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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 10, 2012 |
| Title |
PBS |
| Sample type |
SRA |
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| Source name |
PBS
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
age: 9 wk post injection
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file = Expression.txt
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
The raw sequencing data produced was processed removing the sequence reads which were of too low quality (only "passing filter" reads were selected). Each read file (sample), in the FASTQ format, was individually aligned against the mouse reference genome (15 May 2012 NCBI build 38.1) using CLC Bio-Genomic Workbench and the expression abundance for each gene (RPKM) was calculated according to Montazavi et al.
Genome_build: mouse reference genome (15 May 2012 NCBI build 38.1)
Supplementary_files_format_and_content: Spreadsheet including annotation of reads to the reference genome
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| Submission date |
Jul 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Piotr Maczuga |
| E-mail(s) |
p.maczuga@uniqure.com
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| Organization name |
UniQure
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| Street address |
Meibergdreef 61
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| City |
Amsterdam |
| State/province |
Nord Holland |
| ZIP/Postal code |
1105BA |
| Country |
Netherlands |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE39187 |
Embedding siRNA sequences targeting Apolipoprotein B100 in shRNA and miRNA scaffolds results in differential processing and in vivo efficacy |
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| Relations |
| SRA |
SRX158350 |
| BioSample |
SAMN01086230 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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