GEO DataSets

(Submitter supplied) To address how intratumoral heterogeneity affects anti-cancer drug responses, we profiled transcriptomes of single cancer cells originating from lung adenocarcinoma patient-derived xenograft (PDX) tumors.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

208 Samples

Download data: TXT

(Submitter supplied) PURPOSE: Although epidermal growth factor receptor (EGFR) mutated adenocarcinomas initially have very high response rates to EGFR tyrosine kinase inhibitors (TKIs), most atients eventually develop resistance. Patient derived xenografts (PDXs) are considered preferred preclinical models to study the biology of patient tumors. EGFR-mutant PDX models may be valuable tools to study the biology of these tumors and to elucidate mechanisms of resistance to EGFR-targeted therapies. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platform:

GPL14951

25 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27467 GPL28146

6 Samples

Download data: TXT

(Submitter supplied) To identify the therapeutic targets in a treatment-refractroy cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27467

3 Samples

Download data: TXT

(Submitter supplied) To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28146 GPL27467

3 Samples

Download data: TXT, XLSX

(Submitter supplied) A major impediment to the effective treatment of patients with PDAC (Pancreatic Ductal Adenocarcinoma) is the molecular heterogeneity of the disease, which is reflected in an equally diverse pattern of clinical responses to therapy. We developed an efficient strategy in which PDAC samples from 17 consecutively patients were obtained by EUS-FNA or surgery, their cells maintained as a primary culture and tumors as breathing tumors by xenografting in immunosuppressed mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

34 Samples

Download data: CEL

(Submitter supplied) Global gene expression data were generated from cultured non small cell lung cancer cell lines (NSCLC), normalized using MAS 5.0, filtered and used to predict response of cells to EGFR inhibition

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

48 Samples

Download data: CEL

(Submitter supplied) Mice bearing a G12D activating mutation in Kras consistently develop lung adenocarcinomas in a manner analogous to humans. By performing small and large RNA sequencing on KrasG12D tumors from F1 hybrid mice we were able to identify genes and microRNAs differentially expressed in these tumor samples. Quantification of reads that cover single nucleotide polymorphisms that distinguish between the parental mouse strains enabled an analysis of allele specific expression and imprinting status in these tumors.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13112 GPL9250

12 Samples

Download data: TXT

(Submitter supplied) Brain metastases are highly resistance to chemotherapy and have a poor prognosis for cure. Tumor cells are surrounded by activated astrocytes and exploit their cyto-protective properties for protection from apoptosis induced by chemotherapy. The mechanism by which astrocytes protect tumor cells is poorly understood. An important non-mutational mechanism of chemotherapy resistance is regulation of gene translation mediated by small non-coding RNAs (sRNAs), in particular, microRNAs (miRNAs). more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

6 Samples

Download data: CEL

(Submitter supplied) We employed ChIP-seq to detect poised and active chromatin regions in cisplatin sensitive and resistant head neck squamous cell carcinoma patient derived primary and lymph node cell lines.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

17 Samples

Download data: WIG

(Submitter supplied) We employed Single cell RNA-seq to identify the transcriptome of cisplatin sensitive, resistant and drug-holiday cells from patient-derived OSCC cells isolated from primary and metastatic sites.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1431 Samples

Download data: TXT

(Submitter supplied) Purpose: Malignant ascites is an abnormal accumulation of fluid within the peritoneal cavity, caused by metastasis of several cancer types including colorectal cancer. Cancer cells in ascites reflect poor prognosis and can be a source of recurrence. They also represent a good source of specimens for the study of tumor heterogeneity. Single-cell RNA-sequencing (scRNA-seq) has recently emerged as a powerful tool for exploring and characterizing cellular heterogeneity in both normal tissues and cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(Submitter supplied) Primary tumors and their corresponding P2 mouse xenografts were surveyed for gene expression using the RNA-sequencing approach.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

57 Samples

Download data: TXT

(Submitter supplied) To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data. By combining allele frequency and expression magnitude deviations, HoneyBADGER is able to infer the presence of subclone-specific alterations in individual cells and reconstruct subclonal architecture. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

174 Samples

Download data: TXT

(Submitter supplied) We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas of lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

58 Samples

Download data: RDS, TXT, XLSX

(Submitter supplied) We developed 3'-TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with high throughput 3'-biased whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of 2798 Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with JAK2-V617F mutant myelofibrosis and normal controls using 3'-TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2798 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3436 Samples

Download data

(Submitter supplied) We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

458 Samples

Download data: TXT

(Submitter supplied) We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome analysis of JURKAT, SET2 and HSPCs using SMART-seq+, mRNA targeting (tSMARTseq) or TARGET-seq reveals very good correlations between methods.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

180 Samples

Download data: TXT

(Submitter supplied) We measured 720 HeLa-CCL2 cells (288 from the 9th passage, 288 from the 14th passage and 144 from the 20th passage) in this work on an Illumina HiSeq 4000 platform (sequenced by Novogene, China) for 150 bp paired-end sequencing. The protocol was based on Tang’s modification on SMART-Seq2. Single cells were captured by mouth pipette under the stereomicroscope（Nikon SZM745）and followed by the protocol. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT