Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transient GFP-fused DARPin expression effects on transcription

ABSTRACT: Transient GFP-fused DARPin expression effects on transcription

PROVIDER: PRJEB51294 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR8982140.fastq.gz	Fastqsanger.gz
	ERR8982141.fastq.gz	Fastqsanger.gz
	ERR8982142.fastq.gz	Fastqsanger.gz
	ERR8982143.fastq.gz	Fastqsanger.gz
	ERR8982144.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

Transient GFP-fused DARPin expression effects on transcription

Project description:GFP-tagged DARPin F10 and CTR are expressed in A549 cells, then GFP positive cells are sorted by GFP positive with FACS. Cells are pelleted and total RNA is extracted. The aim is to check DARPin F10 effects on gene expression.

2022-03-12 | E-MTAB-11496 | biostudies-arrayexpress

Full list of co-purified proteins as determined by LC-MS/MS using transiently expressing the TaRACK1B-GFP,TaSGT1-GFP and TaHSP90-GFP fusion protein in wheat protoplasts

Project description:We immunoprecipitated exogengusly expressed TaRACK1B-GFP，TaSGT1-GFP and TaHSP90-GFP fused protein in wheat protoplasts.A high-throughput technology, LC-MS/MS, was applied to identify the candidate interacting proteins of TaRACK1B-GFP，TaSGT1-GFP and TaHSP90-GFP

2024-08-28 | PXD055046 | Pride

GFP-fused 53BP1 interacting proteins in HEK293-T cells with and without irradiation

Project description:Experiment: proteins immunoprecipitated with a GFP-fused 53BP1 fragment. Description: GFP-fused 53BP1 fragment was conditionally expressed (Tet-ON) in HEK293-T cells in duplicate. Cells were irradiated (6 Gy) or not, allowed to recover for 24 hours, cross linked with 0.05% paraformaldehyde, lysed with the EZ-ChIP lysis buffer. Lysates were incubated with anti-GFP beads, washed, and eluted by heating in Laemmli buffer. Eluents were run on an SDS-PAGE gel, lanes were cut into four equally sized sections. Sections were separately in-gel digested with trypsin. Non-Irradiated control sample was labeled with O18 by digesting in the presence of O18 water. Duplicates per section of both samples (non-irradiated and irradiated) were combined to give four samples (one per MW range section). Samples were run on the LTQ Orbitrap XL. Data were searched with Mascot (once including both O16 and O18 at the C-terminus, once allowing only O16, once allowing only O18), and analyzed in Scaffold.

2019-01-03 | MSV000083293 | MassIVE

Transient side effects of CRISPR/Cas9-VP160 for gene activation

Project description:Cas9 fused to VP16 repeats have been used in several systems of gene activation. Here we aimed to evaluate the undesirable effects of this system whether in presence or absence of gRNAS targeting a specific gene, CD34.

2021-05-21 | GSE118277 | GEO

RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

Project description:RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

| PRJNA544322 | ENA

Transient genome-wide adaptations of nascent RNAPII transcription triggered by low temperature

Project description:We determined RNA polymerase (RNAPII) transcription at single-nucleotide resolution in Arabidopsis during early stages of exposure to low temperature. Our data inform on the dynamics of RNAPII transcription and detect thousands of often short-lived uncharacterized transcripts. We demonstrate that low temperature triggers transient genome-wide effects on RNAPII activity, in particular the stalling of RNAPII at both gene ends and the distance of read-through transcription.

2019-12-11 | GSE131733 | GEO

Development of a method for quantitative analysis of in vivo interactions of pluripotency transcription factors Sox2, Oct4, Nanog by mass spectrometry

Project description:Protein-protein proximity of core pluripotency transcription factors plays an important role during cell reprogramming. Pluripotent embryonic stem (ES) cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. These proteins often bind to closely localized genomic sites. The precise mode by which Sox2, Oct4, and Nanog interact with DNA is likely to make a crucial contribution to their function. Here, a detailed protocol for in vivo detection and quantitative analysis of protein-protein proximity of Sox2 and Oct4 using Proximity Utilizing Biotinylation (PUB) method based on the use of the BAP/BirA (target/enzyme) system is described. The method includes design and cloning of DNA plasmid construct, transient transfection of HEK293T cells, Western blot analysis of nuclei fraction and LC-MS/MS analysis. Experiments with coexpression of BAP-X+BirA-Y (X, Y=Sox2, Oct4 and GFP as control) revealed strong biotinylation level of target proteins when X and Y were pluripotency transcription factors compared with control when X=GFP. Since mass spectrometry provides both high sensitivity and more accurate quantification of data a modified workflow was used, in which SDS-PAGE step was eliminated and His-tagged BAP-fused proteins from cell lysate were purified in 6M guanidine HCl buffer, washed, propionylated, digested directly on the Ni sepharose beads using trypsin and analysed on Q-TOF Impact II instrument. Using mass spectrometry allows making quantitative estimation of in vivo interaction of BAP-Sox2 and BirA-Oct4 which was demonstrated by measuring ratios of biotinylation levels of BAP fused either with Sox2 or GFP at different biotin pulse times. After vector preparation this protocol can be completed in seven working days.

2020-01-21 | PXD015756 | Pride

Insulin fused to apolipoprotein A-I

Project description:Insulin fused to apolipoprotein A-I

| PRJNA671860 | ENA

greenCUT&RUN: a rapid and efficient genome profiling approach for transcription and chromatin regulatory proteins

Project description:Chromatin modifiers, transcription factors and cofactors regulate gene expression through engagement with chromatin and DNA, which can be detected by a variety of genomic techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulatory factors, which has higher sensitivity, resolution, accuracy and reproducibility than existing methods, whilst assuring specificity as assessed for the gene specific transcription factors NFY and c-FOS, and for the basal transcription factor TBP. Our strategy begins with tagging the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. Since the nanobody targets GFP, the greenCUT&RUN approach eliminates dependency on protein-specific antibodies, which makes it widely applicable. To examine, if GFP-tagged proteins form complex with known interactors and GFP did not interfere in the formation of protein complex, mass spectrometry was performed.

2021-01-13 | PXD021089 | Pride

Transient side effects of CRISPR/Cas9-VP160 for gene activation

Project description:Transient side effects of CRISPR/Cas9-VP160 for gene activation

| PRJNA485052 | ENA