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| Status |
Public on Dec 09, 2022 |
| Title |
CVX7_C2D07 |
| Sample type |
SRA |
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| Source name |
Fingerstick
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| Organism |
Homo sapiens |
| Characteristics |
patientid: CVX7
timepoint: C2D07
turbo_reatment: Not treated
vaccine_dose: BOOST
tissue: Peripheral blood
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
700858291
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| Data processing |
Encoding Sanger/Illumina 1.9 software used for basecalling.
Quality trimming is performed to remove adapter sequences and polyA tails. Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Dec 02, 2021 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Darawan Rinchai |
| E-mail(s) |
drinchai@gmail.com
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| Organization name |
Sidra Medicine
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| Department |
Research
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| Lab |
Cancer program
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| Street address |
Al Gharrafa St
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| City |
Doha |
| State/province |
Qatar |
| ZIP/Postal code |
PO BOX 26999 |
| Country |
Qatar |
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| Platform ID |
GPL30296 |
| Series (1) |
| GSE190001 |
Detailed delineation of the immune response to COVID-19 mRNA vaccination via high-temporal frequency blood transcriptomics |
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| Relations |
| BioSample |
SAMN23530926 |
| SRA |
SRX13271386 |
| 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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