Illumina Genome Analyzer IIx paired end sequencing; GSM3589856: KO_37; Rattus norvegicus; RNA-Seq

KO_37

We found that the previously published Fmr1 knockout rat model of FXS expresses an Fmr1 transcript with an in-frame deletion of exon 8, which encodes for the K-homology (KH) RNA-binding domain, KH1. We observed that the deletion of exon 8 in 10 male rats within the medial prefrontal cortex (mPFC) led to transcriptional alterations compared to 12 WT rats using RNAseq. Additionally, we used weighted gene co-expression network analysis to generate 23 modules specific to the mPFC with tissue from 35 WT rat samples. Overall design: RNAseq using WT and Fmr1 delta exon 8 mPFC samples

Deletion of the KH1 domain coding sequence of Fmr1 leads to transcriptional alterations and attentional deficits in rats

Submitted by Gene Expression Omnibus on 28-APR-2019

RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Subsequently, the quantity of all purified RNA samples was measured on a nanodrop (2.07±0.01 A260/280; 2.11±0.19 A260/230) and the quality and integrity were measured with the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). All RNA integrity numbers were greater than 9 (9.6±0.3). 1µg of total RNA was used for the preparation of the RNAseq library using the Illumina Genome Analyzer IIx TruSeq mRNA Seq Kit supplied by Illumina (Cat number: RS-122-2001). A poly-A-based mRNA enrichment step was carried out and cDNA was synthesized and used for library preparation using the Illumina TruSeqTM RNA sample preparation kit as previously described (Tariq MA et al. 2011), except for the following step: adapter-ligated DNA fragments were size-selected by gel-free size selection using appropriate concentration of SPRI AMPure beads to get an average 200bp peak size in adaptor ligated DNA. The size selected adaptor-ligated DNA fragments were amplified by LM-PCR. Then, Illumina recommended 6bp barcode bases were introduced at one end of the adaptors during PCR amplification step. The amplified PCR products were then purified with SPRI AMPure XP magnetic beads to get the final RNAseq library, which was used for high-throughput RNAseq. All samples were sequenced on the Illumina Genome Analyzer IIx.

Deletion of the KH1 domain coding sequence of Fmr1 leads to transcriptional alterations and attentional deficits in rats

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