{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Daniela Ávila-González"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17092"],"description":["Identify differentially expressed genes between the different anatomical regions of the human amnion tissue (placental amnion, reflected amnion, and umbilical amnion)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated from both tissue samples and cultured cells using TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.","Sample Collection - Human fetal membranes were obtained from uncomplicated full-term pregnancies (37–40 weeks gestation) delivered via cesarean section, excluding any cases with active labor, premature rupture of membranes, or signs of chorioamnionitis or genital tract infections. Written informed consent was obtained, along with ethical approval from the responsible institutional committee. The amniotic tissue was transported from the operating theater to the laboratory in a sterile container with saline solution. Under sterile conditions, the amnion was mechanically peeled from the underlying chorion, washed repeatedly with saline to remove blood and clots, and then dissected into three distinct anatomical regions: reflected amnion, placental amnion, and umbilical amnion.","Library Construction - The extracted and reverse-transcribed cDNA was processed using the Illumina TruSeq RNA Sample Preparation Kit.","Sequencing - The prepared libraries were sequenced on an Illumina Genome Analyzer GAIIx platform at a genome sequencing facility. The minimum sequencing configuration required was paired-end reads with a read length of 75 base pairs"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quality Control (QC) of raw reads was performed using FASTQC software33 and contamination and adapter removal was carried out using in-house Perl scripts. Filtered reads were mapped to the human reference genome GRCh38.p9 using SMALT v0.7.6. The index and mapping were performed using default options. After mapping, duplicated reads were marked using Picard Tools v2.18.2 in resulting BAM files. From the marked-duplicate BAMs total effective counts for each sample were calculated using coverageBed from BEDtools and all samples were merged using an in-house Perl script."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina Genome Analyzer IIx"],"pubmed_abstract":["Studies have described the presence of pluripotent markers in vivo and in vitro in human amnion. However, the amnion can be divided into reflected, placental and umbilical regions that are anatomically and functionally heterogeneous. Here, we evaluated the expression of pluripotency markers in tissue and cultivated cells in vitro of different regions of human amnion. To this end, we determined the presence of the core pluripotency factors OCT-4, NANOG and SOX-2 by immunofluorescence and RT-PCR and also performed transcriptome analysis of the different regions of amnion tissue. We identified the mRNA and protein of the pluripotency factors in the different regions of human amnion tissue. However, the OCT-4 and NANOG immunolocalization was cytoplasmic, whereas SOX-2 immunolocalization was nuclear regardless of the region analyzed. Moreover, we found three subpopulations of cells in the in vitro cultures of reflected and placental amnion: cells with immunostaining only in the nucleus, only in the cytoplasm, or in both compartments. Yet no statistically significant differences were found between the reflected and placental amnion. These results suggest a homogeneous distribution of the pluripotency transcription factors of the different regions of human amnion to isolate stem cells that can be used in regenerative medicine."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Pluripotency markers in tissue and cultivated cells in vitro of different regions of human amniotic epithelium"],"pubmed_authors":["Fabian Díaz-Martínez","Guadalupe García-López, Daniela Ávila-González, Irma Lydia García-Castro, Héctor Flores-Herrera, Anayansi Molina-Hernández, Wendy Portillo, Néstor Emmanuel Díaz-Martínez, Alejandro Sanchez-Flores, Jerome Verleyen, Horacio Merchant-Larios, Néstor Fabián Díaz","Wendy Portillo","Daniela Ávila-González"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of the three anatomical regions (reflected, placental and umbilical) of the amniotic membrane in the fetal annexes at term","description":"Identify differentially expressed genes between the different anatomical regions of the human amnion tissue (placental amnion, reflected amnion, and umbilical amnion).","dates":{"release":"2026-05-29T00:00:00Z","modification":"2026-05-29T01:00:47.329Z","creation":"2026-05-26T14:59:34.209Z"},"accession":"E-MTAB-17092","cross_references":{"pubmed":["30557557"],"ENA":["ERP193972"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1016/j.yexcr.2018.12.007"]}}