12214 results for "cancer rna-seq"

in 26.19 milliseconds.

• Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers

  Background The encoding of cell intrinsic drug resistance states in breast cancer reflects the contributions of genomic and non-genomic variations and requires accurate estimation of clonal fitness from co-measurement of transcriptomic and genomic data. Somatic copy number (CN) variation is the dominant mutational mechanism leading to transcriptional variation and notably contributes to platinum chemotherapy resistance cell states. Here, we deploy time series measurements of triple negative breast cancer (TNBC) single-cell transcriptomes, along with co-measured single-cell CN fitness, identifying genomic and transcriptomic mechanisms in drug associated transcriptional cell states. Results We present scRNA-seq data (53,641 filtered cells) from serial passaging TNBC patient-derived xenograft (PDX) experiments spanning 2.5 years, matched with genomic single-cell CN data from the same samples. Our findings reveal distinct clonal responses within TNBC tumors exposed to platinum. Clones with high drug fitness undergo clonal sweeps and show subtle transcriptional reversion, while those with weak fitness exhibit dynamic transcription upon drug withdrawal. Pathway analysis highlights convergence on epithelial-mesenchymal transition and cytokine signaling, associated with resistance. Furthermore, pseudotime analysis demonstrates hysteresis in transcriptional reversion, indicating generation of new intermediate transcriptional states upon platinum exposure. Conclusions Within a polyclonal tumor, clones with strong genotype-associated fitness under platinum remained fixed, minimizing transcriptional reversion upon drug withdrawal. Conversely, clones with weaker fitness display non-genomic transcriptional plasticity. This suggests CN-associated and CN-independent transcriptional states could both contribute to platinum resistance. The dominance of genomic or non-genomic mechanisms within polyclonal tumors has implications for drug sensitivity, restoration and re-treatment strategies.

  Study EGAS00001007242

• Single cell RNAseq of PDAC organoids

  To study the role of WNT7B, three organoid lines were sequenced using SORT-Seq

  Study EGAS50000001544

• Patient data used in FLTseq paper

  Apply newly developed FLT-seq protocol and package FLAMES on a primary patient sample

  Study EGAS00001005597

• EM-seq converted WGS for CSF-derived cfDNA from pediatric brain tumor patients

  EM-seq converted WGS for CSF-derived cfDNA from pediatric brain tumor patients

  Dataset EGAD50000001975

• Reference epigenome DB31_N_Alpha_mRNA-Seq data generated from KEP study

  A DB31_N_Alpha_mRNA-Seq paired end data for alpha cells(PSA-NCAM(-), pancreas)

  Dataset EGAD00001003485

• Reference epigenome DB31_N_Alpha_smRNA-Seq data generated from KEP study

  A DB31_N_Alpha_smRNA-Seq single end data for alpha cells(PSA-NCAM(-), pancreas)

  Dataset EGAD00001003494

• Reference epigenome ADMSC01_smRNA-Seq data generated from KEP study

  A ADMSC01_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003867

• Reference epigenome ADMSC02_smRNA-Seq data generated from KEP study

  A ADMSC02_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003868

• Reference epigenome ADMSC03_smRNA-Seq data generated from KEP study

  A ADMSC03_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003869

• ChIP-Seq files for RMS.

  ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".

  Dataset EGAD00001004312

• BLUEPRINT Bisulfite-seq and Whole Genome Sequencing of mantle cell lymphoma

  BLUEPRINT Bisulfite-seq and Whole Genome Sequencing of mantle cell lymphoma

  Dataset EGAD00001001892

• 4C-Seq datasets of EndoC-bh1

  2 Circular chromosome conformation capture (4C-Seq) datasets of the human beta cell line EndoC-bh1.

  Dataset EGAD00001005210

• Reference epigenome IPS-NPC02 h3k36me3 ChIP-Seq data generated from KEP study

  IPS-NPC02 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007286

• Reference epigenome IPS-NPC02 h3k4me1 ChIP-Seq data generated from KEP study

  IPS-NPC02 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007287

• Reference epigenome IPS-NPC02 h3k9me3 ChIP-Seq data generated from KEP study

  IPS-NPC02 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007289

• Reference epigenome IPS-NPC02 input ChIP-Seq data generated from KEP study

  IPS-NPC02 input ChIP-Seq paired end data

  Dataset EGAD00001007290

• Reference epigenome IPS-ENeuron01 h3k27ac ChIP-Seq data generated from KEP study

  IPS-ENeuron01 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007291

• Reference epigenome IPS-ENeuron01 h3k27me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron01 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007292

• Reference epigenome IPS-ENeuron01 h3k36me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron01 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007293

• Reference epigenome IPS-ENeuron01 h3k4me1 ChIP-Seq data generated from KEP study

  IPS-ENeuron01 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007294

• Reference epigenome IPS-ENeuron01 h3k4me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron01 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007295

• Reference epigenome IPS-ENeuron01 h3k9me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron01 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007296

• Reference epigenome IPS-ENeuron01 input ChIP-Seq data generated from KEP study

  IPS-ENeuron01 input ChIP-Seq paired end data

  Dataset EGAD00001007297

• Reference epigenome IPS-ENeuron02 h3k27me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron02 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007299

• Reference epigenome IPS-ENeuron02 h3k36me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron02 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007300

• Reference epigenome IPS-ENeuron02 h3k4me1 ChIP-Seq data generated from KEP study

  IPS-ENeuron02 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007301

• Reference epigenome IPS-ENeuron02 h3k4me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron02 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007302

• Reference epigenome IPS-ENeuron02 h3k9me3 ChIP-Seq data generated from KEP study

  IPS-ENeuron02 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007303

• Reference epigenome IPS-ENeuron02 input ChIP-Seq data generated from KEP study

  IPS-ENeuron02 input ChIP-Seq paired end data

  Dataset EGAD00001007304

• Reference epigenome Pancreas-Islet02 h3k27ac ChIP-Seq data generated from KEP study

  Pancreas-Islet02 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007193

• Reference epigenome Pancreas-Islet02 h3k27me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet02 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007194

• Reference epigenome Pancreas-Islet02 h3k4me1 ChIP-Seq data generated from KEP study

  Pancreas-Islet02 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007196

• Reference epigenome Pancreas-Islet02 h3k4me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet02 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007197

• Reference epigenome Pancreas-Islet02 h3k9me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet02 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007198

• Reference epigenome Pancreas-Islet02 input ChIP-Seq data generated from KEP study

  Pancreas-Islet02 input ChIP-Seq paired end data

  Dataset EGAD00001007199

• Reference epigenome Pancreas-Islet03 h3k27ac ChIP-Seq data generated from KEP study

  Pancreas-Islet03 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007200

• Reference epigenome Pancreas-Islet03 h3k27me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet03 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007201

• Reference epigenome Pancreas-Islet03 h3k36me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet03 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007202

• Reference epigenome Pancreas-Islet03 h3k4me1 ChIP-Seq data generated from KEP study

  Pancreas-Islet03 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007203

• Reference epigenome Pancreas-Islet03 h3k4me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet03 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007204

• Reference epigenome Pancreas-Islet03 h3k9me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet03 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007205

• Reference epigenome Pancreas-Islet03 input ChIP-Seq data generated from KEP study

  Pancreas-Islet03 input ChIP-Seq paired end data

  Dataset EGAD00001007206

• Reference epigenome Pancreas-Islet04 h3k27ac ChIP-Seq data generated from KEP study

  Pancreas-Islet04 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007207

• Reference epigenome Pancreas-Islet04 h3k27me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet04 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007208

• Reference epigenome Pancreas-Islet04 h3k36me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet04 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007209

• Reference epigenome Pancreas-Islet04 h3k4me1 ChIP-Seq data generated from KEP study

  Pancreas-Islet04 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007210

• Reference epigenome Pancreas-Islet04 h3k4me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet04 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007211

• Reference epigenome Pancreas-Islet04 h3k9me3 ChIP-Seq data generated from KEP study

  Pancreas-Islet04 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007212

• Reference epigenome Pancreas-Islet04 input ChIP-Seq data generated from KEP study

  Pancreas-Islet04 input ChIP-Seq paired end data

  Dataset EGAD00001007213

• Reference epigenome Pancreas-beta01 h3k27ac ChIP-Seq data generated from KEP study

  Pancreas-beta01 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007214