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Sample GSM1924186 Query DataSets for GSM1924186
Status Public on Nov 04, 2015
Title PX2
Sample type SRA
 
Source name Oviduct
Organism Bos taurus
Characteristics tissue: oviduct
treatment: Pregnant - transfer of 50 in vitro produced presumptive zygotes
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from oviduct epithelial cells using the Trizol method as per manufacturers' instructions (Invitrogen, Carlsbad, CA, USA) and RNA clean up and on-column DNAse digestion was perfored using the Qiagen Rneasy columns as per manufacturers' instructions (Qiagen, Crawley, West Sussex, UK).
Standard Illumina TruSeqstranded mRNA HT library construction. One microgram of total RNAwas used as input material. mRNA was enriched using oligo-dT magnetic beads and fragmented to 100-300 bp with a single shearing and RT primer hybridization before generating cDNA. Following adapter ligation and PCR amplification (14 cycles), library validation was perfomred using the Fragment Analyzer (Advanced Analytical) with the hiSens NGS reagents followed by quantitation using the QuBit HS DNA assay (Life Technologies) and qPCR kit for Illumina (Kapa Biosystems, Inc.).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Libraries were sequenced on the HiSeq 2500 platform (50bp PE) and basecalls were made by HiSeq Control Software.
Reads were quality trimmed (error probability 0.001) and 13 bp were removed from the 5’ end of each read with CLC Genomics Server 6.0
Mapped to Ensembl gene UMD 3.1.75 with CLC Genomics Server 6.0
Statistical analysis was completed using the Empirical Analyisis of DGE (EDGE) tool in CLC Genomics Workbench with default settings
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: RPKM data
 
Submission date Nov 03, 2015
Last update date May 15, 2019
Contact name Peadar O'Gaora
Organization name UCD
Street address Belfield
City Dublin
ZIP/Postal code Dublin 4
Country Ireland
 
Platform ID GPL19172
Series (2)
GSE74612 Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? [RNA-Seq]
GSE74613 Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?
Relations
BioSample SAMN04231322
SRA SRX1410418

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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