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| Status |
Public on Jul 26, 2018 |
| Title |
wP_PT_TCM (14) |
| Sample type |
SRA |
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| Source name |
wP, cells Pertussis-specific, TCM
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| Organism |
Homo sapiens |
| Characteristics |
individual id: 1584
disease group: San Diego whole Pertussis (wP) Vaccine
cell type: Cryopreserved PBMC
stimulation: PT
cell subset: TCM 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, stimulated with peptides in a 24h AIM assay (Dan et al. 2016), stained with antibodies, and an average of 10,000 antigen-specfic cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. TCM and TEM were defined as the combination of CCR7+CD45RA- or CCR7-CD45RA- populations respectively. 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 (microscaled) 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 |
PT_all_TPM.tsv
PT_all_TPM.tsv
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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 matrix tables
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| Submission date |
May 01, 2018 |
| Last update date |
Jul 26, 2018 |
| Contact name |
Mariana Babor |
| E-mail(s) |
mbabor@lji.org
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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 (1) |
| GSE113891 |
Transcriptomic profile of circulating CD4+ T cells from TCM and TEM memory compartments from donors vaccinated at birth either with whole or acellular Pertussis vaccine |
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| Relations |
| BioSample |
SAMN09005882 |
| SRA |
SRX4016713 |
| 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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