{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dylan Siriwardena"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15846"],"description":["Non-invasive prenatal testing (NIPT) using cell free fetal DNA has transformed prenatal care by allowing risk assessment for a number of fetal genetic conditions without posing risk to the pregnancy. However, its limitations, including low fetal fraction and high DNA fragmentation, restrict its capacity for comprehensive genomic analysis. As an alternative, cell-based NIPT offers the potential to capture intact fetal cells for more detailed genetic interrogation. Cervical mucosa is a promising source for fetal DNA as it can be collected non-invasively as early as 5 weeks into the pregnancy and contains intact fetal cells.   We performed single cell mRNA squencing of transcervical swabs and placental samples from pregant donors at multiple gestational ages to identify potential fetal cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Libraries were constructed as described in the Chromium Next GEM Single Cell 3' v3.1 kit.","Nucleic Acid Extraction - RNA was extracted after cells were encapsulated in GEMS as described in the Chromium Next GEM Single Cell 3' v3.1 kit.","Sample Collection - 3 transcervical swab samples were transferred to a 50mL falcon tube and centrifuged at 300xg for 10 minutes to collect any cells in the supernatant. PBS volume was adjusted to 25 mL and 25 mL of DMEM with dithithreitol (DTT), sodium bicarbonate (Na2CO3) and Benzonase ® was added to a final concentration of 10 mM DTT, 1 mM Na2CO3, and 28 mU Benzonase ® to remove mucus. Samples were placed on a variable speed rocker (BR2000-GM 2D rocker, VWR) for 30 minutes at 37°C. Samples were centrifuged at 300xg for 10 minutes to collect transcervical swabs in solution. Placental tissue was collected from pregnancy termination. Gestational age week 7.6 placental tissue was dissociated with trypsin for 30 minutes at 37°C. Cell suspension was filtered through a 40 μm filter to remove clumps of tissue. Cellular suspension was centrifuged at 300xg for 10 minutes to collect placental cells in solution.","Sequencing - 10X Chromium single-cell libraries were sequenced on a Novaseq 6000 for 100 cycles to obtain ~ 500 Million reads/sample"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","Basic laboratory equipment"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["From Concept to Challenge: Microfluidic Approach for Cell-Based Non-Invasive Testing"],"pubmed_authors":["Dylan Siriwardena","Dylan Siriwardena1,2, Michael Dryden1,2,3, M. Dean Chamberlain1,2,4, Chloe Taylor1,2, Louise Dupoiron1,2, Farhana Abbas1,2, Julian Lamanna1,2, David Chitayat5,6, Aaron R. Wheeler1,2,7 and Elena Greenfeld8,9,*"],"additional_accession":[]},"is_claimable":false,"name":"10x single cell mRNA sequencing of transcervical swabs of pregnant donors at 5.2, 7.6, and 10.2 weeks of gestation","description":"Non-invasive prenatal testing (NIPT) using cell free fetal DNA has transformed prenatal care by allowing risk assessment for a number of fetal genetic conditions without posing risk to the pregnancy. However, its limitations, including low fetal fraction and high DNA fragmentation, restrict its capacity for comprehensive genomic analysis. As an alternative, cell-based NIPT offers the potential to capture intact fetal cells for more detailed genetic interrogation. Cervical mucosa is a promising source for fetal DNA as it can be collected non-invasively as early as 5 weeks into the pregnancy and contains intact fetal cells.   We performed single cell mRNA squencing of transcervical swabs and placental samples from pregant donors at multiple gestational ages to identify potential fetal cells.","dates":{"release":"2026-05-31T00:00:00Z","modification":"2026-05-31T01:01:14.467Z","creation":"2025-10-23T23:48:06.192Z"},"accession":"E-MTAB-15846","cross_references":{"ENA":["ERP182853"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}