Comprehensive Transcriptomic and Translational Profiling of Human Embryonic Stem Cell Differentiation to Definitive Endoderm and Pancreatic Progenitors via RNA-seq and Ribo-seq
RNA-seq (gene expression) · human · 14 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
- 14 samples: 6 conditions, mostly in duplicateGroups 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.
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 GSE277202_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 PRJNA1161172 and SRA study SRP532749. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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.
- GSM8516495 RNA_seq_DE_rep1 RNA_seq_DE
- GSM8516496 RNA_seq_DE_rep2 RNA_seq_DE
- GSM8516497 RNA_seq_PP1_rep1 RNA_seq_PP1
- GSM8516498 RNA_seq_PP1_rep2 RNA_seq_PP1
- GSM8516499 RNA_seq_PP2_rep1 RNA_seq_PP2
- GSM8516500 RNA_seq_PP2_rep2 RNA_seq_PP2
- GSM8516501 RNA_seq_PP2_rep3 RNA_seq_PP2
- GSM8516502 RIBO_seq_DE_rep1 RIBO_seq_DE
- GSM8516503 RIBO_seq_DE_rep2 RIBO_seq_DE
- GSM8516504 RIBO_seq_PP1_rep1 RIBO_seq_PP1
- GSM8516505 RIBO_seq_PP1_rep2 RIBO_seq_PP1
- GSM8516506 RIBO_seq_PP2_rep1 RIBO_seq_PP2
- GSM8516507 RIBO_seq_PP2_rep2 RIBO_seq_PP2
- GSM8516508 RIBO_seq_PP2_rep3 RIBO_seq_PP2
- GSE335452 Single-cell RNA-seq and spatial transcriptomics characterize CD8+ exhausted T cells in pancreatic ductal adenocarcinoma 15 samples shares pancreatic, rna-seq
- GSE275610 scRNA-seq and snATAC-seq reveal differentiation trajectories of several pancreatic islet induction protocols 341 samples shares pancreatic, rna-seq
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares pancreatic, rna-seq
- GSE310388 In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment. [RNA-Seq] 171 samples shares pancreatic, rna-seq
- GSE208732 Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-seq] 102 samples shares pancreatic, rna-seq
- GSE288966 Multi-omics analysis identifies progenitors of CD4-CTLs [bulk RNA-seq] 70 samples shares progenitors, rna-seq
- GSE305132 Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Progenitors in vitro - Treatment with Antisense Oligonucleotides for PKNOX1, BACH1 and GABPA (Bulk RNA-seq Dataset) 68 samples shares progenitors, rna-seq
- GSE296649 Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scRNA-Seq] 58 samples shares progenitors, rna-seq
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.