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Sample GSM3454289 Query DataSets for GSM3454289
Status Public on Dec 04, 2018
Title 5_Cas9-2
Sample type SRA
 
Source name striatal tissue
Organism Mus musculus
Characteristics tissue: striatal tissue
treatment (viral injection): Cas9
age: 3 weeks-old
Treatment protocol Injected with adeno-associated virus into the striatum.
Growth protocol 3-month old wild type mice
Extracted molecule total RNA
Extraction protocol Total RNA was purified using RNAeasy Mini Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
Libraries were prepared on cDNA generated using Clontech SmartER kits. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description 5_Cas9-2_alaHtseq.txt
Data processing Reads were aligned to an assembly of Mus musculus (house mouse) (Genome Reference Consortium Mouse Build 38 patch release 3 (GRCm38.p3)) using STAR software (v2.5.2b).
Transcripts were annotated with GENCODE M3 release
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
 
Submission date Nov 01, 2018
Last update date Dec 04, 2018
Contact name Gregory K Tharp
E-mail(s) gktharp@emory.edu
Phone 404-727-7797
Organization name Yerkes National Primate Research Center
Department Developmental and Cognitive Neuroscience
Lab Genomics Core
Street address 954 Gatewood Dr
City Atlanta
State/province GA
ZIP/Postal code 30329-4208
Country USA
 
Platform ID GPL21493
Series (1)
GSE122072 Shortening the half-life of Cas9 maintains its gene editing ability and reduces neuronal toxicity
Relations
BioSample SAMN10359412
SRA SRX4965981

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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