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GenomicsPantoea sp. MBD-2R isolate:MBD-2R
Pantoea sp. MBD-2R isolate:MBD-2R Genome sequencing
PRJNA1102620 | ENA
GenomicsMethyl-CpG-binding domain (MBD) sequencing of 15 primary stage 4S neuroblastoma tumors
The DNA methylome of 15 primary stage 4S neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing DNA of 15 primary stage 4S tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, libr...
ORGANISM(S): Homo sapiens 
2015-12-15 | E-GEOD-69268 | biostudies-arrayexpress
GenomicsExtra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [MBD-seq]
This dataset contains whole-genome MBD (methylbinding domain) sequencing results from cortical neuronal cultures and serves as the basis for characterization of DNA methylation profiles from neuronal systems. This experiment contains three sequencing datasets from 2 biological samples. Two datasets ...
ORGANISM(S): Rattus norvegicus 
2016-05-31 | E-GEOD-64987 | biostudies-arrayexpress
GenomicsMethyl-CpG-binding domain (MBD) sequencing of 45 primary neuroblastoma tumors
The DNA methylome of 45 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing DNA of 45 primary tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation an...
ORGANISM(S): Homo sapiens 
2015-11-19 | E-GEOD-69243 | biostudies-arrayexpress
GenomicsGenome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [MBD-Seq]
Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained. MBD-sequencing of 8 colorectal cancer cell lines.
ORGANISM(S): Homo sapiens 
2013-10-01 | E-GEOD-45333 | biostudies-arrayexpress
GenomicsQuality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing
Purpose: to compare different Methyl Binding Domain (MBD) based kits for DNA-methylation sequencing using Reduced Representation Bisulfite Sequencing (RRBS) data for validation, and to determine whether data quality can also be derived from inherent sequence data characteristics MBD-seq using 5 diff...
ORGANISM(S): Homo sapiens 
2013-01-23 | E-GEOD-42790 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human fibroblast cells transfected with a MDB-VP16 fusion to identify possible target genes for MBD1
We compared cells transfected with a MBD-VP16 fusion, with cells transfected with a control construct.
The purpose was to turn a repressor protein (MBD1) into an activator, and use differences in transcription to identify possible gene promoter targets.
A common reference was employed for all ...
ORGANISM(S): Homo sapiens 
2009-06-30 | E-MTAB-103 | biostudies-arrayexpress
GenomicsEpigenome signatures during gastric carcinogenesis based on next generation sequencing analysis [MBD-Seq]
Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing. MBD and RRBS sequencing of gast...
ORGANISM(S): Homo sapiens 
2015-09-01 | E-GEOD-55157 | biostudies-arrayexpress
GenomicsGenome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [ChIP-Seq, MBD-Seq]
Purpose: The aim of this study is (1) to identify the chromatin occupancy of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain; (2) to profile key epigenetic marks H3K4me3, H3K27me3 and DNA methylation in wild type and Smchd1 null NSCs; (3) to identify the ch...
ORGANISM(S): Mus musculus 
2015-06-11 | E-GEOD-65748 | biostudies-arrayexpress
TranscriptomicsMBD-R2(Q4167).S2
modENCODE_submission_3039 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under s...
ORGANISM(S): Drosophila melanogaster 
2011-03-09 | E-GEOD-27802 | biostudies-arrayexpress
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