Transcriptome Analysis of Developing Brain

Microarray experiments and analysis were performed as we previously described^{81 (link),89 (link)}. Total RNA was extracted (Qiagen RNA extraction kit) from one brain hemisphere of the 24-h and 13 weeks’ old pups according to the manufacturer’s protocol. RNA samples with A260/A280 absorbance ratios between 2.00 and 2.20 were reverse-transcribed into cDNA and analyzed by “whole-transcript transcriptomics” using the GeneAtlas microarray system (Affymetrix) and manufacturer’s protocols. MoGene 2.1 ST array strips (Affymetrix) were used to hybridize to newly synthesized ss-cDNA. Each array comprised 770,317 distinct 25-mer probes to probe an estimated 28,853 transcripts, with a median 27 probes per gene. Only annotated genes were included in the differential analysis.

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Alhassen S., Chen S., Alhassen L., Phan A., Khoudari M., De Silva A., Barhoosh H., Wang Z., Parrocha C., Shapiro E., Henrich C., Wang Z., Mutesa L., Baldi P., Abbott G.W, & Alachkar A. (2021). Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction. Communications Biology, 4, 783.

Publication 2021

RNA extraction kit GeneAtlas microarray system MoGene 2.1 ST array strips

Brain hemisphere Cdna Genes Microarray Transcriptomics

Corresponding Organization :

Other organizations : University of California, Irvine, University of Rwanda

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Variable analysis

independent variables

Age of pups (24-h and 13 weeks)

dependent variables

Whole-transcript transcriptomics (gene expression) using GeneAtlas microarray system

control variables

One brain hemisphere of the pups
RNA samples with A260/A280 absorbance ratios between 2.00 and 2.20
Reverse-transcription of RNA samples into cDNA
Use of MoGene 2.1 ST array strips (Affymetrix) with 770,317 distinct 25-mer probes to probe an estimated 28,853 transcripts

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

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