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| Status |
Public on Sep 27, 2017 |
| Title |
GS0259_naive_secondary |
| Sample type |
SRA |
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| Source name |
Cryopreserved PBMC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
disease group: Sri Lanka Secondary
cell subset: NAIVE CD3+CD4+CCR7+CD45RA+ T cells
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| Treatment protocol |
No specific treatment involved
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| Growth protocol |
Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Naive, TCM, TEM and TEMRA cells were defined as the combination of CCR7+CD45RA+, CCR7+CD45RA-, CCR7-CD45RA- and CCR7-CD45RA+ populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Microscaled (SmartSeq2) cDNA amplification - RNA seq
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| Data processing |
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files. The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table
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| Submission date |
Apr 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mariana Babor |
| E-mail(s) |
[email protected]
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| Organization name |
La Jolla Institute for Allergy and Immunology
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| Street address |
9420 Athena Cir
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| City |
La Jolla |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE97862 |
Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls from San Diego [Cohort 2 & Cohort 3] |
| GSE97863 |
Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls |
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| Relations |
| BioSample |
SAMN06759560 |
| SRA |
SRX2741733 |
| 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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