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Series GSE208330 Query DataSets for GSE208330
Status Public on Jul 19, 2022
Title Detailed analysis of dorsal-ventral gradients of gene expression in the rat hippocampus
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Dorsal and ventral parts of the hippocampus despite similar histological structure are known to be involved in performance of different functions. Previous studies using next generation sequencing showed that these two hippocampal parts differ in the expression of many genes, however, stability of dorsoventral gradient of gene expression remains open question. Here, we analyzed differential expression of genes between the dorsal and ventral hippocampus of rats in polyA-enriched samples and samples subjected to depletion of ribosomal RNA. We present here a detailed analysis of differentially expressed genes between the dorsal and ventral parts of the hippocampus. Intersection of our dataset with data of previous RNAseq studies revealed 544 genes are stably differentially expressed between the hippocampal parts suggesting that, despite strongly variability between the animals and sequencing approaches, there is a subset of genes whose expression stably differs between the dorsal and ventral hippocampus. Analysis of differential splicing showed that the dorsal and ventral parts of the hippocampus express 64 genes whose splice isoforms are different between the hippocampal parts. Furthermore, we show that depletion of ribosomal RNA increases representation of transposable elements in the RNAseq libraries and helps to detect a weak predominance of expression of these elements in the ventral hippocampus.
 
Overall design 7 male rats were analyzed using polyA-enrichment RNAseq and 3 male rats were analyzed using RNAseq after depletion of ribosomal RNA. Dorsal and ventral parts of the hippocampus were dissected in every animal.
 
Contributor(s) Beletskiy A, Positselskaya E, Vinarskaya A, Spivak Y, Dobryakova Y, Tyulenev I, Markevich V, Bolshakov A
Citation(s) 36077346
Submission date Jul 16, 2022
Last update date Oct 26, 2022
Contact name Alexander Beletsky
E-mail(s) apbeletskiy@gmail.com
Organization name IHNA
Street address Butlerova street, building 5a
City Moscow
ZIP/Postal code 117290
Country Russia
 
Platforms (1)
GPL30103 DNBSEQ-G400 (Rattus norvegicus)
Samples (20)
GSM6341127 Dorsal polyA-enriched 1
GSM6341128 Ventral polyA-enriched 1
GSM6341129 Dorsal polyA-enriched 2
Relations
BioProject PRJNA859286

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE208330_PolyA_RBD_counts.txt.gz 2.6 Mb (ftp)(http) TXT
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Processed data are available on Series record

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