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Sample GSM3743503

Query DataSets for GSM3743503

Status

Public on Jul 20, 2021

Title

ND_3 decidual leukocytes-scRNA-seq

Sample type

SRA

Source name

CD45+ leukocytes

Organism

Homo sapiens

Characteristics

ethnicity: Chinese
tissue: Uterus
age: 30
disease: normal pregnancy

Treatment protocol

The fresh tissue samples were gently triturated with GentelMACS Dissociator (Miltenyi Biotec, Germany) in the RPMI-1640 medium (Invitrogen) and enzymatically digested twice for 30 minutes in 37℃ shaker with 1.6 mg/ml type IV collagenase (9001121, Gibco) and 10U/ml type I DNase (DN25, Sigma). the suspended cells were subsequently passed through 60 mesh and 200 mesh cell strainers, and centrifuged at 1000rpm for 10 min. After the supernatant was removed, the pelleted cells diluted 1:1 by PBS, followed by Ficoll-Paque Plus (17-1440-02, GE Healthcare,) separation, after washing with 1x PBS, then the lymphocytes were centrifuged at 1000rpm for 10 min. the cell pellets were resuspended in PBS, The lymphocytes were stained with eFluor 506-viability dye (65-0866-14, ebioscience) and FITC-labeled anti-CD45 antibody (11-0459-42, ebioscience), then subjected to FACS sorting to obtain CD45+ lymphocytes.

Extracted molecule

polyA RNA

Extraction protocol

RNA were prepared for sequencing
Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v2 (10X Genomics)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

scRNA-Seq: We checked the quality of raw sequencing data by FastQC software. We used 10x genomics cellranger count pipeline 2.0.0 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were merged together by cellranger aggr pipeline and normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

Submission date

May 01, 2019

Last update date

Jul 20, 2021

Contact name

Yan-Ling Wang

E-mail(s)

wangyl@ioz.ac.cn

Phone

8601064807195

Organization name

Institute of Zoology, Chinese Academy of Sciences