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GenomicsSingle-cell DNA methylome sequencing and bioinformatic inference of epigenetic cell state dynamics
Here we describe a method for whole genome bisulfite sequencing in very small cell populations (µWGBS) and in single cells (scWGBS). Our method is optimized for profiling DNA methylation in many samples at low coverage, and we developed a bioinformatic method that uses collections of single-cell met...
ORGANISM(S): Mus musculus 
2015-02-25 | E-GEOD-65196 | biostudies-arrayexpress
GenomicsChromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks
Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ...
ORGANISM(S): Homo sapiens 
2016-06-26 | E-GEOD-81274 | biostudies-arrayexpress
TranscriptomicsSingle-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
We report the single-cell RNA-seq based identification of 6 known human islet cell types (alpha cells, beta cells, delta cells, pp cells, acinar cells and duct cells) based on the expression of known marker genes. We further assess cell type specific gene expression and suggest novel marker genes fo...
ORGANISM(S): Homo sapiens 
2016-01-05 | E-GEOD-73727 | biostudies-arrayexpress
TranscriptomicsDifferentiation and specification of resident tissue macrophages [MARS-seq]
Tissue resident macrophages are functionally diverse cells that share an embryonic mesodermal origin. However, the mechanism(s) that control their specification remain unclear. We performed transcriptional, molecular and in situ spatio-temporal analyses of macrophage development in mice. We report t...
ORGANISM(S): Mus musculus 
2016-08-08 | E-GEOD-81760 | biostudies-arrayexpress
TranscriptomicsDifferentiation and specification of resident tissue macrophages [SMART-Seq2]
Tissue resident macrophages are functionally diverse cells that share an embryonic mesodermal origin. However, the mechanism(s) that control their specification remain unclear. We performed transcriptional, molecular and in situ spatio-temporal analyses of macrophage development in mice. We report t...
ORGANISM(S): Mus musculus 
2016-08-08 | E-GEOD-81686 | biostudies-arrayexpress
TranscriptomicsDifferentiation and specification of resident tissue macrophages [ID3-KO RNA-seq]
Tissue resident macrophages are functionally diverse cells that share an embryonic mesodermal origin. However, the mechanism(s) that control their specification remain unclear. We performed transcriptional, molecular and in situ spatio-temporal analyses of macrophage development in mice. We report t...
ORGANISM(S): Mus musculus 
2016-08-08 | E-GEOD-83854 | biostudies-arrayexpress
Genomicsena-DATASET-CeMM-13-05-2016-20:41:19:139-66 - samples
Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ...
EGAD00001002110 | EGA
GenomicsEpigenome and transcriptome profiling of chronic lymphocytic leukemia patients
Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ...
EGAS00001001821 | EGA
GenomicsDAC of the chronic lymphocytic leukemia epigenome and transcriptome profiling project
Data Access Committee EGAC00001000486
EGAC00001000486 | EGA
Genomics5a9f4bd6-d795-47e9-9690-979bf5b1df6b - samples
The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samp...
EGAD00001006995 | EGA
2019 novel coronavirus infection 2019-nCoV infection coronavirus disease 2019 COVID-19 SARS-coronavirus 2 SARS-CoV-2 severe acute respiratory syndrome coronavirus 2 
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