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Sample GSM4887042 Query DataSets for GSM4887042
Status Public on Feb 04, 2021
Title R6/1-vehicle_rep3
Sample type SRA
Source name Striatum
Organism Mus musculus
Characteristics model: R6/1
genotype: R6/1
treatment: vehicle
tissue: Striatum
Treatment protocol The HDAC1 and HDAC3 inhibitor RGFP109 (RG2833; CAS No. 1215493-56-3) was purchased from Selleckchem. RGFP109 was dissolved in dimethyl sulfoxide and diluted in 0.9% NaCl (1:2) directly before use (final concentration: 15 mg/ml). Mice were administered RGFP109 (30 mg/kg body weight) or an equal volume of vehicle solution by intraperitoneal injections five times a week for three weeks (total of 23 days) starting at the age of 11 to 14 weeks. Mice were deeply anesthetized using isoflurane and sacrificed by cervical dislocation 18 h after the final injection.
Extracted molecule total RNA
Extraction protocol Brain tissues were removed and flash frozen in liquid nitrogen. Flash-frozen tissues were homogenized in QIAzol Lysis Reagent (Qiagen) followed by RNA extraction using the miRNeasy Kit (Qiagen).
Illumina TruSeq RNA Sample Prep Kit was used with 380 ng of total RNA for the construction of sequencing libraries. Two pools with twelve libraries each were sequenced on a Illumina HiSeq 4000 instrument (1x51bp).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description RNAseq_Cuffdiff__WT-vehicle_vs_R6-1-vehicle.txt
Data processing Raw single-end reads of cDNA fragments were aligned to the mouse transcriptome (RefSeq, mm10) using the ‘RNA-Seq Alignment Workflow’ from BaseSpace, Illumina (version 1.1.0) with STAR aligner (version STAR_2.5.0b) for mapping.
Differential gene expression analysis was performed using ‘Cufflinks Assembly & DE Workflow' from BaseSpace, Illumina (version 2.1.0) with Cuffdiff 2 (Cufflinks, version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain cuffdiff output with columns: (1) tested id, (2) gene id, (3) gene, (4) locus, (5) sample 1, (6) sample 2, (7) test status, (8) FPKM of the gene in sample 1, (9) FPKM of the gene in sample 2, (10) log2(FPKM_2/FPKM_1), (11) test statistic, (12) p-value, (13) q-value, (14) significant (yes or no). WT=wild type, MUT=R6/1.
Submission date Nov 06, 2020
Last update date Feb 04, 2021
Contact name Katharina Hecklau
Organization name Charité-Universitätsmedizin Berlin
Lab Yildirim Lab
Street address Charitéplatz 1, Virchowweg 6
City Berlin
ZIP/Postal code 10117
Country Germany
Platform ID GPL21103
Series (1)
GSE160967 The effects of selective inhibition of histone deacetylase 1 and 3 in Huntington’s disease mice
BioSample SAMN16686521
SRA SRX9450321

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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