Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [PAR-CLIP]

ABSTRACT: Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [PAR-CLIP]

PROVIDER: PRJNA474443 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7253210.fastq.gz	Fastqsanger.gz
	SRR7253211.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [PAR-CLIP]

Project description:PAR-CLIP sequencing experiments for SOX2 in HEK293T cells.

2020-01-30 | GSE115273 | GEO

Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [RNA-Seq]

Project description:Total RNA was extracted at different stages of somatic cell reprogramming of OG2-MEFs to induced pluripotent stem cells to analyse the effect of a Sox2 mutant lacking a putative RNA binding motif on genes expression and post-transcriptional processing

2020-01-30 | GSE115451 | GEO

Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif

Project description:Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif

| PRJNA475049 | ENA

Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [RNA-Seq]

Project description:Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [RNA-Seq]

| PRJNA475064 | ENA

Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-01-29 | GSE115452 | GEO

Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs

Project description:We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis. To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP. After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE. Reads were sequenced by Illumina HiSeq. PAR-CLIP was also performed for HuR. Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).

2013-11-07 | E-GEOD-50989 | biostudies-arrayexpress

PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif [PAR-CLIP]

Project description:PAPD5 is one of the seven members of non-canonical poly(A) polymerases in human cells. There are previous reports about polyadenylation dependent degradation of pre-ribosomal RNAs and uridylation dependent degradation of histone mRNAs in vivo. In this study, we observed polyadenylation but not polyuridylation activity of PAPD5 with in vitro assays. We aimed to get genome-wide targets of PAPD5 and used PAR-CLIP and deep sequencing for this purpose. Recombinant version of PAPD5 is expressed in HEK293 human cell lines and its genome wide targets are obtained with PAR-CLIP and deep sequencing as two replicate experiments. The short reads in the deep sequencing libraries of PAPD5 replicates and an unrelated protein to polymerization from a previous study, IGF2BP1, are aligned to the hg18 human genome assembly. The biological variance of the read counts in overlapping 100-nucleotide-long-windows is estimated between the PAPD5 replicates and further used in the differential expression estimations between the 100-nucleotide windows in PAPD5 replicates and IGF2BP1. The top differentially expressed windows in PAPD5 and IGF2BP1 are further annotated using gene and repeat tracks from UCSC.

2012-04-02 | E-GEOD-36987 | biostudies-arrayexpress

PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif [PAR-CLIP]

2012-04-03 | GSE36987 | GEO

PAR-CLIP-seq of HA-METTL14 in HepG2 cells

Project description:The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. To identify METTL14 binding sites in the transcriptome, we overexpressed HA-tagged METTL14 in HepG2 cells and performed PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using HA antibody. Subsequent deep sequencing identified 5,961 METTL14 binding sites, in which the GGAC motif was enriched.

2019-02-21 | GSE121948 | GEO

Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs

2013-11-07 | GSE50989 | GEO