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Sample GSM5400870 Query DataSets for GSM5400870
Status Public on Aug 18, 2022
Title Nor_17
Sample type SRA
 
Source name extracellular vesicles from endometrial fluid
Organism Homo sapiens
Characteristics sample type: Endometrial fluid
tissue: Non-implantative endometrium
Treatment protocol Endometrial fluid was aspirated with a catheter used for embryo transfer (Frydman, Instrumentos Médicos Estériles SA, Spain) connected to a 10 mL syringe, under abdominal ultrasound guidance. Sample extraction was performed by gentle manual application of negative pressure with the syringe. To prevent contamination with cervical mucus, aspiration was interrupted at the internal cervical os. Aspirate volumes ranged from 5 uL up to 50 uL. After the aspiration, the 10 mL syringe was replaced with a 2 mL syringe containing 1.5 mL saline solution and the aspirates were mixed and expelled in a cryogenic tube (5-50 uL of EF + 1500 uL 1XDPBS (Gibco, Thermo Fisher Scientific #14190250). The mixed samples were centrifuged to remove contaminants at 2,000 x g for 5 min and the supernatants were then frozen at −80 °C until processed. The dilution of the supernatants was 1:30 and they had a volume comprised between 400uL and 1300uL. Extracellular vesicle enrichment was done with Total Exosome Isolation Reagent from cell culture media (Invitrogen by ThermoFisher Scientific, #4478359). The EF supernatants were centrifuged at 3000 g for 30 min at 4 ºC, then 400uL were transferred to a fresh tube and 1 volume of the Total Exosome Isolation Reagent (1:1) was added. The mixture was incubated for 30 min at room temperature and then centrifuged at 10,000 g for 1 hour at 4 ºC. The supernatant was discarded and the EVs that were in the pellet were resuspended in 100 uL of 1 x DPBS.
Extracted molecule total RNA
Extraction protocol Total RNA from extracellular vesicles from endometrial fluid was extracted using either the mirVana PARIS kit (Ambion) or the Plasma/Serum RNA Purification kit (Norgen), as detailed in the SAMPLES section
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description Plasma/Serum RNA Purification kit (Norgen)
Data processing FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers.
We used Bowtie 1.0.1 to align the reads against the human genome (GRCh38), with a mismatch 0, to avoid false positives. We select mirbase v22 to quantify mature micrornas employing Partek Flow application, software version 7.0. Only the miRNAs with 10 or more reads were considered.
Mapped reads were quantified to GENCODE-v26 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: read count table
 
Submission date Jun 25, 2021
Last update date Aug 18, 2022
Contact name Ana Maria Aransay
E-mail(s) amaransay@cicbiogune.es
Phone 0034944061325
Organization name CIC bioGUNE
Department Genome Analysis Platform
Street address Parque tecnologico de Bizkaia, Building 801-A
City Derio
State/province BIZKAIA
ZIP/Postal code 48160
Country Spain
 
Platform ID GPL16791
Series (1)
GSE178917 MicroRNA-based signatures obtained from endometrial fluid identify implantative endometrium
Relations
SRA SRX11230271
BioSample SAMN19896377

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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