{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kazuya Masuda"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14727"],"description":["A cryovial that contains frozen PBMCs (10^6 cells/vial) from each of 11 COVID-19 patients was thawed in 37oC water bath. Immediately after, thawed cells were transferred to 15-mL Falcon tube that contained 10 mL of cold culture medium.  After centrifugation at 150g for 5 min, the cell pellets were resuspended in complete RPMI + 10% heat-inactivated FCS medium and plated onto 12-well plate at a concentration of 5 x 10^6 cells/3 mL/well. Then a peptide cocktail was added at a concentration of 5 μg/mL for 16hr in 5% CO2 37oC incubator.  After 16-hour incubation, cells were washed 3 times and incubated for 10 minutes with Fc receptor block, following each sample was stained with a total of 6 HLA-A2+/peptide fluorescent tetramer (Tet) and pentamer (Pent) for 10 min. After cell washing at twice, each sample was stained with cell hashing antibodies for 20 min, respectively and then washed at three times and finally pooled. The combined cells were stained with CITE-seq and anti-human CD8 FACS antibody for 30 minutes. After cell washing at twice, viable HLA-A2+/peptide Tet/Pent positive CD8+ T cells were sorted by FACS Aria II. The scRNA-Seq libraries including GEX and CITE-seq libraries were prepared using the 10x Chromium single-cell 3’ reagent kits (v3.1 Chemistry), per manufacturer’s instructions. As a result, we have 2 separate groups of the single cell datasets. MKH datasets (MKH_GEX_... and MKH_FB...) contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 5 COVID-19 patients. MKK datasets contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 6 COVID-19 patients. Cell hashing and CITE-seq antibody information is available in the csv files."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 10x Genomics 3' v3.1 protocol. In brief, after cell sorting, single-cell suspensions were loaded into the Chromium controller to make nanoliterscale droplets with uniquely barcoded 3’ gel beads called GEMs (gel bead-in emulsions). After GEM-RT, GEMs were cleaned up by Dyna beads MyOne Silane beads (Thermo Fisher Scientific, 37002D). According to the manufacturer’s instructions, the cDNA was amplified and size-selected by SPRI-beads (Beckman Coulter, B23317). Finally, the 3’ transcript and feature barcode libraries were pooled","Sequencing - The Illumina sequencing protocol (Illumina NovaSeq 6000 sequencing system)","Sample Collection - HLA-A2+/peptide pentamer and tetramer selection from patient PBMCs","Library Construction - 10x Genomics 3' v3.1 protocol. In brief, after cell sorting, single-cell suspensions were loaded into the Chromium controller to make nanoliterscale droplets with uniquely barcoded 3’ gel beads called GEMs (gel bead-in emulsions). After GEM-RT, GEMs were cleaned up by Dyna beads MyOne Silane beads (Thermo Fisher Scientific, 37002D). According to the manufacturer’s instructions, the cDNA was amplified and size-selected by SPRI-beads (Beckman Coulter, B23317). Finally, the 3’ transcript and feature barcode libraries were pooled"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - FASTQ files were processed by Cell Ranger v.6.1.2 (10x Genomics) software using the GRCm38 (GENCODE vM23/Ensembl 98) genome as a reference"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["N/A","10x Chromium controller","FACS Aria II","10x Genomics","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Kazuya Masuda","Moriya Tsuji"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 11 COVID-19 patients","description":"A cryovial that contains frozen PBMCs (10^6 cells/vial) from each of 11 COVID-19 patients was thawed in 37oC water bath. Immediately after, thawed cells were transferred to 15-mL Falcon tube that contained 10 mL of cold culture medium.  After centrifugation at 150g for 5 min, the cell pellets were resuspended in complete RPMI + 10% heat-inactivated FCS medium and plated onto 12-well plate at a concentration of 5 x 10^6 cells/3 mL/well. Then a peptide cocktail was added at a concentration of 5 μg/mL for 16hr in 5% CO2 37oC incubator.  After 16-hour incubation, cells were washed 3 times and incubated for 10 minutes with Fc receptor block, following each sample was stained with a total of 6 HLA-A2+/peptide fluorescent tetramer (Tet) and pentamer (Pent) for 10 min. After cell washing at twice, each sample was stained with cell hashing antibodies for 20 min, respectively and then washed at three times and finally pooled. The combined cells were stained with CITE-seq and anti-human CD8 FACS antibody for 30 minutes. After cell washing at twice, viable HLA-A2+/peptide Tet/Pent positive CD8+ T cells were sorted by FACS Aria II. The scRNA-Seq libraries including GEX and CITE-seq libraries were prepared using the 10x Chromium single-cell 3’ reagent kits (v3.1 Chemistry), per manufacturer’s instructions. As a result, we have 2 separate groups of the single cell datasets. MKH datasets (MKH_GEX_... and MKH_FB...) contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 5 COVID-19 patients. MKK datasets contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 6 COVID-19 patients. Cell hashing and CITE-seq antibody information is available in the csv files.","dates":{"release":"2025-12-01T00:00:00Z","modification":"2025-12-01T02:01:51.667Z","creation":"2024-12-24T16:52:24.286Z"},"accession":"E-MTAB-14727","cross_references":{"ENA":["ERP167409"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}