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| Status |
Public on Jun 15, 2021 |
| Title |
28-42FJy-mDC-SM_S121 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Cercocebus atys |
| Characteristics |
batch id: 277
subject id: FJy
infected: SIVpos
cell type: mDC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Qiagen miRNeasy Mini Kit
cDNA was generated using the Clontech SMARTseq v4 Ultra Low Input kit and libraries were prepared for sequencing using the Illumina HiSeq3000
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
RawCounts_mDC_MacaM.txt
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| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped using STAR v2.5.2b with default alignment parameters.
For SIV+ vs SIV- pDC samples (Figures 1 & 2), alignment was done to either MacaM v7 (rhesus macaque samples) or Caty 1.0 (sooty mangabey samples). Only gene names that were common between the two were used
For ranking genes expressed on surface and transcription factors, samples were aligned to MacaM v7 and GRCh38
For all other analyses, samples were aligned to MacaM v7
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: Rhesus macaque (MacaM v7.8.2 - https://www.unmc.edu/rhesusgenechip/index.htm#Rhesus), sooty mangabey (Caty 1.0 - NCBI GCF_000955945.1), human(GRCh38 ensembl relase 86).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jun 15, 2021 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Steven E. Bosinger |
| E-mail(s) |
steven.bosinger@emory.edu
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| Organization name |
Emory University
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| Street address |
954 Gatewood Rd NE
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| City |
Atlanta |
| ZIP/Postal code |
30329 |
| Country |
USA |
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| Platform ID |
GPL23805 |
| Series (1) |
| GSE178225 |
Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection |
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| Relations |
| BioSample |
SAMN19712301 |
| SRA |
SRX11148757 |
| 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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