Trajectory modeling of first trimester placenta highlight differences between cytotrophoblast progenitors and trophoblast stem cells [scRNA-seq]
Single-cell RNA-seq · human · 13 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 13 samples: 3 × TSC, patient vs 2 × Basal Plate, patient vs 2 × Chorionic Plate, patientGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Single-cell transcriptomics reveal differences between chorionic and basal plate cytotrophoblasts and trophoblast stem cellsbioRxiv : the preprint server for biology · 2024
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE270170_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1125368 and SRA study SRP514630. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 7 samples.
How we read this: 3 replicated groups read from 13 sample titles; they account for 7 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8335886 Whole Placenta, patient 856, 5000, rep1
- GSM8335887 Whole Placenta, patient 856, 10000, rep2
- GSM8335888 Whole Placenta, patient 860, 5000, rep1
- GSM8335889 Whole Placenta, patient 860, 10000, rep2
- GSM8335890 Whole Placenta, patient 861, 10000, rep1
- GSM8335891 Whole Placenta, patient 866, 10000, rep1
- GSM8335892 Basal Plate, patient 1276 Basal Plate, patient
- GSM8335893 Chorionic Plate, patient 1276 Chorionic Plate, patient
- GSM8335894 Basal Plate, patient 1290 Basal Plate, patient
- GSM8335895 Chorionic Plate, patient 1290 Chorionic Plate, patient
- GSM8335896 TSC, patient 906 TSC, patient
- GSM8335897 TSC, patient 1000 TSC, patient
- GSM8335898 TSC, patient 1278 TSC, patient
- GSE296649 Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scRNA-Seq] 58 samples shares progenitors, scrna-seq
- GSE290353 Temporal Differences in Progenitor Metabolism Shape Regional Brain Growth during Development [scRNA-seq] 12 samples shares differences, scrna-seq
- GSE307832 DEVELOPMENTAL LANDMARKS AND CELLULAR TRANSITIONS DURING EXTRAVILLOUS TROPHOBLAST CELL DIFFERENTIATION [scRNA-Seq] 11 samples shares trophoblast, scrna-seq
- GSE236796 Specificity protein 6 governs human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements 42 samples shares cytotrophoblast, trophoblast
- GSE255685 Age-related transcriptomic differences in peripheral blood of adolescents with major depressive disorder 279 samples shares differences
- GSE293398 Sex-related differences in gene expression in early-stage bladder cancer revealed by whole-transcriptome sequencing 186 samples shares differences
- GSE243579 iPSC-based modeling of preeclampsia identifies defects in extravillous trophoblast differentiation 144 samples shares trophoblast
- GSE268230 Extracellular vesicles alter trophoblast function in pregnancies complicated by COVID-19 129 samples shares trophoblast
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.