Hidden outcomes of CRISPR/Cas9 genome editing revealed by targeted sequencing in isogenic human iPSC clones [RNA-seq]
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: 10 samples, each with a distinct title — no replicated groupsGroups 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 GSE341489_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 PRJNA1502830. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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.
- GSM9907741 CRISPR/Cas9-edited human iPSC clone 146-1-2v1, RNA-seq coverage
- GSM9907742 CRISPR/Cas9-edited human iPSC clone 149-4-4v1, RNA-seq coverage
- GSM9907743 CRISPR/Cas9-edited human iPSC clone 146-7-3v1, RNA-seq coverage
- GSM9907744 CRISPR/Cas9-edited human iPSC clone 149-4-3v1, RNA-seq coverage
- GSM9907745 CRISPR/Cas9-edited human iPSC clone 149-1-20v6, RNA-seq coverage
- GSM9907746 CRISPR/Cas9-edited human iPSC clone 149-4-1v6, RNA-seq coverage
- GSM9907747 CRISPR/Cas9-edited human iPSC clone 149-1-6v1, RNA-seq coverage
- GSM9907748 CRISPR/Cas9-edited human iPSC clone 146-1-5v1, RNA-seq coverage
- GSM9907749 CRISPR/Cas9-edited human iPSC clone 149-4-7v6, RNA-seq coverage
- GSM9907750 CRISPR/Cas9-edited human iPSC clone 146-1-2v6, RNA-seq coverage
- GSE290621 Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [RNA-seq] 33 samples shares crispr, cas9, rna-seq
- GSE244257 Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells 83 samples shares crispr, cas9, editing
- GSE327354 Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-seq Exp3] 18 samples shares crispr, targeted, rna-seq
- GSE243185 Activation of the imprinted Prader-Willi Syndrome locus by CRISPR-based epigenome editing [RNA-seq] 18 samples shares crispr, editing, rna-seq
- GSE327357 Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-Seq Exp1] 14 samples shares crispr, targeted, rna-seq
- GSE327352 Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-seq Exp2] 12 samples shares crispr, targeted, rna-seq
- GSE303100 Dissecting Resistance to CDK4/6 Inhibition in Experimental Glioma via Genome-wide CRISPR-Cas9 Screening 24 samples shares crispr, cas9
- GSE240468 Silencing of NFYC-AS1 by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion. 23 samples shares crispr, cas9
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.