Single cell RNA-seq analysis on human endometrium across the natural menstrual cycle

Experiment ID:SRP135922
Technology:scRNA-Seq
Description:To unbiasedly and systematically characterize endometrial transformation across the human menstrual cycle in preparation for embryo implantation, we analyzed the transcriptomic transformation of human endometrium at single cell resolution, dissecting multidimensional cellular heterogeneity of the tissue across the entire natural menstrual cycle. Overall design: We collected single cell transcriptome profile of endometrium biopsies sampled from 19 healthy and fertile females, at 4-27 days of their menstrual cycle. [10x dataset] - collected to validate main findings drawn from the original C1 dataset of this study. In this dataset, we collected additional data from 10 endometrial biopsies using the 10x Chromium system. Importantly, we collected both C1 and 10x data for two biopsies, one from mid-secretory phase and the other early-secretory. They served as anchors for a direct comparison between the two datasets, and were referred as ?anchor biopsies? in the manuscript of this study. Biopsies in the 10x dataset were obtained following the same protocol used for the C1 dataset, as described in the manuscript.
DOI:10.1038/s41591-020-1040-z
Source:SRP135922 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

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Showing 1 to 20 of 68 entries

Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX8419314CL:0002149 epithelial cell of uterusUnciliated epithelia 2UBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired553541529338667952032578341865229353.5Browse results
SRX8419314CL:0000067 ciliated epithelial cellCiliatedUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55354152933866795205358741532827884.5Browse results
SRX8419314CL:0002255 stromal cell of endometriumStromal fibroblastsUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired553541529338667952011111380593028775.5Browse results
SRX8419314CL:0000542 lymphocyteLymphocytesUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55354152933866795201672506309826247.5Browse results
SRX8419314CL:0009095 endothelial cell of uterusEndotheliaUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55354152933866795201320388270126176.5Browse results
SRX8419314CL:0002601 uterine smooth muscle cellSmooth muscle cellsUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired5535415293386679520390548115324791Browse results
SRX8419314CL:0000235 macrophageMacrophagesUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 20, early-mid-secretoryfemaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired553541529338667952029295797824164Browse results
SRX8419315CL:0002149 epithelial cell of uterusUnciliated epithelia 2UBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired500563247322662779021472995943028740Browse results
SRX8419315CL:0000235 macrophageMacrophagesUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired5005632473226627790355190116224263.5Browse results
SRX8419315CL:0002601 uterine smooth muscle cellSmooth muscle cellsUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired5005632473226627790871201307725584.5Browse results
SRX8419315CL:0009095 endothelial cell of uterusEndotheliaUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired50056324732266277901978877474526267.5Browse results
SRX8419315CL:0000542 lymphocyteLymphocytesUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired50056324732266277901606192222026334Browse results
SRX8419315CL:0002255 stromal cell of endometriumStromal fibroblastsUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired5005632473226627790438130091038929831Browse results
SRX8419315CL:0000067 ciliated epithelial cellCiliatedUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 23femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired50056324732266277909151288835428343Browse results
SRX8419316CL:0002601 uterine smooth muscle cellSmooth muscle cellsUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 19femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired501306179340089050012067792022931.5Browse results
SRX8419316CL:0000235 macrophageMacrophagesUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 19femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired50130617934008905001319112619018Browse results
SRX8419316CL:0000542 lymphocyteLymphocytesUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 19femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired50130617934008905001622087246926261Browse results
SRX8419316CL:0000067 ciliated epithelial cellCiliatedUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 19femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired5013061793400890500158101751018728572.5Browse results
SRX8419316CL:0002149 epithelial cell of uterusUnciliated epithelia 1UBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 19femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired5013061793400890500283554591065428925.5Browse results
SRX8419316CL:0002255 stromal cell of endometriumStromal fibroblastsUBERON:0001295 endometriumendometrium biopsyHsapDv:0000266 young adult stage (human)18-34 years, menstrual cycle day 19femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired501306179340089050016498792923422.5Browse results

Showing 1 to 20 of 68 entries

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