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Mus musculus

ABSTRACT: High-throughput sequencing of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) targets

PROVIDER: PRJNA172921 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR539129.fastq.gz	Fastqsanger.gz
	SRR539130.fastq.gz	Fastqsanger.gz
	SRR539131.fastq.gz	Fastqsanger.gz
	SRR539132.fastq.gz	Fastqsanger.gz
	SRR539133.fastq.gz	Fastqsanger.gz

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High-throughput sequencing of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) targets

Project description:We conducted RNA/RNA binding protein immunoprecipitation (RIP) followed by high throughput sequencing to identify mRNA targets of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) in mouse embryonic stem cells. We collected over 190 million sequencing reads and identified many highly enriched protein coding mRNAs. Gene ontology analysis of enriched genes reveals that transcription factors and intercellular signaling proteins account for a large fraction of the targets, many of which are important for pluripotency and differentiation. Identification of Brf1 and Brf2 mRNA targets

2014-04-30 | E-GEOD-40104 | biostudies-arrayexpress

High-throughput sequencing of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) targets

2014-04-30 | GSE40104 | GEO

RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.

Project description:Purpose: Conditional knockout of Zfp36l1 Zfp36l2 early in lymphocyte development leads to a bypass of beta-selection and subsequently T cell acute lymphoblastic leukemia. This RNA seq experiment aimed to determine the molecular pathways affected by loss of Zfp36l1 and Zfp36l2, and to deduce direct targets of these RNA binding proteins. Methods: RNA was isolated from sorted Zfp36l1fl/fl; Zfp36l2fl/fl DN3a (Lineage-negative, CD44-, Kitlow, CD25+, CD98low) and DN3b (Lineage-negative, CD44-, Kitlow, CD25intermediate, CD98+) cells as well as Zfp36l1fl/fl; Zfp36l2fl/fl; CD2cre DN3 (Lineage-negative, CD44-, Kitlow, CD25+) cells with the RNeasy Micro Kit (Qiagen). RNAseq libraries were prepared from 20-200ng RNA using the TruSeq Stranded Total RNA and rRNA Removal Mix â?? Gold from Illumina. Libraries were sequenced by Hiseq in 100bp single-end reads. The reads were trimmed to remove adapter sequences using Trim Galore then mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly; reads with an identical sequence to more than one genomic locus were not mapped. Quality control analysis was carried out with FastQC. Reads were counted using htseq-count tool and mouse gtf file version 78. Results: Differences in the abundance of transcripts between DCKO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3). Adjusted P values for differential expression were calculated in DESeq2 using a Benjamini-Hochberg correction: genes with an adjusted p-value of less than 5% were considered significant. Differentially expressed mouse transcripts identified using DESeq2 were analyzed for gene set enrichment using Toppfun. Conclusions: We identified an enrichment of mRNAs involved in cell cycle progression within Zfp36l1 Zfp36l2 double conditional knockouts. 4 biological replicates of control DN3a, control DN3b and DCKO DN3-like cells were analyzed

2016-09-05 | E-GEOD-79174 | biostudies-arrayexpress

Mus musculus

Project description:Late pre-B cell transcriptomes from Zfp36l1 Zfp36l2 double knockout mice [iCLIP]

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Roles of Zfp36l1 and Zfp36l1 in retinal development

Project description:We report our study of the function of two members of the TTP (tristetraprolin) mRNA binding protein family, Zfp36l1 and Zfp36l2, in retinal development. We found that Zfp36l1 and Zfp36l2 were expressed in retinal progenitor cells during development and Müller glial cells and photoreceptors in the mature retina. Our analysis of the mutant retinas showed that, whereas the single knockout retinas appeared largely normal, the double knockout (DKO) retina manifested decreased RPC proliferation and increased differentiation of multiple retinal cell types. RNA-seq analysis not only confirmed the imbalance of proliferation and differentiation in the DKO retina but also revealed Zfp36l1 and Zfp36l2 interact with multiple signaling pathways including the sonic hedgehog pathway and the Notch pathway, to regulate this process.

2021-09-01 | GSE158718 | GEO

Mus musculus

Project description:Late pre-B cell transcriptomes from Zfp36l1 Zfp36l2 double knockout mice [RNA-Seq]

| PRJNA313058 | ENA

Mus musculus

Project description:Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice. [iCLIP]

| PRJNA315111 | ENA

Transcriptome of ZFP36L1-sufficient and ZFP36L1-deficient Fo B cells

Project description:High-throughput sequencing analysis of transcriptome from LPS-activated B cells from Lymph node of Zfp36l1(fl/fl) and Zfp36l1(fl/fl) x Cd79a(Cre/+) mice

2020-11-20 | GSE146073 | GEO

Mus musculus

Project description:RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.

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The RNA binding proteins ZFP36L1 and ZFP36L2 modulate transcriptional and post-transcriptional genome wide effects of glucocorticoids

Project description:To investigate the genome-wide role of RNA binding proteins ZFP36L1 and ZFP36L2 in glucocorticoid mechanisms of action in bronchial epithelial cells

2023-11-21 | GSE213495 | GEO

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