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| Status |
Public on Feb 02, 2016 |
| Title |
220814 0444-312 ILC3 |
| Sample type |
SRA |
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| Source name |
Peripheral Blood
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| Organism |
Homo sapiens |
| Characteristics |
individual: 0444-312
cell type: Innate Lymphoid Cell 3
hiv status: HIV+
days post hiv-infection: 41
treatment: ART
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| Treatment protocol |
Cells were sorted into RLT buffer by FACS, spun down, and snap frozen on dry ice.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Due to low cell counts, lysates were treated as single cells in an adapted SMART-Seq II protocol (Trombetta et al., Current Protocols in Molecular Biology, 2014, 107:II:4:22). Briefly, mRNA was extracted from lystates using SPRI beads and then reverse transcribed and amplified using a poly-adenylated RT primer and template switching SMART oligo.
Library construction followed from the protocol above (Trombetta et al.,).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ILC_matrix_processed.txt
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| Data processing |
Illumina bcl2fastq2.15.0.4 was used to generate .fastq files from .bcl files.
tophat2 was used to align the scRNA-seq data
rsem-1.2.3 generated an expression matrix in psuedocounts
Genome_build: hg19 ucsc genomestudio
edgeR modeled dispersion, normalized for library size, and conducted differential expression likelihood ratio tests
Supplementary_files_format_and_content: edgeR normalized counts per million with genes as rows and cell populations (samples) as columns
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| Submission date |
Jan 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alasdair Leslie |
| E-mail(s) |
[email protected]
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| Organization name |
African Health Research Institute
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| Lab |
Leslie Lab
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| Street address |
719 Umbilo Road
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| City |
Durban |
| ZIP/Postal code |
4001 |
| Country |
South Africa |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE77088 |
Time course RNA-Seq of Innate Lymphoid Cells in Early Acute HIV Infection |
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| Relations |
| BioSample |
SAMN04432860 |
| SRA |
SRX1539842 |
| 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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