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Sample GSM2451685 Query DataSets for GSM2451685
Status Public on Jun 12, 2017
Title HUH-AAV_RNA-Seq
Sample type SRA
 
Source name viral transcripts
Organism Adeno-associated virus
Characteristics virus serotype: AAV2
cell line: HuH7
Treatment protocol Wild-type AAV serotype 2 was added at an MOI of 5000. Cells were cultured a further 48 hours before recovery using trypsin
Growth protocol HuH-7 cells were seeded at 5 × 10(E)5 cells per T25 and cultured for 24 hours.
Extracted molecule total RNA
Extraction protocol Cells were processed using an RNeasy kit (QIAGEN) to recover total RNA
Illumina TruSeq Stranded mRNA LT Sample Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Adaptor trimming using Trimmomatic with parameters: 2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:25 MINLEN:18
Alignment to the human genome (hg19) using RNA-STAR with parameters --outFilterMismatchNoverLmax 0.05 --twopassMode Basic --twopass1readsN -1.
Alignment to the AAV genome (J01901.1_modified) using RNA-STAR with parameters --outFilterMismatchNoverLmax 0.05 --twopassMode Basic --twopass1readsN -1.
Bedtools genomecov –d –split to determine the strand specific coverage on reads with flags 99 and 147 for the negative strand and flags 83 and 163 for the positive strand
Genome_build: J01901.1_modified. The fasta file for this genome is available on the series record.
Supplementary_files_format_and_content: genomic coverage for viral genome only generated by bedtools genomecov
 
Submission date Jan 09, 2017
Last update date May 15, 2019
Contact name Grant Joseph Logan
E-mail(s) glogan@cmri.org.au
Organization name CHildren's Medcial Research institute
Street address 214 Hawkesbury Road
City Westmead
ZIP/Postal code 2145
Country Australia
 
Platform ID GPL22169
Series (1)
GSE93341 Identification of liver-specific enhancer-promoter activity in the 3’ UTR of the wild-type AAV2 genome
Relations
BioSample SAMN06213944
SRA SRX2480773

Supplementary file Size Download File type/resource
GSM2451685_HUH7-AAV_anti_sense_coverage.txt.gz 13.5 Kb (ftp)(http) TXT
GSM2451685_HUH7-AAV_sense_coverage.txt.gz 18.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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