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Sample GSM5572243 Query DataSets for GSM5572243
Status Public on Sep 16, 2022
Title RIF3
Sample type SRA
 
Source name endometrium
Organism Homo sapiens
Characteristics tissue: endometrium
Stage: 5 days after ovulation
group: RIF
Treatment protocol none
Growth protocol none
Extracted molecule total RNA
Extraction protocol Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 40%;  Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes
 
Submission date Sep 09, 2021
Last update date Sep 16, 2022
Contact name li mingqing
E-mail(s) mqli@fudan.edu.cn
Organization name Affiliated obstetrics and Gynecology Hospital of Fudan University
Street address NO.419 fangxie Road, Shanghai
City shanghai
ZIP/Postal code 200011
Country China
 
Platform ID GPL24676
Series (1)
GSE183837 Single-cell transcriptome profiling of the human endometrium from patients with recurrent implantation failure
Relations
BioSample SAMN21371334
SRA SRX12124992

Supplementary file Size Download File type/resource
GSM5572243_RIF-3.barcodes.tsv.gz 31.2 Kb (ftp)(http) TSV
GSM5572243_RIF-3.genes.tsv.gz 222.2 Kb (ftp)(http) TSV
GSM5572243_RIF-3.matrix.mtx.gz 61.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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