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Status |
Public on Feb 02, 2016 |
Title |
130115 0629-453 Acute ILC2 |
Sample type |
SRA |
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Source name |
Peripheral Blood
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Organism |
Homo sapiens |
Characteristics |
individual: 0629-453 cell type: Innate Lymphoid Cell 2 hiv status: HIV+ days post hiv-infection: 40 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) |
al.leslie@ahri.org
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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 |
SAMN04432855 |
SRA |
SRX1539837 |
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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