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TranscriptomicsEfficient cellular fractionation of RNA
The aim of this experiment was to develop new methods to extract pure fractions of nuclear and cytoplasmic RNA. We compared the results of nuclear and cytoplasmic RNA-sequencing to results of the total and polyA+ RNA-sequencing. Cytoplasmic, nuclear, total and polyA+ RNA was extracted from two human...
ORGANISM(S): Homo sapiens 
2013-10-22 | E-MTAB-1898 | biostudies-arrayexpress
TranscriptomicsVAPB regulates proliferation in medulloblastoma
RNA sequencing of medulloblastoma cell lines DAOY and USP13-med; wild type and VAPB KO.
ORGANISM(S): Homo sapiens 
2023-06-28 | E-MTAB-11914 | biostudies-arrayexpress
TranscriptomicsRNA-seq of human hepatic arteries in a study of primary sclerosing cholangitis
PSC is a chronic inflammatory condition of the biliary tree causing biliary strictures and fibrosis and predisposes to cholangiocarcinoma. Traditionally it is considered a primary disorder of the bile duct epithelia. Here we investigate whether injury to the arterial blood supply may contribute to P...
ORGANISM(S): Homo sapiens 
2023-07-01 | E-MTAB-11917 | biostudies-arrayexpress
TranscriptomicsRNA-seq of murine bone marrow-derived macrophages (mBMDM) of the wild type (WT) group versus the RBP-J conditionally knockout (CKO) group at 36 hours post HTNV (Hantaan orthohantavirus) infection
Total RNA was extracted from WT and RBP-JCKO mBMDMs at 36 hpi (HTMV, MOI=1), using TRIzol (Invitrogen). Ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre Biotechnologies). Fragmented RNA (the average length was approximately 200 bp) was subjected to first-strand and second-strand cDNA sy...
ORGANISM(S): Mus musculus 
2022-07-22 | E-MTAB-11926 | biostudies-arrayexpress
GenomicsWhole genome bisulfite sequencing of liver samples of five mammals (human, rhesus macaque, mouse, rat and dog)
This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and ...
ORGANISM(S): Homo sapiens 
2022-10-20 | E-MTAB-11946 | biostudies-arrayexpress
TranscriptomicsSingle cell RNA sequencing of iPSC-derived lung organoid models
Here, we used single cell RNA sequencing of iPSC17 WT 7B2-derived day 10 lung spheroids, unsorted 3-, 6-, and 10-week lung progenitor organoids (LPOs) and induced bud tip progenitor organoids (iBTOs) sorted from 4- and 10-week LPOs, sequenced 4 weeks post-sort. All cultures were grown in serum-free ...
ORGANISM(S): Homo sapiens 
2022-07-24 | E-MTAB-11953 | biostudies-arrayexpress
TranscriptomicsDifferences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China
We recruited 24 Mongolian volunteers,6 of which were T2D cases(sample T1-T6), 6 were prediabetes cases(sample P1-P6), and 12 were health cases(sample C1-C12). The metagenomic analysis of gut microbiota from the volunteers’ fecal samples was performed. We compared the microbial differences in the thr...
ORGANISM(S): Homo sapiens 
2022-07-30 | E-MTAB-11957 | biostudies-arrayexpress
TranscriptomicsDifferential gene expression profiles associated with CAIX expression in patients with ER negative breast cancer
Breast cancer is a heterogeneous disease classified into 3 major subtypes based on the presence or absence of molecular markers for oestrogen receptors (ER), progesterone receptors (PR) and human epidermal growth factor-2 (Her2) . Hormone receptor-positive BC (ER+, PR+ and Her-2-), accounts for app...
ORGANISM(S): Homo sapiens 
2023-07-31 | E-MTAB-11955 | biostudies-arrayexpress
TranscriptomicsCUT&RUN LoV-U of beta-catenin, TCF/LEF transcription factors and histone modifications in HEK293T and mouse embryonic hindlimb tissue at 11.5 days post coitum
In our attempts to profile different regulators of the WNT/b-catenin transcriptional complex, CUT&RUN failed to produce consistent binding patterns of the non-DNA-binding b-catenin. We developed a modified CUT&RUN protocol, which we refer to as LoV-U (Low Volume and Urea), that enables the generatio...
ORGANISM(S): Mus musculus 
2022-07-16 | E-MTAB-11951 | biostudies-arrayexpress
ProteomicsAntibody arrays for identification of biomarkers of Immunoglobulin A nephropathy
Immunoglobulin A nephropathy (IgAN) is the most common glomerulonephritis worldwide. However, biomarkers for predicting the progression or regression of IgAN remain a clinical challenge. In the present study, we aim to identify novel diagnostic and prognostic markers of IgAN. Using the cytokine anti...
ORGANISM(S): Homo sapiens 
2022-07-13 | E-MTAB-11972 | biostudies-arrayexpress
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