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Single cell gene expression in Dlxi1/2b::eGFP+ cells before and after migration

GSE96045 Homo sapiens (human) Single-cell RNA-seq 410 samples Submitted 2017/04/26 Platform GPL16791
At a glance

Single-cell RNA-seq · human · 410 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
410 samples: 211 × hSS vs 189 × hCSGroups 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.
Summary (written by the submitters)
We report the expression of selected genes associated with cortical, striatal and olfactory interneurons in hSS-derived Dlxi1/2::eGFP cells before (in hSS) and after migration (in hCS). By fusing hiPSC-derived fusions that were separately patterned to generate either human subpallial spheroids (hSS) or human cortical spheroids (hCS) we are able to model human interneuron migration in vitro. The aim of this experiment is to examine the gene expression of hSS-derived Dlxi1/2::eGFP cells before and after migration.
This dataset
Open GSE96045 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE96045_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA378657 and SRA study SRP096334. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28445465) ↗
Study design
211 × hSS vs 189 × hCS

Supports a between-group comparison across 400 samples.

How we read this: 2 replicated groups read from the first 400 of 410 sample titles; they account for 400 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.

Samples in this study

+ 370 more — browse all 410 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.