Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP (PDX samples from different disease statuses)
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: 5 × Primary vs 5 × Residual vs 5 × RelapsedGroups 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 GSE301872_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 PRJNA1287680 and SRA study SRP599006. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 3 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.
- GSM9091042 Primary-Rep1 Primary
- GSM9091043 Primary-Rep2 Primary
- GSM9091044 Primary-Rep3 Primary
- GSM9091045 Primary-Rep4 Primary
- GSM9091046 Primary-Rep5 Primary
- GSM9091047 Residual-Rep1 Residual
- GSM9091048 Residual-Rep2 Residual
- GSM9091049 Residual-Rep3 Residual
- GSM9091050 Residual-Rep4 Residual
- GSM9091051 Residual-Rep5 Residual
- GSM9091052 Relapsed-Rep1 Relapsed
- GSM9091053 Relapsed-Rep2 Relapsed
- GSM9091054 Relapsed-Rep3 Relapsed
- GSM9091055 Relapsed-Rep4 Relapsed
- GSM9091056 Relapsed-Rep5 Relapsed
- GSE301870 Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP (KHSRP knockdown in CAL-1 cells) 9 samples shares slc23a1, khsrp, therapy-persistent, selectively, restoration, vulnerable, targeting
- GSE337663 Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP (AML patient samples) 8 samples shares slc23a1, khsrp, therapy-persistent, selectively, restoration, vulnerable, targeting
- GSE228260 RNA-seq study of a helicon peptide targeting β-Catenin/TCF transcription factor [PDX] 31 samples shares pdx, targeting
- GSE261999 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1(PDX tumors) 8 samples shares pdx, targeting
- GSE266207 Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma [SSPDX.RNA-seq] 6 samples shares pdx, targeting
- GSE229230 Targeting novel m6A reader KHSRP impairs pancreatic ductal adenocarcinoma progression via attenuating FAK signaling 31 samples shares khsrp, targeting
- GSE255095 An in vivo screening platform using PDX models reveals KEAP1, USP22 and other drivers of chemoresistance in small cell lung cancer 67 samples shares pdx
- GSE245474 RFX6 Regulates Human Intestinal Patterning and Function Upstream of PDX1 55 samples shares pdx
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.