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Sample GSM5224705

Query DataSets for GSM5224705

Status

Public on Apr 03, 2021

Title

CNTRL_3_villi, scRNA-seq

Sample type

SRA

Source name

placental villi

Organism

Homo sapiens

Characteristics

sars-cov-2 status: negative
tissue: placental villi

Extracted molecule

polyA RNA

Extraction protocol

Dissected tissues were rinsed thoroughly in PBS and minced with scissors in a tissue digestion buffer of Liberase TM (0.28 WU/ml) and DNase I (30 μg/ml) in HBSS with Ca2+ and Mg2+. Finely minced tissue was enzymatically digested at 37°C for 1 hour with agitation, pipetting, and further mincing every 10 minutes until disaggregated. The suspension was passed through sterile gauze, centrifuged at 1000 x g for 5 minutes at 4°C to pellet cells, and washed with fresh digestion buffer. After centrifugation, the supernatant was aspirated and the cell pellet was resuspended in ACK lysing buffer for 5 minutes. Cells were centrifuged and resuspended in RPMI media before filtering through a 70-μm mesh cell strainer.
scRNA-seq libraries were generated using the 10x Chromium Single Cell 3’ Reagent Kit.
single cell RNA-seq

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

counts.tsv.gz
metadata.tsv.gz

Data processing

Sequencing results were demultiplexed into FASTQ files using the Cell Ranger (10x Genomics, 3.0.2) mkfastq function.
Samples were aligned to GRCh38 10x genome and the count matrix was generated using the cellranger count function with default settings.
Low quality cells containing <500 or >6000 genes detected were removed, as well cells with >20% of transcripts mapping to mitochondrial genes. Genes that were present in less than 3 cells were excluded from analysis.
Gene expression values were then normalized, log-transformed, and scaled.
Single cell transcriptomes from COVID-19 cases and healthy controls were pooled prior to unsupervised cluster analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.tsv.gz is a tab-delimited file that contain cell by gene matrix of raw counts
Supplementary_files_format_and_content: metadata.tsv.gz is tab-delimited file that contains cell-level metadata including cell QC metrics and cell type annotations

Submission date

Apr 02, 2021

Last update date

Apr 04, 2021

Contact name

Arun Rajendra Chavan

E-mail(s)

arun.chavan@yale.edu

Organization name

Yale University

Department

Ecology and Evolutionary Biology