeq™ 2500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description New Zealand White
mRNA(polyA+)
Data processing After sequencing, a computational pipeline was used to process RNA-seq data. Raw sequence data in fastq format were filtered to remove reads with more than 10% unknown nucleotides. Clean reads were mapped to rabbit reference genome OryCun2 with Tophat v1.4.0 allowing no more than two mismatches. Transcript isoforms were assembled using Cufflinks v1.3.0 and combined with the gene annotations from ENSEMBL database release 81. Gene expression levels were measured using reads per Kilobase of transcript per million mapped reads (RPKM). To compare profile differences between two groups, a t-test with Benjamini-Hochberg multiple test correction was employed. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.01.
Genome_build: OryCun2
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. The first column is gene name, the second column is ENSEMBL ID, and the third column is RPKM value.
 
Submission date Dec 17, 2015
Last update date May 15, 2019
Contact name Ji-Long Liu
E-mail(s) jilongliu@scau.edu.cn
Organization name South China Agricultural University
Street address 483 Wushan Rd
City Guangzhou
ZIP/Postal code 510642
Country China
 
Platform ID GPL21255
Series (1)
GSE76115 Identification of gene expression changes in rabbit uterus during embryo implantation
Relations
BioSample SAMN04348743
SRA SRX1489437

Supplementary file Size Download File type/resource
GSM1974444_IS3.txt.gz 147.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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