This RNAsequencing_of_endomtrial_explants_readme.txt file was generated on 2021-01-15 by Sandra Recuero 
GENERAL INFORMATION
1. Title of Dataset: RNA-sequencing of endometrial explants
2. Author Information
	A. Principal Investigator Contact Information
		Name: Beatriz Fernandez-Fuertes
		Institution: Instituto Nacional de Tecnología Agraria y Alimentaria (INIA)
		Address: Av. Puerta de Hierro, 18, Madrid, Spain
		Email: beatriz.fernandez@inia.es

	B. Associate or Co-investigator Contact Information
		Name: Sandra Recuero Cobos
		Institution: University of Girona
		Address: Maria Aurelia Capmany, 69, Girona, Spain
		Email: sandra.recuero@udg.edu

	C. Alternate Contact Information
		Name: 
		Institution: 
		Address: 
		Email: 

3. Date of data collection (single date, range, approximate date) 
Sample collection 2018-03-08
Sequencing and data analysis: 2019-03-19 – 2019-04-09

4. Geographic location of data collection:
Sample collection: Dublin, Ireland
Sequencing and data analysis: Missouri, USA
5. Information about funding sources that supported the collection of the data: 
EU Horizon 2020 Marie Sklodowska-Curie (No 792212) and Science Foundation Ireland (Grant No. 16/IA/4474).

SHARING/ACCESS INFORMATION
1. Licenses/restrictions placed on the data: N/A

2. Links to publications that cite or use the data: manuscript currently under review

3. Links to other publicly accessible locations of the data: N/A

4. Links/relationships to ancillary data sets: N/A

5. Was data derived from another source? yes/no: No
	A. If yes, list source(s): 

6. Recommended citation for this dataset: 


DATA & FILE OVERVIEW
1. File List: 
1 file with 6 sheets:
Sheet 1 (Global_gene_expression_data): Transcript length of each gene found in bovine endometrial tissue (total and for each sample)
Sheet 2 (Ctr vs Ejac Overall): gene expression data of all genes found in endometrial tissue comparing control explants and explants exposed to ejaculated sperm
Sheet 3 (Ctr vs Epid Overall): gene expression data of all genes found in endometrial tissue comparing control explants and explants exposed to epididymal sperm
Sheet 4 (Ctr vs Epid Significant): gene expression data of genes found differentially expressed comparing control explants and explants exposed to epididymal sperm
Sheet 5 (Epid vs Ejac Overall): gene expression data of all genes found in endometrial tissue comparing explants exposed to epididymal sperm and explants exposed to ejaculated sperm
Sheet 6 (Epid vs Ejac Significant): gene expression data of genes found differentially expressed comparing explants exposed to epididymal sperm and explants exposed to ejaculated sperm

2. Relationship between files, if important: N/A

3. Additional related data collected that was not included in the current data package: No

4. Are there multiple versions of the dataset? yes/no: No
	A. If yes, name of file(s) that was updated: 
		i. Why was the file updated? 
		ii. When was the file updated? 

METHODOLOGICAL INFORMATION
1. Description of methods used for collection/generation of data: 
Six crossbreed beef heifers were oestrous synchronised and slaughtered at a commercial abattoir approximately 24 h after the onset of oestrus. Reproductive tracts were recovered three endometrial explants from each animal were obtained from intercaruncular. Explants were cultured endometrial side up at 39 °C under an atmosphere of 5% CO2 for 4 h before incubation with: 1) RPMI medium alone (Control), 2) RPMI medium + 5 × 106 epididymal sperm (Epididymal sperm) or 3) RPMI medium + 5 × 106 ejaculated sperm (Ejaculated sperm).  Explants were incubated with the three treatments for 6 h at 39 °C under an atmosphere of 5% CO2, after which they were washed twice in RPMI media to remove sperm, snap frozen, and stored at −80 °C. Six replicates were carried out, each replicate corresponding to a synchronised heifer (n = 6). To minimise variation, explants from the same uterus were used across all treatments in a given replicate.
For mRNA extraction, endometrial samples were first homogenized in Trizol reagent (Invitrogen, Carlsbad, CA) using a steel bead and the Qiagen tissue lyzer (2 x 120 s at 30 Hz). On-column RNA purification was performed using the Qiagen RNeasy kit per the manufacturer’s instructions. The quantity of RNA was determined using the Nano Drop 1000 spectrophotometer. Prior to RNA sequencing analysis, the RNA quality was assessed by the Agilent Bioanalyzer. 
2. Methods for processing the data: 
RNA library preparation and sequencing were performed by the University of Missouri DNA Core Facility as described previously (Moraes et al., Proc Natl Acad 115, E1749-E1758, 2018).
The raw sequences (fastq) were subjected to quality trimming control using fqtrim (https://ccb.jhu.edu/software/fqtrim/). Then, the quality reads were mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/), which is a fast and sensitive alignment program of next-generation sequencing data (Kim et al., Nat Methods 12, 357-360, 2015). Read counts mapping to each gene were determined from the mapping data using FeatureCounts (Liao et al., Bioinformatics 30, 923-930, 2014). Differential expression analysis between different sample groups was performed by robustly fitting the expression data to a weighted generalized linear model using edgeR robust (Zhou et al., Nucleic Acids Res 42, e921, 2014).
3. Instrument- or software-specific information needed to interpret the data: 

4. Standards and calibration information, if appropriate: 

5. Environmental/experimental conditions: 
Bovine endometrial explants incubated with ejaculated sperm or epididymal sperm or RPMI medium (control explants).

6. Describe any quality-assurance procedures performed on the data: 

7. People involved with sample collection, processing, analysis and/or submission: 
Mrs. Sandra Recuero, Dr. José María Sánchez, Dr. Sandra Bagés-Arnal, Mr. Michael McDonald, Dr. Susanta K Behura, Dr. Thomas E Spencer, Dr. Marc Yeste, Dr. Pat Lonergan and Dr. Beatriz Fernandez-Fuertes

DATA-SPECIFIC INFORMATION FOR: Global_gene_expression_data
1. Number of variables: 

2. Number of cases/rows: 

3. Variable List: 

4. Missing data codes: 

5. Specialized formats or other abbreviations used:
Epid: Explants exposed to epididymal sperm 
Ejac: Explants exposed to ejaculated sperm  
Ctr: Control explants