Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA315111 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3223780.fastq.gz | Fastqsanger.gz | |||
| SRR3223781.fastq.gz | Fastqsanger.gz | |||
| SRR3223782.fastq.gz | Fastqsanger.gz | |||
| SRR3223783.fastq.gz | Fastqsanger.gz | |||
| SRR3223779.fastq.gz | Fastqsanger.gz |
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Project description:Late pre-B cell transcriptomes from Zfp36l1 Zfp36l2 double knockout mice [RNA-Seq]
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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
Project description:Purpose: Conditional knockout of Zfp36l1 Zfp36l2 in pro-B cells perturbs B cell development leading to reduced V(D)J recombination and diminished numbers of cells in successive stages of development. 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: RNAseq libraries were prepared from 0.1 µg of RNA from sorted control and DCKO late pre-B cells using TruSeq RNA sample preparation kit v2 modified to be strand specific using the dUTP method. Libraries were sequenced by an Illumina genome analyzer II measuring 54bp single-end reads. Over 30 million reads were measured from each sample. The reads were trimmed to remove adapter sequences using Trim Galore then mapped using Tophat (version 1.1.4) to the NCBIm37 mouse assembly (April 2007, strain C57BL/6J); reads with an identical sequence to more than one genomic locus were not mapped. Quality control analysis was carried out with FastQC. Results: Read counts for each gene were generated in SeqMonk: transcripts from the same gene were collapsed into a single transcript containing all exons, so total reads were counted without considering alternative splice forms. Since the libraries were strand-specific only reads on the opposing strand were counted. Differences in the abundance of transcripts between DCKO and control late pre-B cells were calculated in the R/Bioconductor program DESeq (version 1.12.1). Adjusted P values for differential expression were calculated in DESeq using a Benjamini-Hochberg correction: genes with an adjusted p-value of less than 5% were considered significant. Differentially expressed mouse transcripts identified using DESeq 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.
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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.
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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 – 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.
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