Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LIN-41 RIP-Seq

ABSTRACT: FLAG-GFP tagged LIN-41 was immunoprecipitated using FLAG dynabeads (Sigma) from lysates of young adult C.elegans. After washing steps, bound fraction (IP) was eluted from beads and associated RNAs were isolated by using the Pico pure RNA isloation kit (Invitrogen)

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE106814 | GEO | 2018/04/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

LIN-41 RIP-Seq

Project description:LIN-41 RIP-Seq

| PRJNA418125 | ENA

BRD4 regulates the osteogenic differentiation of MSCs

Project description:MSCs were lysed in cell lysis buffer for Western blotting and IP (Beyotime, Cat. No. P0013). A Dynabeads™ protein G immunoprecipitation kit (Invitrogen, Cat. No. 10007D) was used for Co-IP according to the manufacturer’s instructions. Dynabeads were resuspended and placed on a magnet to remove the supernatant then incubated with Ab Binding & Washing Buffer containing an anti-BRD4 antibody for 10 min at room temperature with rotation. The supernatant was removed by placing tubes on a magnet, and the Dynabeads-antibody complex was washed with Ab Binding & Washing Buffer. MSC lysates were added to the Dynabeads-antibody mixture and incubated for 10 min at room temperature with rotation. The supernatant was removed, the Dynabeads-antibody complex mixture was washed with washing buffer, and the proteins were separated using a standard SDS–PAGE system.

2022-06-16 | PXD034615 | iProX

RNA immunoprecipitation (RIP)-Chip analysis for EWS-bound mRNA

Project description:Although EWS/FLI-1 fusion protein is responsible for most EwingM-bM-^@M-^Ys sarcoma family tumors (ESFT), the function of native EWS remains largely unknown. Here, we first showed that EWS repressed protein expression in a tethering assay. mRNAs bound to EWS were determined by RNA-immunoprecipitation Chip assay, and one of them, proline-rich Akt substrate of 40 kDa (PRAS40) mRNA, directly interacted with EWS. The inhibitor of AKT, API-2, repressed ESFT cell proliferation. We demonstrate that EWS negatively regulated PRAS40 protein expression through binding to PRAS40 3M-bM-^@M-^YUTR. Furthermore, PRAS40 knockdown inhibited the proliferation and metastatic potential of ESFT cells. Cytoplasmic lysates or whole cell lysates were prepared from HeLa S3 cells transfected with pFLAG-EWS , and incubated with anti-FLAG M2 Affinity Gel (Sigma) at 4M-BM-0C for 2 h. RNAs from lysates and immunoprecipitates were analysed using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).

2012-01-16 | E-GEOD-29313 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RIP-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins (YBPs) in C. elegans. YBPs in other organisms are known RNA-binding proteins. Our global analysis of associated mRNAs supports a role of YBPs as general mRNA binders in C.elegans. FLAG IPs were performed on transgenic animals expressing FLAG-tagged versions of either CEY-1, CEY-2, or CEY-4. MYC IPs served as controls. All IPs were performed in duplicates. 12 samples in total.

2015-01-08 | E-GEOD-62856 | biostudies-arrayexpress

sox6 interacting protiens identification

Project description:Dynabeads Protein A (Invitrogen) were prepared according to the manufacturer’s protocol. The nuclear lysates were incubated with DynaBeads Protein A coated with appropriate antibodies for 4 hours at 4°C. After washing the beads for 5 times in wash buffer (PBST) to remove non-specific proteins, the beads-bound proteins were analysed by mass spectrometry.

2020-12-17 | PXD016780 | JPOST Repository

IRF3-binding RNA RIP-seq

Project description:Flag-taged IRF3-binding RNAs were analyzed by imprinting RNA-sequencing of anti-flag antibody-retrieved complexes from macrophages lysate.

2021-11-09 | GSE138699 | GEO

GOT2 binding RNA RIP-seq

Project description:Flag-taged GOT2 binding RNAs were analyzed by imprinting RNA-sequencing of Flag antibody-retrieved complexes from MEF cells lysis.

2017-12-14 | GSE100229 | GEO

Genome-wide identification of CCA1-bound genes in Arabidopsis by ChIP-Seq

Project description:LHY and CCA1 encode single MYB transcription factors, involved in circadian clock. However, direct target genes of LHY and CCA1 in a genomic scale were largely unknown. To reveal bound genes by CCA1, chimeric protein CCA1-FLAG was expressed under CCA1 promoter in cca1 lhy (CCA1pro:CCA1-FLAG/ cca1 lhy). ChIP was performed using anti-FLAG antibody (F3165; SIGMA), which was bound to Dynabeads Protein G (100-03D; Life Technologies), and ChIP DNA were analyzed by IonPGM or Illumina GAII.

2016-03-11 | GSE67903 | GEO

Genome-wide maps of PRR5 binding loci in Arabidopsis thaliana

Project description:PRR5 transcription factor acts in the circadian clock system. To elucidate bound genes by PRR5, Chimeric protein FLAG-PRR5-GFP, was expressed under PRR5 promoter in Col-0 (PRR5pro:FLAG-PRR5-GFP/prr5). ChIP was performed using anti-GFP antibody (ab290;Abcam), which was bound to Dynabeads Protein G (100-03D;Life technologies), and ChIP DNA and input DNA were analyzed by Illumina GA II.

2012-09-20 | GSE36361 | GEO

Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [BEND2_ChIPseq]

Project description:To characterize BEND2-binding sites on the genome, we conducted ChIP-seq analyses by using testicular lysates from FLAG-BEND2 KI mice. We found BEND2 preferentially binds to simple sequence repeats.

2022-06-01 | GSE189594 | GEO

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