Prime Editing Enables Isogenic Modeling of PNPLA3-I148M-Associated Lipotoxicity in Hepatocytes
RNA-seq (gene expression) · human · 16 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
- 16 samples: 3 × HepG2-GG vs 3 × HepG2-GC vs 2 × HepG2-CCGroups 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 GSE313544_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 PRJNA1380303 and SRA study SRP654747. 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 16 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.
- GSM9369967 HepG2-GG1 HepG2-GG
- GSM9369968 HepG2-GG2 HepG2-GG
- GSM9369969 HepG2-GG6 HepG2-GG
- GSM9369970 HepG2-GC2 HepG2-GC
- GSM9369971 HepG2-GC3 HepG2-GC
- GSM9369972 HepG2-GC4 HepG2-GC
- GSM9369973 HepG2-CC1 HepG2-CC
- GSM9369974 HepG2-CC3 HepG2-CC
- GSM9369975 HepG2-GG1_PA
- GSM9369976 HepG2-GG2_PA
- GSM9369977 HepG2-GG6_PA
- GSM9369978 HepG2-GC2_PA
- GSM9369979 HepG2-GC3_PA
- GSM9369980 HepG2-GC4_PA
- GSM9369981 HepG2-CC1_PA
- GSM9369982 HepG2-CC3_PA
- GSE275241 Genome engineering of primary and pluripotent stem cell-derived hepatocytes for modeling liver tumor formation 18 samples shares hepatocytes, modeling
- GSE341489 Hidden outcomes of CRISPR/Cas9 genome editing revealed by targeted sequencing in isogenic human iPSC clones [RNA-seq] 10 samples shares isogenic, editing
- GSE226482 Single cell RNA sequencing of spinal motor neurons and interneurons differentiated from isogenic FUS and TARDBP human induced pluripotent stem cell lines harbouring ALS-causative mutations 1415 samples shares isogenic
- GSE190185 Cholesterol and matrisome pathways dysregulated in APOE ε4 human microglia and astrocytes [isogenicAPOE] 94 samples shares isogenic
- GSE228249 Transcriptome analysis of primary human hepatocytes-derived organoids [RNA-seq] 82 samples shares hepatocytes
- GSE293032 Transcriptomic comparison of hepatocytes derived from a panel of human induced pluripotent stem cells with different ethnicities 54 samples shares hepatocytes
- GSE307755 Direct contact between iPSC-derived macrophages and hepatocytes drives reciprocal acquisition of Kupffer cell identity and hepatocyte maturation 53 samples shares hepatocytes
- GSE264742 Isogenic hiPSC models of Turner syndrome development reveal shared roles of inactive X and Y in the human cranial neural crest network 52 samples shares isogenic
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.