title: cerebellar organoid, organoid, replicate 1

city: Oxford

first: John

last: Jacob

address: Headley Way

department: NDCN

country: United Kingdom

institute: University of Oxford

description:
10X Genomics 3pr v3.1 Chemistry
07_CBO_GEX-v3.1

data_processing:
Analysis pipeline was applied to process Chromium single-cell data to align reads, and generate feature-barcode matrices. Illumina’s bcl2fastq and cellranger mkfastq demultiplexes were used to convert the raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
Cellranger count (v7.0.0) took FASTQ files from cellranger mkfastq and performed alignment, filtering, barcode counting, and UMI counting. It used the Chromium cellular barcodes to generate feature-barcode matrices. In the count pipeline, one sample was processed through one GEM well and sequenced on one flowcell.
Assembly: GRCh38
Supplementary files format and content: Seurat object  (counts of all samples)

source_name: cerebellar organoid

extract_protocol:
Day 60 organoids and organoid-tumour co-culture samples were collected using a wide bore pipette tip and placed in a 6 well plate. Using micro-scissors, organoids were cut in four pieces before placing a total of five organoids in an Eppendorf tube. After removal of excess medium, 200 uL of pre-warmed (to 37°C) Neuron isolation enzyme was added and the tube was placed in a 37°C water bath. Organoids were incubated with the enzyme for 30 minutes with intermittent agitation. The enzyme was removed and organoids were washed once with HHGN medium (HBSS + 2.5mM HEPES + 35mM Glucose + 4mM NaHCO3). Organoids were then dissociated in differentiation medium by gentle trituration. Afterwards, the cell suspension was enriched for viable cells using the dead cell removal kit (Miltenyi Biotec) following the manufacturers protocol. Cell viability was determined using Trypan Blue staining and counted using an automated cell counter (Applied Biosystems Countess 3). Cells were centrifuged at 300 x g for 5 minutes and resuspended in the appropriate volume of resuspension buffer (HBSS + 0.04% BSA) to a final concentration of 2 x 10^3 cells / uL before proceeding with single cell RNA sequencing. Thirty tumour spheroids were collected using a wide bore pipette tip and placed in an Eppendorf tube. Excess medium was removed and 200 uL of pre-warmed Neuron isolation enzyme (Gibco) was added. The tube was placed in a 37°C water bath for 20 minutes and agitated every 5 minutes. Subsequent processing was performed following the same steps as described above. DAOY and ONS-76 cell monolayer cultures were dissociated by incubation with pre-warmed TrypLE for 5 minutes. TrypLE was then diluted in PBS before centrifugation at 400 x g for 5 minutes to collect the cells. Cells were washed once in differentiation medium before processing as described above.
Single cell barcoding and reverse transcription of poly-A mRNA was performed using the 10X Chromium controller (3’ version 3.1 chemistry) and sequencing of single cell libraries was performed on an Illumina NovaSeq6000 sequencing system according to the manufacturer’s instructions

value: cerebellar organoid

tag: cell line

tag: cell type

value: wild-type

value: in vitro culture


title: EDTA-K3 plasma anticoagulant tubes [9-OSA52]

status: Public on Apr 01 2024

type: SRA

city: Lleida

first: David

last: de Gonzalo-Calvo

state: Lleida

address: Rovira Roure 80

country: Spain

institute: IRBLleida

description:
HTG EdgeSeq miRNA WTA Sequencer NB551420
GEO_data HTG OSA Processed TB.txt

library_source: transcriptomic

data_processing:
FASTQ files were processed by HTG EdgeSeq parser software. Parser produces text file of counts per target miRNA. Differential gene expression analysis based on the negative binomial distribution (DESeq package (R version 4.1.1)
biocLite("DESeq2"): 1. Quality assess and clean raw sequencing data; 2. Align reads to a reference; 3. Count the number of reads assigned to each contig/gene; 4. Extract counts and store in a matrix; 5. Create column metadata table; 6. Analyze count data using DESEQ2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RAW data (total counts) and analyzed count data for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasma samples were collected in the early morning and after 10-14 h of overnight fasting and after sleep test.

extract_protocol:
HTG EdgeSeq extraction-free chemistry can detect miRNA targets without the requirement for RNA extraction, adaptor ligation, cDNA synthesis or pre-amplification of the sample by PCR.  Plasma samples were thawed and 15µl of each sample was plated in 24 wells and loaded onto the HTG EdgeSeq instrument.
HTG EdgeSeq miRNA following manufacture's protocols. Set of 2083 targets used, plus 5 negative controls, 1 positive control and 13 housekeeping genes - total of 2102 observations per sample

tag: tissue

tag: Sex

value: Male

tag: age

tag: body mass_index

tag: apnea hypoapnea_index


title: DAOY-cerebellar organoid, coculture, replicate 1

description:
10X Genomics 3pr v3.1 Chemistry
06_DAOY_CBO_GEX-v3.1

library_source: transcriptomic single cell

source_name: DAOY-cerebellar organoid coculture

value: DAOY-cerebellar organoid coculture

value: DAOY

value: cell line and cerebellar organoid

tag: genotype

value: malignant and wild-type

tag: treatment


title: EDTA-K3 plasma anticoagulant tubes [9-OSA51]

value: Plasma samples were collected in the early morning and after 10-14 h of overnight fasting and after sleep test.

value: female


title: EDTA-K3 plasma anticoagulant tubes [9-OSA50]


title: ONS76, tumour-spheroid, replicate 1

description:
10X Genomics 3pr v3.1 Chemistry
03_ONS76_SPHER_GEX-v3.1

source_name: ONS-76 tumour-spheroid

value: ONS-76 tumour-spheroid

value: cell line

value: malignant


title: EDTA-K3 plasma anticoagulant tubes [9-OSA49]


title: ONS76-cerebellar organoid, coculture, replicate 1

description:
10X Genomics 3pr v3.1 Chemistry
05_ONS76_CBO_GEX-v3.1

source_name: ONS-76-cerebellar organoid coculture

value: ONS-76-cerebellar organoid coculture


title: EDTA-K3 plasma anticoagulant tubes [8-OSA45]


title: ONS76, monolayer, replicate 1

description:
10X Genomics 3pr v3.1 Chemistry
01_ONS76_2D_GEX-v3.1

source_name: ONS-76 cell line

value: ONS-76 cell line


title: EDTA-K3 plasma anticoagulant tubes [9-OSA48]


title: EDTA-K3 plasma anticoagulant tubes [9-OSA46]


title: nPOD6407, snRNA-seq with citric acid isolation method

city: Tallahassee

first: Yue

middle: Julia

last: Wang

state: FL

address: 1115 West Call Street

department: Biomedical Sciences

country: USA

institute: Florida State University

description: 10X Genomics

data_processing:
FASTQ files were aligned to GRCh38-3.0.0 using Cell Ranger V.5.0.1 and Include introns=TRUE. The raw gene expression matrices were input to Soup X 1.6.2  for ambient RNA removal using autoEstCont to automatically estimate the contamination fraction. Contamination was then removed from the original count matrix to generate a corrected gene expression matrix. All the downstream analysis was performed in Seurat V4.3.0 (34), with the  Soupx corrected gene expression matrix as input.
Assembly: GRCh38
Supplementary files format and content: seurat objects containing gene expression matrix post ambient RNA removal, cell type annotation, and other metadata

molecule: nuclear RNA

source_name: pancreas

extract_protocol:
Nuclei were extracted from frozen human pancreata using GRO-seq or citic acid method. For those experiment with FANS, nuclei were  labeled with the primary antibody against NKX2-2 (DSHB,  74.5A5, 1:100) and  Cy3 donkey-anti-mouse secondary antibody (Jackson ImmunoResearch, 715-165-151, 1:200).
Sorted nuclei were loaded onto a 10x Genomics Chromium Next GEM Chip G (10X Genomics, PN1000127) and library preparation was perfrmed according to the manufacturer's protocol (Chromium Next GEM Single Cell 3' reagent kits v3.1 (dual index)).

value: pancreas

value: pancreatic cells

tag: protocol


title: nPOD6292, snRNA-seq with endocrine population enrichment

description: 10X Genomics


title: Choroid_hsa, scRNAseq

city: Bentley

first: Paul

middle: James

last: Whatmore

state: Western Australia

address: Kent St

department: eResearch

country: Australia

institute: Curtin University

description: 10x Genomics

data_processing:
Demultiplexing, barcoding processing, gene counting and aggregation were completed using Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov)
Downstream analysis (see below) was completed in R v4.0.5
QC, dimensionality reduction, clustering, and differential expression analysis was completed using the R package Seurat (https://satijalab.org/seurat/)
Functional annotation of GE genes to KEGG pathways and GO terms was completed using the R package clusterProfiler (https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html)
Assembly: mm10, hg38
Supplementary files format and content: Quality-filtered barcodes (cell IDs), features (genes) and count matrix, generated by Cell Ranger.

source_name: Choroid

extract_protocol:
Mouse samples: Immune cells (CD45+ cells) were isolated from the choroid and pia mater of n=20 C57Bl/6J female mice (7 weeks of age) by FACS. Freshly dissected choroid and pia mater were pooled to obtain sufficient numbers of cells. The dissected tissues were transferred to 50 mL tubes containing dissection buffer (1x HBSS, no calcium, no magnesium, no phenol red; 5 mM glucose; 15 mM HEPES) and all processing was performed on ice. The tissues were passed through a 70 μm nylon cell strainer (Falcon 352350) using the plunger of a 5 mL syringe to obtain single cell suspensions, and then pelleted by centrifugation at 400 g for 5 min at 4 °C.  Pia mater-enriched tissue was subsequently resuspended in 30% (v/v) Percoll (GE Healthcare 17089102) in 1 x PBS and centrifuged at 700 g for 10 min at 4 °C without a brake being applied. The myelinated (i.e., hydrophobic) layer formed at the top of the tube was discarded prior to resuspending the cell pellet. The number of viable cells was determined by exclusion of trypan blue stain as viewed by microscopy, assisted by use of a hemocytometer. Cells were subsequently resuspended in FACS buffer (3 mM EDTA, 0.1% (w/v) BSA, 1 x PBS, 100 μg/mL DNase I) and stained with fluorescent-conjugated antibodies (rat anti- mouse CD45-BV605, BD Biosciences 563890) for 30 min on ice, then centrifuged and resuspended in FACS buffer. Immune cells (CD45+) were isolated from stained cell suspensions using a BD FACS Aria IIIu (100 µm nozzle) at QIMR Berghofer Flow Cytometry Facility. Dead cells were identified and excluded from analysis by staining with propidium iodide (PI, 1 μg/ mL, BD Biosciences, Franklin Lakes, NJ, 556463).  Human samples: Fresh (unfixed) human eye cups from a 45-year-old male donor with no history of eye disease or diabetes was obtained within 17 hours post-mortem from the Queensland Eye Bank. The vitreous and retinas were removed from the eye cups and choroid-RPE was subsequently dissected from the sclera. Choroid-RPE tissue was transferred into a 12-well plate and subjected to enzymatic digestion with collagenase type II (200 U/mL in HBSS (calcium, magnesium, no phenol red)) for 60 minutes at 37 °C, with tissue triturated every 15 minutes. After 60 minutes, choroid tissue was triturated with a pipette and then passed through a 70 µm cell strainer to generate a single cell suspension. The cell suspension was pelleted by centrifugation at 400 x g for 5 mins, resuspended in freezing media (DMEM/F12 containing 10% (v/v) DMSO and 10% (w/v) bovine serum albumin) and transferred to a Cool Cell freezing chamber at -80 °C for controlled freezing. Cells then were transferred to liquid nitrogen storage. For scRNA-seq studies, cells were thawed and pre-warmed DMEM/F12 containing 10% (w/v) BSA was added in a dropwise manner. The viability and yield of thawed cells were determined by trypan blue staining using a haemocytometer. Human choroidal immune cells were isolated from thawed cell suspensions by FACS. Briefly, thawed cell suspensions were incubated with 2.5 µg anti-human Fc block (BD Pharmingen 564220) for 15 mins, then centrifuged at 400 x g for 5 mins. The pellet was resuspended in FACS buffer containing BV421 Mouse Anti-Human CD45 antibody (BD Biosciences 563879) and incubated on ice for 30 mins. Cells were centrifuged at 400 x g for 5 mins then resuspended in FACS buffer for sorting. Live (propidium iodide negative) immune cells (CD45+) were sorted using a BD FACS Aria IIIu with a 100 µm nozzle.
scRNA-seq libraries were prepared using a Chromium single cell reaction 3’ v3.1 kit, following the manufacturer's instructions.

value: Choroid


title: nPOD6407, snRNA-seq with GRO-seq isolation method

description: 10X Genomics

value: snRNA-seq with GRO-seq isolation method


title: EDTA-K3 plasma anticoagulant tubes [8-OSA41]


title: DAOY, monolayer, replicate 1

description:
10X Genomics 3pr v3.1 Chemistry
01_DAOY_2D_rep_GEX-v3.1

source_name: DAOY cell line

value: DAOY cell line

value: in vitro culture


title: COVIDTet_S919_TP8_CD8_041_TCR

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

description: 22 years old male, 1 week after receiving the third shot

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system. The Variable (V) and Joining (J) segments of TCRs were represented in IMGT gene nomenclature. T-cell clones were determined as TCR reads with the same TCR V segment, J segment, and CDR3 nucleotide sequence.
Inter-sample contamination within samples using same UDIs were excluded by "Decontaminate" function of vdjtools with the parameter "-r 10".
The sequencing reads of samples were normalized to 16 times the cell count in each sample by the “DownSample” command of VDJtools-1.2.1, and TCR clones with 15 or fewer reads were regarded as sampling noise and removed from the dataset.
Assembly: IMGT reference sequences of human TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated from whole blood with BD vacutainer CPT tubes (BD), resuspended in CELLBANKER 1 (Takara), and stored in -80°C.
For preparing Peptides-HLA class I tetramers for SARS-CoV-2 Spike epitopes, S448 and S1208 peptides were purchased from GenScript. S269 and S919 peptides were purchased from GL Biochem Ltd. (Shanghai, China). Tetramers for S448, S1208, and S269 were generated by QuickSwitchTM Quant HLA-A*24:02 Tetramer Kit-BV421, HLA-A*24:02 Tetramer Kit -PE, and HLA-A*02:01 Tetramer Kit-PE (MBL), respectively, according to the manufacturer’s protocol. Tetramer for S919 was generated using Flex-T™ HLA-B*15:01 Monomer UVX (BioLegend) with D-Biotin (Nacalai) and BV421 Streptavidin (BD) according to the manufacturer’s protocol. The rate of peptide exchange was reported to be more than 95% in our previous report32. Thawed PBMCs were treated with a protein kinase inhibitor, Dasatinib (50 nM, AdooQ), for 30 min at 37 °C, and Human TruStain FcX for 5 minutes at room temperature. Then, PBMCs were stained with tetramers for 30 minutes at room temperature. After tetramer staining, cells were stained for antibody mix 3 (anti-CD4 (PerCP/Cyanine5.5), anti-CD14 (PE/Dazzle™ 594), anti-CD19 (PE/Dazzle™ 594), anti-CD45RA (APC/Cyanine7), anti-CD27 (APC), anti-CD8 (FITC, clone HIT8a)) for 20 minutes at room temperature. After washing twice with FACS buffer, CD8+ tetramer+ cells were sorted using FACS Aria II or Aria III and FACSDiva software (v8.0.1). Nonviable cells were excluded from the analysis based on forward and side scatter profiles and PI staining. Data were analyzed using FlowJo software (v10.8.1).
TCR-seq libraries of tetramer+ T cells were prepared on sample with (i) more than 100 tetramer+ cells and (ii) the proportion of tetramer+ cells was more than 0.1% in CD8+ T cells. S1208-tetramer+ sample with high background (ID22) was excluded from the analysis. Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2023).  In brief, mRNA in T-cell lysates were captured by incubating with 10 μL of Dynabeads M270 streptavidin (Thermo Fisher Scientific) bound to 2.5 pmol of BioEcoP-dT25-adapter primers for 30 minutes at room temperature under gentle rotation. mRNA-trapped beads were suspended in 10 µL of RT mix and incubated for 60 min at 42ºC to perform reverse transcription (RT) and template-switching. The composition of the RT mix was as follows; 1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of i5-TSO. To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed using KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), followed by the purification of PCR product using an AM Pure XP kit (Beckman Coulter) at a 0.7:1 beads-to-sample ratio. The third PCR was performed to amplify TCR libraries and add adaptor sequences for the next-generation sequencer. The third-PCR products were purified as second PCR. Final TCR libraries, whose lengths were about 600 base pairs, were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems), and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu). TCR libraries were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina) using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles, Illumina). Only read2 contained the sequence regarding the definition of T-cell clones. Oligonucleotides and reaction conditions for library preparation were summarized in Table S1 and S2, respectively.
Bulk TCR-seq

treatment_protocol: 38 healthcare workers (over 20 years old) at Nara Medical University in Japan received two doses of Pfizer-BNT162b2 vaccine between 10 March and 30 March 2021.

value: Peripheral blood

value: CD14- CD19- CD8+ S919-B15:01-tetramer+ T cells

value: Three doses of Pfizer-BNT162b2 vaccine


title: EDTA-K3 plasma anticoagulant tubes [9-OSA47]

value: Male


title: HPAP080, snRNA-seq with endocrine population enrichment

description: 10X Genomics


title: EDTA-K3 plasma anticoagulant tubes [8-OSA39]

value: Plasma samples were collected in the early morning and after 10-14 h of overnight fasting and after sleep test.


title: EDTA-K3 plasma anticoagulant tubes [8-OSA40]


title: EDTA-K3 plasma anticoagulant tubes [8-OSA44]

value: female


title: EDTA-K3 plasma anticoagulant tubes [8-OSA42]


title: EDTA-K3 plasma anticoagulant tubes [8-OSA38]


title: COVIDTet_S919_TP8_CD8_005_TCR

description: 39 years old male, 1 week after receiving the third shot


title: DAOY, tumour-spheroid, replicate 1

description:
10X Genomics 3pr v3.1 Chemistry
04_DAOY_SPHER_GEX-v3.1

source_name: DAOY tumour-spheroid

value: DAOY tumour-spheroid

value: DAOY


title: COVIDTet_S919_TP3_CD8_022_TCR

description: 33 years old male, 1 week after receiving the second shot


title: EDTA-K3 plasma anticoagulant tubes [7-OSA37]


title: COVIDTet_S919_TP3_CD8_005_TCR

description: 39 years old male, 1 week after receiving the second shot


title: nPOD6292, snRNA-seq without endocrine population enrichment

description: 10X Genomics


title: EDTA-K3 plasma anticoagulant tubes [7-OSA36]


title: EDTA-K3 plasma anticoagulant tubes [8-OSA43]


title: EDTA-K3 plasma anticoagulant tubes [7-OSA34]


title: COVIDTet_S919_TP2_CD8_037_TCR

description: 36 years old female, 1 week after receiving the first shot


title: EDTA-K3 plasma anticoagulant tubes [7-OSA35]


title: COVIDTet_S919_TP2_CD8_025_TCR

description: 50 years old male, 1 week after receiving the first shot


title: COVIDTet_S919_TP2_CD8_022_TCR

description: 33 years old male, 1 week after receiving the first shot


title: EDTA-K3 plasma anticoagulant tubes [7-OSA32]


title: EDTA-K3 plasma anticoagulant tubes [7-OSA33]


title: COVIDTet_S919_TP2_CD8_007_TCR

description: 49 years old male, 1 week after receiving the first shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA29]


title: EDTA-K3 plasma anticoagulant tubes [7-OSA30]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA28]


title: EDTA-K3 plasma anticoagulant tubes [7-OSA31]


title: COVIDTet_S919_TP2_CD8_005_TCR

description: 39 years old male, 1 week after receiving the first shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA27]


title: COVIDTet_S448_TP8_CD8_039_TCR

description: 33 years old male, 1 week after receiving the third shot

value: CD14- CD19- CD8+ S269-A02:01-tetramer+ T cells


title: COVIDTet_S448_TP8_CD8_033_TCR

description: 33 years old female, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_036_TCR


title: COVIDTet_S448_TP8_CD8_031_TCR

description: 36 years old male, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA26]

description:
HTG EdgeSeq miRNA WTA Sequencer NB551420
GEO_data HTG OSA Processed TB.txt


title: EDTA-K3 plasma anticoagulant tubes [6-OSA25]


title: COVIDTet_S448_TP8_CD8_037_TCR

description: 36 years old female, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_029_TCR

description: 57 years old female, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA24]


title: COVIDTet_S919_TP2_CD8_041_TCR

description: 22 years old male, 1 week after receiving the first shot


title: COVIDTet_S448_TP8_CD8_027_TCR

description: 35 years old male, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA23]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA22]


title: COVIDTet_S448_TP8_CD8_024_TCR

description: 43 years old female, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA20]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA21]


title: COVIDTet_S448_TP8_CD8_021_TCR

description: 45 years old male, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA19]


title: COVIDTet_S448_TP8_CD8_023_TCR

description: 47 years old male, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_035_TCR


title: COVIDTet_S448_TP8_CD8_019_TCR


title: COVIDTet_S448_TP8_CD8_015_TCR

description: 42 years old male, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_014_TCR

description: 28 years old female, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_018_TCR

description: 53 years old male, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA17]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA13]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA16]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA15]


title: COVIDTet_S448_TP8_CD8_012_TCR


title: EDTA-K3 plasma anticoagulant tubes [6-OSA11]


title: COVIDTet_S448_TP8_CD8_013_TCR


title: EDTA-K3 plasma anticoagulant tubes [6-OSA10]


title: COVIDTet_S448_TP8_CD8_011_TCR

description: 40 years old male, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [6-OSA12]


title: COVIDTet_S448_TP8_CD8_006_TCR

description: 46 years old male, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_010_TCR

description: 41 years old male, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [5-OSA08]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA09]


title: COVIDTet_S448_TP8_CD8_001_TCR

description: 43 years old male, 1 week after receiving the third shot


title: COVIDTet_S448_TP8_CD8_020_TCR

description: 44 years old female, 1 week after receiving the third shot


title: COVIDTet_S448_TP3_CD8_039_TCR

description: 33 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP8_CD8_004_TCR


title: COVIDTet_S448_TP8_CD8_016_TCR

description: 35 years old female, 1 week after receiving the third shot


title: EDTA-K3 plasma anticoagulant tubes [5-OSA06]

description:
HTG EdgeSeq miRNA WTA Sequencer NB551420
GEO_data HTG OSA Processed TB.txt


title: EDTA-K3 plasma anticoagulant tubes [5-OSA05]


title: EDTA-K3 plasma anticoagulant tubes [5-OSA07]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA18]


title: COVIDTet_S448_TP3_CD8_037_TCR

description: 36 years old female, 1 week after receiving the second shot


title: EDTA-K3 plasma anticoagulant tubes [5-OSA04]


title: EDTA-K3 plasma anticoagulant tubes [6-OSA14]


title: EDTA-K3 plasma anticoagulant tubes [5-OSA03]


title: EDTA-K3 plasma anticoagulant tubes [5-OSA01]


title: COVIDTet_S448_TP3_CD8_027_TCR

description: 35 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_024_TCR

description: 43 years old female, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_031_TCR

description: 36 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_036_TCR


title: EDTA-K3 plasma anticoagulant tubes [5-OSA02]


title: Pt2 iPSC-HPCs, KRASG13C, stimulated_STF3

city: Sagamihara

first: Makoto

last: Otsu

state: Kanagawa

address: 1-15-1 Kitasato, Minami-ku

institute: Kitasato University School of Medicine

data_processing:
Genedata Profiler Genome (GPG) v 11.0.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using GPG workflow.
Trimmed sequence reads (100bp) were mapped to GRCh37/hg19 using GPG and STAR sotwares.
Read count extraction and normalization were performed using GPG and STAR workflow.
All the above procedures were performed by TAKARA Bio.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet files include FPKM values and read counts for each sample

source_name: induced pluripotent stem cells

extract_protocol:
RNA was harvested using NucleoSpinRNA XS kit (MACHEREY-NAGEL). 1-10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: hematopoietic progenitor cells

tag: patient


title: COVIDTet_S448_TP3_CD8_022_TCR


title: Pt2 iPSC-HPCs, KRASG13C, stimulated_SF


title: Pt2 iPSC-HPCs, KRASG13C, unstimulated


title: Pt2 iPSC-HPCs, WTcontrol, stimulated_STF3

value: WT/WT


title: COVIDTet_S448_TP3_CD8_021_TCR

description: 45 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_019_TCR


title: Pt2 iPSC-HPCs, WTcontrol, stimulated_SF


title: Pt2 iPSC-HPCs, WTcontrol, unstimulated


title: COVIDTet_S448_TP3_CD8_016_TCR

description: 35 years old female, 1 week after receiving the second shot


title: 3T3_CDX2, CTCF, Dox, rep2

city: Lausanne

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

library_source: genomic

data_processing:
Reads were aligned to the mouse reference genome mm10 and the Drosophila reference genome dm6 using STAR with settings ‘--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’. Duplicate reads were removed with Picard (Broad Institute) and reads not mapping to chromosomes 1–19, X, or Y were removed. Normalization factors were calculated on the number of non-duplicated reads uniquely mapped to Drosophila genome for each sample and applied to downsample the total number of reads mapped to mouse genome. For each sample, peaks were called with MACS2 with settings ‘-f BAMPE -g mm’. Peaks overlapping peaks called for input (non-immunoprecipitated chromatin) from NIH-3T3 cells and ENCODE blacklisted peaks were discarded.
Assembly: mm10
Supplementary files format and content: bigWig files include RPKM normalized reads

molecule: genomic DNA

organism: Mus musculus

source_name: 3T3 iCDX2

growth_protocol: NIH3T3 cell lines stably expressing H2B-mCherry, the rtTA3G transactivator, and TRE3G-controlled (doxycycline (dox)-inducible) CDX2were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with Glutamax, 2 μg/ml Puromycin, and 1% Penicillin-Streptomycin, 10% Fetal bovine serum , and 1 mM sodium pyruvate  at 37°C with 5% CO2

extract_protocol:
5 million cells were fixed in 1% formaldehyde for 10 min at room temperature, quenched with 250 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at −80 °C. The cell pellet was resuspended in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100), incubated 10 min at 4 °C, spun down, and resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min at 4 °C. The pellet was spun down and rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and finally resuspended in 0.9 ml SDS shearing buffer. All buffers contain 1:100 diluted Protease Inhibitor Cocktail in DMSO (Sigma). The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicatedon a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken.5μg of sonicated chromatin was incubated with 5μg CTCF antibody (#61932 Active Motif) and for normalization 50ng Drosophila chromatin (Active Motif) and 2.5μg anti-H2Av drosophila-specific antibody (Active Motif). ChIP was performed using ChIP-IT High Sensitivity kit (Active Motif) following manufacturer protocol.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 37 nt paired end reads on an Illumina NextSeq 500.

treatment_protocol: CDX2 expression was induced by 6-hour treatment with 500ng/µL Doxycycline

value: 3T3 iCDX2

tag: chip antibody

value: CTCF ((#61932 Active Motif)

value: +Dox (6h)


title: COVIDTet_S448_TP3_CD8_010_TCR

description: 41 years old male, 1 week after receiving the second shot


title: 3T3_CDX2, CTCF, noDox, rep2

value: -Dox (6h)


title: 3T3_CDX2, CTCF, Dox, rep1


title: 3T3_CDX2, CTCF, noDox, rep1


title: COVIDTet_S448_TP3_CD8_014_TCR

description: 28 years old female, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_023_TCR

description: 47 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_015_TCR

description: 42 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP3_CD8_004_TCR


title: 3T3_CDX2, Input, noDox, rep1

value: input


title: COVIDTet_S448_TP2_CD8_039_TCR

description: 33 years old male, 1 week after receiving the first shot


title: Day2_SatelliteCells_NEMO_biol_rep2_ATAC

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

data_processing:
RNA-seq: Paired-end RNA-seq samples from Illumina were aligned to the mm10 reference genome with the STAR aligner (STAR_2.5.0a)(Dobin et al. 2013) using default parameters.
RNA-seq: RSEM (Applied Research Applied Research Press 2015) quantification was applied to the aligned reads. All replicates were aligned and quantified separately -- there were two technical replicates for each timepoint/condition (WT vs KO).
Supplementary files format and content: RNA-seq: .tsv tab-separated text files containing the RSEM quantified expected count, FPKM, TPM at both the isoform and gene level. Rows indicate unique gene / transcript identifiers. Columns indicate unique replicates
ATAC-seq: The ATAC-Seq samples were analyzed with the ENCODE ATAC-seq processing pipeline( https://github.com/ENCODE-DCC/atac-seq-pipeline, version 1.1.1)(Lee et al. 2016). The cutadapt algorithm(Martin 2011) was used to trim adapters, and the Bowtie2(Langmead and Salzberg 2012) aligner was used to align the reads to an mm10 index. Duplicates were then removed from the aligned reads, and the MACS2(Langmead and Salzberg 2012; Zhang et al. 2008) peak caller was used to call peaks from the aligned ATAC-seq samples. The naive overlap peak set from all replicates for a given sample was used. Such peak sets from all samples were concatenated and merged using the bedtools merge command to produce a master peak set across all samples. The read counts for each sample at each peak were obtained by running bedtools coverage on the shifted de-deplicated tagAlign files generated by the pipeline.
Assembly: mm9
Supplementary files format and content: ATAC-seq: tagAlign (alignments to mm9)
Supplementary files format and content: ATAC-seq:  narrowPeak peak calls for top 500K peaks with p-value from MACS2 < 0.01, TN5-shifted
Supplementary files format and content: ATAC-seq:  narrowPeak peak calls for top 500K peaks with p-value from MACS2 < 0.01, TN5-shifted; with peaks derived from overlap of pseudo reps via ENCODE processing pipeline (“naive overlap”)
Supplementary files format and content: ATAC-seq: bigWigs, fold-change (from MACS2)
Supplementary files format and content: ATAC-seq: bigWigs, p-value (from MACS2)

source_name: Satellite Cells

extract_protocol:
RNA-seq: At least 10,000 FACS sorted muscle stem cells were deposited into Trizol (Thermo Fisher) and snap frozen immediately thereafter. After thawing, total RNA was isolated using the miRNeasy Micro Kit (Qiagen) as per the manufacturer’s instructions. The isolated RNA was quantitated and the integrity of the samples were verified with a Bioanalyzer (Agilent 2100).
RNA-seq:  Approximately 10ng of isolated total RNA from biological replicates was used to produce cDNA libraries using the SmartSeq4 protocol (Clontech), as per the manufacturer’s instructions. Individual libraries were pooled and sequenced using one lane of 76-bp paired-end reads on an Illumina High-Seq 2500 to an average depth of 50M reads per library.
ATAC-seq: At least 10,000 sorted muscle stem cells were sorted into 1.5 mL centrifuge tubes, spun down at 500xg for 5 min at 4˚C and the supernatant removed. After re-suspension in cold 1x PBS and centrifugation again at 500xg for 5 min at 4˚C, the cell pellets were re-suspended in 50 µL of cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360), and centrifuged at 750xg for 15 min at 4˚C to pellet the nuclei. The nuclei were then re-suspended transposase reaction mix (12.5 µL 2x TD buffer, 1.25 µL TN5 transposase (Illumina) and 11.25 µL nuclease-free water), incubated at 37˚C for 35 min under mild agitation (300 rpm on a Thermo-Mixer C, Eppendorf). The transposed DNA fragments were purified (Qiagen MinElute PCR Purification Kit) as per manufacturer’s instructions, amplified using barcoded PCR primers and NEB Next High Fidelity 2x PCR Master Mix (New England Bio Labs) on a thermal cycler and purified again using double concentrated SPRI beads.
ATAC-seq: The concentration and size distribution of each was determined (Agilent 2100 Bioanalyzer), pooled and sequenced on a NextSeq (Illumina) using 76-bp paired-end reads to greater than 50M reads per library.

value: Satellite Cells

value: NEMO KO

tag: timepoint

value: Day 2


title: Day2_SatelliteCells_NEMO_biol_rep1_ATAC


title: Day2_SatelliteCells_Control_biol_rep2_ATAC

value: WT


title: COVIDTet_S448_TP2_CD8_036_TCR

value: Peripheral blood

value: Three doses of Pfizer-BNT162b2 vaccine


title: COVIDTet_S448_TP2_CD8_035_TCR

description: 36 years old female, 1 week after receiving the first shot


title: COVIDTet_S448_TP3_CD8_001_TCR

description: 43 years old male, 1 week after receiving the second shot


title: HFD, large nuclei, replicate4

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Sequence reads were pre-processed by fastp for adaptor trimming and filtering, and then aligned to GrCM38/mm10 using STAR. Filtered reads were assigned to transcriptome and quantified by featureCounts.
Assembly: mm10
Supplementary files format and content: txt (raw counts from each sample)

source_name: adipose

extract_protocol:
Nuclei were isolated from frozen inguinal (iWAT) white adipose tissues by pulverizing the tissues in liquid nitrogen and homogenizing in chilled Douncers. Next, the nucleus suspension was subject to nucleus sorting to remove debris and multiplets. RNA was extracted using TRIzol and used for constructing sequencing libraries.
The extracted RNA (100ng) was first purified using the TURBO DNase Kit and processed by NEBNext rRNA Depletion Kit for removing ribosomal RNA. Then, RNA was converted to cDNA using Maxima Reverse Transcriptas and NEBNext mRNA Second Strand Synthesis Kit following manufacturer's protocols. After purification of cDNA based on size, sequencing libraries were generated using Nextera XT DNA Library Preparation Kit and subsequent PCR amplification.

treatment_protocol: Adipoq-NuTRAP male C57BL/6J mice were subject to either a normal chow diet or a high-fat diet (HFD) for 12 weeks.

tag: strain

value: adipose

value: Adipoq-NuTRAP

value: High-fat diet (HFD)


title: COVIDTet_S448_TP2_CD8_037_TCR

value: CD14- CD19- CD8+ S269-A02:01-tetramer+ T cells


title: COVIDTet_S448_TP2_CD8_033_TCR

description: 33 years old female, 1 week after receiving the first shot


title: Day2_SatelliteCells_Control_biol_rep1_ATAC


title: COVIDTet_S448_TP3_CD8_018_TCR

description: 53 years old male, 1 week after receiving the second shot


title: COVIDTet_S448_TP2_CD8_031_TCR

description: 36 years old male, 1 week after receiving the first shot


title: COVIDTet_S448_TP2_CD8_027_TCR

description: 35 years old male, 1 week after receiving the first shot


title: HFD, large nuclei, replicate3


title: HFD, large nuclei, replicate1


title: HFD, large nuclei, replicate2


title: COVIDTet_S448_TP2_CD8_024_TCR

description: 43 years old female, 1 week after receiving the first shot


title: COVIDTet_S448_TP2_CD8_023_TCR

description: 47 years old male, 1 week after receiving the first shot


title: HFD, small nuclei, replicate3


title: HFD, small nuclei, replicate4


title: COVIDTet_S448_TP2_CD8_022_TCR


title: HFD, small nuclei, replicate2


title: HFD, small nuclei, replicate1


title: COVIDTet_S448_TP2_CD8_021_TCR

description: 45 years old male, 1 week after receiving the first shot


title: COVIDTet_S448_TP2_CD8_019_TCR


title: NCD, replicate3

value: Chow diet


title: COVIDTet_S448_TP2_CD8_018_TCR

description: 53 years old male, 1 week after receiving the first shot


title: COVIDTet_S448_TP2_CD8_020_TCR

description: 44 years old female, 1 week after receiving the first shot


title: COVIDTet_S448_TP2_CD8_016_TCR

description: 35 years old female, 1 week after receiving the first shot


title: NCD, replicate1


title: BCP, Preleukemic, rep4

city: Vancouver

first: Ali

last: Farrokhi

state: BC

address: BC Childrens Hospital Research Institute, 950 west 28th Ave- Ro0m 3062

country: Canada

institute: University of British Columbia

data_processing:
Basepace RNA-Seq Alignment app Version: 1.1.0 (Illumina) | Includes: Isis (Analysis Software) 2.6.25.18, STAR 2.5.0b, Isaac Variant Caller (2.3.13-31-g3c98c29-dirty), BEDTools (2.17.0), Cufflinks (2.2.1), BLAST (2.2.26+) | Parameters: {Stranded = First Strand, Panel = None, Aligner = STAR, QC Mode = False, Novel Transcript Assembly = False, FusionCalling = False, ERCC Spike-in controls = None, Trim TruSeq Adapters = True, Advanced Options = False, VariantCalling = True}
De-multiplexed input reads filtered against abundant sequences using Bowtie, adaptors trimmed, and aligned against mm10 reference sequence using STAR (default parameters as specified by pipeline).
Basepace Cufflinks Assembly & DE app Version: 2.1.0 (Illumina) | Includes: Isis (Analysis Software) 2.6.25.17, STAR (Aligner) STAR_2.5.0b, BEDTools 2.17.0, Cufflinks 2.2.1, BLAST 2.2.26+ | Parameters {Strandedness = First Strand, Aligner = STAR, Novel Transcript Assembly = Not Completed in RNA-Seq Alignment, Panel = None, Group 1 = Leukemic, Group 2 = Pre-Leukemic, PolyA = Yes, Enable Pairwise Diff Expression Analysis = True, Control = Pre-Leukemic, Advanced Options = False}
Aligned read assembly and abundance estimation (FPKM) carried out using Cufflinks (default parameters as specified by pipeline)
Genes with row-wise count <= 10 removed
Normalization and differential-expression analysis carried out in DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Spleen

growth_protocol: BCP were FACS sorted from preleukemic and leukemic mice into RNA later.

extract_protocol:
Total RNA was isolated from sorted BCP using AllPrep DNA/RNA Mini kit (Qiagen)
Sample quality control performed on Agilent 2100 Bioanalyzer. Qualifying samples were prepared for RNA-seq using NEBnext Ultra ii Stranded mRNA Library Prep Kit (New England Biolabs) following manufacturers protocol.

value: Spleen

value: B-cell precursor (BCP)

tag: disease state

value: Preleukemia

value: Emu-Ret hemizygote

value: BALB/c background


title: COVIDTet_S448_TP2_CD8_014_TCR

description: 28 years old female, 1 week after receiving the first shot


title: BCP, Preleukemic, rep3


title: BLAS Tat 48h 2

city: Villejuif

first: Anna

last: Schwager

state: Please Select

address: 114 Rue Edouard Vaillant

country: France

institute: Institut Gustave Roussy

data_processing:
The reads were trimmed with trimgalore (0.6.7) and cutadapt (3.4) to remove the Illumina adapter sequences from the 3′-ends. The trimmed reads were mapped to the GRCh38 genome from the Illumina iGenomes using Hisat2 and quantified with FeatureCounts.
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: blood

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA isolation kit (Macherey-Nagel, Germany) following manufacturer’s instructions
Novogene NGS RNA Library Prep Set (PT042)

value: blood

value: BLAS

value: B cells

value: Tat 48h


title: COVIDTet_S448_TP2_CD8_015_TCR

description: 42 years old male, 1 week after receiving the first shot


title: BCP, Preleukemic, rep2


title: COVIDTet_S448_TP2_CD8_013_TCR


title: COVIDTet_S448_TP2_CD8_012_TCR


title: BCP, Preleukemic, rep1


title: BCP, Leukemic, rep3

value: Overt Disease


title: BCP, Leukemic, rep2


title: BCP, Leukemic, rep1


title: COVIDTet_S448_TP2_CD8_006_TCR

description: 46 years old male, 1 week after receiving the first shot

value: Peripheral blood


title: KOOTI-WT2

city: Yangsan

first: YUNA

last: JO

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan National University

data_processing:
Analysis of ATAC-seq data was very similar to the analysis of ChIP Seq data. Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: mm10
Supplementary files format and content: bw

source_name: tumor

extract_protocol:
To analyze the function of CD8+ T cells in the TME, we sorted tumor-infiltrating CD8+ T cells from tumor-bearing mice.
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented , with some = modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

value: tumor

value: primary cells

value: Tumor-infiltrating CD8 T cells


title: COVIDTet_S448_TP2_CD8_011_TCR

description: 40 years old male, 1 week after receiving the first shot

value: Three doses of Pfizer-BNT162b2 vaccine


title: COVIDTet_S269_TP8_CD8_032_TCR

description: 33 years old male, 1 week after receiving the third shot

value: CD14- CD19- CD8+ S269-A02:01-tetramer+ T cells


title: COVIDTet_S269_TP8_CD8_026_TCR

description: 44 years old male, 1 week after receiving the third shot


title: COVIDTet_S448_TP2_CD8_004_TCR

description: 41 years old male, 1 week after receiving the first shot


title: COVIDTet_S269_TP8_CD8_017_TCR

description: 47 years old male, 1 week after receiving the third shot


title: NCD, replicate2

value: adipose

value: Adipoq-NuTRAP

value: Chow diet


title: OTI-WT2


title: OTI-WT1


title: COVIDTet_S269_TP8_CD8_007_TCR

description: 49 years old male, 1 week after receiving the third shot


title: MYC control 2

city: Cincinnati

first: Yunguan

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads with phred quality scores less than 25 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.1.0) (Pertea et al., 2016) aligner using default settings.
The alignment files, that is, SAM files were converted to BAM files and then sorted by 'coordinate' using sambamba 0.6.6.
Aligned reads were quantified using featureCounts (v1.6.3) (Liao et al., 2014) per gene ID against GRCm38 GENCODE version M20.
Differential gene expression analysis was done using the R package DEseq2 (v 1.20.0).
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Liver

extract_protocol:
Total liver RNA was isolated using TRIzol (Invitrogen #15596018) followed by purification using the RNeasy Mini kit (Qiagen #74104). The RNA was further treated with DNase (Invitrogen #AM1906).
The RNA-seq library was prepared using the Nugen Ovation Mouse RNA-seq System (Nugen #0348-32) and quantified with the Qubit dsDNA BR Assay kit.

value: hepatocytes

value: Liver

value: LAP-tTA

value: Dox was given for the same schedule


title: COVIDTet_S269_TP8_CD8_003_TCR

description: 31 years old male, 1 week after receiving the third shot


title: MYC OE -3

value: LAP-tTA; TRE-MYC

value: MYC was induced at ~E8 by withdrawing dox water from pregnant mothers


title: COVIDTet_S269_TP3_CD8_032_TCR

description: 33 years old male, 1 week after receiving the second shot


title: COVIDTet_S269_TP3_CD8_026_TCR

description: 44 years old male, 1 week after receiving the second shot


title: MYC OE -1


title: COVIDTet_S448_TP2_CD8_010_TCR


title: COVIDTet_S269_TP3_CD8_017_TCR

description: 47 years old male, 1 week after receiving the second shot


title: COVIDTet_S1208_TP8_CD8_039_TCR

value: CD14- CD19- CD8+ S1208-A24:02-tetramer+ T cells


title: YAP OE 4 weeks -2

value: Col-TRE-YAPS127A; Rosa26-LSL-rtTA

value: YAPS127A was induced by Dox for 4 weeks


title: COVIDTet_S269_TP3_CD8_004_TCR

description: 41 years old male, 1 week after receiving the second shot

value: Peripheral blood


title: YAP OE 2 weeks -2

value: YAPS127A was induced by Dox for 2 weeks


title: KOOTI-WT1

value: tumor

value: primary cells

value: Tumor-infiltrating CD8 T cells


title: YAP control 2

value: YAPS127A was not induced


title: YAP control 1


title: COVIDTet_S1208_TP8_CD8_033_TCR

description: 33 years old female, 1 week after receiving the third shot

value: Three doses of Pfizer-BNT162b2 vaccine


title: COVIDTet_S1208_TP8_CD8_031_TCR

description: 36 years old male, 1 week after receiving the third shot


title: COVIDTet_S1208_TP8_CD8_035_TCR

description: 36 years old female, 1 week after receiving the third shot


title: COVIDTet_S1208_TP8_CD8_037_TCR


title: COVIDTet_S1208_TP8_CD8_027_TCR

description: 35 years old male, 1 week after receiving the third shot


title: MYC control 1


title: Male sham_rep3

city: Seoul

first: Eun-Mi

last: Hur

address: 1, Gwanak-ro, Gwanak-gu

department: College of Veterinary Medicine

institute: Seoul National University

data_processing:
Raw reads from the sequencere were processed to remove low quality and adapter sequence using fastx_trimmer (Bolger et al., Bioinformatics, 2014).
Bowtie2 was used to align the processed reads, estimate the abundance, and detect differentially expressed genes (DEGs) (Langmead & Salzberg, Nature methods, 2012). DEGs were determined on the basis of counts from alignments using the Bedtools. (Quinlan & Hall, Bioinformatics, 2010)
The relative abundance estimates of genes expressed were processed and normalized with respect to library size with Edge R (R Development Core Team, 2016).
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Matrix table with raw gene counts and normalized expression levels for every gene and every sample

source_name: dorsal root ganglion

extract_protocol:
Total RNA was extracted from L3-L5 DRGs of injured and sham mice using Nucleopsin RNA isolation kit.
cDNA libraries were prepared for sequencing using Quant Seq 3’ mRNA-Seq Library Prep Kit which includes procedures for polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription, and single-end sequencing by Illumina NextSeq 500.

value: dorsal root ganglion

value: post natal week 8

value: Male

value: sham


title: COVIDTet_S1208_TP8_CD8_024_TCR

description: 43 years old female, 1 week after receiving the third shot


title: MYC OE -2

value: hepatocytes

value: Liver


title: Male sham_rep1


title: COVIDTet_S1208_TP8_CD8_019_TCR


title: Male sham_rep2


title: Male SNI_rep3

value: SNI


title: YAP OE 4 weeks -3


title: COVIDTet_S1208_TP8_CD8_018_TCR

description: 53 years old male, 1 week after receiving the third shot

value: CD14- CD19- CD8+ S1208-A24:02-tetramer+ T cells


title: COVIDTet_S269_TP3_CD8_003_TCR

description: 31 years old male, 1 week after receiving the second shot

value: CD14- CD19- CD8+ S269-A02:01-tetramer+ T cells


title: Male SNI_rep2


title: COVIDTet_S1208_TP8_CD8_014_TCR

description: 28 years old female, 1 week after receiving the third shot


title: COVIDTet_S1208_TP8_CD8_011_TCR

description: 40 years old male, 1 week after receiving the third shot


title: YAP OE 4 weeks -1

value: Col-TRE-YAPS127A; Rosa26-LSL-rtTA

value: YAPS127A was induced by Dox for 4 weeks


title: Female sham_rep3

value: Female


title: COVIDTet_S1208_TP3_CD8_037_TCR

description: 36 years old female, 1 week after receiving the second shot

value: Peripheral blood


title: YAP OE 2 weeks -1

value: YAPS127A was induced by Dox for 2 weeks


title: Male SNI_rep1


title: Female sham_rep2


title: COVIDTet_S1208_TP3_CD8_031_TCR

description: 36 years old male, 1 week after receiving the second shot


title: Female sham_rep1


title: Female SNI_rep3


title: COVIDTet_S1208_TP3_CD8_024_TCR

description: 43 years old female, 1 week after receiving the second shot


title: COVIDTet_S1208_TP3_CD8_027_TCR

description: 35 years old male, 1 week after receiving the second shot


title: COVIDTet_S1208_TP3_CD8_019_TCR


title: Female SNI_rep1


title: Female SNI_rep2


title: COVIDTet_S1208_TP3_CD8_018_TCR

description: 53 years old male, 1 week after receiving the second shot


title: Bmpr1a_CKO_rep2

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

data_processing:
Cutadapt 1.13
Trimmomatic 0.35
RNA-star 2.5.2b
Htseq-count 0.6.1p2
EdgeR 3.16.5
Genome_build: Gencode M8, GRCm38, Ensembl 83
Supplementary_files_format_and_content: 01Feb16_WS_EdgeR_DE_24810_genes.xlsx: Differential gene expression analysis
Supplementary_files_format_and_content: 22Feb16_WS_Raw_Data_RPKM_ALL.csv: Raw Data, Counts and RPKM values for every genomic feature
Supplementary_files_format_and_content: gencode_vM8_ERCC.gtf: Table of genomic features and ERCC controls useful for reprocessing the data

source_name: Lung

growth_protocol: Bmpr1a flox mice were crossed with Tbx4-rtTA/TetO-Cre transgenic mice

extract_protocol:
Lung were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and purified using the RNeasy Micro Kit (QIAGEN, Cat #74004).
Illumina TruSeq v2

treatment_protocol: Doxycycline was gived in drinking water (1mg/ml) and in food from E6.5 to E15.5.

value: Lung

value: embryonic day 15.5 (E15.5)


title: Bmpr1a_CKO_rep3


title: COVIDTet_S1208_TP3_CD8_010_TCR

value: Three doses of Pfizer-BNT162b2 vaccine


title: COVIDTet_S1208_TP3_CD8_014_TCR

description: 28 years old female, 1 week after receiving the second shot


title: WT_rep2

value: wild type


title: Bmpr1a_CKO_rep1


title: WT_rep3


title: COVIDTet_S1208_TP3_CD8_036_TCR

description: 33 years old male, 1 week after receiving the second shot


title: COVIDTet_S1208_TP2_CD8_031_TCR

description: 36 years old male, 1 week after receiving the first shot


title: WT_rep1


title: COVIDTet_S1208_TP2_CD8_024_TCR

description: 43 years old female, 1 week after receiving the first shot


title: LuCaP 170.2, input [170.2_TE]

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description: input

data_processing:
Sequence analysis was conducted using Nextflow Core analysis pipeline (10.5281/zenodo.3240506)
Assembly: hg19
Supplementary files format and content: bigwig, NarrowPeak
Supplementary files format and content: concensus peaks and counts files for H3K27ac and HNF1A ChIPs

source_name: prostate cancer

growth_protocol: PDX tumors were passaged in NOD scid gamma (NSG) mice at the NCI and propagated in vitro as 3-dimensional organoid cultures. PDXs were enzymatically degraded using the MACS human Tumor Dissociation Kit

extract_protocol:
Chromatin sample preparation was obtained using the Active Motif ChIP-IT High Sensitivity kit per manufacturer instructions. Samples were immunoprecipitated overnight using ChIP-seq grade H3K27ac antibody or HNF1A, bound to protein G dynabeads.  A fraction of sample was not exposed to antibody and used as input control.
Samples underwent crosslink reversal with RNase and proteinase K, and DNA sequencing libraries were prepared using the Accel-NGS-2S DNA Library Kit.
Libraries were sequenced using 100-bp paired end reads using NovaSeq 6000 on the Illumina platform at the CCR-Sequencing Facility.

treatment_protocol: LuCaP 23.1 cells were transduced with generated lentivirus via centrifugation and LentiBOOST.

value: prostate cancer

value: LuCaP 170.2

value: Wild-type

value: male


title: LuCaP 23.1 ectopically expressing HNF1A, input [H1r2_TE]

description: input

value: LuCaP 23.1

value: HNF1A expressing


title: LuCaP 170.3, input [170.3_TE]

description: input

value: LuCaP 170.3


title: COVIDTet_S1208_TP2_CD8_014_TCR

description: 28 years old female, 1 week after receiving the first shot

value: CD14- CD19- CD8+ S1208-A24:02-tetramer+ T cells


title: LuCaP 23.1 empty vector, input [M1r2_TE]

description: input

value: Empty Vector


title: LuCaP 23.1 empty vector, HNF1A, ChIP, rep2 [M2r2_HNF1A]

value: HNF1A (Cell Signaling cat. No 89670)


title: MUSIC_H1_E14_mix_species

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: University of California, San Diego

library_source: other

data_processing:
The raw pair-end read pairs with a 28bp read1 and 150bp read2. Read1 contains 16bp 10X Barcode and 12bp 10X UMI sequence. The 150bp Read2 sequence contains the 3rd, 2nd, 1st Cell Barcodes, the RNA Linker sequence or the DNA-Linker(bt) sequence, the RNA insert or the DNA insert.
Three rounds of cell barcodes, DNA/RNA identifier (Linker) and 10X Barcode are extracted using customized code following the pipeline described in http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/intro.html
Consecutive As or Gs from the 3' of the DNA insert that regarded as artifacts and are removed using cutadaptor (v2.8) with parameters "-q 15 -m 20". For RNA reads, we will detect the ssDNA region of the RNA Linker sequence “CGAGGAGCGCTT” and remove any sequence following it.
Cleaned DNA reads were mapped to the genome (hg38/mm10) using "bowtie2 -p 10 -t -phred33 -x" and cleaned RNA reads were mapped to the genome in a splice aware manner using "bwa mem" with parameters "-SP5M".
Customized deduplication script was applied to remove PCR duplicates. Any read that satisfies all the following criteria is flagged as a duplicate: 1) it maps to a location within 8 base pairs of the previous read, 2) it shares the same cell barcode and molecular barcode with the previous read, and 3) its UMI exhibits a Levenshtein distance of less than 2 base pairs from the UMI of the previous read. All identified PCR duplicates are subsequently removed to ensure the integrity of downstream analyses.
Finally we consolidated all deduplicated BAM files obtained from each I7 index-marked library into a unified bam file for each sample. The read name in the bam file records cell barcodes, molecular barcode and mapping location of the insert for both DNA and RNA.
Assembly: hg38; mm10
Supplementary files format and content: The processed data ended with DNA.reads.csv.gz or RNA.reads.csv.gz recorded the cell barcode (CB), molecular complex barcode (CBMB), genomic region and strand information of each DNA/RNA read. The Filtered_human(mouse) files only include cells passed purity threshold (more than 95% of DNA reads mapped to a single species, and have at least 1000 DNA reads per cell). We have provided information on DNA and RNA reads for each brain sample, including all detected cells from that donor without undergoing quality control and filtering. To work with the same group of brain cells presented in the manuscript, kindly refer to the cells outlined in the FrontalCortex_sample_meta_data.tsv file.

molecule: other

organism:
Homo sapiens
Mus musculus

source_name: cell line

growth_protocol: H1 human embryonic stem cells and E14 mouse embryonic stem cells were cultured according to the 4D Nucleome Consortium approved protocols (https://www.4dnucleome.org/).

extract_protocol:
Cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) and 3% formaldehyde (FA). The crosslinking reaction was quenching by adding 3 mL of 2.5 M glycine per 10 mL of 3% formaldehyde. Five million cells were lysed in 1.4 mL of cell lysis buffer A (50 mM HEPES pH 7.4, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 140 mM NaCl, 0.25% Triton X-100, 0.5% IGEPAL CA-630, 10% glycerol, 1X proteinase inhibitor cocktail (PIC)) followed by a 10-min incubation in lysis buffer B (10 mM Tris-HCl pH 8, 1.5 mM EDTA, 1.5 mM EGTA, 200 mM NaCl, 1X PIC) for 10 min. Isolated nuclei were further permeabilized in 0.25% SDS solution at 62°C for 10 min, and the reaction was quenched with 10% Triton X-100 (wt/vol) at 37°C for 15 min.
After the RNA and DNA linker ligations, three rounds of cell barcode ligations, dA-tailling, 10X barcode addition, and library amplification with multiple indexed i7, the molarity of the sequencing library was measured by Qubit 4.0 Fluorometer (Invitrogen, Q33238) using Qubit dsDNA HS assay kit (Invitrogen, Q33231). Fragment size distribution was assessed by Agilent bioanalyzer with High sensitivity DNA ChIP. The library was sequenced by UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000. The sequencer is set to read a 28 bp sequence next to the Universal Adapter as the Read1, a 8 bp index sequence from the I7 region inside the Index Adapter, and a 150 bp sequence next to the Index Adapter as the Read2.

treatment_protocol: There was no cell treatment during cell growth.

value: cell line

value: H1-hESC, E14-mESC

value: Human embryonic, Mouse embryonic

value: WT

value: Mixed species sample


title: Gastric cancer

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: This total RNA is cell-free RNA extracted from a mixed urine sample of three individuals.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Urine in gastric cancer

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted from 400 μl of urine after removal of cellular components using the mirVana PARIS Kit (Ambion, Austin, TX).

treatment_protocol: PC and GC were surgically resected and pathologically diagnosed cases. Healthy volunteers were required to undergo medical tests, including computed tomography and endoscopy, with no indication of pancreatic or stomach disease or cancer.

value: Gastric cancer


title: LuCaP 23.1 empty vector, H3K27ac, ChIP, rep2 [M2r2_H3K27Ac]

value: H3K27ac (Diagenode, cat. No C15410196)


title: LuCaP 23.1 empty vector, HNF1A, ChIP, rep1 [M1r2_HNF1A]

value: prostate cancer


title: Pancreatic cancer

source_name: Urine in pancreatic cancer

value: Pancreatic cancer


title: Healthy volunteer

source_name: Urine in healthy volunteer

value: Healthy volunteer


title: Peripheral blood mononuclear cells (PBMCs) 6a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac

city: shaoxing

first: guanguan

last: qiu

state: zhejiang

address: Yanan Road123

country: China

institute: shaoxing second hospital

description: Peripheral blood samples 6a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac,total RNA was extracted from PBMC

hyb_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood samples were obtained from the subjects 1-2 weeks after the third dose of CoronaVac.

label_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

growth_protocol: Percoll density gradient followed by plastic adherence was used for PBMC separation. Nine milliliters of heparinized peripheral blood from  healthy volunteers was mixed with 9 ml phosphate-buffered saline (PBS). Aliquots of the mixture (6 ml) were overlaid onto 6 ml Ficoll-Paque density gradient (Cedarlane, Burlington, NC, USA) in 15 ml tubes, which were then centrifuged at 2000 rpm for 20 min. Peripheral blood mononuclear cells (PBMC) at the interface were collected and washed twice with PBS.

extract_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: PBMC


title: LuCaP 23.1 ectopically expressing HNF1A, H3K27ac, ChIP, rep2 [H2r2_H3K27Ac]

value: LuCaP 23.1

value: male


title: LuCaP 23.1 ectopically expressing HNF1A, HNF1A, ChIP, rep2 [H2r2_HNF1A]

value: HNF1A expressing


title: Peripheral blood mononuclear cells (PBMCs) 5b was obtained from the subjects before the third dose of CoronaVac

description: Peripheral blood samples 5b was obtained from the subjects before the third dose of CoronaVac,total RNA was extracted from PBMC

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood samples were obtained from the subjects before the third dose of CoronaVac.


title: Peripheral blood mononuclear cells (PBMCs) 5a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac

description: Peripheral blood samples 5a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac,total RNA was extracted from PBMC


title: LuCaP 23.1 ectopically expressing HNF1A, H3K27ac, ChIP, rep1 [H1r2_H3K27Ac]


title: LuCaP 170.3, H3K27ac, ChIP, rep 1 [170.3T_H3K27Ac]

value: LuCaP 170.3

value: Wild-type


title: Peripheral blood mononuclear cells (PBMCs) 4b was obtained from the subjects before the third dose of CoronaVac

description: Peripheral blood samples 4b was obtained from the subjects before the third dose of CoronaVac,total RNA was extracted from PBMC


title: LuCaP 170.2, H3K27ac, ChIP, rep 1 [170.2_H3K27Ac]

value: LuCaP 170.2


title: LuCaP 170.2, H3K27ac, ChIP, rep 2 [170.2r2_H3K27Ac]


title: Peripheral blood mononuclear cells (PBMCs) 4a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac

description: Peripheral blood samples 4a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac,total RNA was extracted from PBMC


title: Peripheral blood mononuclear cells (PBMCs) 3b was obtained from the subjects before the third dose of CoronaVac

description: Peripheral blood samples 3b was obtained from the subjects before the third dose of CoronaVac,total RNA was extracted from PBMC


title: Peripheral blood mononuclear cells (PBMCs) 2a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac

description: Peripheral blood samples 2a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac,total RNA was extracted from PBMC


title: Peripheral blood mononuclear cells (PBMCs) 6b was obtained from the subjects before the third dose of CoronaVac

description: Peripheral blood samples 6b was obtained from the subjects before the third dose of CoronaVac,total RNA was extracted from PBMC


title: Peripheral blood mononuclear cells (PBMCs) 2b was obtained from the subjects before the third dose of CoronaVac

description: Peripheral blood samples 2b was obtained from the subjects before the third dose of CoronaVac,total RNA was extracted from PBMC


title: Peripheral blood mononuclear cells (PBMCs) 3a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac

description: Peripheral blood samples 3a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac,total RNA was extracted from PBMC


title: Peripheral blood mononuclear cells (PBMCs) 1b was obtained from the subjects before the third dose of CoronaVac

description: Peripheral blood samples 1b was obtained from the subjects before the third dose of CoronaVac,total RNA was extracted from PBMC


title: HCT116 cells, miR-8485 mimics, rep3

city: Beijing

first: Yingxing

last: Li

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wa

institute: Peking Union Medical College Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Fastp (version 0.23.1).
paired-end clean reads were aligned to the reference genome using hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples

extract_protocol:
Total RNA was extracted following the standard Trizol protocol (15596026, Invitrogen, Carlsbad, CA, USA).
RNA libraries from three independent biological replicates were generated using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605, Vazyme, Nanjing, China) according to the manufacturer’s instruction.

value: human colorectal cancer cells

value: miR-8485 mimics


title: HCT116 cells, miR-8485 mimics, rep2


title: LuCaP 23.1 empty vector, H3K27ac, ChIP, rep1 [M1r2_H3K27Ac]

value: Empty Vector


title: VUMC1000

city: Nashville

first: Cong

last: Wang

state: TN

address: 2525 West End Ave

institute: Vanderbilt University

hyb_protocol: NanoString nCounter miRNA Expression Assay manufacturer's protocol

data_processing: miRNAs were normalized in the following steps: 1) background correction to remove non-specific binding. The background level was calculated as an aggregate summary of seven negative control probes with no target transcript. Mean of the calculated background level for each sample was then subtracted from the adjusted probe value to remove background noise. 2) Normalization of miRNA counts using mean counts of three spike-in synthetic control miRNAs (ath-miR159a, cel-miR-248, and osa-miR414) to control for variances on the starting material and the miRNA purification efficiency. 3) Sample content normalization using geometric mean counts of the top 50 miRNAs expressed excluding hsa-miR-320e, hsa-miR-16-5p and hsa-miR-451a because these miRNAs may be related to red blood cell contamination or hemolysis. After these steps, the expression level of each miRNA was calculated.

label: NanoString

source_name: plasma

extract_protocol: Qiagen’s miRNeasy Plasma Kit manufacturer's protocol

tag: study site (plco=1 swmhs=2 sccs=3 mec=4)

tag: case control status (control=0 case=1)

tag: sets

tag: sex (female=0 male=1)

tag: age at diagnosis

tag: race (white=1 black=2 other=3)


title: VUMC0999


title: HCT116 cells, control, rep2

tag: cell line

tag: cell type

value: WT


title: HCT116 cells, control, rep1


title: LuCaP 23.1 ectopically expressing HNF1A, HNF1A, ChIP, rep1 [H1r2_HNF1A]

tag: tissue

value: HNF1A (Cell Signaling cat. No 89670)

tag: Sex


title: LuCaP 170.3, H3K27ac, ChIP, rep 2 [170.3r2_H3K27Ac]

tag: genotype


title: Peripheral blood mononuclear cells (PBMCs) 1a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac

description: Peripheral blood samples 1a was obtained from the subjects 1-2 weeks after the third dose of CoronaVac,total RNA was extracted from PBMC


title: VUMC0995


title: HCT116 cells, control, rep3


title: H2170_CRISPRi_MYCp1_RNA_seq

city: Salt Lake City

first: Xiaoyang

last: Zhang

state: Utah

address: 1950 Circle of Hope Drive

department: Oncological Sciences

institute: University of Utah

data_processing:
Bowtie2 to align sequencing reads
RSEM to quanitfy expression for each GENCODE gene
Assembly: hg19
Supplementary files format and content: RSEM text file

extract_protocol:
Quick-RNA miniprep kit (ZYMO R1055)
NEBNext Ultra Directional RNA library prep kit (NEB E7760S)

value: Lung squamous cancer cell line

tag: treatment

value: CRISPRi sg_MYCp1


title: VUMC0993


title: B2V2

city: Jinan

first: Yi

last: Han

address: 16766 Jingshi Road, Lixia District

institute: The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: control


title: B2V3


title: VUMC0990


title: VUMC0991


title: B2P3

value: pentamethylquercetin(PMQ)(100 μM) for 24 h


title: VUMC0992


title: VUMC0998


title: VUMC0989


title: HCT116 cells, miR-8485 mimics, rep1


title: B2P2


title: B2V1


title: B2P1


title: VUMC0997


title: VUMC0996


title: VUMC0986


title: VUMC0988


title: H2170_CRISPRi_MYCp2_RNA_seq

value: CRISPRi sg_MYCp2


title: DJ004

city: New York City

first: Joshua

middle: Ian

last: Gray

state: New York

address: 630 168th Street

department: CCTI

institute: Columbia University

description: 10x Genomics

data_processing:
ADT barcodes were extracted from demultiplexed fastq files using custom scripts (https://github.com/simslab/DropSeqPipeline8). Hashtag barcodes from cell-identifying barcodes containing >1,000 unique transcripts were demultiplexed using the Hashsolo with default parameters.
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: gd T cells

extract_protocol:
Single cell suspensions were thawed from liquid nitrogen by resuspending in warmed IMDM, before incubation with 20ul/ml of Dnase for 20 minutes at 37degrees. gd T cells were enriched by FACS-sorting. Enriched gd T cell populations from each sample were resuspended in PBS FBS EDTA and stained with 3ul of a unique TotalSeq-C DNA-barcoded hashtag for 30 minutes on ice. For libraries DJ001A1, DJ001A2, DJ001B1 and DJ001B2 the hashtags were paired as follows: HDL141 spleen - TotalSeq-C0251_Hashtag_1; HDL141 lung - TotalSeq-C0252_Hashtag_2; HDL141 LLN - TotalSeq-C0253_Hashtag_3; HDL141 jejunum - TotalSeq-C0254_Hashtag_4; HDL141 MLN - TotalSeq-C0255_Hashtag_5. For libraries DJ001-4 hashtages were paired with the following samples: HDL138 lung - TotalSeq-C0251_Hashtag_1; HDL138 spleen - TotalSeq-C0252_Hashtag_2 ;HDL138 LLN - TotalSeq-C0253_Hashtag_3; HDL138 jejunum - TotalSeq-C0254_Hashtag_4 ; HDL138 MLN - TotalSeq-C0255_Hashtag_5 ; HDL131 spleen - TotalSeq-C0256_Hashtag_6; HDL142 lung - TotalSeq-C0257_Hashtag_7; HDL142 LLN - TotalSeq-C0258_Hashtag_8; HDL142 jejunum - TotalSeq-C0259_Hashtag_9; HDL142 MLN - TotalSeq-C0260_Hashtag_10. Cells were washed, counted and combined ensuring equal numbers of cells were present from each sample.
CITE libraries were constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics) with a 5’ Feature Barcode Kit (10x Genomics) for antibody-derived tag (ADT) amplification according to the manufacturer’s instructions. The ADT library pool and scRNA-seq library pool were each sequenced on one lane of an S4 flow cell on an Illumina NovaSeq 6000 (~2.5 billion 2x100 bp reads per lane). Quantification of scRNA-seq library pools was performed by pseudoalignment to the human transcriptome (Gencode v24 annotation derived from GRCh38) using kallisto v0.46.2 in “BUS” mode

value: gd T cells

tag: donors

tag: age


title: VUMC0984


title: VUMC0983


title: DJ002

description: 10x Genomics


title: VUMC0982


title: VUMC0994


title: DJ001

description: 10x Genomics


title: DJ003

description: 10x Genomics


title: VUMC0981


title: VUMC0980


title: DJ001B

description: 10x Genomics

value: 2 years


title: VUMC0979


title: VUMC0985


title: human oocytes,fresh group_3

city: taiyaun

first: Lu

address: Wuyi Road, Xinghualing District, Taiyuan City, Shanxi Province

institute: The Second Hospital of Shanxi Medical University

description: fresh group

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9) was used to remove the reads that contained adaptor contamination. And after removed the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-1.3.4d). The expression levels of all transcripts were estimated and performed as calculating FPKM (FPKM = [total exon fragments / mapped reads (millions) × exon length (kB)] ).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). And then the GO terms (http://www.geneontology.org/) and KEGG Pathway (http://www.genome.jp/kegg/) of these differentially expressed mRNAs were also annotated.
Assembly: GRCH38
Supplementary files format and content: file includes raw counts for each sample
Supplementary files format and content: files includes FPKM for each sample

source_name: oocytes

extract_protocol:
According to the experimental requirements, a control group (0M), 100 µg/mL AfrLEA2 group, 100 µg/mL AfrLEA3m group and fresh group were set up with 3 replicates in each group, and a total of 12 human oocytes were collected from the corresponding condition groups. After washing each oocyte twice in PBS, a volume of less than 5 µl of cells and fluid was aspirated and quickly transferred under a microscope to a clean 200 µl PCR (RNase-free) tube containing lysate, and each sample was placed on dry ice and frozen immediately after the addition of lysate for the next sample.
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Japan) was used to prepare the low-input library following the procedures below: 1)Preparing cDNA library; 2)cDNA Purification and size selection (150-300bp); 3)Preparing sequencing ready library (add i5/i7adaptor using PCR method); 4)Library quality control (assess the size and concentration of the library using Agilent 2100 Bioanalyzer ); Library sequencing performed on Illumina platforms using a 2x150bp paired-end sequencing protocol

value: oocytes


title: DJ001A

description: 10x Genomics


title: human oocytes,fresh group_1

description: fresh group


title: human oocytes, 100 µg/mL AfrLEA3m_3

description: 100 µg/mL AfrLEA3m

value: 100 ug/mL AfrLEA3m


title: human oocytes,fresh group_2

description: fresh group


title: VUMC0976


title: VUMC0977


title: VUMC0975


title: VUMC0978


title: human oocytes, 100 µg/mL AfrLEA3m_2

description: 100 µg/mL AfrLEA3m


title: human oocytes, 100 µg/mL AfrLEA3m_1

description: 100 µg/mL AfrLEA3m


title: human oocytes, 100 µg/mL AfrLEA2_3

description: 100 µg/mL AfrLEA2

value: 100 ug/mL AfrLEA2


title: human oocytes, 100 µg/mL AfrLEA2_2

description: 100 µg/mL AfrLEA2


title: human oocytes, 100 µg/mL AfrLEA2_1

description: 100 µg/mL AfrLEA2


title: VUMC0973


title: VUMC0974


title: VUMC0972


title: human oocytes, control 3

description: control group (0M)


title: VUMC0971


title: human oocytes, control 2

description: control group (0M)


title: human oocytes, control 1

description: control group (0M)


title: VUMC0970


title: VUMC0969


title: VUMC0968


title: Post-Treatment Non-Lesional

city: New York

first: Shruti

last: Naik

address: 1 Gustave L. Levy Pl

department: Immunology & Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics).  The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FATSQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Skin punch biopsy

growth_protocol: Three to four millimeter skin punch biopsies were obtained from pre- and post-treatment lesional and non-lesional psoriatic skin.

extract_protocol: Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within5 minutes of devascularization.10-µm cryosections were mounted onto the ST arrays (10X Visium) where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.

value: Skin punch biopsy

value: secukinumab


title: VUMC0967


title: VUMC0966


title: VUMC0964


title: VUMC0965


title: Post-Treatment Lesional


title: Pre-Treatment Lesional


title: Pre-Treatment Non-Lesional


title: Psoriatic lesional skin, Standard of care, replicate 2

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned using STAR. Human samples were aligned to the human genome (hg38) and mouse samples aligned to the mouse genome (mm10/GRCm38).
The featureCounts program was used to generate raw counts for each gene.
Assembly: hg38/mm10 for human/mouse respectively
Supplementary files format and content: tab-delimited text files, include raw counts for each sample. human_raw_counts contains all raw counts for human samples and mouse_raw_counts contains all raw counts for mouse samples.

source_name: lesional skin

extract_protocol:
Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen) per manufacturer’s instructions.
Libraries were generated with Ribo-Zero Plus rRNA Depletion Kit (Illumina).

value: lesional skin


title: VUMC0963


title: VUMC0961


title: Psoriatic lesional skin, Standard of care, replicate 3


title: Psoriatic lesional skin, Standard of care, replicate 4


title: Psoriatic lesional skin, Standard of care, replicate 1


title: Psoriatic lesional skin, HIF1⍺ inhibitor, replicate 3


title: Psoriatic lesional skin, HIF1⍺ inhibitor, replicate 4


title: VUMC0953


title: VUMC0959


title: VUMC0954


title: Psoriatic lesional skin, vehicle control, replicate 5

value: vehicle (DMSO)


title: VUMC0960


title: Psoriatic lesional skin, HIF1⍺ inhibitor, replicate 2


title: VUMC0952


title: Psoriatic lesional skin, HIF1⍺ inhibitor, replicate 1


title: Psoriatic lesional skin, vehicle control, replicate 4


title: VUMC0951


title: VUMC0958


title: VUMC0955


title: Psoriatic lesional skin, vehicle control, replicate 3


title: VUMC0962


title: Psoriatic lesional skin, vehicle control, replicate 2


title: Healthy skin, Standard of care, replicate 3

source_name: healthy skin

value: healthy skin


title: Healthy skin, Standard of care, replicate 2


title: VUMC0949


title: VUMC0950


title: VUMC0948


title: Psoriatic lesional skin, vehicle control, replicate 1


title: VUMC0947


title: Healthy skin, Standard of care, replicate 1


title: Healthy skin, HIF1⍺ inhibitor, replicate 3


title: VUMC0956


title: VUMC0946


title: Healthy skin, HIF1⍺ inhibitor, replicate 2


title: VUMC0944


title: VUMC0945


title: VUMC0943


title: Healthy skin, vehicle control, replicate 1


title: Healthy skin, vehicle control, replicate 3


title: Healthy skin, vehicle control, replicate 2


title: Healthy skin, HIF1⍺ inhibitor, replicate 1


title: NaraCOVID_TP11_CD8_040_TCR

city: Noda

first: Hiroyasu

last: Aoki

address: 2669 Yamazaki

institute: Tokyo University of Science

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system. The Variable (V) and Joining (J) segments of TCRs were represented in IMGT gene nomenclature. T-cell clones were determined as TCR reads with the same TCR V segment, J segment, and CDR3 nucleotide sequence.
Inter-sample contamination within samples using same UDIs were excluded by "Decontaminate" function of vdjtools with the parameter "-r 10".
For bulk TCRseq data, we regarded the CD4+-CD8+ overlapping clones in the same participant as contamination during T-cell isolation from PBMC because CD4+ and CD8+ T-cell repertoire are mutually exclusive (Aoki 2021). Thus, these overlapping clones were categorized into either CD4+ or CD8+ according to their dominance in CD4+ and CD8+ repertoire using VDJtools-1.2.1. The sequencing reads of bulk TCR-seq samples were normalized to 100,000 reads by the “DownSample” command of VDJtools-1.2.1. To preserve the minor clonotypes, we performed the normalization ten times and pooled these down-sampled repertoire data for each sample, by “JoinSamples” command of VDJtools-1.2.1.
Assembly: IMGT reference sequences of human TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones
Library strategy: Bulk TCR-seq

source_name: Peripheral blood T cells

extract_protocol:
PBMCs were isolated from whole blood with BD vacutainer CPT tubes (BD), resuspended in CELLBANKER 1 (Takara), and stored in -80°C.
CD4+ and CD8+ T cells were magnetically isolated from PBMC. PBMC were thawed by warming frozen cryovials in a 37°C water bath. Cells were stained for 20 minutes at 4°C with 1st antibody mix (Antibody Mix 1 in Supplementary Table S1). After washing with MACS buffer [0.5% BSA (Nacalai), 2 mmol/L EDTA (NIPPON GENE) in PBS (Nacalai)], Cells were stained for 20 minutes at 4°C with 2nd antibody mix; BD IMag anti-PE Magnetic Particles-DM (Clone E31-1459, BD) and anti-APC-Biotin (clone APC003, BioLegend). Then, the cell suspension was diluted with MACS buffer and set on a magnet plate (DynaMag96SideSkirted, Veritas). The positive fraction was collected as CD4+ T cells. The negative fraction was stained with BD IMag Streptavidin Particles Plus-DM (BD) for 20 minutes at 4°C. Then, the cell suspension was diluted with MACS buffer and set on a magnet plate. The positive fraction was collected as CD8+ T cells and B cells. The counts of CD4+ T cells, CD8+ T cells, and B cells were determined using Flow-Count fluorospheres (Beckman) and a Cytoflex flow cytometer (Beckman) and FlowJo software (version 10.8.1; BD Biosciences).
Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2023).  In brief, mRNA in T-cell lysates were captured by incubating with 10 μL of Dynabeads M270 streptavidin (Thermo Fisher Scientific) bound to 2.5 pmol of BioEcoP-dT25-adapter primers for 30 minutes at room temperature under gentle rotation. mRNA-trapped beads were suspended in 10 µL of RT mix and incubated for 60 min at 42ºC to perform reverse transcription (RT) and template-switching. The composition of the RT mix was as follows; 1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of i5-TSO. To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed using KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), followed by the purification of PCR product using an AM Pure XP kit (Beckman Coulter) at a 0.7:1 beads-to-sample ratio. The third PCR was performed to amplify TCR libraries and add adaptor sequences for the next-generation sequencer. The third-PCR products were purified as second PCR. Final TCR libraries, whose lengths were about 600 base pairs, were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems), and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu). TCR libraries were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina) using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles, Illumina). Only read2 contained the sequence regarding the definition of T-cell clones. Oligonucleotides and reaction conditions for library preparation were summarized in Table S2 and S3, respectively.

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD8+ T cells and CD19+ B cells

value: male

tag: date

value: 6 month after receiving the third shot


title: Healthy skin, vehicle control, replicate 4


title: VUMC0935


title: VUMC0938


title: VUMC0937


title: VUMC0934


title: NaraCOVID_TP11_CD8_038_TCR


title: VUMC0942


title: VUMC0940


title: VUMC0941


title: VUMC0930


title: NaraCOVID_TP11_CD8_037_TCR

value: female


title: VUMC0931


title: NaraCOVID_TP11_CD8_033_TCR


title: NaraCOVID_TP11_CD8_031_TCR


title: VUMC0929


title: VUMC0932


title: VUMC0928


title: VUMC0936


title: NaraCOVID_TP11_CD8_032_TCR


title: NaraCOVID_TP11_CD8_036_TCR


title: NaraCOVID_TP11_CD8_041_TCR


title: NaraCOVID_TP11_CD8_035_TCR


title: NaraCOVID_TP11_CD8_039_TCR


title: NaraCOVID_TP11_CD8_030_TCR


title: VUMC0933


title: NaraCOVID_TP11_CD8_027_TCR


title: NaraCOVID_TP11_CD8_026_TCR


title: VUMC0923


title: VUMC0925


title: VUMC0926


title: VUMC0924


title: NaraCOVID_TP11_CD8_023_TCR


title: NaraCOVID_TP11_CD8_025_TCR


title: NaraCOVID_TP11_CD8_022_TCR


title: VUMC0922


title: NaraCOVID_TP11_CD8_024_TCR


title: VUMC0927


title: VUMC0921


title: VUMC0920


title: NaraCOVID_TP11_CD8_021_TCR


title: NaraCOVID_TP11_CD8_019_TCR


title: VUMC0919


title: NaraCOVID_TP11_CD8_017_TCR


title: NaraCOVID_TP11_CD8_016_TCR


title: VUMC0914


title: NaraCOVID_TP11_CD8_015_TCR


title: NaraCOVID_TP11_CD8_029_TCR


title: VUMC0913


title: VUMC0917


title: VUMC0915


title: NaraCOVID_TP11_CD8_020_TCR


title: VUMC0918


title: NaraCOVID_TP11_CD8_014_TCR


title: NaraCOVID_TP11_CD8_012_TCR


title: VUMC0912


title: NaraCOVID_TP11_CD8_013_TCR


title: VUMC0909


title: VUMC0908


title: NaraCOVID_TP11_CD8_010_TCR


title: VUMC0911


title: NaraCOVID_TP11_CD8_011_TCR


title: NaraCOVID_TP11_CD8_007_TCR


title: VUMC0906


title: VUMC0907


title: NaraCOVID_TP11_CD8_004_TCR


title: NaraCOVID_TP11_CD8_005_TCR


title: NaraCOVID_TP11_CD8_002_TCR


title: VUMC0902


title: VUMC0904


title: NaraCOVID_TP11_CD8_001_TCR


title: VUMC0901


title: VUMC0903


title: NaraCOVID_TP11_CD8_003_TCR


title: NaraCOVID_TP11_CD4_041_TCR

value: CD4+ T cells


title: NaraCOVID_TP11_CD4_040_TCR


title: NaraCOVID_TP11_CD4_039_TCR


title: VUMC0898


title: NaraCOVID_TP11_CD8_008_TCR


title: VUMC0897


title: VUMC0899


title: VUMC0900


title: NaraCOVID_TP11_CD4_037_TCR


title: NaraCOVID_TP11_CD4_038_TCR


title: VUMC0905


title: NaraCOVID_TP11_CD4_036_TCR


title: VUMC0895


title: VUMC0896


title: VUMC0891


title: VUMC0892


title: VUMC0893


title: NaraCOVID_TP11_CD4_033_TCR


title: NaraCOVID_TP11_CD4_032_TCR


title: NaraCOVID_TP11_CD4_031_TCR


title: NaraCOVID_TP11_CD4_030_TCR


title: NaraCOVID_TP11_CD4_029_TCR


title: VUMC0890


title: NaraCOVID_TP11_CD4_027_TCR


title: VUMC0887


title: VUMC0888


title: NaraCOVID_TP11_CD4_024_TCR


title: NaraCOVID_TP11_CD4_025_TCR


title: NaraCOVID_TP11_CD4_026_TCR


title: VUMC0885


title: NaraCOVID_TP11_CD4_023_TCR


title: VUMC0886


title: VUMC0884


title: VUMC0883


title: NaraCOVID_TP11_CD4_035_TCR


title: VUMC0882


title: VUMC0881


title: VUMC0879


title: VUMC0889


title: NaraCOVID_TP11_CD4_022_TCR


title: VUMC0880


title: NaraCOVID_TP11_CD8_006_TCR


title: NaraCOVID_TP11_CD4_017_TCR


title: VUMC0877


title: VUMC0878


title: NaraCOVID_TP11_CD4_015_TCR


title: NaraCOVID_TP11_CD4_016_TCR


title: VUMC0876


title: NaraCOVID_TP11_CD4_014_TCR


title: NaraCOVID_TP11_CD4_013_TCR


title: VUMC0874


title: VUMC0875


title: NaraCOVID_TP11_CD4_021_TCR


title: NaraCOVID_TP11_CD4_012_TCR


title: VUMC0872


title: VUMC0873


title: NaraCOVID_TP11_CD4_010_TCR


title: NaraCOVID_TP11_CD4_020_TCR


title: NaraCOVID_TP11_CD4_019_TCR


title: VUMC0868


title: VUMC0869


title: NaraCOVID_TP11_CD4_005_TCR


title: NaraCOVID_TP11_CD4_006_TCR


title: VUMC0867


title: NaraCOVID_TP11_CD4_007_TCR


title: NaraCOVID_TP11_CD4_003_TCR


title: VUMC0865


title: VUMC0864


title: VUMC0863


title: NaraCOVID_TP11_CD4_002_TCR


title: VUMC0860


title: NaraCOVID_TP11_CD4_001_TCR


title: NaraCOVID_TP11_CD4_004_TCR


title: NaraCOVID_TP11_CD4_011_TCR


title: VUMC0862


title: VUMC0870


title: NaraCOVID_TP10_CD8_041_TCR

value: 3 month after receiving the third shot


title: VUMC0859


title: NaraCOVID_TP10_CD8_040_TCR


title: VUMC0910


title: VUMC0858


title: NaraCOVID_TP10_CD8_039_TCR


title: NaraCOVID_TP10_CD8_038_TCR


title: NaraCOVID_TP11_CD4_008_TCR


title: VUMC0857


title: VUMC0866


title: NaraCOVID_TP10_CD8_037_TCR


title: NaraCOVID_TP10_CD8_036_TCR


title: NaraCOVID_TP10_CD8_035_TCR


title: VUMC0856


title: VUMC0855


title: VUMC0854


title: NaraCOVID_TP10_CD8_033_TCR


title: VUMC0851


title: NaraCOVID_TP10_CD8_032_TCR


title: VUMC0852


title: VUMC0853


title: NaraCOVID_TP10_CD8_031_TCR


title: NaraCOVID_TP10_CD8_030_TCR


title: NaraCOVID_TP10_CD8_029_TCR


title: VUMC0849


title: NaraCOVID_TP10_CD8_027_TCR


title: VUMC0848


title: VUMC0844


title: VUMC0847


title: NaraCOVID_TP10_CD8_024_TCR


title: NaraCOVID_TP10_CD8_023_TCR


title: VUMC0846


title: VUMC0841


title: VUMC0843


title: NaraCOVID_TP10_CD8_025_TCR


title: VUMC0842


title: NaraCOVID_TP10_CD8_022_TCR


title: NaraCOVID_TP10_CD8_020_TCR


title: VUMC0840


title: VUMC0839


title: NaraCOVID_TP10_CD8_017_TCR


title: VUMC0837


title: NaraCOVID_TP10_CD8_016_TCR


title: VUMC0836


title: VUMC0834


title: VUMC0835


title: NaraCOVID_TP10_CD8_019_TCR


title: NaraCOVID_TP10_CD8_015_TCR


title: VUMC0833


title: NaraCOVID_TP10_CD8_014_TCR


title: NaraCOVID_TP10_CD8_013_TCR


title: NaraCOVID_TP10_CD8_021_TCR


title: VUMC0838


title: VUMC0829


title: VUMC0832


title: NaraCOVID_TP10_CD8_010_TCR


title: VUMC0827


title: NaraCOVID_TP10_CD8_018_TCR


title: NaraCOVID_TP10_CD8_026_TCR


title: VUMC0825


title: VUMC0824


title: NaraCOVID_TP10_CD8_007_TCR


title: NaraCOVID_TP10_CD8_006_TCR


title: NaraCOVID_TP10_CD8_008_TCR


title: NaraCOVID_TP10_CD8_005_TCR


title: VUMC0822


title: VUMC0826


title: VUMC0823


title: NaraCOVID_TP10_CD8_004_TCR


title: NaraCOVID_TP10_CD8_002_TCR


title: NaraCOVID_TP10_CD8_003_TCR


title: VUMC0821


title: VUMC0828


title: NaraCOVID_TP10_CD8_001_TCR


title: VUMC0818


title: VUMC0819


title: NaraCOVID_TP10_CD8_012_TCR


title: VUMC0820


title: NaraCOVID_TP10_CD8_011_TCR


title: NaraCOVID_TP10_CD4_040_TCR


title: NaraCOVID_TP10_CD4_041_TCR


title: NaraCOVID_TP10_CD4_039_TCR


title: VUMC0815


title: NaraCOVID_TP10_CD4_038_TCR


title: NaraCOVID_TP10_CD4_036_TCR