Gene expression changes of CRISPR/Cas13d-mediated HoxB13 knockdown in 293FT cells and LNCaP95 mouse liver metastasis
RNA-seq (gene expression) · human · 14 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
- 14 samples: 10 distinct titles, 2 of them repeatedGroups 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
- SCORT-Cas13d Nanotherapy Precisely Targets the 'Undruggable' Transcription Factor HoxB13 in Metastatic Prostate Cancer In VivoAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
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 GSE264062_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 PRJNA1100904 and SRA study SRP502003. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 4 as controls.
How we read this: Read from 14 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.
- GSM8209443 293FT_gCtrl_rep1 24h
- GSM8209444 293FT_gCtrl_rep2 24h
- GSM8209445 293FT_gCtrl_rep3 24h
- GSM8209446 293FT_gCtrl_rep4 24h
- GSM8209447 293FT_gHoxB13_rep1 24h
- GSM8209448 293FT_gHoxB13_rep2 24h
- GSM8209449 293FT_gHoxB13_rep3 24h
- GSM8209450 293FT_gHoxB13_rep4 24h
- GSM8209451 LNCaP95_mouse liver metastasis-gCtrl-1
- GSM8209452 LNCaP95_mouse liver metastasis-gCtrl-2
- GSM8209453 LNCaP95_mouse liver metastasis-gCtrl-3
- GSM8209454 LNCaP95_mouse liver metastasis-gHoxB13-1
- GSM8209455 LNCaP95_mouse liver metastasis-gHoxB13-2
- GSM8209456 LNCaP95_mouse liver metastasis-gHoxB13-3
- GSE268709 Transcriptomic changes in HT29 cells and a patient-derived CRC 3D model after CRISPRi-based KAT2A knockdown 12 samples shares crispr, knockdown, changes
- GSE181389 Transcriptome profiling of HOXA13 and HOXB13 expression knockdown in bladder cancer cell lines. 59 samples shares hoxb13, knockdown
- GSE295649 In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [RNASeq_knockdown] 15 samples shares crispr, knockdown
- GSE296250 Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis 43 samples shares hoxb13, metastasis
- GSE317890 Transcriptomic profiling of interferon responses induced by IVT sgRNAs in CRISPRi HEK293T cells 360 samples shares crispr
- GSE271359 Identifying modulators of inflammation in an in vitro airway epithelial inflammation model using an arrayed CRISPRi screen 186 samples shares crispr
- GSE224986 Single-cell CRISPRi screens of breast cancer associated enhancers 94 samples shares crispr
- GSE298803 ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC [CRISPRi RNA-seq] 70 samples shares crispr
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.