Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell ATAC-Seq of Adult GBM surgical specimens

ABSTRACT: Single-cell ATAC-Seq of Adult GBM surgical specimens

PROVIDER: PRJNA578617 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10315835.fastq.gz	Fastqsanger.gz
	SRR10315835_1.fastq.gz	Fastqsanger.gz
	SRR10315835_2.fastq.gz	Fastqsanger.gz
	SRR10315836.fastq.gz	Fastqsanger.gz
	SRR10315836_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Expression data from glioblastoma surgical specimens

Project description:Expression data from glioblastoma surgical specimens

| PRJNA741898 | ENA

Single-cell ATAC-Seq of Adult GBM surgical specimens

Project description:We performed scATAC-seq on primary glioblastoma tissue samples taken at time of initial resection to map the global chromatin profiles of glioblastoma cells and associated non-neoplastic cells

2021-01-27 | GSE139136 | GEO

Genome-wide analysis of microRNA expression in surgical specimens of primary glioblastoma multiform

Project description:MicroRNA has a great potential in predicting survival of cancer patient. We used a genome-wide microRNA expression profiling to identify a miRNA signature for the prediction of clinical outcome of primary GBM patients. Total RNA obtained from 82 surgical specimens of primary glioblastoma multiform and 5 normal brain tissues from areas surrounding arteriovenous malformations (AVM) as control.

2012-07-12 | E-GEOD-25631 | biostudies-arrayexpress

DNA methylation arrays for 8 Surgical specimens (DNA extracted from FFPE slides) after cetuximab treatment

Project description:DNA methylation arrays for 8 Surgical specimens(DNA extracted from FFPE slides) after cetuximab treatment

2020-01-17 | GSE110995 | GEO

Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS)

Project description:Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. This study aims to compare genome-scale DNA methylation between core biopsies (in this GEO accession) and surgical specimens (previously published in GSE66313; see Overall Design below). Within-subject variability in DNA methylation was significantly lower than between-subject variability (all P < 2.20E-16). In 641 CpGs whose methylation was related with increased hazard of invasive breast cancer, lower within-subject than between-subject variability was observed in 92.3% of the study participants (P < 0.05). Between patient-matched core biopsy and surgical specimens, < 0.6% of CpGs measured had changes in median DNA methylation > 15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making.

2018-02-15 | GSE100503 | GEO

Genome-wide analysis of gene expression in surgical specimens of primary glioblastoma multiform

Project description:We used a genome-wide coding gene expression profiling to identify a gene signature for the molecular classification or prognostic prediction of primary GBMs. Total RNA obtained from 21 surgical specimens of primary glioblastoma multiform.

2012-07-12 | E-GEOD-25630 | biostudies-arrayexpress

Longitudinal epigenome analysis of IDH-mutant astrocytomas from initial and recurrent surgical specimens

Project description:Genome-wide DNA methylation profiling of 31 IDH-mutant astrocytoma tumor specimens, of which 14 are from initial surgical resections prior to any radiation or chemotherapy and 17 of which are from a second surgical resection at time of recurrence/progression usually following radiation and/or chemotherapy. For 7 patients (#201-#207), there are paired initial and recurrent tumor samples that were analyzed. For the remaining 17 patients, there are 7 (#208-#214) with only an initial tumor sample analyzed and 10 (#215-#224) with only a recurrent tumor sample analyzed. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of the 31 IDH-mutant astrocytomas.

2024-11-19 | GSE260850 | GEO

Expression data from breast cancer FNA and surgical specimens from patients

Project description:The behavior of breast cancers and their response to neoadjuvant systemic therapy depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell. The purpose of the analysis was to compare matched gene expression profiles of pretreatment cancer with post-neoadjuvant systemic therapy, residual cancer. Pre-treatment FNA from primary tumors or post-treatment surgical specimens were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

2012-01-17 | E-GEOD-32072 | biostudies-arrayexpress

microRNAseq of clear-cell renal cell carcinoma on surgical resection specimens of untreated primary tumors in humans

Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).

2020-07-22 | E-MTAB-9380 | biostudies-arrayexpress

Longitudinal epigenome analysis of IDH-wildtype glioblastomas from initial and recurrent surgical specimens

Project description:Longitudinal epigenome analysis of IDH-wildtype glioblastomas from initial and recurrent surgical specimens

| PRJNA1170304 | ENA