GSE87354: RNAseq analysis of Rpl13a-snoless and wild type islets

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GROUP CONDITION SAMPLES
Pancreatic islets
GSM2328743 GSM2328744 GSM2328745 GSM2328746
GSM2328739 GSM2328740 GSM2328741 GSM2328742
Description

Submission Date: Sep 26, 2016

Summary: Purpose: To gain further mechanistic insight into phenotypic differences between wild type pancreatic islets and islets with loss of function of 4 Box C/D snoRNAs from the Rpl13a locus (U32a, U33, U34 and U35a).

Methods:High quality total RNA (RIN ≥ 8.5) was prepared from hand-picked islets (n = 4 mice/genotype) using TRIZOL reagent, treated with Turbo DNAse (Thermo Fisher), and used to prepare SeqPlex RNAseq libraries (Sigma). Sequencing was performed by the Washington University Genome Technology Access Center using two lanes of Illumina HiSeq 2500, 1x50. Reads were demultiplexed and trimmed, and STAR alignment and quantification analysis was carried out using the Partek Flow platform. Uniquely aligned reads were quantified to identify genes with at least a two-fold change between genotypes with p < 0.05 and FDR step-up of 0.05.

Results:We observed 2-fold or greater differences in the expression of only six genes.

Conclusions: Our data indicate that loss-of-function of snoRNAs from the Rpl13a locus is associated with modest changes in mRNA abundance.

GEO Accession ID: GSE87354

PMID: 27820699

Description

Submission Date: Sep 26, 2016

Summary: Purpose: To gain further mechanistic insight into phenotypic differences between wild type pancreatic islets and islets with loss of function of 4 Box C/D snoRNAs from the Rpl13a locus (U32a, U33, U34 and U35a).

Methods:High quality total RNA (RIN ≥ 8.5) was prepared from hand-picked islets (n = 4 mice/genotype) using TRIZOL reagent, treated with Turbo DNAse (Thermo Fisher), and used to prepare SeqPlex RNAseq libraries (Sigma). Sequencing was performed by the Washington University Genome Technology Access Center using two lanes of Illumina HiSeq 2500, 1x50. Reads were demultiplexed and trimmed, and STAR alignment and quantification analysis was carried out using the Partek Flow platform. Uniquely aligned reads were quantified to identify genes with at least a two-fold change between genotypes with p < 0.05 and FDR step-up of 0.05.

Results:We observed 2-fold or greater differences in the expression of only six genes.

Conclusions: Our data indicate that loss-of-function of snoRNAs from the Rpl13a locus is associated with modest changes in mRNA abundance.

GEO Accession ID: GSE87354

PMID: 27820699

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