Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ago2-bound ShortRnas in HCT116 cell line and Dicer_hypomorphic(DICER_Ex5 cells) HCT116 cell line

ABSTRACT: DICER_Ex5 cells were created by disrupting exon 5 of the human Dicer gene using an AAV targeting construct, thereby interrupting a well conserved segment of the N-terminal helicase domain while sparing the RNase III domains. In DICER_Ex5 cells, Dicer is expressed at a level lower than the wild type. This experiment started with RIP-anti-Ago2 pull-down, followed by high throughput sequencing analysis in wild type and Dicer-hypomorphic HCT116 cell lines.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-2056 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Ago2-bound short RNAs in HeLaS3 cell line

Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of HeLaS3 cell line. Nuclei were isolated from HeLaS3 cells; a fraction of Nuclear lysates was harvsted and sequenced as the 'input' samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2084 | biostudies-arrayexpress

AGO2 bound short RNAs in Jurkat cell line

Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of Jurkat cell line. Nuclei were isolated from cells; a fraction of Nuclear lysates was harvested and sequenced as the input samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2104 | biostudies-arrayexpress

Ago1-bound short RNAs in HeLaS3 cell line

Project description:Characterization of AGO1 bound short RNAs from nuclear extracts of HeLaS3 cell line. Nuclei were isolated from HeLaS3 cells; a fraction of Nuclear lysates was harvsted and sequenced as the input samples. The rest of nuclear lysates were immunoprecipitated using AGO1 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO1 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2129 | biostudies-arrayexpress

Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines

Project description:Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines RIP-seq with multiple antibodies to two proteins in two Drosophila cell lines, at least 2 replicates for each IP and input

2014-07-29 | E-GEOD-55894 | biostudies-arrayexpress

Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. Three replicates of Su(Hw), dCTCF, and CP190 ChIP-chip experiments in both Kc and Mbn2 cells as well as two replicates of BEAF ChIP-chip experiments in both Kc and Mbn2 cells were compared.

2010-05-19 | E-GEOD-15661 | biostudies-arrayexpress

Insulator protein binding profiles and gene expression analysis of Drosophila melanogaster Kc and Mbn2 cell lines

Project description:This SuperSeries is composed of the following subset Series: GSE15660: Gene Expression analysis of Kc and Mbn2 cell lines from Drosophila melanogaster. GSE15661: Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells (Set1) GSE15662: Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells (Set2) GSE15663: Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells (Set3) Refer to individual Series

2010-05-19 | E-GEOD-15664 | biostudies-arrayexpress

Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi

Project description:A variety of small RNAs, including the Dicer-dependent miRNAs and the Dicer-independent Piwi-interacting RNAs, associate with Argonaute family proteins to regulate gene expression in diverse cellular processes. These two species of small RNA have not been found in fungi. Here, by analyzing small RNA associated with the Neurospora Argonaute protein QDE-2, we show that diverse pathways generate miRNA-like small RNAs (milRNAs) and Dicer-independent small interfering RNAs (disiRNAs) in this filamentous fungus. Surprisingly, milRNAs are produced by at least four different mechanisms that use a distinct combination of factors, including Dicers, QDE-2, the exonuclease QIP and an RNAse III domain-containing protein MRPL3. In contrast, disiRNAs originate from loci producing overlapping sense and antisense transcripts, and do not require the known RNAi components for their production. Taken together, these results uncover several pathways for small RNA production in filamentous fungi, shedding light on the diversity and evolutionary origins of eukaryotic small RNAs. One small RNA library was generated using QDE-2 immunoprecipitate from Neurospora crassa.

2010-07-01 | E-GEOD-21175 | biostudies-arrayexpress

CDK8 ChIP-seq from HCT116 cells in normoxia and hypoxia

Project description:To test if CDK8 acts directly at HIF1A target genes, we performed ChIP-seq experiments in HCT116 cells under normoxic and hypoxic conditions. ChIP-seq for CDK8 versus Input under normoxia and 24hrs hypoxia (1% O2).

2013-03-01 | E-GEOD-38258 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells

Project description:Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B. Examination of 4 different insulator proteins at 3 time points of ecdysone treatment.

2011-10-13 | E-GEOD-30740 | biostudies-arrayexpress

Two isoforms of Fs(1)h ChIP-seq

Project description:ChIP-seq was performed using Drosophila Kc167 cells using antibodies against the two isoforms of Fs(1)h, the Brd4 homologue. Differences in binding patterns between the two isoforms are described. We examined the differences in Fs(1)h isoform binding across the genome and describe the short isoform to be correlated with transcription at enhancers and promoters. The long isoform is found predominately at insulator binding sites where multiple insulators are bound.

2012-11-15 | E-GEOD-42086 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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