Development-inspired approach for the derivation of functional and transplantable salivary gland organoids from human pluripotent stem cells [RNA-Seq]
RNA-seq (gene expression) · human · 16 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 16 samples: 8 × BXS0114 - Day vs 8 × WA09 - DayGroups 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.
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 GSE342790_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1508898 and SRA study SRP724918. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 2 replicated groups read from 16 sample titles; they account for 16 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.
- GSM9939349 BXS0114 - Day 0 BXS0114 - Day
- GSM9939350 BXS0114 - Day 3 BXS0114 - Day
- GSM9939351 BXS0114 - Day 10 BXS0114 - Day
- GSM9939352 BXS0114 - Day 13 BXS0114 - Day
- GSM9939353 BXS0114 - Day 17 BXS0114 - Day
- GSM9939354 BXS0114 - Day 25 BXS0114 - Day
- GSM9939355 BXS0114 - Day 32 BXS0114 - Day
- GSM9939356 BXS0114 - Day 46 BXS0114 - Day
- GSM9939357 WA09 - Day 0 WA09 - Day
- GSM9939358 WA09 - Day 3 WA09 - Day
- GSM9939359 WA09 - Day 10 WA09 - Day
- GSM9939360 WA09 - Day 13 WA09 - Day
- GSM9939361 WA09 - Day 17 WA09 - Day
- GSM9939362 WA09 - Day 25 WA09 - Day
- GSM9939363 WA09 - Day 32 WA09 - Day
- GSM9939364 WA09 - Day 46 WA09 - Day
- GSE286998 High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans [RNA-Seq] 26 samples shares pluripotent, derivation, rna-seq
- GSE239843 Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [RNA-seq I] 134 samples shares pluripotent, rna-seq
- GSE224698 Gene expression profiles of human dermal fibroblasts and human pluripotent stem cells analyzed by bulk RNA-seq 69 samples shares pluripotent, rna-seq
- GSE255982 Persistent epigenome anomalies in induced pluripotent stem cells from late-onset sporadic Alzheimer’s disease cases [RNA-seq] 52 samples shares pluripotent, rna-seq
- GSE290316 Human amygdala-like telencephalic organoids from Pluripotent Stem Cells 39 samples shares pluripotent, organoids
- GSE264658 A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells [RNA-seq] 31 samples shares pluripotent, rna-seq
- GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares pluripotent, rna-seq
- GSE249826 Human-induced pluripotent Stem Cell-Derived Hepatic Stellate Cells in Liver Organoids: Maturation Promotion and Essential Role in Vascularization 26 samples shares pluripotent, organoids
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.