LINE-1 locus transcription nucleates oncogenic chromatin architecture [RNA-Seq]
RNA-seq (gene expression) · human · 80 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
- 80 samples: 32 conditions, mostly in duplicateGroups 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
- LINE-1 Locus Transcription Nucleates Oncogenic Chromatin ArchitectureCancer discovery · 2026
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 GSE296212_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 PRJNA1255274 and SRA study SRP582275. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 78 samples.
How we read this: 32 replicated groups read from 80 sample titles; they account for 78 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.
- GSM8967181 CaCo2_chrRNA_rep1 CaCo2_chrRNA
- GSM8967182 CaCo2_chrRNA_rep2 CaCo2_chrRNA
- GSM8967183 GM12878_chrRNA_rep1 GM12878_chrRNA
- GSM8967184 GM12878_chrRNA_rep2 GM12878_chrRNA
- GSM8967185 H460_chrRNA_rep1 H460_chrRNA
- GSM8967186 H460_chrRNA_rep2 H460_chrRNA
- GSM8967187 Huh7_chrRNA_rep1 Huh7_chrRNA
- GSM8967188 Huh7_chrRNA_rep2 Huh7_chrRNA
- GSM8967189 K562_chrRNA_rep1 K562_chrRNA
- GSM8967190 K562_chrRNA_rep2 K562_chrRNA
- GSM8967191 MCF7_chrRNA_rep1 MCF7_chrRNA
- GSM8967192 MCF7_chrRNA_rep2 MCF7_chrRNA
- GSM8967193 MDA-MB-231_chrRNA_rep1 MDA-MB-231_chrRNA
- GSM8967194 MDA-MB-231_chrRNA_rep2 MDA-MB-231_chrRNA
- GSM8967195 MOLM13_chrRNA_rep1 MOLM13_chrRNA
- GSM8967196 MOLM13_chrRNA_rep2 MOLM13_chrRNA
- GSM8967197 T47D_chrRNA_rep1 T47D_chrRNA
- GSM8967198 T47D_chrRNA_rep2 T47D_chrRNA
- GSM8967199 THP1_chrRNA_rep1 THP1_chrRNA
- GSM8967200 THP1_chrRNA_rep2 THP1_chrRNA
- GSM8967201 MCF7_LINE1_ASO1_RNA_rep1 MCF7_LINE1_ASO1_RNA
- GSM8967202 MCF7_LINE1_ASO1_RNA_rep2 MCF7_LINE1_ASO1_RNA
- GSM8967203 MCF7_LINE1_ASO1_RNA_rep3 MCF7_LINE1_ASO1_RNA
- GSM8967204 MCF7_LINE1_ASO2_RNA_rep1 MCF7_LINE1_ASO2_RNA
- GSM8967205 MCF7_LINE1_ASO2_RNA_rep2 MCF7_LINE1_ASO2_RNA
- GSM8967206 MCF7_LINE1_ASO2_RNA_rep3 MCF7_LINE1_ASO2_RNA
- GSM8967207 MCF7_SCR_ASO_RNA_rep1 MCF7_SCR_ASO_RNA
- GSM8967208 MCF7_SCR_ASO_RNA_rep2 MCF7_SCR_ASO_RNA
- GSM8967209 MCF7_SCR_ASO_RNA_rep3 MCF7_SCR_ASO_RNA
- GSM8967210 ER_tumor_patient1 ER_tumor_patient
- GSM8967211 ER_tumor_patient2 ER_tumor_patient
- GSM8967212 TNBC_tumor_patient1 TNBC_tumor_patient
- GSM8967213 TNBC_tumor_patient2 TNBC_tumor_patient
- GSM8967214 MCF7_chr_Takara_rep1
- GSM8967215 MCF7_cyto_Takara_rep1
- GSM8967216 T47D_chr_Takara_rep1 T47D_chr_Takara
- GSM8967217 T47D_chr_Takara_rep2 T47D_chr_Takara
- GSM8967218 T47D_cyto_Takara_rep1 T47D_cyto_Takara
- GSM8967219 T47D_cyto_Takara_rep2 T47D_cyto_Takara
- GSM8967220 K562_chr_Takara_rep1 K562_chr_Takara
+ 40 more — browse all 80 samples with per-sample file links →
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares architecture, chromatin, rna-seq
- GSE274546 The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X] 121 samples shares transcription, architecture
- GSE269826 Conserved patterns of transcriptional dysregulation, heterogeneity and cell states in clear cell kidney cancer [scRNA-seq] 79 samples shares transcription, rna-seq
- GSE189357 Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [scRNA-seq] 9 samples shares transcription, rna-seq
- GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares architecture, chromatin
- GSE296192 Hypoxic regulation of chromatin and gene transcription 98 samples shares transcription, chromatin
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares transcription, chromatin
- GSE273326 A trimeric USP11-USP7-TCEAL1 complex stabilizes paused RNAPII to sustain oncogenic transcription 63 samples shares transcription, oncogenic
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.