biostudies-arrayexpressQian LiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14088To understand how the human macrophages and monocytes (of both fetal and maternal origin) isolated from first-trimester and term placentas differ, we profiled and compared the transcriptomes of cells freshly isolated by fluorescence-activated cell sorting, including fetal Hofbauer cells, placenta-associated maternal macrophages (PAMM), decidual macrophages, maternal and fetal monocytes using the SMART-Seq® v4 PLUS Kit (Takara Bio).biostudies-arrayexpressLibrary Construction - Library preparation for bulk RNA-seq was performed using the SMART-Seq® v4 PLUS Kit (Takara Bio) as per the manufacturer’s instructions. Quality of libraries was assessed on the Agilent D5000 ScreenTape System.Nucleic Acid Extraction - Freshly isolated cells were immediately lysed in RLT buffer (Qiagen) supplemented with 1% β-ME (Sigma-Aldrich) and stored at -80°C. RNA was extracted using the Single Cell RNA Purification Kit (Norgen) with on-column DNA digestion. Total RNA quality was assessed using the Qubit™ RNA HS Assay Kit (Invitrogen).Sequencing - Libraries were pooled in equimolar ratios and sequenced at CRUK genomics core (Cambridge) on NovaSeq 6000 S4 lanes (Illumina).Sample Collection - All tissue samples used were obtained with written informed consent from participants in accordance with the guidelines in The Declaration of Helsinki 2000. First-trimester and term placental tissues were obtained from healthy women with apparent normal pregnancies undergoing medical elective first-trimester terminations (6-13 weeks estimated gestational age (EGA)) and non-labour, elective caesarean sections from uncomplicated pregnancies (36+ weeks EGA) respectively. Ethical approval for the use of first-trimester tissues was obtained from the Cambridge Local Research Ethics Committee (REC 04/Q0108/23), part of the Centre for Trophoblast Research biobank for the ‘Biology of the Human Uterus in Pregnancy and Disease Tissue Bank’ at the University of Cambridge. Overall biobank ethical approval is from the East of England–Cambridge Central Research Ethics Committee (17/EE/0151). Full-term placental tissues were obtained from the Cambridge Blood and Stem Cell Biobank (REC 18/EE/0199).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - STAR (version 2.7.8a) was used to map the sequencing reads to the reference human genome (GRCh38_release37_PRI) by requiring the aligned percentage per read > 95%.Data Transformation - Only uniquely mapped reads were considered for the quantification of gene expression based on the human gene annotation (GENCODE v37) using featureCounts in the R package Rsubread (version 2.4.3). This was followed by the calculation of the reads per kilobase per million mapped reads (RPKM) to further normalize the read abundance by the total number of reads and gene length.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of total RNAHomo sapiensNagisa YoshidaQian LiNaomi McGovernfalseBulk RNA-seq of human macrophages and monocytes from first-trimester and term placentasTo understand how the human macrophages and monocytes (of both fetal and maternal origin) isolated from first-trimester and term placentas differ, we profiled and compared the transcriptomes of cells freshly isolated by fluorescence-activated cell sorting, including fetal Hofbauer cells, placenta-associated maternal macrophages (PAMM), decidual macrophages, maternal and fetal monocytes using the SMART-Seq® v4 PLUS Kit (Takara Bio).2025-08-04T00:00:00Z2025-08-05T00:02:28.055Z2024-05-17T13:27:54.566ZE-MTAB-14088ERP160358E-MTAB-14087E-MTAB-14086EFO_0002944EFO_0004170EFO_0009653EFO_0004917EFO_0005518EFO_0003816EFO_0004184