|
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 |