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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
Phone 8601064807195
Organization name Institute of Zoology, Chinese Academy of Sciences
Department State Key Laboratory of Stem Cell and Reproductive Biology
Street address Beichen West Rd., Chaoyang, Beijing
City Beijing
State/province Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL24676
Series (1)
GSE130560 Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies
BioSample SAMN11548015
SRA SRX5773319

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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