Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A0a336ba-b915-4fc1-9baa-9626ea367ce5 - samples

ABSTRACT: Single-cell RNA sequencing of 18 peripheral blood samples from six melanoma patients. The raw data is available as fastq files.

PROVIDER: EGAD00001009807 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-seq analysis of benign prostatic hyperplasia prostate specimens stratified by prostate weight

Project description:Six de-identified benign prostatic hyperplasia prostate specimens were profiled by 10x Genomics single-cell RNA-seq. Samples were stratified into Large BPH and Small BPH groups by prostate weight. Raw FASTQ files and sequencing-provider CellRanger filtered feature-barcode matrices are provided; downstream quality control, integration, annotation, and endothelial-focused analyses were performed by the authors.

2026-07-20 | GSE330752 | GEO

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (ChIP-seq)

Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.

2013-05-04 | GSE46607 | GEO

Affymetrix 250K StyI SNP array data from PBMCs and cell lines of metastatic melanoma patients

Project description:Allele call files from on 250K StyI SNP array using DNA from 60 human cell lines from metastasized melanoma and from 44 corresponding peripheral blood mononuclear cells (CEL and CHP files provided). Analysis of the 250K StyI arrays was performed for 60 malignant melanoma cell lines derived from metastatic tumors of melanoma patients with GCOS and GTYPE (Affymetrix). In addition, DNA from peripheral blood mononuclear cells (PBMC) was available for 44 of the 60 samples.

2010-04-13 | E-GEOD-17534 | biostudies-arrayexpress

Spatial transcriptomic characterization of obesity-associated gene expression programs in endometrial cancer

Project description:This study investigates spatial transcriptomic alterations associated with obesity in endometrial cancer using NanoString GeoMx Digital Spatial Profiling. Tumor samples from obese and non-obese patients were profiled to identify gene expression programs linked to metabolic and oncogenic pathways. NOTE ON RAW DATA COMPLETENESS: 4 FASTQ files (F03_S3_L003_R1, F06_S6_L003_R2, F11_S11_L004_R1, F12_S12_L002_R2) were lost due to a server crash at the USC Center for Advanced Research Computing (CARC) and could not be recovered. All remaining raw and processed data files are complete and available.

2026-05-15 | GSE330215 | GEO

Single-cell analysis of chromatin accessibility in the adult mouse brain

Project description:Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated through examination of the chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1482 distinct brain cell populations, adding over 446,000 new cCREs to the most recent such annotation in the mouse genome. Raw fastq files are demultiplexed. Out of 234 samples, fastq files for 6 samples are available in NCBI under the accession number GSE126724 (CEMBA180308_3B, CEMBA180312_3B, CEMBA180226_1A, CEMBA180227_1A, CEMBA180305_2B, CEMBA180306_2B). Processed data are SnapATAC2 (<= 2.4.0) h5ad files per sample, with raw fragments and 500-bp bmat. Important note: - Due to the break changes in SnapATAC2 >= 2.5.0, the data can not be handled rightly in SnapATAC2 >= 2.5.0. - In GSE246791_wmb_enhancer.tar.gz, the subclass-specific bedpe files can be downloaded here: https://catlas.org/catlasv1/wholemousebrain/data/pdc/.

2023-11-02 | GSE246791 | GEO

The influence of nt-LNA on cell composition and phenotypees in the atherosclerotic lesion.

Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000

2021-11-01 | GSE160791 | GEO

High-throughput RNA Sequencing of THP-1 macrophages treated with or without native LDL for 24h.

Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000

2021-11-01 | GSE160615 | GEO

The transitional cerebellar progenitor is a technical artifact driven by low-quality cells [re-analysis]

Project description:We reprocessed the raw FASTQ files from the published single-cell RNA-seq atlas of the developing human cerebellum (accession GSE198565) and, following rigorous quality control, removed low-quality cells and refined the cell-type annotations.

2025-07-30 | GSE295804 | GEO

Human melanoma cell lines treated with G007-LK

Project description:18 human melanoma cell lines were treated with G007-LK in order to investigate the effect and compare it with a similar experiment from a mouse melanoma cell line. Due to regulations regarding human data the fastq files are not provided.

2023-11-02 | E-MTAB-8438 | biostudies-arrayexpress

Integrated RNA, translation, and proteome profiling reveals midbody remnants as selectively organized signaling vesicles

Project description:This study investigates the differences in mRNA payloads between midbody remnants (MBRs) and whole cell of origin for six cell types, in order to determine type-specific and common enriched genes in MBRs. RNA-seq was performed by the Skop lab for all six cell types. Ribo-seq was performed by the Iwasaki lab on one of the cell types to assess translational differences. Data include raw FASTQ files, processed count tables, and metadata describing each sample.

2026-08-04 | GSE305263 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data