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Sample GSM4201887 Query DataSets for GSM4201887
Status Public on Feb 24, 2020
Title pregnant embryo mRNA rep 3
Sample type SRA
 
Source name embryo
Organism Equus caballus
Characteristics tissue: embryo
Stage: pregnant
Treatment protocol cyclic mares: no treatment, pregnant mares: inseminated and confirmed to be pregnant
Growth protocol Samples were collected from cycling or pregnant mares 13 days after ovulation
Extracted molecule total RNA
Extraction protocol For RNA extraction from the B and the E tissue samples, the RNeasy Mini Kit (Qiagen) was combined with the RNeasy MinElute Cleanup Kit (Qiagen) in order to extract both small RNAs and larger RNAs (>200 nt) separately from the same tissue sample for mRNA- and miRNA-Sequencing respectively.
1 µg of RNA was used to perform an Illumina sequencing library preparation using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. During library preparation, 12 PCR cycles were used.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads were trimmed using cutadapt version 1.11 to remove the Illumina adaptor sequence.
The trimmed reads were mapped against the equine EquCab 2.80 reference genome using CLC genomics workbench version 9.0.1 (CLC).
Count tables were made by counting the reads that mapped against the genes defined by the Ensembl EquCab 2.80 Gene transfer format file and exported from CLC.
Genome_build: EquCab 2.80
Supplementary_files_format_and_content: comma separated values files including Gene counts and Gene ID
 
Submission date Dec 03, 2019
Last update date Feb 25, 2020
Contact name Laurentijn Tilleman
Organization name Ghent University
Street address Ottergemsesteenweg 460
City Gent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL21401
Series (2)
GSE141360 Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? [RNA-seq]
GSE141450 Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers?
Relations
BioSample SAMN13471459
SRA SRX7262494

Supplementary file Size Download File type/resource
GSM4201887_P3Erna.csv.gz 122.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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