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| Status |
Public on Jun 07, 2023 |
| Title |
CD56dim, ART, rep1 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: CD56dim NK cells
treatment: HIV positive under ART
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| Growth protocol |
CD56hi, CD56dim, CD56negNK cells and ILCs were sorted from the PBMCs of HIV-1 negative people, HIV-1+ viremic people, HIV-1+ people under ART, and HIV-1+ spontaneous controllers.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The RNA of sorted cells were extracted with Trizol.
The mRNA library was constructed by CEL-Seq2 method.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
cutadapt v2.9 was used to trim and move the first 6 bases (UMIs) of the reads to the read header; demultiplex fastq files based on the inline sample barcodes to generate per-sample fastq files and remove adapter sequences.
Star v2.6.1 was used to align reads to human genome hg38 assembly.
UMI-tools v1.1.2 was used to deduplicate PCR duplicates based on the UMI sequences.
Deduplicated bam files were converted to fastq using samtools v1.9.
Kalliso v0.46.0 was used to quantify gene expression from deduplicated fastq files.
Assembly: hg38
Supplementary files format and content: Tab separated values and matrix file.
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| Submission date |
May 13, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Jeremy Luban |
| Organization name |
UMass Medical School
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| Street address |
373 Plantation Street Biotech 2, Suite 319
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| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE203002 |
Clarification of human blood ILC subtype interrelatedness and discovery of amphiregulin production by human NK cells shed light on HIV-1 pathogenesis |
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| Relations |
| BioSample |
SAMN28293287 |
| SRA |
SRX15271029 |
| 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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