Guided self-organization recapitulates tissue architecture in a bioengineered brain organoid model
RNA-seq (gene expression) · human · 24 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
- 24 samples: 12 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 GSE80538_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 PRJNA319262 and SRA study SRP073683. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.
- GSM2130401 20D_Fiber_1_techReplicate1 20D_Fiber_1_tech
- GSM2130402 20D_Fiber_2_techReplicate1 20D_Fiber_2_tech
- GSM2130403 20D_Fiber_3_techReplicate1 20D_Fiber_3_tech
- GSM2130404 20D_Round_1_techReplicate1 20D_Round_1_tech
- GSM2130405 20D_Round_2_techReplicate1 20D_Round_2_tech
- GSM2130406 20D_Round_3_techReplicate1 20D_Round_3_tech
- GSM2130407 60D_Fiber_1_techReplicate1 60D_Fiber_1_tech
- GSM2130408 60D_Fiber_2_techReplicate1 60D_Fiber_2_tech
- GSM2130409 60D_Fiber_3_techReplicate1 60D_Fiber_3_tech
- GSM2130410 60D_Round_1_techReplicate1 60D_Round_1_tech
- GSM2130411 60D_Round_2_techReplicate1 60D_Round_2_tech
- GSM2130412 60D_Round_3_techReplicate1 60D_Round_3_tech
- GSM2130413 20D_Fiber_1_techReplicate2 20D_Fiber_1_tech
- GSM2130414 20D_Fiber_2_techReplicate2 20D_Fiber_2_tech
- GSM2130415 20D_Fiber_3_techReplicate2 20D_Fiber_3_tech
- GSM2130416 20D_Round_1_techReplicate2 20D_Round_1_tech
- GSM2130417 20D_Round_2_techReplicate2 20D_Round_2_tech
- GSM2130418 20D_Round_3_techReplicate2 20D_Round_3_tech
- GSM2130419 60D_Fiber_1_techReplicate2 60D_Fiber_1_tech
- GSM2130420 60D_Fiber_2_techReplicate2 60D_Fiber_2_tech
- GSM2130421 60D_Fiber_3_techReplicate2 60D_Fiber_3_tech
- GSM2130422 60D_Round_1_techReplicate2 60D_Round_1_tech
- GSM2130423 60D_Round_2_techReplicate2 60D_Round_2_tech
- GSM2130424 60D_Round_3_techReplicate2 60D_Round_3_tech
- GSE301846 co-cultures of mesenchymal cells with epithelial organoids promote fusion into bioengineered liver tissues by ECM remodeling 31 samples shares bioengineered, organoid
- GSE324454 Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes 128 samples shares architecture, brain
- GSE322943 Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [RNA-Seq] 100 samples shares architecture, brain
- GSE245467 Immunogenomics and spatial proteomic mapping highlight distinct neuro-immune architectures in melanoma vs. non-melanoma-derived brain metastasis 54 samples shares architecture, brain
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares architecture, organoid
- GSE324453 Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [snRNA-Seq] 28 samples shares architecture, brain
- GSE111672 Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas 23 samples shares architecture
- GSE274546 The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X] 121 samples shares architecture
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.