Mapping origins of variation in neural trajectories of human pluripotent stem cells [SOX21 KO RNA-seq]
RNA-seq (gene expression) · human · 18 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
- 18 samples: 16 distinct titles, 2 of them repeatedGroups 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
- Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cellsStem cell reports · 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 GSE164053_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 PRJNA688714 and SRA study SRP299817. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 sample titles: 16 distinct titles with little repetition. 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.
- GSM4995770 SA01_sox21KO7_SR_2_days
- GSM4995771 SA01_sox21KO7_SR_4_days
- GSM4995772 SA01_sox21KO7_SR_6_days
- GSM4995773 SA01_sox21WT8_SR_2_days
- GSM4995774 SA01_sox21WT8_SR_4_days
- GSM4995775 SA01_sox21WT8_SR_6_days
- GSM4995776 SA01_sox21KO7_SR_2_days.1
- GSM4995777 SA01_sox21WT8_SR_2_days.1
- GSM4995778 SA01_sox21KO7_SR_3_days
- GSM4995779 SA01_sox21WT8_SR_3_days
- GSM4995780 SA01_sox21KO7_NSB_2_days
- GSM4995781 SA01_sox21KO7_NSB_4_days
- GSM4995782 SA01_sox21KO7_NSB_6_days
- GSM4995783 SA01_sox21WT8_NSB_2_days
- GSM4995784 SA01_sox21WT8_NSB_4_days
- GSM4995785 SA01_sox21WT8_NSB_6_days
- GSM4995786 SA01_sox21KO7_BMP4day2_3_days
- GSM4995787 SA01_sox21WT8_BMP4day2_3_days
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- GSE239843 Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [RNA-seq I] 134 samples shares pluripotent, rna-seq
- GSE247367 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [bulk RNA-seq] 80 samples shares trajectories, 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
- GSE282876 Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a neurons [Bulk RNA-seq] 48 samples shares trajectories, rna-seq
- GSE309941 Immunometabolic Endotypes Define Distinct Clinical Trajectories in Type 2 Diabetes [bulk RNA-seq] 42 samples shares trajectories, rna-seq
- GSE264658 A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells [RNA-seq] 31 samples shares pluripotent, 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.