|
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 |