Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RIP-seq to identify transcripts interacting with pluripotency factors in mouse embryonic stem cells

ABSTRACT: RIP-seq to identify transcripts interacting with pluripotency factors in mouse embryonic stem cells

PROVIDER: PRJEB31024 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3132310.fastq.gz	Fastqsanger.gz
	ERR3132320_1.fastq.gz	Fastqsanger.gz
	ERR3132320_2.fastq.gz	Fastqsanger.gz
	ERR3132311.fastq.gz	Fastqsanger.gz
	ERR3132321_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

RIP-seq to identify transcripts interacting with pluripotency factors in mouse embryonic stem cells

Project description:Sox2 is a master transcriptional regulator of embryonic development. Having found that Sox2 interacts with RNA-binding proteins, we designed an experiment to discover RNAs associated with Sox2 and other pluripotency factors. Briefly, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) to sequence transcriptomes enriched for RNAs associated with Klf4, Nanog, Oct4, Sox2 and Suz12. For completeness, this submission includes all RIP-seq data from this study, although some of the data was only used for exploratory analyses. Such analysis indicated that it was important to include input samples for each of the the cell lines that were to be compared, to account for differences in gene expression (e.g. between J1-birA with and without bioSox2), and that overnight IP was more informative than 3 h IP. Therefore, the analysis described in the associated manuscript used samples from experiment batch 3 and 4 only (samples 11-18).

2019-02-11 | E-MTAB-7640 | biostudies-arrayexpress

RIP-seq analysis of Isw1 interacting transcripts

Project description:RIP-seq analysis of Isw1 interacting transcripts

| PRJEB14710 | ENA

Identify Flag-bound transcripts via RIP-seq

Project description:To identify the directly bound transcripts of Flag antibody (the backgroud control for our METTL16 RIP-seq), RNA immunoprecipitation sequencing (RIP-seq) was conducted HEK293T. Briefly, HEK293T cells were infected with pmiRNA1-empty vector. Only the GFP-positive cells were used for study and expanded in DMEM medium.

2021-10-28 | GSE182620 | GEO

Identify QKI7-bound transcripts via RIP-seq

Project description:Identify QKI7-bound transcripts via RIP-seq

| PRJNA793437 | ENA

Identify Flag-bound transcripts via RIP-seq

Project description:Identify Flag-bound transcripts via RIP-seq

| PRJNA757015 | ENA

Identify QKI-bound transcripts via RIP-seq

Project description:Identify QKI-bound transcripts via RIP-seq

| PRJNA794165 | ENA

Identify METTL3, 14 and 16-bound transcripts via RIP-seq

Project description:Identify METTL3, 14 and 16-bound transcripts via RIP-seq

| PRJNA659039 | ENA

Identify METTL3, 14 and 16-bound transcripts via RIP-seq

Project description:To identify the directly bound transcripts of METTL3, METTL14, and METTL16, RNA immunoprecipitation sequencing (RIP-seq) was conducted HEK293T stablely expressing METTL3, METTL14, and METTL16, respectively. Briefly, HEK293T cells were infected with lentivirus, pmiRNA1-3 x Flag-METTL3, pmiRNA1-3 x Flag-METTL14, and pmiRNA1-3 x Flag-METTL14, to overexpress the three METTL family members with 3 x Flag fused in the N-terminal. Only the GFP-positive cells were used for study and expanded in DMEM medium.

2021-10-28 | GSE156797 | GEO

Identify QKI-bound transcripts via RIP-seq

Project description:N7-methylguanosine (m7G) modification, routinely occurring at the 5’ cap of mRNA or within tRNA and rRNA, also exists internally in mRNA. Although essential for mRNA translation as well as stress response, the “reader” protein for mRNA internal m7G modification is still unrevealed. Here, we reported that Quaking protein (QKI), especially QKI7, can selectively recognize the internal mRNA m7G decoration in the cytosol of various cell types. We identified over 1000 confident m7G-modified and QKI binding RNA targets with a conserved motif, “GANGAN (N=A/U/G)”. More strikingly, internal m7G reader QKI7 directly interacts with the SG core protein G3BP1 and can shuttle a subset of m7G-modified transcripts into SG mRNA pool under oxidative stress condition. Additionally, by sequestering mRNA within SGs, QKI7 modulates the translation efficiency of selected transcripts. Moreover, in line with the observation that doxorubicin triggers the assembly of SGs, QKI7 mediates the sensitivity of cancer cells to chemotherapy drug treatment.

2023-05-17 | GSE193036 | GEO

Identify QKI7-bound transcripts via RIP-seq

2023-05-17 | GSE192847 | GEO