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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 30, 2023 |
| Title |
Patient 1, scRNAseq |
| Sample type |
SRA |
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| Source name |
Endometrium
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Endometrium
Sex: female
fecundity: infertile
disease state: recurrent implantation failure
endometrial preparation: hormonal replacement therapy
phase: mid-secretory
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| Extracted molecule |
total RNA |
| Extraction protocol |
After the biopsy, the endometrial tissues were processed immediately. The two-stage dissociation protocol was performed. Briefly, the tissues were washed with DMEM/F12 medium (Gibco) and subsequently minced into small pieces. Then, the minced tissues were dissociated in DMEM/F12 supplemented with 1% Penicillin-Streptomycin (Gibco, 15140122), 0.4 mg/mL Collagenase V (Sigma, C9263), 1.25 U/mL Dispase II (Sigma, D4693) at 37 °C for 1 h with agitation. The supernatant was collected as the stromal fibroblast-enriched suspension. The pellet was the glandular and luminal fragments, which was further dissociated in TrypLE Select (Gibco, 12563-011) at 37 °C for 20 min. The cells were collected as the epithelium-enriched portion.
Cell counting and quality control were performed following the manufacturer’s instructions. Then, the two portions were mixed and loaded into Chromium microfluidic chips (Chromium Next GEM Chip G Single Cell Kit, 10X Genomics) with 3’ chemistry and barcoded with a 10×Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed to generate barcoded cDNA. Next, sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics) and Dynabeads™ MyOne™ SILANE (Life, 37005D) according to the manufacturer’s instructions. The single-cell libraries were sequenced in paired-end reads on a NovaSeq 6000 platform (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jan 25, 2023 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Shen Zhang |
| E-mail(s) |
zhangshen09@126.com
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| Phone |
8619823579016
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| Organization name |
The Second Affiliated Hospital of Chongqing Medical University
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| Department |
Obstetrics and Gynecology Department
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| Street address |
No. 288 Tianwen avenue, Nanan district
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| City |
Chongqing |
| ZIP/Postal code |
400010 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE223672 |
Single-Cell RNA Transcriptome of the Human Endometrium Reveals Epithelial Characterizations Associated with Recurrent Implantation Failure |
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| Relations |
| BioSample |
SAMN32906635 |
| SRA |
SRX19164641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6970370_RIF1_barcodes.tsv.gz |
53.6 Kb |
(ftp)(http) |
TSV |
| GSM6970370_RIF1_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM6970370_RIF1_matrix.mtx.gz |
108.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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