WDFY3 loss-of-function leads to increased proliferation and altered differentiation of neuronal cells underlying the haploinsufficient human phenotype
RNA-seq (gene expression) · human · 10 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
- 10 samples: 4 × Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD vs 2 × Undifferentiated SH-SY5Y Neuronal Cell line, p9, DLD vs 2 × Undifferentiated SH-SY5Y Neuronal Cell line, p11, DLDGroups 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 GSE271636_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 PRJNA1132536 and SRA study SRP518303. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 3 replicated groups read from 10 sample titles; they account for 8 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.
- GSM8380945 Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_01 Undifferentiated SH-SY5…
- GSM8380946 Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_02 Undifferentiated SH-SY5…
- GSM8380947 Undifferentiated SH-SY5Y Neuronal Cell line, p9, DLD_05 Undifferentiated SH-SY5…
- GSM8380948 Undifferentiated SH-SY5Y Neuronal Cell line, p9, DLD_06 Undifferentiated SH-SY5…
- GSM8380949 Undifferentiated SH-SY5Y Neuronal Cell line, p11, DLD_09 Undifferentiated SH-SY5…
- GSM8380950 Undifferentiated SH-SY5Y Neuronal Cell line, p11, DLD_10 Undifferentiated SH-SY5…
- GSM8380951 Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_13 Undifferentiated SH-SY5…
- GSM8380952 Undifferentiated SH-SY5Y Neuronal Cell line, p8, DLD_14 Undifferentiated SH-SY5…
- GSM8380953 Undifferentiated SH-SY5Y Neuronal Cell line, p10, DLD_17
- GSM8380954 Undifferentiated SH-SY5Y Neuronal Cell line, p19, DLD_18
- GSE299964 Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia [RNA-Seq] 50 samples shares proliferation, increased
- GSE265940 Overexpression of extracellular matrix proteins, increased cell death and reduced cell proliferation contribute to the pathophysiology of microphthalmia across in vitro patient-derived models 48 samples shares proliferation, increased
- GSE276630 Somatic loss-of-function variants in leptin alter adipose tissue physiology by promoting proliferation and impairing differentiation 26 samples shares loss-of-function, proliferation
- GSE301142 Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses 18 samples shares loss-of-function, phenotype
- GSE266990 Haploinsufficient phenotypes promote selection of PTEN and ARID1A deficient clones in human colon. 16 samples shares haploinsufficient, phenotype
- GSE330233 CHD8 haploinsufficiency impairs ventral progenitor proliferation and inhibitory neuronal maturation in human ventral forebrain organoids 12 samples shares proliferation, neuronal
- GSE329548 Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses II 9 samples shares loss-of-function, phenotype
- GSE299960 Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia [CUT&Run] 70 samples shares proliferation, increased
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.