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Status |
Public on Jul 20, 2021 |
Title |
PD_2 decidual leukocytes-scRNA-seq |
Sample type |
SRA |
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Source name |
CD45+ leukocytes
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Organism |
Homo sapiens |
Characteristics |
ethnicity: Chinese tissue: Uterus age: 26 disease: recurrent spontaneous abortion (RSA) patient
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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.
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
May 01, 2019 |
Last update date |
Jul 20, 2021 |
Contact name |
Yan-Ling Wang |
E-mail(s) |
wangyl@ioz.ac.cn
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Phone |
8601064807195
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Organization name |
Institute of Zoology, Chinese Academy of Sciences
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Department |
State Key Laboratory of Stem Cell and Reproductive Biology
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Street address |
Beichen West Rd., Chaoyang, Beijing
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City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100101 |
Country |
China |
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Platform ID |
GPL24676 |
Series (1) |
GSE130560 |
Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies |
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Relations |
BioSample |
SAMN11548013 |
SRA |
SRX5773321 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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