title: BAM file of sample MPE-A 14

description:
Library name: MPE_A_14
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)

data_processing:
Demultiplexed fastq format data (cellranger mkfastq) were received from the sequencing facilities. Cellranger v7.2.0 was used to generate feature-barcode matrices using the command cellranger multi with default parameters. GRCh38 was used as the reference genome (version refdata-gex-GRCh38-2020-A) together with the probe set file Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv. One sequencing library of this project contained samples of different, unpublished project. Therefore, fastq data of this library is not provided here. Instead, bam files of the cellranger v7.2.0 multi function are provided for these samples.
One sequencing library of this project contained samples of a different, unpublished project. Therefore, fastq data of this library is not provided here. Instead, bam files of the cellranger v7.2.0 multi function output are provided for the respective samples (SPEPN_B_3, SPEPN_B_4, MPE_A_4, MPE_A_5, MPE_A_6, MPE_A_7, MPE_A_12, MPE_A_13, MPE_A_14, and MPE_A_15).
Assembly: refdata-gex-GRCh38-2020-A together with the probe set file Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv (files downloaded from 10x genomics website)
Supplementary files format and content: Processed 10x Genomics snRNAseq data is provided as filtered feature-barcode matrices reveived from the output of the cellranger multi function (barcodes.tsv, features.tsv, and matrix.mtx).

molecule: nuclear RNA

source_name: FFPE-tumor tissue

extract_protocol:
The tumor material was first subjected to 4% formaldehyde fixation for approximately 24h and subsequently dehydrated and embedded in paraffin (FFPE) for long-term storage. For the generation of single nucleus RNA sequencing data, we performed the 10x Genomics Chromium Single Cell Flex Gene Expression (specific workflow is currently termed Next GEM). The preparation of single nucleus solutions from archival FFPE-tissue was performed according to the instructions of the 10x Genomics protocol CG000632 (RevB). The sample input varied between 3 to 22 slices of 25 µm thickness. For different subsets of samples, the pestle-based dissociation or the gentleMACS™ OctoDissociator (Miltenyi Biotec) protocol arm was performed. Deviating from the original protocol, we stained all single nucleus solutions after the FFPE-tissue dissociation with 4',6-diamidino-2-phenylindole (DAPI, 1:5000). Immediately afterwards, fluorescence activated cell sorting (FACS) on a BD FACSAria-Fusion™ Flow Cytometer was conducted at the technology platform FACS of the Leibniz Institute of Virology (Hamburg, Germany). The experiment was performed at 4°C and the gating strategy first excluded obvious debris and subsequently sorted for DAPI-positive nuclei at the wavelength of 450 nm. This sorting step was performed to remove debris and non-DAPI-stained erythrocytes that otherwise skewed cell counting results of the following protocol steps.
The generation of single nucleus RNA sequencing libraries was performed at the single cell core facility of the University Medical Center Hamburg-Eppendorf (Germany) according to the 10x Genomics protocol CG000527 (Rev. D). The Chromium Fixed RNA (Human Transcriptome) kits PN-1000475 (4 rxns x 4 BC) or PN-1000476 (4 rxns x 16 BC) were used on different samples. The hybridization was conducted at a maximum of 7 days after the DAPI-sorting in appropriate storage buffer according to 10x Genomics protocol CG000632. No fluorescence-based cell counter was available for the experiments. Instead, a TC20 Automated Cell Counter (Bio-Rad Laboratories) was used for every cell counting step. Libraries were sequenced at different facilities (Leibniz Institute of Virology in Hamburg, Germany or CeGaT GmbH in Tübingen, Germany).

value: FFPE-tumor tissue


title: BAM file of sample MPE-A 13

status: Public on Sep 12 2025

type: SRA

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: MPE_A_13
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)

library_source: transcriptomic single cell

organism: Homo sapiens

tag: tissue

tag: batch


title: BAM file of sample MPE-A 7

description:
Library name: MPE_A_7
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: BAM file of sample MPE-A 6

description:
Library name: MPE_A_6
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: BAM file of sample SP-EPN-B 4

description:
Library name: SPEPN_B_4
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A5

city: South San Francisco

first: Elysia

middle: Cecilia

last: Saputra

state: CA

address: 213 E Grand Ave

department: Data, AI, and Genome Sciences

country: USA

institute: Merck & Co., Inc.

description:
Library name: coculture_poolA5_CRISPR
sgRNA

library_source: other

data_processing:
The demultiplexing of sequencing reads, gene counting, and generation of gene expression matrices were performed using the 10X Genomics Cell Ranger v7.0.1 software. Quality control, normalization, library integration, identification of non-perturbed cells, label transfer, and subtype identification were performed using Seurat 4.1.1.
Assembly: Homo sapiens hg38
Supplementary files format and content: RDS files

molecule: other

source_name: fibroblast

growth_protocol: hTERT-immortalized CAF cell lines were suspended in 20mL of FBM with polybrene (16 ug/mL), and then aliquoted to 6-well plates.

extract_protocol:
After aspirating media, 350uL accutase is added to the cell culture, followed by 350uL FBM when the cells have detached. Then, cells are spun (300g, 5 minutes) and resuspended in 2% FBS RPMI to get ~2000/uL. The cells were then loaded to 10X 5'HT Chip based on 10X protocol and run in Chromium X. Afterwards, cDNA amplification was performed following 10X protocol. Libraries were quantified using qubit and sequenced using S4 Illumina flow cell.
Library construction was performed according to the 10X 5' CRISPR protocol following the manufacturer's instruction.

treatment_protocol: 500uL of lentivirus/guide was added to the solution to a final polybrene concentration of 8ug/mL. Then, the media was replaced, and then 1mL of 1.5ug/mL puromycin was added to each well to a final concentration of 0.5ug/mL. After adding 0.5mL accutase and 0.5mL media, the cells were split in 6-well plates (400uL cells/well). Then, 600uL media and 1ug/mL puromycin was added to a final concentration of 0.5ug/mL. The solution was then replaced with fresh FBM without puromycin. To set up the monocultures and cocultures, media was first aspirated, and 500uL accutase was added. After the cells have detached, 500uL media was added. After that, 1e5 of the perturbed CAF cells were added to each well in 12-well plates. To set up the monocultures, 1mL of 2% FBS RPMI was added. To set up the cocultures, 1mL of tumor cells were added. The cultures were incubated for 2 days.

value: fibroblast

tag: cell line

tag: cell type


title: BAM file of sample MPE-A 15

description:
Library name: MPE_A_15
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A16

description:
Library name: coculture_poolA16_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A6

description:
Library name: coculture_poolA6_GEX
mRNA

molecule: polyA RNA


title: Pooled library of MPE-A 8 (BC-001), MPE-A 9 (BC-002), MPE-A 10 (BC-003), and MPE-A 11 (BC-004)

description:
Library name: S11531Nr1
10x Genomics Flex Gene Expression (1000475, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 4 BC)


title: KT00287-VDJ_CON2

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: KT00287-VDJ
H5 file contains RNA
Cell Ranger vdj annotation files

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
For multimodal data: Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using  bcl2fastq vv2.20.0.422 (Illumina)
For multimodal data: 10x cellranger/cellranger-arc 2.0 was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome. The output files for rna and atac were h5 files and fragments.tsv.gz respectively, which were utilized for downstream processing and quality control analysis.
For multimodal data: HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
For multimodal data: Fragments files were then construct into arrow file for analysis in ArchR package
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix
Supplementary files format and content: Fragment files (tsv.gz)
Supplementary files format and content: Fragment file metadata (csv.gz)
Supplementary files format and content: ADT counts and BCR contig counts (csv)

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and immediately thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (71) to generate sample-specific output files.

value: Blood

tag: Sex

value: Female

tag: birth year

tag: race

value: Caucasian

tag: subject

tag: cohort


title: KT01565-VDJ_CON2

description:
Library name: KT01565-VDJ
H5 file contains RNA
Cell Ranger vdj annotation files

value: Asian


title: BAM file of sample MPE-A 5

description:
Library name: MPE_A_5
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: KT00257-VDJ_CON2

description:
Library name: KT00257-VDJ
H5 file contains RNA
Cell Ranger vdj annotation files


title: KT01606-VDJ_CON2

description:
Library name: KT01606-VDJ
H5 file contains RNA
Cell Ranger vdj annotation files


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A15

description:
Library name: coculture_poolA15_CRISPR
sgRNA


title: KT00331-TEA_CON2

description:
H5 file contains RNA
Fragment file contains scATAC data
Metadata file contains scATAC metadata
ADT counts file

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
For multimodal data: Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using  bcl2fastq vv2.20.0.422 (Illumina)
For multimodal data: 10x cellranger/cellranger-arc 2.0 was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome. The output files for rna and atac were h5 files and fragments.tsv.gz respectively, which were utilized for downstream processing and quality control analysis.
For multimodal data: HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
For multimodal data: Fragments files were then construct into arrow file for analysis in ArchR package
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix
Supplementary files format and content: Fragment files (tsv.gz)
Supplementary files format and content: Fragment file metadata (csv.gz)
Supplementary files format and content: ADT counts (csv)


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A14

description:
Library name: coculture_poolA14_CRISPR
sgRNA


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, sgRNA, Pool A12

description:
Library name: coculture_poolA12_CRISPR
sgRNA


title: KT00561-TEA_CON2


title: KT00501-TEA_CON2


title: hTERT-immortalized PDAC CAFs, BxPC3 co-cultured, mRNA, Pool A13

description:
Library name: coculture_poolA13_GEX
mRNA


title: KT00332-TEA_CON2


title: KT00219-TEA_ARI

value: ARI


title: KT00569-TEA_CON2


title: BAM file of sample SP-EPN-B 3

description:
Library name: SPEPN_B_3
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: KT00060-TEA_ARI


title: BAM file of sample MPE-A 12

description:
Library name: MPE_A_12
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: KT00067-TEA_ARI


title: BAM file of sample MPE-A 4

description:
Library name: MPE_A_4
10x Genomics Flex Gene Expression (1000476, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 16 BC)


title: KT00065-TEA_ARI


title: KT01585_CON2

description: H5 file contains RNA

molecule: total RNA

value: Other


title: KT00599_CON2

description: H5 file contains RNA


title: KT02540_CON2

description: H5 file contains RNA


title: KT00096-TEA_ARI


title: KT00073-TEA_ARI


title: KT00602_CON2

description: H5 file contains RNA


title: KT01509_CON2

description: H5 file contains RNA


title: KT02530_CON2

description: H5 file contains RNA


title: KT02342_CON2

description: H5 file contains RNA

value: Male


title: KT00564_CON2

description: H5 file contains RNA


title: KT01447_CON2

description: H5 file contains RNA


title: KT00545_CON2

description: H5 file contains RNA


title: KT02503_CON2

description: H5 file contains RNA


title: KT01418_CON2

description: H5 file contains RNA


title: KT01427_CON2

description: H5 file contains RNA


title: KT00516_CON2

description: H5 file contains RNA


title: KT00649_CON2

description: H5 file contains RNA


title: KT02469_CON2

description: H5 file contains RNA


title: KT02464_CON2

description: H5 file contains RNA


title: KT01428_CON2

description: H5 file contains RNA


title: KT00394_CON2

description: H5 file contains RNA


title: KT00212-TEA_ARI


title: KT00501_CON2

description: H5 file contains RNA


title: KT02320_CON2

description: H5 file contains RNA


title: KT00648_CON2

description: H5 file contains RNA


title: KT00526_CON2

description: H5 file contains RNA


title: KT02318_CON2

description: H5 file contains RNA


title: KT00561_CON2

description: H5 file contains RNA


title: KT00608_CON2

description: H5 file contains RNA


title: KT02536_CON2

description: H5 file contains RNA


title: KT02272_CON2

description: H5 file contains RNA


title: KT00629_CON2

description: H5 file contains RNA


title: KT02328_CON2

description: H5 file contains RNA


title: KT00288_CON2

description: H5 file contains RNA


title: KT00568_CON2

description: H5 file contains RNA


title: KT00539_CON2

description: H5 file contains RNA


title: KT00300_CON2

description: H5 file contains RNA


title: KT00289_CON2

description: H5 file contains RNA


title: KT00277_CON2

description: H5 file contains RNA


title: KT00377_CON2

description: H5 file contains RNA


title: KT00611_CON2

description: H5 file contains RNA


title: KT00264_CON2

description: H5 file contains RNA


title: KT01594_CON2

description: H5 file contains RNA


title: KT02474_CON2

description: H5 file contains RNA


title: KT00593_CON2

description: H5 file contains RNA


title: KT00157_CON2

description: H5 file contains RNA


title: KT01433_CON2

description: H5 file contains RNA


title: KT02337_CON2

description: H5 file contains RNA


title: KT00170_CON2

description: H5 file contains RNA


title: KT00326_CON2

description: H5 file contains RNA


title: KT00549_CON2

description: H5 file contains RNA


title: KT02519_CON2

description: H5 file contains RNA


title: KT00342_CON2

description: H5 file contains RNA


title: KT00575_CON2

description: H5 file contains RNA


title: KT01454_CON2

description: H5 file contains RNA


title: KT01519_CON2

description: H5 file contains RNA


title: KT00278_CON2

description: H5 file contains RNA


title: KT00628_CON2

description: H5 file contains RNA


title: KT00325_CON2

description: H5 file contains RNA


title: KT00271_CON2

description: H5 file contains RNA


title: KT00164_CON2

description: H5 file contains RNA


title: KT00048_CON2

description: H5 file contains RNA


title: KT00616_CON2

description: H5 file contains RNA


title: KT00283_CON2

description: H5 file contains RNA


title: KT00039_CON2

description: H5 file contains RNA


title: KT00331_CON2

description: H5 file contains RNA


title: KT02267_CON2

description: H5 file contains RNA


title: KT00016_CON2

description: H5 file contains RNA


title: KT00257_CON2

description: H5 file contains RNA


title: KT00273_CON2

description: H5 file contains RNA


title: KT00158_CON2

description: H5 file contains RNA


title: KT01410_CON2

description: H5 file contains RNA


title: KT01426_CON2

description: H5 file contains RNA


title: KT02253_CON2

description: H5 file contains RNA


title: KT00149_CON2

description: H5 file contains RNA


title: KT00299_CON2

description: H5 file contains RNA


title: KT00514_CON2

description: H5 file contains RNA


title: KT00030_CON2

description: H5 file contains RNA


title: KT00373_CON2

description: H5 file contains RNA


title: KT00355_CON2

description: H5 file contains RNA


title: KT00022_CON2

description: H5 file contains RNA


title: KT00259_CON2

description: H5 file contains RNA


title: KT00012_CON2

description: H5 file contains RNA


title: KT00035_CON2

description: H5 file contains RNA


title: KT00003_CON2

description: H5 file contains RNA


title: KT00284_CON2

description: H5 file contains RNA


title: KT00631_CON2

description: H5 file contains RNA


title: CLD4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

library_source: transcriptomic

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build GENCODE Ghomo sapiens GRCh38.p31 Release 37
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GENCODE Homo sapiens GRCh38.p13 Release 37
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: Liver

extract_protocol:
RNA was extracted following the manual of the Qiagen RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: group

value: CLD


title: CLD5


title: CLD2


title: HCC7

value: HCC


title: CLD1


title: HCC6


title: HCC5


title: HCC1


title: HCC4


title: HCC3


title: Normal6

value: Normal


title: Normal5


title: Normal1


title: Normal2


title: Normal4


title: KT00047_CON2

description: H5 file contains RNA


title: HCC2


title: Normal3


title: KT00586_CON2

description: H5 file contains RNA


title: PB03296-001 flex scRNA-seq

description:
SRR30204383, SRR30204382, SRR30204381, SRR30204380, SRR30204379, SRR30204378, SRR30204376, SRR30204375
10x Flex ligation probe-based sequencing

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For all initial analyses, we used a Python single-cell data analysis package – Scanpy (v1.9.6). High quality cells were selected based on the following cutoffs: <4.5% mitochondria reads, number of genes detected between 500 and 5000, RNA UMIs/cells less than 12000 and number of reads less than 30000. Doublets were detected and filtered out with the Scrublet package accessed through scanpy.external.pp.scrublet call and the doublet filtration threshold was set at less than 0.2
After QC filtering, all remaining cells were clustered using a workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; natural log transformation using scanpy.pp.log1p; dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'; nearest neighbor distance matrix and neighborhood graph computed using scanpy.pp.neighbors with the parameters n_neighbors=50, use_rep='X_pca', n_pcs=30;
Assembly: GRCh38/hg38
Supplementary files format and content: h5 files

extract_protocol:
PBMCs were removed from liquid nitrogen and immediately thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics flex single cell gene expression assay. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq 6000 or X platform.

value: PBMC

tag: subject id

tag: age at_enrollment

tag: cmv status

value: Positive

tag: batch id

tag: sample bridging_control

value: FALSE

tag: pooled sample_id

tag: probe barcode_id


title: PB03357-001 flex scRNA-seq

tag: tissue


title: PB03350-001 flex scRNA-seq

description:
SRR30204258, SRR30204257, SRR30204256, SRR30204254, SRR30204387, SRR30204386, SRR30204385, SRR30204384
10x Flex ligation probe-based sequencing

value: African American

value: Negative


title: PB03348-001 flex scRNA-seq


title: CLD3


title: PB03336-001 flex scRNA-seq


title: PB03373-003 flex scRNA-seq


title: PB03403-003 flex scRNA-seq

description:
SRR30204267, SRR30204266, SRR30204264, SRR30204263, SRR30204262, SRR30204261, SRR30204260, SRR30204259
10x Flex ligation probe-based sequencing


title: PB03833-003 flex scRNA-seq


title: PB03781-003 flex scRNA-seq


title: PB03810-001 flex scRNA-seq


title: PB03806-001 flex scRNA-seq

description:
SRR30204300, SRR30204265, SRR30204412, SRR30204377, SRR30204366, SRR30204283, SRR30204272, SRR30204405
10x Flex ligation probe-based sequencing

value: TRUE


title: PB03771-001 flex scRNA-seq

description:
SRR30204414, SRR30204413, SRR30204342, SRR30204246, SRR30204235, SRR30204333, SRR30204322, SRR30204311
10x Flex ligation probe-based sequencing

value: Blood


title: PB03734-003 flex scRNA-seq


title: PB03733-003 flex scRNA-seq

value: Female

value: Pacific Islander


title: PB03741-003 flex scRNA-seq

value: Hispanic or Latino origin


title: PB03757-003 flex scRNA-seq


title: PB03732-003 flex scRNA-seq

value: Asian


title: PB03712-001 flex scRNA-seq


title: PB03725-001 flex scRNA-seq

value: Caucasian


title: PB03702-003 flex scRNA-seq

value: Male


title: PB03861-003 flex scRNA-seq


title: PB03729-003 flex scRNA-seq


title: PB03683-003 flex scRNA-seq


title: PB03688-001 flex scRNA-seq


title: PB03676-001 flex scRNA-seq


title: PB03673-001 flex scRNA-seq


title: PB03671-001 flex scRNA-seq


title: PB03670-001 flex scRNA-seq


title: PB03650-001 flex scRNA-seq


title: PB03624-001 flex scRNA-seq


title: PB03622-001 flex scRNA-seq


title: PB03608-001 flex scRNA-seq


title: PB03603-001 flex scRNA-seq


title: PB03602-001 flex scRNA-seq


title: PB03599-001 flex scRNA-seq


title: PB03587-001 flex scRNA-seq


title: PB03573-001 flex scRNA-seq


title: PB03554-001 flex scRNA-seq


title: PB03543-001 flex scRNA-seq


title: PB03529-001 flex scRNA-seq


title: PB03516-001 flex scRNA-seq


title: PB03505-001 flex scRNA-seq


title: PB03425-001 flex scRNA-seq


title: PB03489-001 flex scRNA-seq


title: PB03514-001 flex scRNA-seq


title: KT04625_ERA

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix


title: PB03165-001 flex scRNA-seq


title: PB03163-001 flex scRNA-seq


title: PB03438-001 flex scRNA-seq


title: PB03426-001 flex scRNA-seq


title: PB03156-001 flex scRNA-seq


title: PB03695-003 flex scRNA-seq


title: PB03147-001 flex scRNA-seq


title: PB03292-001 flex scRNA-seq


title: PB03160-001 flex scRNA-seq


title: KT02981_ERA


title: KT02845_ERA


title: KT02139_ERA


title: PB03556-001 flex scRNA-seq


title: KT02141_ERA


title: KT02140_ERA


title: KT00778_ERA

value: Other


title: KT00474_ERA


title: PB03288-001 flex scRNA-seq


title: KT00777_ERA


title: KT00447_ERA


title: PB03280-001 flex scRNA-seq


title: KT00072_ERA


title: KT04474_LONG


title: KT02968_LONG


title: KT04102_LONG


title: KT04103_LONG


title: KT04105_LONG


title: KT03936_LONG


title: KT03932_LONG


title: KT03939_LONG


title: KT03930_LONG


title: KT02856_LONG


title: KT02854_LONG


title: KT04113_ERA


title: KT02948_LONG


title: KT02853_LONG


title: KT02839_LONG


title: KT02136_LONG


title: KT02164_LONG


title: KT02823_LONG


title: KT02830_LONG


title: KT02133_LONG


title: KT02817_LONG


title: KT00500_LONG


title: KT00493_LONG


title: KT00492_LONG


title: KT00497_LONG


title: KT00482_LONG


title: KT00480_LONG


title: KT00478_LONG


title: KT00055_ERA


title: KT00467_LONG


title: KT00464_LONG


title: KT00443_LONG


title: KT00440_LONG


title: KT00453_LONG


title: KT00424_LONG


title: KT00416_LONG


title: KT00468_LONG


title: KT00409_LONG


title: KT00227_LONG


title: KT00208_LONG


title: KT00465_LONG


title: KT00219_LONG


title: KT00202_LONG


title: KT00105_LONG


title: KT00114_LONG


title: KT00093_LONG


title: KT00118_LONG


title: KT00103_LONG


title: KT00099_LONG


title: KT00097_LONG


title: KT00075_LONG


title: KT00084_LONG


title: PB03503-001 flex scRNA-seq


title: KT00057_LONG


title: KT00082_LONG


title: KT00052_LONG


title: KT00056_LONG


title: KT04924_LONG


title: KT04108_LONG


title: KT04085_LONG


title: KT02963_LONG


title: KT04462_LONG


title: KT02135_LONG


title: KT00790_LONG


title: KT02177_ARI


title: KT00109_LONG


title: KT00473_ARI


title: KT00463_ARI


title: KT00477_ARI


title: KT00221_ARI


title: KT00461_ARI


title: KT00436_ARI


title: KT00120_ARI


title: KT00064_LONG


title: KT00420_ARI


title: KT00107_ARI


title: KT00095_ARI


title: KT00108_ARI


title: KT00211_ARI


title: KT00088_ARI


title: KT00086_ARI


title: KT00087_ARI


title: KT00081_ARI


title: KT00092_ARI


title: KT02975_LONG


title: KT02132_LONG


title: KT02844_LONG


title: KT00076_ARI


title: KT00070_ARI


title: KT00077_ARI


title: KT00074_ARI


title: KT00069_ARI


title: KT00067_ARI


title: KT00068_ARI


title: KT00065_ARI


title: KT00063_ARI


title: KT00060_ARI


title: KT00058_ARI


title: KT04937_CON1


title: KT04906_CON1


title: KT04933_CON1


title: KT04671_CON1


title: KT04905_CON1


title: KT00090_ARI


title: KT04652_CON1


title: KT04633_CON1


title: KT04115_CON1


title: KT04118_CON1


title: KT04445_CON1


title: KT04072_CON1


title: KT03931_CON1


title: KT02992_CON1


title: KT02985_CON1


title: KT02978_CON1


title: KT00073_ARI


title: KT02974_CON1


title: KT02969_CON1


title: KT02958_CON1


title: KT02953_CON1


title: KT02303_CON1


title: KT02957_CON1


title: KT02952_CON1


title: KT02298_CON1


title: KT02287_CON1


title: KT02286_CON1


title: KT04634_CON1


title: PB03079-001 Flu Year 2 Day 90

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

tag: days since_first_visit

tag: visit

value: Flu Year 2 Day 90


title: KT04092_CON1


title: PB02525-001 Flu Year 2 Day 7

tag: cell type

value: Flu Year 2 Day 7


title: PB02508-001 Flu Year 2 Day 0

tag: Sex

value: Flu Year 2 Day 0


title: PB02004-01 Immune Variation Day 0

value: PBMC

tag: birth year

value: Immune Variation Day 0


title: PB00625-02 Flu Year 1 Day 0

tag: race

value: Positive

value: Flu Year 1 Day 0

value: FALSE


title: PB00639-02 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB03913-001 Flu Year 3 Stand-Alone

value: Blood

value: Flu Year 3 Stand-Alone


title: KT02284_CON1

value: Female


title: PB03094-001 Flu Year 2 Day 90


title: KT02971_CON1


title: KT02970_CON1


title: PB02551-001 Flu Year 2 Day 7


title: PB02335-002 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02540-001 Flu Year 2 Day 0


title: PB02239-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB02229-01 Immune Variation Day 0


title: PB00599-01 Flu Year 1 Day 0


title: PB00604-01 Flu Year 1 Day 7


title: KT02292_CON1

value: Caucasian


title: PB03914-001 Flu Year 3 Stand-Alone


title: PB03093-001 Flu Year 2 Day 90


title: PB02542-001 Flu Year 2 Day 7


title: PB02530-001 Flu Year 2 Day 0


title: PB02331-001 Immune Variation Day 90

value: Male


title: PB03900-001 Flu Year 3 Stand-Alone


title: PB02011-01 Immune Variation Day 7


title: PB02327-002 Immune Variation Day 90


title: PB01990-01 Immune Variation Day 0


title: PB01997-01 Immune Variation Day 7


title: PB01509-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00614-01 Flu Year 1 Day 7


title: PB01543-01 Flu Year 1 Day 90


title: PB03924-002 Flu Year 3 Stand-Alone

value: Negative


title: PB00602-01 Flu Year 1 Day 0


title: PB02497-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02477-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB03102-001 Flu Year 2 Day 90

value: PBMC

value: Flu Year 2 Day 90


title: PB02323-002 Immune Variation Day 90


title: PB01585-01 Flu Year 1 Day 90

value: Other

value: Positive


title: PB01545-01 Flu Year 1 Day 90

value: FALSE


title: PB02588-002 Flu Year 2 Day 90


title: PB01993-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01541-01 Immune Variation Day 7

value: Blood


title: PB02447-001 Flu Year 2 Day 7


title: PB02344-001 Flu Year 2 Day 0


title: PB02234-01 Immune Variation Day 90


title: PB00623-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB01415-01 Flu Year 1 Day 90


title: PB00637-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00540-01 Flu Year 1 Day 7


title: PB03911-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB00523-01 Flu Year 1 Day 0


title: PB02538-002 Flu Year 2 Day 7


title: PB02258-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02522-002 Flu Year 2 Day 0

value: Caucasian


title: PB01582-01 Immune Variation Day 7

value: Male

value: Immune Variation Day 7


title: PB03084-001 Flu Year 2 Day 90


title: PB01568-01 Immune Variation Day 0


title: PB01416-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB01999-01 Immune Variation Day 7

value: Negative


title: PB03918-001 Flu Year 3 Stand-Alone

value: Asian


title: PB00520-01 Flu Year 1 Day 0

value: PBMC


title: PB02554-002 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB03893-001 Flu Year 3 Stand-Alone


title: PB02342-001 Immune Variation Day 90


title: PB02546-002 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB01996-01 Immune Variation Day 7


title: PB01986-01 Immune Variation Day 0


title: PB01527-01 Immune Variation Day 0

value: Positive


title: PB01447-02 Flu Year 1 Day 90

value: FALSE


title: PB00564-04 Flu Year 1 Day 0


title: PB00577-02 Flu Year 1 Day 7


title: PB03110-003 Flu Year 3 Stand-Alone

value: Female


title: PB03064-002 Flu Year 2 Day 90

value: Blood

value: Flu Year 2 Day 90


title: PB02488-002 Flu Year 2 Day 0


title: PB01992-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB02001-01 Immune Variation Day 7


title: PB02329-001 Immune Variation Day 90


title: PB02505-002 Flu Year 2 Day 7


title: PB01451-01 Flu Year 1 Day 90


title: PB00571-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00557-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB02533-001 Flu Year 2 Day 7

value: Caucasian


title: PB03076-001 Flu Year 2 Day 90


title: PB03104-002 Flu Year 2 Day 90

value: Male


title: PB03909-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB02249-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB01570-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00538-01 Flu Year 1 Day 7


title: PB01556-01 Immune Variation Day 0


title: PB00550-01 Flu Year 1 Day 7


title: PB00533-01 Flu Year 1 Day 0


title: PB03088-002 Flu Year 2 Day 90


title: PB03912-002 Flu Year 3 Stand-Alone


title: PB02531-002 Flu Year 2 Day 7


title: PB01572-01 Immune Variation Day 7


title: PB02515-002 Flu Year 2 Day 0


title: PB02240-02 Immune Variation Day 90


title: PB00560-01 Flu Year 1 Day 7


title: PB01423-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00541-01 Flu Year 1 Day 0

value: PBMC


title: PB03066-002 Flu Year 2 Day 90

value: Negative


title: PB02501-002 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB01418-01 Flu Year 1 Day 90


title: PB02516-001 Flu Year 2 Day 0

value: Positive

value: Flu Year 2 Day 0


title: PB01580-01 Immune Variation Day 7

value: Female

value: FALSE


title: PB01566-02 Immune Variation Day 0

value: Blood


title: PB02246-02 Immune Variation Day 90


title: PB00559-01 Flu Year 1 Day 7


title: PB00545-01 Flu Year 1 Day 0


title: PB03921-001 Flu Year 3 Stand-Alone


title: PB02521-001 Flu Year 2 Day 7


title: PB02251-01 Immune Variation Day 90


title: PB01564-01 Immune Variation Day 7


title: PB01431-01 Flu Year 1 Day 90


title: PB02503-001 Flu Year 2 Day 0


title: PB03090-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB01551-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01427-01 Flu Year 1 Day 90


title: PB01558-01 Immune Variation Day 0


title: PB03898-001 Flu Year 3 Stand-Alone


title: PB03067-001 Flu Year 2 Day 90


title: PB02469-001 Flu Year 2 Day 0


title: PB00534-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB02489-001 Flu Year 2 Day 7

value: Caucasian


title: PB00516-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB01529-03 Immune Variation Day 7


title: PB02474-002 Flu Year 2 Day 0


title: PB00649-04 Flu Year 1 Day 90


title: PB01516-03 Immune Variation Day 0


title: PB03894-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB00513-02 Flu Year 1 Day 7


title: PB02528-001 Flu Year 2 Day 7

value: Male


title: PB03092-001 Flu Year 2 Day 90


title: PB00394-02 Flu Year 1 Day 0


title: PB02511-001 Flu Year 2 Day 0


title: PB03919-001 Flu Year 3 Stand-Alone


title: PB01546-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB01528-02 Immune Variation Day 0


title: PB02358-001 Flu Year 2 Day 7


title: PB03099-001 Flu Year 3 Stand-Alone


title: PB01421-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00383-01 Flu Year 1 Day 0

value: PBMC


title: PB02569-001 Flu Year 2 Day 90

value: Negative


title: PB00503-01 Flu Year 1 Day 7


title: PB02008-04 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02339-001 Flu Year 2 Day 0


title: PB01533-01 Immune Variation Day 7


title: PB00603-01 Flu Year 1 Day 90


title: PB00360-01 Flu Year 1 Day 7


title: PB01521-01 Immune Variation Day 0


title: PB02007-02 Immune Variation Day 90


title: PB00339-01 Flu Year 1 Day 0


title: PB02228-03 Immune Variation Day 90


title: PB02356-001 Flu Year 2 Day 7

value: Positive

value: Flu Year 2 Day 7


title: PB02575-001 Flu Year 2 Day 90


title: PB02341-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB01530-01 Immune Variation Day 7

value: FALSE


title: PB01517-02 Immune Variation Day 0

value: Blood


title: PB01998-04 Immune Variation Day 90


title: PB00369-01 Flu Year 1 Day 0


title: PB03081-001 Flu Year 2 Day 90

value: Female

value: Flu Year 2 Day 90


title: PB03908-002 Flu Year 3 Stand-Alone


title: PB02537-001 Flu Year 2 Day 7


title: PB00389-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB02235-04 Immune Variation Day 90

value: Caucasian


title: PB02523-001 Flu Year 2 Day 0


title: PB00393-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB03906-002 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB01518-02 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01537-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00512-01 Flu Year 1 Day 7


title: PB01414-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB02593-001 Flu Year 2 Day 90

value: PBMC


title: PB02458-001 Flu Year 2 Day 7


title: PB03103-001 Flu Year 3 Stand-Alone

value: Male


title: PB00387-01 Flu Year 1 Day 0


title: PB02354-001 Flu Year 2 Day 0


title: PB01555-01 Immune Variation Day 7


title: PB00638-01 Flu Year 1 Day 90


title: PB01542-01 Immune Variation Day 0


title: PB00506-01 Flu Year 1 Day 7


title: PB02237-04 Immune Variation Day 90

value: Immune Variation Day 90


title: PB03063-001 Flu Year 2 Day 90

value: Negative


title: PB02464-001 Flu Year 2 Day 0


title: PB02484-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB01579-01 Immune Variation Day 0


title: PB01593-01 Immune Variation Day 7


title: PB01428-01 Flu Year 1 Day 90


title: PB03073-001 Flu Year 2 Day 90

value: Asian

value: Positive


title: PB03892-001 Flu Year 3 Stand-Alone

value: Blood

value: FALSE


title: PB00519-01 Flu Year 1 Day 7

value: Female


title: PB00626-01 Flu Year 1 Day 90


title: PB02250-02 Immune Variation Day 90


title: PB00501-01 Flu Year 1 Day 0


title: PB02518-001 Flu Year 2 Day 7


title: PB02005-01 Immune Variation Day 90


title: PB01515-01 Immune Variation Day 7


title: PB02502-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB01511-02 Immune Variation Day 0


title: PB00636-01 Flu Year 1 Day 90


title: PB00515-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00390-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB02481-001 Flu Year 2 Day 7

value: Caucasian


title: PB02587-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB02318-002 Immune Variation Day 90


title: PB00648-01 Flu Year 1 Day 90


title: PB02461-001 Flu Year 2 Day 0


title: PB01984-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00543-01 Flu Year 1 Day 7


title: PB03890-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB00526-01 Flu Year 1 Day 0

value: PBMC


title: PB01971-02 Immune Variation Day 0

value: Immune Variation Day 0


title: PB03078-001 Flu Year 2 Day 90

value: Male


title: PB02512-001 Flu Year 2 Day 7

value: Negative


title: PB01983-02 Immune Variation Day 0


title: PB02498-001 Flu Year 2 Day 0


title: PB00581-01 Flu Year 1 Day 7


title: PB00563-01 Flu Year 1 Day 0


title: PB01445-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB01991-01 Immune Variation Day 7


title: PB02500-001 Flu Year 2 Day 0


title: PB02514-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02322-002 Immune Variation Day 90

value: Positive

value: Immune Variation Day 90


title: PB01982-01 Immune Variation Day 7

value: Blood

value: FALSE


title: PB02317-001 Immune Variation Day 90


title: PB03070-001 Flu Year 2 Day 90


title: PB03899-001 Flu Year 3 Stand-Alone

value: Female


title: PB01966-01 Immune Variation Day 0


title: PB01512-02 Flu Year 1 Day 90


title: PB02535-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB03106-001 Flu Year 2 Day 90


title: PB00330-01 Flu Year 1 Stand-Alone

value: Flu Year 1 Stand-Alone


title: PB01981-01 Immune Variation Day 7

value: Caucasian


title: PB02320-001 Immune Variation Day 90


title: PB00600-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB00605-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB02544-001 Flu Year 2 Day 7


title: PB01448-02 Flu Year 1 Day 90


title: PB00574-01 Flu Year 1 Day 7


title: PB01969-01 Immune Variation Day 0


title: PB03069-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB00326-01 Flu Year 1 Stand-Alone

value: PBMC


title: PB00561-04 Flu Year 1 Day 0


title: PB02499-001 Flu Year 2 Day 0


title: PB02002-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB01994-01 Immune Variation Day 0

value: Male

value: Immune Variation Day 0


title: PB01453-02 Flu Year 1 Day 90

value: Negative

value: Flu Year 1 Day 90


title: PB00597-01 Flu Year 1 Day 7


title: PB00588-01 Flu Year 1 Day 0


title: PB02568-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00328-01 Flu Year 1 Stand-Alone


title: PB00333-01 Flu Year 1 Stand-Alone


title: PB02319-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02565-001 Flu Year 2 Day 0

value: Blood


title: PB02513-001 Flu Year 2 Day 7

value: FALSE


title: PB01444-01 Flu Year 1 Day 90


title: PB00566-01 Flu Year 1 Day 0


title: PB03916-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB00580-01 Flu Year 1 Day 7


title: PB00297-02 Flu Year 1 Stand-Alone


title: PB03098-001 Flu Year 2 Day 90


title: PB02545-001 Flu Year 2 Day 7


title: PB02536-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB02252-01 Immune Variation Day 90


title: PB02326-001 Immune Variation Day 90


title: PB01550-01 Immune Variation Day 0


title: PB01563-01 Immune Variation Day 7


title: PB00342-01 Flu Year 1 Day 0


title: PB00608-01 Flu Year 1 Day 90


title: PB02507-001 Flu Year 2 Day 7

value: Female

value: Positive


title: PB02492-001 Flu Year 2 Day 0

value: Caucasian


title: PB01429-01 Flu Year 1 Day 90


title: PB01554-01 Immune Variation Day 0


title: PB03089-001 Flu Year 2 Day 90


title: PB00567-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB02254-02 Immune Variation Day 90


title: PB01973-01 Immune Variation Day 7


title: PB00552-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB00295-02 Flu Year 1 Stand-Alone

value: PBMC

value: Flu Year 1 Stand-Alone


title: PB01964-01 Immune Variation Day 0

value: Male


title: PB02555-001 Flu Year 2 Day 7


title: PB01590-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB02547-001 Flu Year 2 Day 0

value: Negative


title: PB01577-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB02268-01 Immune Variation Day 90


title: PB00579-01 Flu Year 1 Day 7


title: PB01436-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00296-02 Flu Year 1 Stand-Alone


title: PB00562-01 Flu Year 1 Day 0


title: PB02524-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02506-001 Flu Year 2 Day 0

value: Blood


title: PB00358-01 Flu Year 1 Day 7

value: FALSE


title: PB03085-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB02269-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB01597-01 Immune Variation Day 7


title: PB01567-01 Immune Variation Day 7

value: Female


title: PB00527-01 Flu Year 1 Day 7


title: PB03097-001 Flu Year 2 Day 90


title: PB00510-01 Flu Year 1 Day 0


title: PB02532-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00292-02 Flu Year 1 Stand-Alone

value: Caucasian


title: PB02543-001 Flu Year 2 Day 7


title: PB01578-01 Immune Variation Day 0


title: PB01591-01 Immune Variation Day 7


title: PB03100-001 Flu Year 2 Day 90


title: PB01437-01 Flu Year 1 Day 90


title: PB00288-01 Flu Year 1 Stand-Alone


title: PB00568-01 Flu Year 1 Day 0


title: PB00583-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB01988-01 Immune Variation Day 7


title: PB01979-01 Immune Variation Day 0


title: PB00539-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB00556-01 Flu Year 1 Day 7

value: PBMC


title: PB01424-01 Flu Year 1 Day 90


title: PB02504-001 Flu Year 2 Day 7

value: Positive


title: PB00289-01 Flu Year 1 Stand-Alone

value: Male

value: Flu Year 1 Stand-Alone


title: PB02485-001 Flu Year 2 Day 0


title: PB01581-01 Immune Variation Day 0

value: Negative


title: PB01974-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01412-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB02272-01 Immune Variation Day 90


title: PB01449-01 Flu Year 1 Day 90


title: PB00590-01 Flu Year 1 Day 7


title: PB00291-01 Flu Year 1 Stand-Alone


title: PB02583-001 Flu Year 2 Day 90


title: PB02453-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02349-001 Flu Year 2 Day 0

value: Blood


title: PB02309-002 Immune Variation Day 90

value: FALSE


title: PB01600-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB01592-01 Immune Variation Day 0


title: PB00582-01 Flu Year 1 Day 0


title: PB01441-01 Flu Year 1 Day 90


title: PB00584-01 Flu Year 1 Day 7


title: PB03895-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB03061-001 Flu Year 2 Day 90

value: Female

value: Flu Year 2 Day 90


title: PB00287-01 Flu Year 1 Stand-Alone

value: Caucasian


title: PB03086-001 Flu Year 2 Day 90


title: PB01985-01 Immune Variation Day 7


title: PB02313-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB01557-01 Immune Variation Day 0


title: PB00642-01 Flu Year 1 Day 90


title: PB01571-01 Immune Variation Day 7


title: PB02236-01 Immune Variation Day 90


title: PB03891-001 Flu Year 3 Stand-Alone


title: PB00508-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB03071-001 Flu Year 2 Day 90

value: PBMC


title: PB02478-001 Flu Year 2 Day 7


title: PB02000-01 Immune Variation Day 7


title: PB02459-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB02328-001 Immune Variation Day 90


title: PB00388-01 Flu Year 1 Day 0

value: Positive

value: Flu Year 1 Day 0


title: PB01989-02 Immune Variation Day 0

value: Negative


title: PB00629-01 Flu Year 1 Day 90


title: PB00396-01 Flu Year 1 Day 7


title: PB00377-01 Flu Year 1 Day 0


title: PB00569-01 Flu Year 1 Day 0


title: PB02579-001 Flu Year 2 Day 90


title: PB02340-001 Flu Year 2 Day 0


title: PB02357-001 Flu Year 2 Day 7


title: PB01586-01 Immune Variation Day 7


title: PB02457-001 Flu Year 2 Day 7


title: PB02351-001 Flu Year 2 Day 0


title: PB01452-01 Flu Year 1 Day 90


title: PB00553-01 Flu Year 1 Day 7


title: PB00537-01 Flu Year 1 Day 0


title: PB00285-01 Flu Year 1 Stand-Alone

value: Flu Year 1 Stand-Alone


title: PB02574-001 Flu Year 2 Day 90

value: Male


title: PB02456-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02353-001 Flu Year 2 Day 0

value: Blood


title: PB01594-01 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone

value: FALSE


title: PB00641-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00374-01 Flu Year 1 Day 7


title: PB00356-01 Flu Year 1 Day 0


title: PB00269-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00264-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB03907-001 Flu Year 3 Stand-Alone

value: Female

value: Caucasian

value: Flu Year 3 Stand-Alone


title: PB03072-001 Flu Year 2 Day 90

value: PBMC

value: Flu Year 2 Day 90


title: PB02491-001 Flu Year 2 Day 7

value: Positive


title: PB02467-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB02315-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB01995-01 Immune Variation Day 0


title: PB02003-02 Immune Variation Day 7


title: PB02255-01 Immune Variation Day 90


title: PB01569-01 Immune Variation Day 0


title: PB01438-01 Flu Year 1 Day 90


title: PB00548-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00530-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB02576-001 Flu Year 2 Day 90


title: PB02445-001 Flu Year 2 Day 0


title: PB02463-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB01599-01 Flu Year 2 Stand-Alone

value: Blood


title: PB00632-03 Flu Year 1 Day 90


title: PB00371-03 Flu Year 1 Day 7


title: PB00352-04 Flu Year 1 Day 0


title: PB00275-03 Immune Variation Day 90


title: PB00254-01 Immune Variation Day 0


title: PB00260-01 Immune Variation Day 7


title: PB02585-001 Flu Year 2 Day 90

value: Negative


title: PB00300-01 Immune Variation Day 90

value: Male

value: FALSE


title: PB02455-001 Flu Year 2 Day 7


title: PB02310-001 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB00611-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB02231-01 Flu Year 2 Stand-Alone

value: Female


title: PB00334-01 Flu Year 1 Day 0

value: Caucasian


title: PB02450-001 Flu Year 2 Day 7


title: PB00344-01 Flu Year 1 Day 7


title: PB00277-01 Immune Variation Day 90


title: PB00157-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB02347-001 Flu Year 2 Day 0

value: PBMC


title: PB00619-03 Flu Year 1 Day 90


title: PB00353-04 Flu Year 1 Day 0


title: PB00329-01 Immune Variation Day 90


title: PB00148-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00044-01 Immune Variation Day 0


title: PB02452-001 Flu Year 2 Day 7

value: Positive


title: PB02582-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB00395-01 Flu Year 1 Day 7


title: PB00368-07 Flu Year 1 Day 0


title: PB00322-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00036-01 Immune Variation Day 0


title: PB02346-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB01588-02 Flu Year 2 Stand-Alone


title: PB00323-01 Immune Variation Day 90


title: PB00168-01 Immune Variation Day 7


title: PB00379-04 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00160-01 Immune Variation Day 0


title: PB01553-01 Immune Variation Day 7


title: PB00293-02 Flu Year 1 Stand-Alone

value: Flu Year 1 Stand-Alone


title: PB03897-001 Flu Year 2 Day 90

value: Blood


title: PB02586-001 Flu Year 2 Day 90

value: Negative


title: PB00163-01 Immune Variation Day 7


title: PB02230-01 Immune Variation Day 90

value: Male


title: PB02350-001 Flu Year 2 Day 0

value: FALSE


title: PB01540-01 Immune Variation Day 0


title: PB00045-01 Immune Variation Day 7


title: PB00399-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00624-01 Flu Year 2 Day 90


title: PB00151-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00381-01 Flu Year 2 Day 0


title: PB02316-001 Immune Variation Day 90

value: Female


title: PB02560-002 Flu Year 3 Stand-Alone

value: Caucasian

value: Flu Year 3 Stand-Alone


title: PB00015-01 Flu Year 1 Day 0

value: PBMC

value: Flu Year 1 Day 0


title: PB00020-01 Flu Year 1 Day 7


title: PB00627-01 Flu Year 1 Day 90

value: Positive


title: PB01508-01 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB00170-01 Flu Year 1 Day 90


title: PB01977-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00021-01 Flu Year 1 Day 7


title: PB00016-01 Flu Year 1 Day 0


title: PB00598-01 Flu Year 2 Day 7


title: PB02482-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00294-02 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB01978-01 Flu Year 1 Day 90


title: PB02262-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB00593-01 Flu Year 2 Day 0

value: Blood

value: Flu Year 2 Day 0


title: PB02566-001 Flu Year 2 Day 7

value: Male

value: Negative


title: PB03109-001 Flu Year 2 Day 90

value: FALSE


title: PB03917-001 Flu Year 3 Stand-Alone


title: PB01446-01 Flu Year 1 Day 0


title: PB02273-01 Immune Variation Day 7


title: PB01455-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB02563-001 Flu Year 2 Day 0


title: PB03105-001 Flu Year 2 Day 90

value: Female


title: PB03923-001 Flu Year 3 Stand-Alone

value: Caucasian


title: PB02548-001 Flu Year 2 Day 0


title: PB02336-001 Immune Variation Day 90


title: PB02247-01 Immune Variation Day 7


title: PB02238-01 Immune Variation Day 0


title: PB01967-01 Immune Variation Day 0


title: PB01587-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB01434-01 Flu Year 1 Day 7

value: PBMC


title: PB01425-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB03928-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB03904-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB02571-001 Flu Year 2 Day 0


title: PB02578-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02233-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB02333-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02012-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01548-01 Flu Year 1 Day 90

value: Blood


title: PB02556-002 Flu Year 2 Day 7


title: PB02550-001 Immune Variation Day 90


title: PB00646-01 Flu Year 1 Day 7


title: PB03091-001 Flu Year 2 Day 7


title: PB03920-001 Flu Year 2 Day 90


title: PB00645-01 Flu Year 1 Day 0


title: PB03083-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB01514-01 Flu Year 1 Day 90


title: PB02271-01 Immune Variation Day 0


title: PB00621-01 Flu Year 1 Day 0


title: PB00635-01 Flu Year 1 Day 7


title: PB03095-001 Flu Year 2 Day 90

value: Male


title: PB02534-001 Flu Year 2 Day 7

value: Negative


title: PB03927-001 Flu Year 3 Stand-Alone

value: FALSE


title: PB02260-01 Immune Variation Day 90


title: PB01561-01 Immune Variation Day 0


title: PB01575-01 Immune Variation Day 7


title: PB01442-01 Flu Year 1 Day 90


title: PB00578-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00565-01 Flu Year 1 Day 0


title: PB02243-01 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB01507-01 Flu Year 1 Day 90

value: Caucasian


title: PB00596-01 Flu Year 1 Day 7


title: PB03108-002 Flu Year 3 Stand-Alone

value: Asian

value: Positive


title: PB02573-001 Flu Year 2 Day 90

value: PBMC


title: PB00592-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB02311-001 Immune Variation Day 7

value: Female


title: PB02355-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02241-01 Immune Variation Day 90


title: PB01549-01 Immune Variation Day 0


title: PB01433-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00570-01 Flu Year 1 Day 7


title: PB02561-001 Flu Year 2 Day 7


title: PB01562-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB02248-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00549-01 Flu Year 1 Day 0

value: Blood


title: PB01573-01 Immune Variation Day 7


title: PB01435-01 Flu Year 1 Day 90


title: PB02517-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00547-01 Flu Year 1 Day 7


title: PB00529-01 Flu Year 1 Day 0


title: PB03905-002 Flu Year 3 Stand-Alone

value: Male

value: Flu Year 3 Stand-Alone


title: PB03075-001 Flu Year 2 Day 90

value: Negative

value: Flu Year 2 Day 90

value: FALSE


title: PB02526-001 Flu Year 2 Day 7

value: Caucasian


title: PB02509-001 Flu Year 2 Day 0


title: PB02006-01 Immune Variation Day 90


title: PB01522-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01535-01 Immune Variation Day 7


title: PB01417-01 Flu Year 1 Day 90


title: PB00518-01 Flu Year 1 Day 0


title: PB00536-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB02337-001 Flu Year 2 Day 0

value: PBMC

value: Asian

value: Positive


title: PB02562-001 Flu Year 2 Day 0

value: Female


title: PB02564-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB03896-001 Flu Year 2 Day 90


title: PB01440-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00532-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB01552-01 Immune Variation Day 0

value: Blood


title: PB02270-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB03901-001 Flu Year 3 Stand-Alone

value: Male


title: PB03082-001 Flu Year 2 Day 90


title: PB02510-001 Flu Year 2 Day 7


title: PB00555-01 Flu Year 1 Day 7


title: PB01583-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB01565-01 Immune Variation Day 0


title: PB02314-001 Immune Variation Day 90


title: PB02495-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB01968-01 Immune Variation Day 7


title: PB03926-001 Flu Year 3 Stand-Alone

value: Negative

value: Flu Year 3 Stand-Alone


title: PB01605-01 Immune Variation Day 0

value: Caucasian

value: FALSE


title: PB00554-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00522-01 Flu Year 1 Day 7

value: PBMC


title: PB01439-01 Flu Year 1 Day 90


title: PB02552-001 Flu Year 2 Day 0

value: Asian


title: PB00535-01 Flu Year 1 Day 0

value: Positive


title: PB00504-01 Flu Year 1 Day 0


title: PB02009-01 Immune Variation Day 90


title: PB01536-01 Immune Variation Day 7


title: PB00391-01 Flu Year 1 Day 0


title: PB00511-01 Flu Year 1 Day 7


title: PB03903-001 Flu Year 3 Stand-Alone


title: PB02493-001 Flu Year 2 Day 7


title: PB02324-001 Immune Variation Day 90


title: PB02473-001 Flu Year 2 Day 0


title: PB01576-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01589-01 Immune Variation Day 7


title: PB00386-01 Flu Year 1 Day 0


title: PB03915-001 Flu Year 2 Day 90

value: Female

value: Flu Year 2 Day 90


title: PB00398-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB01413-01 Flu Year 1 Day 90

value: Blood

value: Flu Year 1 Day 90


title: PB02590-001 Flu Year 2 Day 0


title: PB02312-001 Immune Variation Day 7


title: PB02519-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02276-02 Immune Variation Day 0


title: PB01454-01 Flu Year 1 Day 90


title: PB00589-01 Flu Year 1 Day 7


title: PB03902-001 Flu Year 3 Stand-Alone

value: Male


title: PB00575-01 Flu Year 1 Day 0


title: PB01513-01 Immune Variation Day 0


title: PB00647-01 Flu Year 1 Day 90


title: PB03080-001 Flu Year 2 Day 90


title: PB01547-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00363-01 Flu Year 1 Day 0

value: Negative


title: PB00382-01 Flu Year 1 Day 7


title: PB02577-001 Flu Year 2 Day 90


title: PB02472-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB03074-001 Flu Year 2 Day 7


title: PB02256-01 Immune Variation Day 90

value: Caucasian


title: PB00517-01 Flu Year 1 Day 7

value: FALSE


title: PB03077-001 Flu Year 2 Day 90


title: PB02338-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00640-01 Flu Year 1 Day 90

value: PBMC


title: PB00505-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB01419-01 Flu Year 1 Day 90

value: Positive


title: PB02352-001 Flu Year 2 Day 7

value: Asian


title: PB00610-02 Flu Year 1 Day 90

value: Female


title: PB01519-01 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB00272-01 Immune Variation Day 7


title: PB00271-03 Immune Variation Day 0

value: Immune Variation Day 0


title: PB00268-01 Immune Variation Day 0

value: Blood

value: Other


title: PB00354-01 Flu Year 1 Day 7


title: PB00166-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB00341-01 Flu Year 1 Day 0


title: PB00270-01 Immune Variation Day 7


title: PB00278-05 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02479-001 Flu Year 2 Day 7

value: Male


title: PB02454-001 Flu Year 2 Day 0

value: Negative


title: PB03065-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB01532-02 Immune Variation Day 0

value: Caucasian


title: PB00256-01 Flu Year 1 Day 7

value: FALSE


title: PB02460-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00357-01 Flu Year 1 Day 0

value: PBMC


title: PB00280-01 Immune Variation Day 90


title: PB02483-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB01975-01 Flu Year 2 Stand-Alone


title: PB02591-001 Flu Year 2 Day 90


title: PB00620-01 Flu Year 1 Day 90

value: Positive

value: Flu Year 1 Day 90


title: PB00375-01 Flu Year 1 Day 7

value: Asian

value: Flu Year 1 Day 7


title: PB00255-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00167-01 Immune Variation Day 0

value: Blood

value: Immune Variation Day 0


title: PB00630-01 Flu Year 1 Day 90

value: Female


title: PB00262-01 Immune Variation Day 0


title: PB00367-01 Flu Year 1 Day 7


title: PB00345-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB00332-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00267-01 Immune Variation Day 7

value: Negative


title: PB03107-001 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB01972-01 Flu Year 2 Stand-Alone

value: Caucasian

value: Flu Year 2 Stand-Alone


title: PB02527-002 Flu Year 2 Day 0

value: Flu Year 2 Day 0

value: FALSE


title: PB00327-01 Immune Variation Day 90

value: PBMC


title: PB02261-01 Flu Year 2 Stand-Alone

value: Male

value: Positive


title: PB00546-01 Flu Year 1 Day 7


title: PB01430-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00161-01 Immune Variation Day 7


title: PB02541-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02462-001 Flu Year 2 Day 0


title: PB01596-01 Flu Year 2 Stand-Alone


title: PB00628-01 Flu Year 1 Day 90


title: PB00162-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00380-01 Flu Year 1 Day 7

value: Blood

value: Flu Year 1 Day 7


title: PB00154-01 Immune Variation Day 0

value: Female

value: Immune Variation Day 0


title: PB03101-001 Flu Year 2 Day 90


title: PB00325-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00362-01 Flu Year 1 Day 0

value: Negative

value: Flu Year 1 Day 0


title: PB03096-001 Flu Year 2 Day 90

value: Caucasian

value: Flu Year 2 Day 90


title: PB00253-01 Immune Variation Day 7


title: PB00164-01 Immune Variation Day 0


title: PB02557-002 Flu Year 2 Day 7


title: PB02465-001 Flu Year 2 Day 7


title: PB01602-01 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB02446-001 Flu Year 2 Day 0

value: Flu Year 2 Day 0

value: FALSE


title: PB00152-01 Immune Variation Day 7

value: PBMC


title: PB00622-01 Flu Year 1 Day 90


title: PB00290-01 Immune Variation Day 90


title: PB00525-01 Flu Year 1 Day 0

value: Positive


title: PB03062-002 Flu Year 2 Day 90


title: PB00155-01 Immune Variation Day 0


title: PB00585-01 Flu Year 1 Day 7


title: PB02470-001 Flu Year 2 Day 0


title: PB00050-01 Immune Variation Day 0


title: PB02529-001 Flu Year 2 Day 0


title: PB01603-01 Flu Year 2 Stand-Alone


title: PB00631-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00370-05 Flu Year 1 Day 7


title: PB00284-01 Immune Variation Day 90


title: PB00349-01 Flu Year 1 Day 0


title: PB00150-01 Immune Variation Day 7


title: PB02570-002 Flu Year 2 Day 90


title: PB02444-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00048-01 Immune Variation Day 0


title: PB01525-01 Flu Year 2 Stand-Alone


title: PB00616-01 Flu Year 1 Day 90


title: PB02343-001 Flu Year 2 Day 0


title: PB00376-01 Flu Year 1 Day 7


title: PB00350-01 Flu Year 1 Day 0


title: PB00347-01 Flu Year 1 Day 0


title: PB00141-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00039-03 Immune Variation Day 0

value: Blood


title: PB00283-01 Immune Variation Day 90


title: PB02592-002 Flu Year 2 Day 90


title: PB02490-001 Flu Year 2 Day 7


title: PB02468-001 Flu Year 2 Day 7


title: PB02449-001 Flu Year 2 Day 0


title: PB00385-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00633-01 Flu Year 1 Day 90

value: Female


title: PB00365-01 Flu Year 1 Day 0


title: PB00046-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB03068-002 Flu Year 2 Day 90


title: PB00286-05 Immune Variation Day 90

value: Immune Variation Day 90


title: PB02496-001 Flu Year 2 Day 7

value: Negative


title: PB01531-01 Flu Year 2 Stand-Alone


title: PB00338-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: PB00359-01 Flu Year 1 Day 7

value: Caucasian


title: PB02476-001 Flu Year 2 Day 0


title: PB00281-01 Immune Variation Day 90


title: PB00617-01 Flu Year 1 Day 90


title: PB00144-01 Immune Variation Day 7


title: PB00042-01 Immune Variation Day 0


title: PB02494-001 Flu Year 2 Day 7


title: PB02267-01 Flu Year 2 Stand-Alone


title: PB00392-01 Flu Year 1 Day 7


title: PB02475-001 Flu Year 2 Day 0


title: PB00366-01 Flu Year 1 Day 0


title: PB00331-01 Immune Variation Day 90


title: PB00257-01 Immune Variation Day 0


title: PB02558-001 Flu Year 3 Stand-Alone

value: Male

value: Flu Year 3 Stand-Alone


title: PB01606-01 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB02334-001 Immune Variation Day 90

value: FALSE


title: PB01970-01 Immune Variation Day 0

value: PBMC


title: PB01980-01 Immune Variation Day 7


title: PB00147-01 Immune Variation Day 7


title: PB01510-01 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: PB00615-01 Flu Year 2 Day 7


title: PB00606-01 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00041-01 Flu Year 1 Day 0


title: PB00397-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00143-01 Flu Year 1 Day 7


title: PB02589-001 Flu Year 2 Day 90


title: PB02486-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00507-01 Flu Year 1 Day 0

value: Blood


title: PB00282-01 Immune Variation Day 90


title: PB00650-01 Flu Year 1 Day 90


title: PB01524-01 Flu Year 2 Stand-Alone


title: PB02466-001 Flu Year 2 Day 0


title: PB00142-01 Immune Variation Day 0


title: PB00524-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: PB00153-01 Immune Variation Day 7

value: Female

value: Immune Variation Day 7


title: PB01595-01 Flu Year 2 Stand-Alone


title: PB00263-03 Immune Variation Day 7


title: PB00384-01 Flu Year 1 Day 0


title: PB00509-01 Flu Year 1 Day 7


title: PB01410-01 Flu Year 1 Day 90


title: PB00273-05 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00165-03 Immune Variation Day 7

value: Negative


title: PB00158-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB00531-01 Flu Year 1 Day 7

value: Other

value: Positive


title: PB00159-01 Immune Variation Day 7

value: Male


title: PB00149-01 Immune Variation Day 0


title: PB03925-001 Immune Variation Day 7

value: Caucasian


title: PB00514-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0

value: FALSE


title: PB01459-01 Flu Year 2 Day 90

value: PBMC

value: Flu Year 2 Day 90


title: PB02244-01 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: PB03922-001 Immune Variation Day 0


title: PB02451-001 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB02584-001 Flu Year 2 Day 90

value: Blood


title: PB00595-01 Flu Year 2 Day 7


title: PB00031-05 Flu Year 1 Day 0


title: PB00591-01 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00032-05 Flu Year 1 Day 7

value: Female

value: Flu Year 1 Day 7


title: PB00298-02 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00544-01 Flu Year 2 Day 7

value: Negative


title: PB02348-001 Flu Year 2 Day 0


title: PB02572-001 Flu Year 3 Stand-Alone


title: PB02520-001 Immune Variation Day 90

value: Immune Variation Day 90


title: PB01426-01 Flu Year 1 Day 90

value: Other


title: Poly A RNA, late S/G2/M population of BJ-Fucci cells, Rep3

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: KI630

data_processing:
RNA-seq reads were aligned to the GRCh38 human reference genome with the Gencode v38 basic gene annotation (60,649 genes) [20] using STAR 2.7.9 [21] with the default alignment parameters except using “clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA”.
Raw read counts were processed in Combat-seq in R to correct for the sorting batch.
The corrected read counts were used to compute transcripts per million (TPM), such that TPM =106 x RPK/sum(RPK), where RPK is [1+corrected read count]/[transcript length in kb], and sum(RPK) is sum of RPKs for all genes.
Assembly: GRCh38
Supplementary files format and content: List of TPM for each gene for each biological replicate in plain text

source_name: cell line

growth_protocol: BJ-Fucci cells are the hTERT-immortalized human dermal fibroblast cell line BJ-5ta (source: foreskin of male neonate; ATCC catalog # CRL-4001) transduced with Fucci4 reporters. To introduce Fucci4 fluorescent markers, BJ-5ta cells were co-transduced with the two lentivirus Clover-Gemininaa1-110-IRES-mKO2-Cdt1aa30-120 (Addgene ID83841) and mTurquoise2- SLBPaa18-126-IRES-H1-mMaroon1 (Addgene ID83842). The transduced cells were selected for their simultaneous expression of Clover and mMaroon1 and then for their simultaneous expression of mKO2 and mMaroon1 using FACS. The resultant double-selected cells are “BJ-Fucci” cells (cell ID cc1357-2ss) used in this study. BJ-Fucci cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS), 90 U/mL penicillin, 90 µg/mL streptomycin streptomycin at 37ºC under 5% CO2.

extract_protocol:
Total RNAs were purified by Trizol LS (Invitrogen 10296028) and treated with DNase I (Invitrogen Turbo DNase AM2238). mRNAs were isolated and fragmented using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490). cDNAs were synthesized using the cDNA synthesis module in NEBNext UltraII Directional RNA Library Prep Kit for Illumina (NEB E7660).
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370).

treatment_protocol: Approximately 20 hours before FACS sorting, BJ-Fucci cells that reached confluency were passaged to 8–20 15-cm culture dishes at a density of 2.5 million cells per dish. Cells were dissociated from the dishes with TrypLE (Thermo Fisher), filtered through a 40-µm cell strainer, resuspended in the complete culture medium, and sorted into the culture medium using BD FACSAriaII (sorting experiment ID: KI2834 and KI2847) or BD FACSAriaIIu (KI2858) sorters. The following populations were sorted: mKO2–Clover–mTurquoise2– (early G1), mKO2+Clover– (G1), mKO2+Clover+mTurquois+ (early S), and mKO2–Clover+ (late-S/G2/M). The following excitation (ex) lasers and emission (em) filter settings were used: mTurquioise2, ex 405 nm, em 450/50 nm; Clover, ex 488 nm, em 530/30 nm; mKO2, ex 561 nm, em 582/15 nm; mMaroon1, ex 561 nm, em 670/30 nm (FACSAriaII) or em 670/14 (FACSAriaIIu). After sorting, cells were stored with Trizol LS (Thermo Fisher) at –80ºC for RNA-seq.

value: cell line

tag: cell line

value: BJ-Fucci

value: fibroblast

tag: treatment

value: Late S/G2/M

tag: batch

value: FACS KI2858


title: PB00299-02 Flu Year 1 Day 90

value: PBMC

tag: subject id

value: Caucasian

value: FALSE


title: PB02259-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB02253-01 Immune Variation Day 0

value: Blood

value: Immune Variation Day 0


title: PB00528-01 Flu Year 2 Day 0

value: Female

value: Flu Year 2 Day 0


title: Poly A RNA, early G1 population of BJ-Fucci cells, Rep3

description: Library name: KI631

value: Early G1


title: PB00033-06 Flu Year 1 Day 7

value: Negative

value: Flu Year 1 Day 7


title: Poly A RNA, G1 population of BJ-Fucci cells, Rep3

description: Library name: KI629


title: Poly A RNA, early S population of BJ-Fucci cells, Rep2

description: Library name: KI624

value: Early S

value: FACS KI2847


title: PB02321-001 Flu Year 3 Stand-Alone

value: Male

value: Positive

value: Flu Year 3 Stand-Alone


title: PB02010-01 Immune Variation Day 90

value: Immune Variation Day 90


title: Poly A RNA, late S/G2/M population of BJ-Fucci cells, Rep2

description: Library name: KI622

value: cell line

value: BJ-Fucci

value: fibroblast

value: Late S/G2/M


title: PB01411-01 Flu Year 2 Day 90

value: Blood

value: PBMC

value: Caucasian

value: Flu Year 2 Day 90

value: FALSE


title: Poly A RNA, early G1 population of BJ-Fucci cells, Rep2

description: Library name: KI623

value: Early G1


title: PB01534-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB00361-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: Poly A RNA, G1 population of BJ-Fucci cells, Rep2

description: Library name: KI621

value: FACS KI2847


title: Poly A RNA, early S population of BJ-Fucci cells, Rep1

description: Library name: KI616

value: Early S

value: FACS KI2834


title: Poly A RNA, late S/G2/M population of BJ-Fucci cells, Rep1

description: Library name: KI614


title: PB01523-01 Immune Variation Day 0

value: Male

value: Positive

value: Immune Variation Day 0


title: PB00607-02 Flu Year 2 Day 90


title: Poly A RNA, early S population of BJ-Fucci cells, Rep3

description: Library name: KI632

value: cell line

value: BJ-Fucci

value: FACS KI2858


title: Poly A RNA, early G1 population of BJ-Fucci cells, Rep1

description: Library name: KI615

value: fibroblast


title: Poly A RNA, G1 population of BJ-Fucci cells, Rep1

description: Library name: KI613


title: PB00340-01 Flu Year 2 Day 0

value: Blood

value: PBMC

value: Flu Year 2 Day 0


title: Wound, 6 dpw

city: Zürich

first: Ismail

last: Kücükaylak

address: Otto-Stern-Weg 7

institute: ETH Zurich

description:
Library name: 169370
10X Genomics

data_processing:
Single cell RNA sequencing data was analyzed using RStudio program with Seurat (V4.3.0) software package for R using standard quality control, normalization, integration and analysis steps.
Assembly: Danio_rerio.GRCz11.106
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Skin

extract_protocol:
Unwounded skin tissue from three adult zebrafish was collected by scraping off the skin and pooling in PBS (Mg2+ and Ca2+-free). In addition, the wound tissues for 2 dpw, 4 dpw and 6 dpw were collected using a biopsy punch with a diameter of 4 mm from three adult zebrafish each. PBS was replaced with 0.25 mg/ml Liberase TM in PBS solution and the tissues were incubated at 30oC for an hour with slow agitation (~300 rpm). The solution was pipetted every 10-15 minutes. After successful digestion of the tissue, the solution was mixed with 5% FBS/PBS and filtered through a cell strainer with 70 μm nylon mesh and then a cell strainer with 40 μm nylon mesh in 50 ml Falcon tubes. The falcon tubes were centrifuged at 500 x g for 5 minutes and the pellet was resuspended with 2% FBS/PBS. The viability of the cells were more than ninety percent. The single cell suspensions were kept on ice until they were processed at the Cologne Center for Genomics, University of Cologne. 10.000 cells per condition was aimed for single cell RNA sequencing.
Single cell suspensions were processed, sequenced and single cell library construction was mapped to the zebrafish transcriptome by Cologne Center for Genomics, University of Cologne using 10x Genomics 3’scRNA seq application (Version 3’v.3.1) with Cell Ranger software (cellranger-6.1.2) used to generate feature-barcode matrices.

treatment_protocol: Wounding

value: Skin

tag: age

value: Adult

value: Skin cells

tag: genotype

value: Wild type

value: Wounding

tag: time

value: 6 dpw


title: PB00252-02 Flu Year 1 Day 90

value: Caucasian

tag: cmv status

value: Flu Year 1 Day 90

tag: batch id

tag: sample bridging_control

value: FALSE


title: PB00030-02 Flu Year 1 Day 0

tag: tissue

value: Female

value: Negative

value: Flu Year 1 Day 0


title: PB00028-05 Flu Year 1 Day 7

value: Male

value: Positive

tag: days since_first_visit

value: Flu Year 1 Day 7


title: ZEN4000,replicate 3

city: Jinan

first: Chenqinyao

last: Li

state: shandong

address: jinshidongroad, 1009, jinan, shandong, china

country: China

institute: Qilu University of Technology

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment.FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Transcript-level quantification, analysis of differentially expressed transcript (DEGs),cluster analysis, GO and KEGG enrichment. If it was transcript-level quantification, FPKM[2] and read counts value of each transcript(protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Gene structure extension and novel transcripts identification The reads were reassembled using StringTie. Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
Alternatively splicing analysis and SNP-INDEL calling. The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile. SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Assembly: GRCz11
Supplementary files format and content: fq

source_name: liver

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min.  B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube.  C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase.  D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.                                                                                E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.  G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μLaliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (Illumina Novaseq 6000) and 125bp/150bp paired-end reads were generated.

value: liver

value: day 6

tag: strain

value: 4000 ng/mL zearalenone exposure


title: Wound, 2 dpw

description:
Library name: 169368
10X Genomics

value: Skin

value: Adult

tag: cell type

value: 2 dpw


title: PB00026-05 Flu Year 1 Day 0

value: Blood

value: PBMC

tag: Sex

tag: visit


title: Wound, 4 dpw

description:
Library name: 169369
10X Genomics

value: Skin cells

value: Wild type

value: Wounding

value: 4 dpw


title: PB01456-01 Immune Variation Day 0

tag: birth year

tag: race

value: African American

value: Negative

value: Immune Variation Day 0

value: FALSE


title: PB00618-01 Flu Year 2 Day 90

value: Male

value: Flu Year 2 Day 90


title: ZEN2000,replicate 2

value: liver

value: day 6

tag: treatment

value: 2000 ng/mL zearalenone exposure


title: Control,replicate 3


title: ZEN2000,replicate 1


title: PB01458-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB01965-01 Immune Variation Day 90

value: Immune Variation Day 90


title: Control,replicate 2


title: PB00025-04 Flu Year 1 Day 0

value: Blood

value: Flu Year 1 Day 0


title: ZEN4000,replicate 2

value: 4000 ng/mL zearalenone exposure


title: PB00336-05 Flu Year 2 Day 0

value: PBMC

value: Flu Year 2 Day 0


title: PB00348-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00029-02 Flu Year 1 Day 7

value: African American

value: Flu Year 1 Day 7


title: ZEN4000,replicate 1


title: ZEN2000,replicate 3


title: PB02274-01 Immune Variation Day 7

value: Female

value: Caucasian

value: Positive


title: PB00258-04 Flu Year 1 Day 90

value: Male

value: Negative

value: Flu Year 1 Day 90

value: FALSE


title: Control,replicate 1

value: liver

value: day 6


title: PB02553-002 Flu Year 3 Stand-Alone

value: Blood

value: Flu Year 3 Stand-Alone


title: HH-TAZ_24h-3

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49, Campus Gasthuisberg, O&N 4, 9e verd, bus 912

country: Belgium

institute: VIB-KU Leuven Center for Cancer Biology

description: Library name: sample 30

data_processing:
cleaning with fastq-mcf
quality control with FastQC
mapping with HISAT2, further processing with SAMTools
counting abundances with htseq-count
Assembly: hg38
Supplementary files format and content: tab delimited text file with raw counts

source_name: HH

extract_protocol:
RNA extraction was performed using a Promega Maxwell, using the Maxwell RSC simplyRNA Cells Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HH

value: cutaneous T-cell leukemia/lymphoma

value: tazemetostat


title: PB02487-001 Immune Variation Day 90

value: PBMC

tag: subject id

value: Immune Variation Day 90


title: HH-TAZ_24h-2

description: Library name: sample 29


title: HH-ROMI_24h-2

description: Library name: sample 26

value: romidepsin


title: HH-ROMI_24h-1

description: Library name: sample 25


title: Unwounded Skin

description:
Library name: 169367
10X Genomics

value: Skin

tag: age

value: Adult

value: Skin cells

value: Wild type

value: No treatment

value: Unwounded Skin


title: HH-TAZ_24h-1

description: Library name: sample 28


title: HH-ROMI_24h-3

description: Library name: sample 27


title: PB02265-02 Flu Year 3 Stand-Alone

value: Male

value: African American

value: Negative

value: FALSE


title: PB01450-01 Flu Year 2 Day 90

value: Blood

value: Female

value: Caucasian

value: Positive

value: Flu Year 2 Day 90


title: PB02263-02 Immune Variation Day 0

value: PBMC

value: Immune Variation Day 0


title: PB00594-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00586-01 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: PB00259-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00024-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: HH-MS+ROMI_24h-1

description: Library name: sample 22

value: HH

value: cutaneous T-cell leukemia/lymphoma

value: MS1943 + romidepsin


title: HH-MS+ROMI_24h-2

description: Library name: sample 23


title: HH-MS+ROMI_24h-3

description: Library name: sample 24


title: PB00022-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: HH-MS_24h-3

description: Library name: sample 21


title: PB02471-001 Immune Variation Day 90

value: Negative

value: Immune Variation Day 90


title: HH-MS_24h-1

description: Library name: sample 19


title: PB02275-01 Immune Variation Day 7

value: Blood

value: Immune Variation Day 7

value: FALSE


title: HH-DMSO_24h-3

description: Library name: sample 18

value: DMSO


title: PB02264-01 Immune Variation Day 0

value: Female

value: Caucasian


title: HH-MS_24h-2

description: Library name: sample 20


title: HH-DMSO_24h-2

description: Library name: sample 17


title: PB01520-01 Flu Year 2 Day 90

value: PBMC

value: Flu Year 2 Day 90


title: PB00612-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: EOL1-TAZ_24h-2

description: Library name: sample 14

value: acute myeloid leukemia

value: tazemetostat


title: EOL1-TAZ_24h-1

description: Library name: sample 13


title: PB00169-03 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: PB00027-05 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: EOL1-ROMI_24h-3

description: Library name: sample 12

value: romidepsin


title: EOL1-ROMI_24h-2

description: Library name: sample 11


title: PB00023-05 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: EOL1-ROMI_24h-1

description: Library name: sample 10


title: PB00634-01 Flu Year 2 Day 90

value: Positive


title: PB00502-01 Flu Year 2 Day 7


title: PB02559-002 Flu Year 3 Stand-Alone

value: Negative

value: Flu Year 3 Stand-Alone


title: PB00373-01 Flu Year 2 Day 0

value: Blood

value: Flu Year 2 Day 0


title: EOL1-MS+ROMI_24h-3

description: Library name: sample 9

value: MS1943 + romidepsin


title: PB00019-01 Flu Year 1 Day 7

value: Female

value: FALSE


title: EOL1-MS_24h-3

description: Library name: sample 6


title: EOL1-MS+ROMI_24h-1

description: Library name: sample 7


title: PB00047-01 Flu Year 1 Day 90

value: PBMC

value: Caucasian


title: EOL1-MS_24h-2

description: Library name: sample 5


title: HH-DMSO_24h-1

description: Library name: sample 16

value: HH

value: cutaneous T-cell leukemia/lymphoma

value: DMSO


title: EOL1-TAZ_24h-3

description: Library name: sample 15

value: acute myeloid leukemia

value: tazemetostat


title: PB02332-001 Flu Year 3 Stand-Alone

value: Male

value: Other


title: PB00012-01 Flu Year 1 Day 0

value: Positive

value: Flu Year 1 Day 0


title: PB02277-01 Immune Variation Day 90

value: Immune Variation Day 90


title: PB00601-01 Flu Year 2 Day 0

value: Blood

value: Negative


title: EOL1-DMSO_24h-2

description: Library name: sample 2


title: PB01604-01 Immune Variation Day 7

value: Immune Variation Day 7


title: EOL1-MS_24h-1

description: Library name: sample 4


title: EOL1-DMSO_24h-3

description: Library name: sample 3


title: PB01598-01 Immune Variation Day 0

value: Immune Variation Day 0


title: EOL1-DMSO_24h-1

description: Library name: sample 1


title: PB01420-01 Flu Year 2 Day 90

value: Flu Year 2 Day 90

value: FALSE


title: LARGE_MYCPOS_9

city: London

first: Mariia

last: Yuneva

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: SET2504A60

data_processing:
RNA-sequencing reads were processed using the nf-core RNA-seq pipeline (version 3.3) with the STAR/RSEM option. Reads were aligned to the mouse genome assembly GRCm38 using Ensembl release 95 transcript annotations. Gene-level abundance estimates were obtained from RSEM and imported into R using the DeSeqDataSetFromMatrix function in DESeq2. Normalization factors were computed per gene, correcting for library size and feature length. Variance stabilizing transformation (VST) was applied to abundance estimates to standardize gene expression across samples.
Assembly: GRCm38 using Ensembl release 95
Supplementary files format and content: VST normalised expression values. Rows are transcripts. Columns are samples.
Supplementary files format and content: Raw counts matrix. Output of RSEM-STAR alignments and counting.. Rows are transcipts. Columns are samples.

organism: Mus musculus

source_name: Mammary gland tumour

extract_protocol:
RNA was extracted from a scoop of frozen tissue and then ground by homogenizing in TRIzol™ following the manufacturer’s protocol.   200ng of extracted RNA was submeeted for RNA sequencing.
KAPA mRNA polyA HyperPrep

value: Mammary gland tumour

tag: genotype

value: MMTV-MYC

value: Tumour

tag: batch

value: FVB/N


title: PB00521-01 Flu Year 2 Day 0

value: PBMC

tag: cmv status

value: Flu Year 2 Day 0


title: LARGE_MYCPOS_8

description: Library name: SET2504A59


title: PB00542-01 Flu Year 2 Day 7

value: Male

value: Flu Year 2 Day 7

tag: batch id


title: PB00049-01 Flu Year 1 Day 90

value: Other

value: Positive

value: Flu Year 1 Day 90

tag: sample bridging_control


title: LARGE_MYCPOS_5

description: Library name: SET2504A56

tag: tissue


title: LARGE_MYCPOS_7

description: Library name: SET2504A58


title: LARGE_MYCPOS_6

description: Library name: SET2504A57


title: EOL1-MS+ROMI_24h-2

description: Library name: sample 8

value: acute myeloid leukemia

value: MS1943 + romidepsin


title: LARGE_MYCPOS_4

description: Library name: SET2504A55


title: PB00018-01 Flu Year 1 Day 7

value: Blood

tag: days since_first_visit

value: Flu Year 1 Day 7


title: PB00014-01 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: LARGE_MYCPOS_3

description: Library name: SET2504A54


title: PB02567-001 Flu Year 3 Stand-Alone

value: Caucasian

value: Negative

value: Flu Year 3 Stand-Alone

value: FALSE


title: LARGE_MYCPOS_2

description: Library name: SET2504A53

value: Mammary gland tumour

value: MMTV-MYC

value: Tumour

value: FVB/N


title: SMALL_MYCPOS_6

description: Library name: SET2504A51


title: PB02325-001 Immune Variation Day 90

value: PBMC

value: Male

value: Immune Variation Day 90


title: PB01976-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB01987-01 Immune Variation Day 7

value: Immune Variation Day 7


title: SMALL_MYCPOS_5

description: Library name: SET2504A50


title: PB00572-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: SMALL_MYCPOS_4

description: Library name: SET2504A49


title: LARGE_MYCPOS_1

description: Library name: SET2504A52


title: PB01443-01 Flu Year 2 Day 90

value: Blood

value: Flu Year 2 Day 90