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| Status |
Public on Aug 30, 2023 |
| Title |
PB013_Liver_SIVhigh |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Liver
treatment: SIV-infected (high viremic)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from samples preserved in TRIzol, using the Qiagen RNeasy Micro kit with DNaseI treatment, following the manufacturer’s protocol.
The NEBNext Ultra II directional RNA library prep kit for Illumina (New England Biolabs Inc., Ipswich, MA, USA) was used to mRNA sequencing libraries, according to the manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
PB013_Liver_SIVhigh
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| Data processing |
Reads were trimmed using fastp v0.20.0.
Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.8 and MultiQC v1.8.
The quantification was performed with Kallisto v0.46.2 against the Macaca mulata transcriptome (Mmul_10 downloaded from Ensemble release 103).
Assembly: Mmul_10
Supplementary files format and content: xlsx file includes TPM values for each sample
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| Submission date |
Jun 07, 2023 |
| Last update date |
Aug 30, 2023 |
| Contact name |
Jérôme Estaquier |
| E-mail(s) |
Jerome.Estaquier@crchudequebec.ulaval.ca
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| Organization name |
Centre de Recherche du CHU de Québec-Université Laval
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| Street address |
2705 Boulevard Laurier
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| City |
Québec |
| State/province |
Québec |
| ZIP/Postal code |
G1V4G2 |
| Country |
Canada |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE234399 |
Gene expression in the liver and lungs of healthy, SIV-infected and ART-treated rhesus macaques |
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| Relations |
| BioSample |
SAMN35668051 |
| SRA |
SRX20631953 |
| 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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