DOI: 10.5061/dryad.66t1g1k9d
title: Transcriptomics in human cumulus cells during oocyte in vitro maturation

description: Advancing human oocyte in vitro maturation (IVM) requires understanding
 the mechanisms that govern this process. The cumulus cells (CCs) that
 surround the oocyte play a crucial role. Our study focused on identifying
 specific genes in human CCs contributing to oocyte maturation in vitro. We
 used microarrays to detail the global transcriptome underlying oocyte
 maturation in cumulus cells and identified distinct up-and-down-regulated
 genes and signaling pathways during this process. Cumulus cells were
 removed from immatures (germinal vesicle - GV) cumulus-oocyte complexes
 (COCs) before IVM (Fresh GV, n = 5) and immature (GV) and mature (MII)
 COCs after IVM (GV-IVM, n=8; and MII-IVM, n=12). All the samples were
 collected ex vivo from 8 women who underwent unilateral ovariectomy and
 ovarian tissue cryopreservation for fertility preservation. Women did not
 receive prior ovarian stimulation
description: Total RNA was individually extracted and purified from each
 sample with TRIzol® reagent and 1-bromo-3-chloropropane and, subsequently,
 with RNeasy® Minikit 250 (Qiagen, Denmark) according to the manufacturer’s
 instructions. All steps were performed on ice. RNA quality and quantity
 were assessed by DeNovix DS-11 FX spectrophotometer and Bioanalyzer RNA
 6000 Pico Kit, respectively. Only samples with RNA integrity (RIN) values
 ≥ 6 were included in the study. Moreover, 25 samples were selected based
 on their RIN values to ensure a similar distribution across all groups:
 Fresh GV (mean RIN 8.9, n = 5), GV (mean RIN 7.9, n = 8), and MII (mean
 RIN 8, n = 12) (Supplementary Table S2). The selected samples were further
 processed using the Clariom<sup>TM</sup> D<sup>
 </sup>arrays<sup> </sup>with GeneChip<sup>TM
 </sup>Whole Transcript (WT) PLUS Reagent Kit according to the
 manufacturer’s instructions. The array was washed and stained with
 phycoerythrin-conjugated streptavidin using the Affymetrix Fluidics
 Station 450 and then scanned with the Affymetrix
 GeneChip<sup>TM</sup> Scanner 3000 7G System to generate
 fluorescent images. The Expression Console Software generated cell
 intensity files (.CEL files). The raw CEL files were imported into the
 Transcriptome Analysis Console (TAC, v4.0.2.15, Applied Biosystems). Data
 summarization, normalization, gene summaries, and statistical analysis
 were performed in one analysis flow. Normalization was performed by the
 signal space transduction-robust multi-array average (SST-RMA) approach.
 The differential expression analysis among CC groups (Fresh GV, GV-IVM,
 and MII-IVM) was set up using ANOVA ebayes comparison and an overall false
 discovery rate (FDR) &lt;0.05. For differential expression between
 groups, an FDR &lt; 0.05 combined with a gene level fold change (FC)
 &lt;−2 or &gt;2 was considered significant. Furthermore, pathway
 analysis, principal component analysis (PCA), and hierarchical clustering
 were performed in TAC.
description: # Transcriptomics in human cumulus cells during oocyte in vitro maturation
 [https://doi.org/10.5061/dryad.66t1g1k9d](https://doi.org/10.5061/dryad.66t1g1k9d) ## Description of the data and file structure Advancing human oocyte in vitro maturation (IVM) requires understanding the mechanisms that govern this process. The cumulus cells (CCs) surrounding the oocyte play a crucial role. Our study focused on identifying specific genes in human CCs that may contribute to oocyte maturation in vitro. Microarray (ClariomTM D arrays with GeneChipTM Whole Transcript (WT) PLUS Reagent Kit) was used to evaluate the overall gene expression of CCs from fresh immature (germinal vesicle - GV) human oocytes (Fresh-GV) and CCs from immature (GV) and mature (metaphase II - MII) oocytes after in vitro maturation (GV-IVM and MII-IVM, respectively). All the samples were collected ex vivo from the surplus ovarian medulla tissue of 8 women who underwent unilateral ovariectomy and ovarian tissue cryopreservation for fertility preservation. None of them had prior ovarian stimulation. All women gave informed consent to donate their surplus ovarian tissue for research purposes. ### Files and variables Dryad_microarray_Human_cumulus_cells_IVM.zip **Description:**   1\) CEL files 2\) CHP files **File naming convention for CEL and CHP files:** \[JCMor]-[RH]-[oocyte number]-[Condition]-[IVM treatment]-[Letter A-H]-[Clariom_D_Human-a1].CEL/CHP Where: \[JCMor] = Person that generated the date - contributor (Jesús Cadenas Moreno) \[RH] = Hospital where the array was performed (Rigshospitalet, University Hospital of Copenhagen, Denmark) \[Oocyte number] = Internal oocyte ID  \[Condition] = Oocyte maturation stage: GV before IVM (GV_Fresh), GV after IVM (GV), or MII after IVM (MII) \[IVM-treatment] = Indicates whether the IVM medium contained the growth factor Midkine (MDK) or no (No MDK) \[Letter A-H]: Internal patient ID. The same letter indicates the cells originated from the same patient. Each letter correspond to a random internal identification patient number (e.g., A = patient 1382) **Description of columns and possible values:**  * Condition: Developmental stage of the oocytes; Fresh GV* *(immature before IVM), GV (immature after IVM), or MII (matured in vitro).  * IVM treatment: Whether the oocytes were exposed to the growth factor Midkine during IVM (MDK or No MDK) or collected before IVM (No IVM).  * Patient ID: Random internal code assigned to each patient (e.g.,, 1382,1384, 1390, etc.) * Diagnosis: Clinical group of the patient (e.g., Breast cancer or Hodgkins lymphoma) # Code/Software Transcriptome Analysis Console (TAC, v4.0.2.15, Applied Biosystems, Thermo Fisher Scientific) is needed to import (CEL files) or open (CHP files) Before using TAC, you must install the required library: Click on the preferences tab, click browse, select Clariom_D_Human library, and download it. You can find them on the product webpage [Clariom™ D Assay, human 10 arrays | thermofisher.com]() in the Section Support Files. They are titled Library Files: Clariom™ D Array, human TAC Analysis Files, r1. Download the files and Unzip the zipped library folder as well as the folder TAC_CONFIG.zip therein. Then transfer all the contents to the TAC library folder, as specified under Preferences in TAC. ## Access information Non-applicable. The data does not derive from another source ## Human subjects data All patients provided explicit informed consent to donate their surplus ovarian tissue for research purposes, including the potential publication of de-identified data in the public domain. The data shared in this submission has been fully de-identified. No personal identifiers (e.g., names, social security numbers, etc.) were collected or accessed. Patients were assigned random internal identification numbers that cannot be traced back to individuals. The only other available information includes diagnosis, which is not sufficient to identify any individual participant.