|
| Status |
Public on Jul 05, 2023 |
| Title |
NC3 |
| Sample type |
SRA |
| |
|
| Source name |
Placenta
|
| Organisms |
Homo sapiens; Severe acute respiratory syndrome coronavirus 2 |
| Characteristics |
tissue: Placenta
cell type: Heterogeneous
condition: NegativeControl
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Spatial transcriptomics. Human placentae from distinct regions including the chorionic villi, decidua, and chorioamniotic membranes, or cross-sections from the parenchyma, were fresh-frozen in optimal cutting temperature solution (FF-OCT). Blocks were cryosectioned and H&E stained directly on 10X Genomics Visium Gene Expression slides (v2) and imaged using a Nikon Eclipse SE Ni microscope using a Nikon DS-Ri1 camera, Nikon Plan Apo objective at 10x magnification (0.45 aperture, 0.91 μm/pixel resolution). Tissues were permeabilized and RNA was subject to spatial transcriptomics library preparation including poly(dT) reverse transcription. Libraries were sequenced on the Illumina NovaSeq S4 platform with 2% PhiX.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics Visium Spatial Gene Expression (v2)
|
| Data processing |
Single-cell and spatial transcriptomics analyses. Reads were demultiplexed and aligned to a custom human (GRCh38) and SARS-CoV-2 reference genome (NC_045512.2) using SpaceRanger (v1.3.0) and custom bash scripts. Downstream analyses were done using the package Seurat (v4.0.3) in rStudio (v4.1.1). Counts matrices were filtered iteratively to exclude low-quality transcriptomes and clusters defined by quality control metrics (e.g. mitochondrial or hemoglobin gene expression). Spatial transcriptomes were normalized and scaled using a negative binomial model (SCTransform) and the top 3,000 most variable transcripts were used for to principal component analysis dimension reduction. The first 30 PCA dimensions were used for K-nearest neighbors’ analysis, clustered using a Louvain algorithm with the default resolution parameter (0.6), and visualized by unique manifold approximation and projection (UMAP) in two dimensions. Significantly upregulated transcripts were manually examined and compared to the term placenta atlas in addition to using EnrichR(58), PlacentaCellEnrich(110), and the Human Protein Atlas(111) to annotate clusters. Pseudotime trajectory analysis was done using Monocle3 (v1.0.0) utilizing gene sets and starting points denoted in the text. Spatial and scRNA-seq datasets were integrated using reciprocal PCA of 3,000 reference transcripts prior to clustering.
Assembly: GRCh38_and_NC_045512.2
Supplementary files format and content: h5 counts matrix
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Jan 16, 2023 |
| Last update date |
Jul 05, 2023 |
| Contact name |
Michael Jochum |
| E-mail(s) |
michael.jochum@bcm.edu, michaeljochumjr@gmail.com
|
| Phone |
5127698372
|
| Organization name |
Baylor College of Medicine
|
| Department |
Obstetrics and Gynecology
|
| Lab |
Aagaard
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77401 |
| Country |
USA |
| |
|
| Platform ID |
GPL29320 |
| Series (1) |
| GSE222987 |
SARS-CoV-2 Niches in Human Placenta Revealed by Spatial Transcriptomics |
|
| Relations |
| BioSample |
SAMN32756902 |
| SRA |
SRX19046552 |
