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E-GEOD-59043 - G9a is essential for epigenetic silencing of K+ channel genes in acute-to-chronic pain transition

Status
Released on 2 November 2015, last updated on 24 November 2015
Organism
Rattus norvegicus
Samples (11)
Protocols (2)
Description
AIM: We performed RNA-sequencing experiments seeking genes whose expression changed due to nerve injury. In addition, we wanted to test whether inhibition of the methyl transferase G9a/GLP, that methylates H3K9me2, could reverse those expression changes due to nerve ligation. G9a/GLP methylase was pharmacologically inhibited using UNC0638. METHOD: We generated cDNA libraries from RNA purified from DRGs obtained from Sham operated (4), SNL (4), and SNL plus UNC0638 (3) rats. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the rat genome rn4 using TopHat RESULTS: We were able to map 16876 genes, from which 2035 changed their expression values at least two fold when we compared SNL to Sham operated (p≤ 0.01). There were 1205 upregulated and 832 down-regulated genes. Next, we focused on genes whose expression was either up or down-regulated 2 fold due to nerve ligation, and the values would be normalized to control level after G9a/GLP inhibito (UNC0638)r treatment. We identified 639 genes in our data set that behave this way We generated cDNA libraries from RNA purified from DRGs obtained from Sham operated (4), SNL (4), and SNL plus UNC0638 (3) rats. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the rat genome rn4 using TopHat
Experiment type
RNA-seq of coding RNA 
Contacts
matteo cesaroni <geo@ncbi.nlm.nih.gov>, Geoffroy Laumet, Judit Garriga, Matteo Cesaroni
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-59043.idf.txt
Sample and data relationshipE-GEOD-59043.sdrf.txt
Additional data (1)E-GEOD-59043.additional.1.zip
Links