Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure
RNA-seq (gene expression) · human · 36 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
- 36 samples: 14 conditions, mostly in triplicateGroups 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
- Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failureNature communications · 2024
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 GSE233916_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 PRJNA978559 and SRA study SRP440685. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 36 samples.
How we read this: 14 replicated groups read from 36 sample titles; they account for 36 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.
- GSM7438707 WT/WT iPSC, rep1 WT/WT iPSC,
- GSM7438708 WT/WT iPSC, rep2 WT/WT iPSC,
- GSM7438709 WT/WT iPSC, rep3 WT/WT iPSC,
- GSM7438710 WT/WT NPC, rep1 WT/WT NPC,
- GSM7438711 WT/WT NPC, rep2 WT/WT NPC,
- GSM7438712 WT/WT NPC, rep3 WT/WT NPC,
- GSM7438713 WT/WT d28 cerebral organoids, rep1 WT/WT d28 cerebral orga…
- GSM7438714 WT/WT d28 cerebral organoids, rep2 WT/WT d28 cerebral orga…
- GSM7438715 WT/WT d28 cerebral organoids, rep3 WT/WT d28 cerebral orga…
- GSM7438716 WT/WT d49 cerebral organoids, rep1 WT/WT d49 cerebral orga…
- GSM7438717 WT/WT d49 cerebral organoids, rep2 WT/WT d49 cerebral orga…
- GSM7438718 WT/WT d49 cerebral organoids, rep3 WT/WT d49 cerebral orga…
- GSM7438719 70Q/70Q iPSC, rep1 70Q/70Q iPSC,
- GSM7438720 70Q/70Q iPSC, rep2 70Q/70Q iPSC,
- GSM7438721 70Q/70Q iPSC, rep3 70Q/70Q iPSC,
- GSM7438722 70Q/70Q NPC, rep1 70Q/70Q NPC,
- GSM7438723 70Q/70Q NPC, rep2 70Q/70Q NPC,
- GSM7438724 70Q/70Q NPC, rep3 70Q/70Q NPC,
- GSM7438725 70Q/70Q d28 cerebral organoids, rep1 70Q/70Q d28 cerebral or…
- GSM7438726 70Q/70Q d28 cerebral organoids, rep2 70Q/70Q d28 cerebral or…
- GSM7438727 70Q/70Q d28 cerebral organoids, rep3 70Q/70Q d28 cerebral or…
- GSM7438728 70Q/70Q d49 cerebral organoids, rep1 70Q/70Q d49 cerebral or…
- GSM7438729 70Q/70Q d49 cerebral organoids, rep2 70Q/70Q d49 cerebral or…
- GSM7438730 70Q/70Q d49 cerebral organoids, rep3 70Q/70Q d49 cerebral or…
- GSM7439035 NGN2, C1, rep 1 NGN2, C1,
- GSM7439036 NGN2, C1, rep 2 NGN2, C1,
- GSM7439037 NGN2, C2, rep 1 NGN2, C2,
- GSM7439038 NGN2, C2, rep 2 NGN2, C2,
- GSM7439039 NGN2, C3, rep 1 NGN2, C3,
- GSM7439040 NGN2, C3, rep 2 NGN2, C3,
- GSM7439041 NGN2, HD1, rep 1 NGN2, HD1,
- GSM7439042 NGN2, HD1, rep 2 NGN2, HD1,
- GSM7439043 NGN2, HD2, rep 1 NGN2, HD2,
- GSM7439044 NGN2, HD2, rep 2 NGN2, HD2,
- GSM7439045 NGN2, HD3, rep 1 NGN2, HD3,
- GSM7439046 NGN2, HD3, rep 2 NGN2, HD3,
- GSE233895 Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure [organoids] 24 samples shares neurodevelopment, chchd2-mediated, neurometabolic, huntingtin, organoids, impairs, failure, mutant
- GSE233914 Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure [NGN2] 12 samples shares neurodevelopment, chchd2-mediated, neurometabolic, huntingtin, organoids, impairs, failure, mutant
- GSE271852 Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure 6 samples shares neurodevelopment, chchd2-mediated, neurometabolic, huntingtin, organoids, impairs, failure, mutant
- GSE289912 APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoids 32 samples shares neurodevelopment, organoids
- GSE231321 Phosphorylation of 53BP1 by ATM enforce neurodevelopmental programs in cortical organoids 30 samples shares neurodevelopment, organoids
- GSE264218 Sequencing-Guided Design of Genetically Encoded Small RNAs Targeting CAG Repeats for Selective Inhibition of Mutant Huntingtin [II] 18 samples shares huntingtin, mutant
- GSE287509 Propofol Differentially Modulates Neurodevelopmental Processes in Region-Specific Human Brain Organoids 12 samples shares neurodevelopment, organoids
- GSE264590 Patient TSC2 Mutant Cells Exhibit Aberrations in Early Neurodevelopment Accompanied by Changes in the DNA Methylome 10 samples shares neurodevelopment, mutant
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.