Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of MEIS2 binding sites through ChIP-seq in the neuroblastoma Kelly and BE(2)-C cell lines.

ABSTRACT: In total, 100x106 SK-N-BE(2)-C and Kelly neuroblastoma cells were processed for ChIP-sequencing. Briefly, pellets were prepared by fixing cells in 1% formaldehyde for 15 minutes, and quenching in 1M Tris pH 7.5. Nuclei were prepared using the Sigma Nuclei Isolation Kit (#NUC-101), and sonicated using a Branson digital sonifier as previously. Antibodies to MEIS2 were from Sigma Aldrich (HPA003256). ChIP-seq libraries were prepared using the KAPA HyperPrep ChIP library kit following the manufacturer’s settings, and were sequenced on an Illumina NextSeq 500 machine.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Sarah-Lee Bekaert

PROVIDER: E-MTAB-10620 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene Expression Analysis of the Neuroblastoma Kelly Cell Line

Project description:Gene expression profililing of the MYCN-amplified Kelly cell line

2011-06-18 | E-MEXP-3121 | biostudies-arrayexpress

Transcription profiling by array of human Kelly cells following transfection with PremiR to miR542-5p compared to a negative control

Project description:Gene expression profiling of Kelly cells following transfection with PremiR to miR542-5p compared to negative control

2011-02-01 | E-MEXP-2895 | biostudies-arrayexpress

Transient expression of CHD5 in KELLY cells

Project description:Loss of the tumor suppressor CHD5 frequently occurs during neuroblastoma progression. We used microarray analyses to identify genes that change expression following transient transfection of human CHD5 into KELLY cells KELLY cells were transiently transfected with the human CHD5 cDNA or the empty vector. RNA was extracted and hybridized on Affymetrix microarrays

2014-09-23 | E-GEOD-59899 | biostudies-arrayexpress

Differential gene expression in neuroblastoma cells after transfection with control siRNA, N-Myc siRNA-1, N-Myc siRNA-2, lncMycN siRNA-1 or lncMycN siRNA-2

Project description:N-Myc oncoprotein induces neuroblastoma by modulating gene transcription, and long noncoding RNAs exert biological effects by regulating gene expression. We analysed whether N-Myc and the long noncoding RNA lncMycN mediate the expression of common subsets of genes. Neuroblastoma Kelly cells were transfected with control siRNA, N-Myc siRNA-1, N-Myc siRNA-2, lncMycN siRNA-1 or lncMycN siRNA-2. RNA was extracted from the cells 48 hours after siRNA transfections, and subjected to differential gene expression studies with Affymetrix microarrays.

2015-03-31 | E-GEOD-50959 | biostudies-arrayexpress

Ian George Kelly

Project description: Not available

| S-EPMC521632 | biostudies-literature

Proteogenomics analysis reveals specific genomic orientations at distal regulatory regions composed by non-canonical histone variants

Project description:Histone variants (H3.1, H3.3, H2A, and macroH2A) were studied about their proteomic and genomic distribution in Hela cells HeLa S3 cells stably expressing either FLAG-tagged H3.1, and H3.3 were grown in suspension in Joklik media containing 10% newborn calf serum (Hyclone), 1% GlutaMAX (Invitrogen), and 1% penicillin-streptomycin, and cells were harvested at log phase. Nuclei were isolated, mononucleosomes were subsequently obtained from these cell lines. Cells were lysed in hypotonic TMSD buffer to isolate nuclei, which were then digested with micrococcal nuclease. The resulting mononucleosomes were immunoprecipitated with anti-FLAG M2-agarose beads (Sigma) and eluted with FLAG peptide (Sigma)

2015-12-22 | E-GEOD-64652 | biostudies-arrayexpress

ChIP-seq for RFX1

Project description:Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the ‘histone code’. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RFX1 in hMDMs cells.

2023-11-08 | GSE210668 | GEO

Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS

2022-11-03 | GSE216732 | GEO

Decoding the protein composition of whole nucleosomes with Nuc-MS

2021-04-20 | GSE149484 | GEO

ChIP-chip by array of Arabidopsis endosperm nuclei expressing a PHE1::PHE1-GFP reporter using H3K27me3 and IgG antibodies

Project description:ChIP was performed using chromatin from sorted endosperm nuclei expressing a PHE1::PHE1-GFP reporter. The following antibodies were used: anti H3K27me3 (Millipore, cat. 07-449) and IgG (Sigma I50006).

2010-12-14 | E-TABM-1008 | biostudies-arrayexpress

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