Dataset

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

Dataset ID Technology Samples
EGAD00001003705 Illumina HiSeq 2000,NextSeq 500 32

Dataset Description

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.

Who controls access to this dataset

For each dataset that requires controlled access, there is a corresponding Data Access Committee (DAC) who determine access permissions. Access to actual data files is not managed by the EGA. If you need to request access to this data set, please contact:

The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)
Contact person: Peiyong Jiang
Email: jiangpeiyong [at] cuhk [dot] edu [dot] hk
More details: EGAC00001000078

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