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TranscriptomicsSingle cell long read genotyping of transcripts reveals discrete mechanisms of clonal evolution in post-MPN AML
Myeloproliferative neoplasm (MPN) or post-MPN acute myeloid leukemia patient bone marrow aspirates were sorted for CD34+ hematopoietic stem and progenitor cells (HSPCs), followed by 10x 3' single cell RNA sequencing and long read sequencing to study the consequences of mutation combination on HSPCs.
ORGANISM(S): Homo sapiens 
2026-06-25 | E-MTAB-15981 | biostudies-arrayexpress
TranscriptomicsGlucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania
Some T's in nuclear DNA of trypanosomes and Leishmania are hydroxylated and glucosylated to yield base J (?-D-glucosyl-hydroxymethyluracil). In Leishmania about 99% of J is located in telomeric repeats. We show here that most of the remaining J is located at chromosome-internal RNA Polymerase II ter...
ORGANISM(S): Leishmania major 
2011-10-15 | E-GEOD-32976 | biostudies-arrayexpress
Metabolomics3D DESI mass spectrometry imaging of 51 serial sections from a human liver metastasis
51 serial sections from a single human liver metastasis are made available in this dataset. Four neighbouring sections were placed on a single slide and analysed together. The tissue sections were analysed by desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) according to the pr...
2016-04-28 | MTBLS282 | MetaboLights
Metabolomics3D DESI mass spectrometry imaging of 52 serial sections from a human colorectal adenocarcinoma
Fifty-two serial sections from a single human adenocarcinama are made available in this dataset. Four neighbouring sections were placed on a single slide and analysed together. The tissue sections were analysed by desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) according to t...
2017-03-21 | MTBLS415 | MetaboLights
GenomicsAuthentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Whole genome sequencing (WGS) from snap-frozen oesophageal tumour tissue and germline nucleic acids isolated from peripheral blood mononuclear cells (PBMC) was performed as part of the International Cancer Genome Consortium project and OCCAMS consortium (1,2). Filtered read sequences were mapped to ...
ORGANISM(S): Homo sapiens 
2016-09-09 | E-MTAB-4600 | biostudies-arrayexpress
TranscriptomicsMapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana
We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes with...
ORGANISM(S): Arabidopsis thaliana 
2013-12-15 | E-GEOD-53322 | biostudies-arrayexpress
TranscriptomicsRNA-seq from sorted population of CD8 T cells (50 cells per sample) of human CD8 T memory stem cells (Tscm) subsets defined by surface expression of CD122 or CXCR3
Although it is recognised that CD8+ T memory stem cells (Tscm) are heterogeneous in phenotype and function, very few studies have sought to systematically examine these characteristics, particularly in human samples, as the population as a whole is rare and antigen-specific cells even more so. For e...
ORGANISM(S): Homo sapiens 
2022-03-10 | E-MTAB-10208 | biostudies-arrayexpress
TranscriptomicsmRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum
Schizophrenia (SCZ) is a common, disabling mental illness with high heritability but complex, poorly understood genetic etiology. As the first phase of a genomic convergence analysis of SCZ, we generated 16.7 billion nucleotides of short read, shotgun sequences of cDNA from post-mortem cerebellar c...
ORGANISM(S): Homo sapiens 
2009-08-29 | E-GEOD-12297 | biostudies-arrayexpress
TranscriptomicsRNA-seq of Vibrio cholerae wild-type and dbfS, dbfQ, and dbfR(D51V) mutant strains
RNA-seq was performed to characterize transcriptional changes governed by the DbfRS two-component signaling system in Vibrio cholerae. The experiment compared global gene expression in wild-type and mutant strains lacking dbfS or dbfQ, as well as a phospho-dead dbfR(D51V) variant. Cultures were grow...
ORGANISM(S): Vibrio cholerae 
2025-11-20 | E-MTAB-16165 | biostudies-arrayexpress
MetabolomicsBenchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry
Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives ...
2016-07-27 | MTBLS176 | MetaboLights
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