Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001003705	10 single-cell placental RNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10X Genomics). All single-cell libraries were sequenced with a customized paired end with dual indexing (98/14/8/10-bp) format according to the recommendation by 10X Genomics. The data were aligned using the Cell Ranger Single-Cell Software Suite (version 1.0). Moreover, plasma RNA from 22 samples were extracted using the RNeasy Mini Kit (Qiagen). cDNA reverse transcription, second-strand synthesis, and RNA-sequencing (RNA-seq) library construction were performed using the Ovation RNA-seq System V2 (NuGEN) kit according to the manufacturer’s protocol. For alignment of the plasma RNA library, adaptor sequences and low-quality bases on the fragment ends (i.e., quality score < 5) were trimmed, and reads were aligned to the human reference genome (hg19) using the TopHat (v2.0.4) software. All aligned reads were deposited in bam file format.	Illumina HiSeq 2000 NextSeq 500	32

Publications	Citations
Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics. Tsang JCH, Vong JSL, Ji L, Poon LCY, Jiang P, Lui KO, Ni YB, To KF, Cheng YKY, Chiu RWK, Lo YMD. Proc Natl Acad Sci U S A 114: 2017 E7786-E7795	146
Current approaches and developments in transcript profiling of the human placenta. Yong HEJ, Chan SY. Hum Reprod Update 26: 2020 799-840	24
MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads. Li WV, Zheng D, Wang R, Tian B. Genome Biol 22: 2021 222	7
Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast. Morey R, Farah O, Kallol S, Requena DF, Meads M, Moretto-Zita M, Soncin F, Laurent LC, Parast MM. Front Cell Dev Biol 9: 2021 702046	15
Human placental biology at single-cell resolution: a contemporaneous review. Barrozo ER, Aagaard KM. BJOG 129: 2022 208-220	6
The Function of the Kynurenine Pathway in the Placenta: A Novel Pharmacotherapeutic Target? Broekhuizen M, Danser AHJ, Reiss IKM, Merkus D. Int J Environ Res Public Health 18: 2021 11545	14
A cost-effective machine learning-based method for preeclampsia risk assessment and driver genes discovery. Wang H, Zhang Z, Li H, Li J, Li H, Liu M, Liang P, Xi Q, Xing Y, Yang L, Zuo Y. Cell Biosci 13: 2023 41	2
Histopathologic and Transcriptomic Profiling Identifies Novel Trophoblast Defects in Patients With Preeclampsia and Maternal Vascular Malperfusion. Horii M, To C, Morey R, Jacobs MB, Li Y, Nelson KK, Meads M, Siegel BA, Pizzo D, Adami R, Zhang-Rutledge K, Lamale-Smith L, Laurent LC, Parast MM. Mod Pathol 36: 2023 100035	2
Placental cell type deconvolution reveals that cell proportions drive preeclampsia gene expression differences. Campbell KA, Colacino JA, Puttabyatappa M, Dou JF, Elkin ER, Hammoud SS, Domino SE, Dolinoy DC, Goodrich JM, Loch-Caruso R, Padmanabhan V, Bakulski KM. Commun Biol 6: 2023 264	7