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Status |
Public on Jul 07, 2019 |
Title |
Day_11_15-181 |
Sample type |
SRA |
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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.
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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
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|
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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 |