RNAseq validation of Neurodevelopmental disorder associated genes knockout efficiency [RNAseq]
RNA-seq (gene expression) · human · 19 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
- 19 samples: 6 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.
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 GSE327684_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 PRJNA1451864 and SRA study SRP690920. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 19 sample titles; they account for 18 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.
- GSM9663172 ASH1L_Induced_R1 ASH1L_Induced
- GSM9663173 ASH1L_Induced_R2 ASH1L_Induced
- GSM9663174 ASH1L_Induced_R3 ASH1L_Induced
- GSM9663175 ASH1L_Uninduced_R1 ASH1L_Uninduced
- GSM9663176 ASH1L_Uninduced_R2 ASH1L_Uninduced
- GSM9663177 ASH1L_Uninduced_R3 ASH1L_Uninduced
- GSM9663178 CHD8_Induced_R1 CHD8_Induced
- GSM9663179 CHD8_Induced_R2 CHD8_Induced
- GSM9663180 CHD8_Induced_R3 CHD8_Induced
- GSM9663181 CHD8_Uninduced_R1 CHD8_Uninduced
- GSM9663182 CHD8_Uninduced_R2 CHD8_Uninduced
- GSM9663183 CHD8_Uninduced_R3 CHD8_Uninduced
- GSM9663184 KMT5B_Induced_R1 KMT5B_Induced
- GSM9663185 KMT5B_Induced_R2 KMT5B_Induced
- GSM9663186 KMT5B_Induced_R3 KMT5B_Induced
- GSM9663187 KMT5B_Uninduced_R1 KMT5B_Uninduced
- GSM9663188 KMT5B_Uninduced_R2 KMT5B_Uninduced
- GSM9663189 KMT5B_Uninduced_R3 KMT5B_Uninduced
- GSM9663190 NRXN1_Induced_R1
- GSE119316 Impaired oxysterol-liver X receptor signaling underlies aberrant cortical neurogenesis in a stem cell model of neurodevelopmental disorder 71 samples shares neurodevelopmental, disorder
- GSE262442 Scaled and efficient derivation of loss-of-function alleles in risk genes for neurodevelopmental and psychiatric disorders in human iPSCs 69 samples shares neurodevelopmental, disorder
- GSE301239 SETBP1 variants outside the degron disrupt DNA-binding, transcription and neuronal differentiation capacity to cause a heterogeneous neurodevelopmental disorder [induced neurons] 51 samples shares neurodevelopmental, disorder
- GSE271268 Gene expression analysis in obsessive-compulsive disorder with and without comorbid neurodevelopmental disorders 28 samples shares neurodevelopmental, disorder
- GSE327685 Neurodevelopmental disorder genes 60 samples shares neurodevelopmental, disorder
- GSE249942 Requirements for the neurodevelopmental disorder-associated gene ZNF292 in human cortical interneuron development and function 55 samples shares neurodevelopmental, disorder
- GSE319096 A CRISPR screen in human iPSC-derived neurons reveals convergent transcriptomic effects of neurodevelopmental disorder genes [CRISPR Screen] 32 samples shares neurodevelopmental, disorder
- GSE288033 Functional dissection of ovarian aging-associated genes NDUFS5 and UBE2L3 through integrated genomic analyses and validation 62 samples shares validation
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.