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Sample GSM2228462 Query DataSets for GSM2228462
Status Public on Jul 07, 2019
Title Day_11_15-181
Sample type SRA
 
Source name Day 11, Human microdissected endometrial gland
Organism Homo sapiens
Characteristics cycle day: LH+11
live births: 1
pregnancy losses: 5
age: 38
bmi: 23.3
tissue: microdissected endometrial gland
Extracted molecule total RNA
Extraction protocol Luteinizing hormone (LH)-timed endometrial biopsies were subjected to laser microdissection of the endometrial glands followed by RNA-sequencing. The biopsies were obtained 5, 8 and 11 days after the LH surge, identified by urine test, immediately frozen in liquid nitrogen and then embedded in cryomatrix OCT. Ten micron slices cut in a cryotome were mounted on a membrane slide and stained with 70% (v/v) cresyl violet and 30% (v/v) eosin Y. Endometrial glands were captured using a laser microdissection system. RNA was extracted, quantity was assessed by spectrophotometry and integrity was checked by Agilent 2100 Bioanalyzer system. For all samples, the RNA integrity number (RIN) was above 5 and the rRNA ratio [28s/18s] above 0.9.
Amplified cDNA was obtained from total RNA using NuGen Ovation RNA-Seq System V2. NuGen Ovation Ultralow System V2 1-16 was applied for library preparation and sample barcoding. A 100bp paired end run with Illumina NGS was performed by Wellcome Trust Centre for Human Genomics - High Throughput Genomics, Oxford, UK.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Transcriptomic maps of paired-end reads were generated using bowtie-2.2.6, samtools-1.2, and tophat-2.1.0 against the University of California Santa Cruz (UCSC) hg19 reference transcriptome (2014) using the fr-unstranded setting.
Transcript counts were assessed by HTSeq-0.6.1 using stranded-no setting and intersection-non-empty mode and counts were assigned to gene IDs. Transcripts per million (TPM) were calculated according to Wagner et al. (2012) http://www.ncbi.nlm.nih.gov/pubmed/22872506.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] A tab-delimited text file including TPM values for each sample
 
Submission date Jul 08, 2016
Last update date Jul 07, 2019
Contact name Jan J Brosens
E-mail(s) j.j.brosens@warwick.ac.uk
Organization name University of Warwick
Department Warwick Medical School
Lab Division of Reproductive Health
Street address University Hospital Coventry and Warwickshire
City Coventry
ZIP/Postal code CV2 2DX
Country United Kingdom
 
Platform ID GPL20301
Series (1)
GSE84169 Changes in human endometrial gland transcriptome over the window of implantation
Relations
BioSample SAMN05366398
SRA SRX1906070

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

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