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| Status |
Public on Nov 04, 2015 |
| Title |
C3 |
| Sample type |
SRA |
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| Source name |
Oviduct
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| Organism |
Bos taurus |
| Characteristics |
tissue: oviduct
treatment: Control - sham transfer
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| 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.).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Nov 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peadar O'Gaora |
| Organization name |
UCD
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| Street address |
Belfield
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| City |
Dublin |
| ZIP/Postal code |
Dublin 4 |
| Country |
Ireland |
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| 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? |
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| Relations |
| BioSample |
SAMN04231306 |
| SRA |
SRX1410414 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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