Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whi3 RIP-Chip

ABSTRACT: Whi3 associated mRNAs were identified by immunoprecipitation of TAP-tagged Whi3 followed by microarray analysis RNA IP of Whi3-TAP and Whi3-dRRM-TAP with total RNA as reference. Each sample has 2 replicates

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Ying Cai

PROVIDER: E-GEOD-51784 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAi profiling to identify RNAs bound to Whi3 and Whi4 in budding yeastá

Project description:Identification of RNAs bound to Whi3 and Whi4. Mock experiment and several other proteins (Dpm1 and Sfb3) were used as controls. TAP versions of the proteins were used for affinity purification. RNAs retained in the columns were identified by microarray hybridizations.

2008-08-05 | E-MEXP-1734 | biostudies-arrayexpress

Whi3 RIP-Chip

Project description:Whi3 associated mRNAs were identified by immunoprecipitation of TAP-tagged Whi3 followed by microarray analysis

2013-10-31 | GSE51784 | GEO

Identification and functional characterization of proteins interacting with cohesin complex in yeast Saccharomyces cerevisiae.

Project description:To ensure equal separation of DNA, sister chromatids are held together from S phase to metaphase–anaphase transition by a multiprotein complex called cohesin. This makes it possible to establish chromosome biorientation, counteracts the pulling force of mitotic spindle microtubules, preventing premature sister chromatid separation, and ensures precise segregation of sister DNAs into daughter cells In order to better understand how the sister chromatid cohesion process is regulated we looked for new cohesin interacors. We constructed a yeast strain endogenously expressing TAP-tagged Scc1 (Scc1-TAP). Next, we performed a single-step TAP purification using an untagged strain (mock sample) or a strain expressing Scc1-TAP, followed by identification of co-purifying proteins by MS.

2023-10-24 | PXD037034 | Pride

CEP215_gallus_interactome - A CEP215-HSET complex links centrosomes with spindle poles and drives centrosome clustering in cancer

Project description:To establish the molecular basis for CEP215 function in centrosome-spindle pole attachment, we employed an unbiased proteomic approach to isolat e and identify CEP215 interactors. To this end, affinity purification tags ( Gs TAP containing protein G and streptavidin-binding protein) were inserted in-frame into both alleles of the CEP215 gene (CEP215-TAP cell line) in the chicken B cell line, DT40. Following affinity purification, protein complexes were analysed by mass spectr ometry

2016-03-31 | PXD003382 | Pride

Transcription profiling of S. cerevisiae to identify Upf1p-associated transcripts in S. cerevisiae

Project description:The goal of this experiment was to identify transcripts associated with the S. cerevisiae Upf1 protein. Experiment Overall Design: The RNA population from four independent pairs of Upf1p-TAP and mock affinity selections were analyzed by using Affymetrix Yeast Genome S98 Arrays.

2008-06-16 | E-GEOD-9486 | biostudies-arrayexpress

Trancriptome-wide association of Not1and Polysomal occupancy in wt and not5 background

Project description:The following data contains sequencing files for RNA IP and Polysome profiling experiments in wt and not5delta strains with background of Not1-TAP tagged strain (MAT_ leu2_20 ura3_ met15_ lys2_ his3delta1 not1::NOT1-Tap-tag-URA3). The RNA IP experiments have been performed as described previously (Gupta et al 2014) and the Polysome profiling experiments have been performed as described in (Albanese 2010). The libraries have been sequenced using polyadenylation isoform specific profiling protocol. The Not1 RIP experiments demonstrate genome-wide association of RNA with the central essential scaffold of the Ccr4-Not complex. The same RIP experiment in the not5delta background demonstrates the specificity of not5 in determining Not1 binding specificity to pulled down RNA. The polysome profiling experiments demonstrate the role of not5 in determining the translatability of ribosomal RNA.

2015-12-19 | E-MTAB-3195 | biostudies-arrayexpress

ChIP-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to investigate histone modification changes during cell cycle progression of human embryonic stem cells (hESCs) during definitive endoderm differentiation. For this, FUCCI hESCs were sorted in Early G1 (EG1), and differentiation into endoderm was performed for up to 72 hours with a combination of cytokines as described in Pauklin and Vallier (2013) and Pauklin et al. (2016). ChIP-seq was generated at 12-hour and 36-hour time-points for H3K4me3, H3K27ac, H3K4me1, H3K36me3 and H3K27me3. Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility on Illumina HiSeq 2000, 2 x 75bp paired-end reads. ChIP-seq data from other time-points (0h, 24h, 48h and 72h) of the same experimental set-up is available elsewhere (GEO DataSet, accession PRJNA593217). All processed ChIP-seq data is publicly available at http://ngs.sanger.ac.uk/production/endoderm

2020-09-07 | E-MTAB-9276 | biostudies-arrayexpress

ChIP-chip from HEK293-RPF-1 stable transfectants expressing the HA-tagged RPF-1 transcription factor

Project description:RPF-1 binds promoters of genes modulated by its induction in HEK/RPF-1 transfectant Chromatin IP (ChIP) combined to chromatin array analysis (ChIP-chip) shows that RPF-1 transcription factor bind to promoter elements of genes repressed or activated by RPF-1 expression Comparison of cells induced for RPF-1 expression (Tet-) over uninduced control cells (Tet+)

2016-09-06 | E-GEOD-55270 | biostudies-arrayexpress

Dynamic binding of RBPJ is determined by Notch signalling status

Project description:Notch signalling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to a neighbouring cell. The DNA-binding protein RBPJ is the principle effector of this pathway in mammals and together with the transcription factor moiety of Notch (NICD) it regulates the expression of target genes. The prevalent view presumes that RBPJ statically occupies consensus binding sites while exchanging repressors for activators in response to NICD. We present the first specific RBPJ chromatin immunoprecipitation and high-throughput sequencing study in mammalian cells. To dissect the mode of transcriptional regulation by RBPJ and identify its direct targets, whole genome binding profiles were generated for RBPJ, its coactivator p300, NICD and the histone H3 modifications H3K4me3, H3K4me1 and H3K27ac in myogenic cells under active or inhibitory Notch signalling conditions. Our results demonstrate dynamic binding of RBPJ in response to Notch activation at essentially all sites co-occupied by NICD. Additionally, we identify a distinct set of sites where RBPJ recruits neither NICD nor p300, and binds DNA statically, irrespective of Notch activity. These findings significantly modify our views on how RBPJ and Notch signalling mediate their activities and consequently impact on cell fate decisions. ChIP (chromatin immunoprecipitation) is followed by deep sequencing to generate genome-wide patterns of RBP-J binding in mouse C2C12 cells under various conditions. Cells were either Notch activated by exposure to immobilized ligand or by overexpression of NICDGFP, or Notch inhibited by treatment with DAPT. Notch activation and inhibition treatments were applied for 6h and 24h. In addition to RBP-J, p300 and NICDGFP were profiled by ChIP-Seq and gene expression was assessed by RNA-Seq.

2013-05-13 | E-GEOD-37184 | biostudies-arrayexpress

Interacting partners of Trypanosoma brucei RBSR1 and RBSR2

Project description:Affinity purification of RBSR1 and RBSR2 endogenously tagged with TAP at the C terminal. A cell line with inducible G-TAP was used as negative control. 3 biological replicates were used for RBSR1 and RBSR2 and 3 technical replicates for GFP

2022-10-15 | PXD033509 | Pride

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