Pervasive off-target activity in CRISPR-interference (CRISPRi) system [RNA-seq]
RNA-seq (gene expression) · human · 15 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
- 15 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.
- Paper
- Seed sequences mediate off-target activity in the CRISPR-interference systemCell genomics · 2024
Read the full summary ↓
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 GSE252977_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 PRJNA1063363 and SRA study SRP482977. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 6 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8011766 Jurkat_sgHMGB1_infected_rep2 Jurkat_sgHMGB1_infected
- GSM8011767 Jurkat_sgADAT1_infected_rep2 Jurkat_sgADAT1_infected
- GSM8011768 Jurkat_sgADAT1_infected_rep3 Jurkat_sgADAT1_infected
- GSM8011769 Jurkat_sgHMGB1_infected_rep1 Jurkat_sgHMGB1_infected
- GSM8011770 Jurkat_sgHMGB1_infected_rep3 Jurkat_sgHMGB1_infected
- GSM8011771 Jurkat_uninfected_rep3 Jurkat_uninfected
- GSM8011772 Jurkat_sgADAT1_infected_rep1 Jurkat_sgADAT1_infected
- GSM8011773 Jurkat_uninfected_rep2 Jurkat_uninfected
- GSM8011774 Jurkat_uninfected_rep1 Jurkat_uninfected
- GSM8011775 EAhy926_sgGRK4_infected_rep1 EAhy926_sgGRK4_infected
- GSM8011776 EAhy926_sgLRRC34_infected_rep2 EAhy926_sgLRRC34_infect…
- GSM8011777 EAhy926_uninfected_rep2 EAhy926_uninfected
- GSM8011778 EAhy926_sgGRK4_infected_rep2 EAhy926_sgGRK4_infected
- GSM8011779 EAhy926_uninfected_rep1 EAhy926_uninfected
- GSM8011780 EAhy926_sgLRRC34_infected_rep1 EAhy926_sgLRRC34_infect…
- GSE305224 Covalent pan-TEAD inhibitors block YAP activity and demonstrate brain penetrance in Hippo-dependent cancer models [RNA-seq] 120 samples shares activity, rna-seq
- GSE286949 Neuronal hyperactivity becomes mTORC1 independent due to epigenetic changes in Tuberous Sclerosis Complex [RNA-seq] 96 samples shares activity, rna-seq
- GSE227973 MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells [RNA-seq] 21 samples shares activity, rna-seq
- GSE238112 ABI1 regulates transcriptional activity of Androgen Receptor by novel DNA and AR binding mechanism [RNA-seq] 18 samples shares activity, rna-seq
- GSE229736 Therapy Induced Senescence Promotes Immunogenicity in Acute Myeloid Leukemia through Reduced EZH2 Activity (RNA-seq AraC) 12 samples shares activity, rna-seq
- GSE300083 The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma [RNA-Seq] 12 samples shares activity, rna-seq
- GSE279480 Longitudinally stable T cell and innate immune activity distinguish healthy adult immunotypes I 1021 samples shares activity
- GSE279552 Longitudinally stable T cell and innate immune activity distinguish healthy adult immunotypes [II] 864 samples shares activity
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.