title: ExT28_day21_Tumor_Tim3_FTY_11

description: Library name: Sample 119

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5.
In MiXCR, Filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics information system: -starting-material=rna, -5-end=no-v-primers-, -3-end=c-primers, -adapters=no-adapters, vParameters.geneFeatureToAlign=VTranscript, -vjAlignmentOrder=JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=15, –separateByV=true, –separateByJ=true, -only-productive=true, –region-of-interest=CDR3.
The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature. List of final clones were analyzed by VDJtools-1.2.1. Then, the sequencing reads of sample was normalized to the six times of cell count in each sample by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR V segment, J segment and CDR3 nucleotide sequence.
Assembly: IMGT reference sequences of mouse TRB
Supplementary files format and content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

extract_protocol:
Tumors were cut into small fragments and digested for 45 minutes at 37°C with 0.2% collagenase (FUJIFILM Wako) and DNase I (Sigma-Aldrich), except for experiments for single-cell analysis, in which tumors were digested with 0.2% collagenase NB8 (Nordmark Pharma GmbH). The cells were then subjected to two-phase density separation with upper 35% Percoll PLUS (GE Healthcare) (1000g, 10 minutes at room temperature). Leukocytes were recovered, washed and resuspended in preparation medium (PM) [5%FBS, 10mM HEPES (Nacalai), Penicillin-Streptomycin (Nacalai) in RPMI-1640 (Nacalai)]. After RBC lysis with ACK buffer [155mM of NH4Cl (Nacalai), 10mM of KHCO3 (Nacalai), and 0.5mM EDTA pH8.0 (NIPPON GENE)] for 1 minute at room temperature, cells were washed and resuspended in PM, and the cell concentrations were measured using Flow-Count fluorospheres (Beckman Coulter) and a CytoFLEX S flow cytometer (Beckman Coulter).Cells were stained with a mix of Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioLegend) and fluorophore-conjugated anti-mouse monoclonal antibodies (Supplementary Table 5). Antibody mixtures were prepared using BD Horizon Brilliant Stain Buffer Plus (BD) diluted 5x with FACS buffer (D-PBS(-) supplemented with 2% FBS, and 0.05% Sodium Azide). Staining was performed for 20 minutes at 4°C. Before sorting, T cells were enriched from tumor suspensions by further staining with BD IMag APC Magnetic Particles-DM (BD Biosciences), then placed on magnetic plate. After washing by MACS buffer (D-PBS(-) supplemented with 10% BSA, and 2 mM EDTA pH8.0), APC and APC-Cy7(CD8, mouse TCRb)-positive cells were collected as positive fraction. Cell sorting was performed using a FACS Aria II or Aria III (BD Biosciences). Cells were stained with 5µg/mL of propidium iodide (PI, Sigma-Aldrich) immediately before sorting. Nonviable cells were excluded from the analysis based on forward and side scatter profiles and PI staining. For bulk TCR repertoire analysis and bulk RNA-seq analysis, cells were sorted into Lysis buffer [1% w/v LiDS, 100 mM Tris-HCl pH7.5, 500 mM LiCl, 5 mM dithiothreitol, and 10 mM EDTA pH8.0] and stored at −80°C. For the bulk TCR-seq experiments, cells were sorted from the CD8+, CD8+PD-1+Ly108+TIM-3-, CD8+PD-1+Ly108+TIM-3+, CD8+PD-1+Ly108-TIM-3+ and CD8+PD-1- fractions to produce five datasets per mouse.
TCR libraries were prepared on purified T cells lysed in lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, and 10 mM EDTA]. PolyA RNAs were isolated according to a previous report with some modifications (GSE110711).To perform reverse transcription and template-swiching, beads were then suspended in 10 µL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2, 1 U/µL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1µM of i5-TSO], and incubated for 60 min at 42ºC and immediately cooled on ice. Beads were washed once with with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads with containing cDNA was resuspended with the 25 µL of first PCR mixture [0.4 µM of primers (i5, Trac_ex, and Trbc_ex), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, #KK2602)], and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min. Then, 2.5 µL of first PCR product was mixed with the 22.5 µl of second PCR mixture [0.35 µM of primers (i5_2nd, i7-BC_mTrac, and i7-BC_mTrbc), and 1x KAPA Hifi Hotstart ReadyMix], , and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 18 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min.. The second-PCR products were purified by an Agencort AM Pure XP kit (Bexkman-Coulter, CA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 20 µL of Tris-HCl (pH 8.0).To amplify TCR library and add adaptor sequence for next generation sequencer, the third PCR was performed as follows. 5µL of purified second PCR product was mixed with the 20 µl of third PCR mixture [0.4 µM of primers (i5-BC and i7-BC), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, USA, #KK2602)], and the thermal cycling was performed under the same condition as first PCR, excepted for the number of cycles (23 cycles). The third-PCR products were purified as second PCR. The products were pooled and then purified and subjected to dual size selection using ProNex size-selective purification system (Promega) and eluted with 25 μL of Tris-HCl (pH 8.5). Final TCR libraries, whose lengths were about 600 base pairs were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina, USA). Only read2 contained the sequence regarding the definition of T cell clones.

treatment_protocol: For the FTY720 experiment, FTY720 (Selleck) was injected intraperitoneally at a dose of 20μg per mice on days 14, 16, 18 and 20.

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108- and Tim3+ T cells


title: ExT28_day21_Tumor_Tim3_FTY_9

status: Public on Jul 29 2025

type: SRA

city: Noda-shi

first: Mikiya

last: Tsunoda

state: Chiba

department: Molecular Preventive Medicine

country: Japan

institute: The University of Tokyo

description: Library name: Sample 117

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: Tumor

growth_protocol: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left and right flanks of C57BL/6 mice.

tag: tissue

value: Tumor

tag: cell line

value: Lewis lung carcinoma

tag: cell type

tag: genotype

value: WT


title: ExT28_day21_Tumor_Tim3_FTY_12

description: Library name: Sample 120


title: ExT28_day21_Tumor_Tim3_FTY_7

description: Library name: Sample 115


title: ExT28_day21_Tumor_Tim3_cont_6

description: Library name: Sample 114


title: ExT28_day21_Tumor_Tim3_FTY_8

description: Library name: Sample 116


title: ExT28_day21_Tumor_Tim3_cont_4

description: Library name: Sample 112


title: ExT28_day21_Tumor_Tim3_FTY_10

description: Library name: Sample 118


title: ExT28_day21_Tumor_PD1nega_FTY_12

description: Library name: Sample 108

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+ and PD-1- T cells


title: ExT28_day21_Tumor_Tim3_cont_5

description: Library name: Sample 113


title: ExT28_day21_Tumor_Tim3_cont_1

description: Library name: Sample 109


title: ExT28_day21_Tumor_PD1nega_FTY_10

description: Library name: Sample 106


title: ExT28_day21_Tumor_PD1nega_FTY_9

description: Library name: Sample 105


title: ExT28_day21_Tumor_Tim3_cont_3

description: Library name: Sample 111


title: ExT28_day21_Tumor_PD1nega_FTY_8

description: Library name: Sample 104


title: ExT28_day21_Tumor_PD1nega_cont_5

description: Library name: Sample 101


title: ExT28_day21_Tumor_PD1nega_cont_6

description: Library name: Sample 102


title: ExT28_day21_Tumor_PD1nega_cont_3

description: Library name: Sample 99


title: ExT28_day21_Tumor_PD1nega_cont_2

description: Library name: Sample 98


title: ExT28_day21_Tumor_PD1nega_cont_1

description: Library name: Sample 97


title: ExT28_day21_Tumor_PD1nega_FTY_7

description: Library name: Sample 103


title: ExT28_day21_Tumor_PD1nega_cont_4

description: Library name: Sample 100


title: ExT28_day21_Tumor_Ly108_FTY_11

description: Library name: Sample 95

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108+ and Tim3- T cells


title: ExT28_day21_Tumor_Ly108_FTY_10

description: Library name: Sample 94


title: ExT28_day21_Tumor_Tim3_cont_2

description: Library name: Sample 110


title: ExT28_day21_Tumor_PD1nega_FTY_11

description: Library name: Sample 107


title: ExT28_day21_Tumor_Ly108_FTY_8

description: Library name: Sample 92


title: ExT28_day21_Tumor_Ly108_cont_6

description: Library name: Sample 90


title: ExT28_day21_Tumor_Ly108_FTY_7

description: Library name: Sample 91


title: ExT28_day21_Tumor_Ly108_cont_5

description: Library name: Sample 89


title: ExT28_day21_Tumor_Ly108_cont_4

description: Library name: Sample 88


title: ExT28_day21_Tumor_Ly108_cont_2

description: Library name: Sample 86


title: ExT28_day21_Tumor_DP_FTY_11

description: Library name: Sample 83

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108+ and Tim3+ T cells


title: ExT28_day21_Tumor_DP_FTY_12

description: Library name: Sample 84


title: ExT28_day21_Tumor_DP_FTY_10

description: Library name: Sample 82


title: ExT28_day21_Tumor_Ly108_cont_1

description: Library name: Sample 85


title: ExT28_day21_Tumor_Ly108_cont_3

description: Library name: Sample 87


title: ExT28_day21_Tumor_DP_FTY_9

description: Library name: Sample 81


title: ExT28_day21_Tumor_DP_FTY_8

description: Library name: Sample 80


title: ExT28_day21_Tumor_Ly108_FTY_12

description: Library name: Sample 96


title: ExT28_day21_Tumor_DP_FTY_7

description: Library name: Sample 79


title: ExT28_day21_Tumor_DP_cont_6

description: Library name: Sample 78


title: ExT28_day21_Tumor_DP_cont_5

description: Library name: Sample 77


title: ExT28_day21_Tumor_Ly108_FTY_9

description: Library name: Sample 93


title: ExT28_day21_Tumor_DP_cont_1

description: Library name: Sample 73


title: ExT28_day21_Tumor_CD8_FTY_11

description: Library name: Sample 71

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+ T cells


title: ExT28_day21_Tumor_CD8_FTY_12

description: Library name: Sample 72


title: ExT28_day21_Tumor_CD8_FTY_10

description: Library name: Sample 70


title: ExT28_day21_Tumor_CD8_FTY_9

description: Library name: Sample 69


title: ExT28_day21_Tumor_CD8_FTY_7

description: Library name: Sample 67


title: ExT28_day21_Tumor_CD8_FTY_8

description: Library name: Sample 68


title: ExT28_day21_Tumor_CD8_cont_4

description: Library name: Sample 64


title: ExT28_day21_Tumor_CD8_cont_5

description: Library name: Sample 65


title: ExT28_day21_Tumor_CD8_cont_6

description: Library name: Sample 66


title: ExT28_day21_Tumor_CD8_cont_3

description: Library name: Sample 63


title: ExT28_day14_Tumor_Tim3_FTY_12

description: Library name: Sample 60


title: ExT28_day21_Tumor_CD8_cont_2

description: Library name: Sample 62


title: ExT28_day14_Tumor_Tim3_FTY_11

description: Library name: Sample 59


title: ExT28_day14_Tumor_Tim3_FTY_8

description: Library name: Sample 56


title: ExT28_day14_Tumor_Tim3_FTY_7

description: Library name: Sample 55


title: ExT28_day21_Tumor_CD8_cont_1

description: Library name: Sample 61


title: ExT28_day14_Tumor_Tim3_cont_4

description: Library name: Sample 52


title: ExT28_day14_Tumor_Tim3_cont_5

description: Library name: Sample 53


title: ExT28_day14_Tumor_Tim3_FTY_10

description: Library name: Sample 58


title: ExT28_day21_Tumor_DP_cont_3

description: Library name: Sample 75


title: ExT28_day14_Tumor_Tim3_FTY_9

description: Library name: Sample 57


title: ExT28_day14_Tumor_Tim3_cont_3

description: Library name: Sample 51


title: ExT28_day14_Tumor_PD1nega_FTY_12

description: Library name: Sample 48


title: ExT28_day14_Tumor_Tim3_cont_1

description: Library name: Sample 49


title: ExT28_day14_Tumor_PD1nega_FTY_11

description: Library name: Sample 47


title: ExT28_day14_Tumor_Tim3_cont_6

description: Library name: Sample 54


title: ExT28_day14_Tumor_PD1nega_FTY_7

description: Library name: Sample 43


title: ExT28_day14_Tumor_PD1nega_FTY_9

description: Library name: Sample 45


title: ExT28_day14_Tumor_PD1nega_cont_5

description: Library name: Sample 41


title: ExT28_day14_Tumor_PD1nega_FTY_10

description: Library name: Sample 46


title: ExT28_day14_Tumor_PD1nega_cont_6

description: Library name: Sample 42


title: ExT28_day14_Tumor_PD1nega_FTY_8

description: Library name: Sample 44


title: ExT28_day14_Tumor_PD1nega_cont_1

description: Library name: Sample 37


title: ExT28_day14_Tumor_Tim3_cont_2

description: Library name: Sample 50


title: ExT28_day14_Tumor_PD1nega_cont_3

description: Library name: Sample 39


title: ExT28_day14_Tumor_PD1nega_cont_2

description: Library name: Sample 38


title: ExT28_day14_Tumor_PD1nega_cont_4

description: Library name: Sample 40


title: ExT28_day14_Tumor_Ly108_FTY_12

description: Library name: Sample 36


title: ExT28_day14_Tumor_Ly108_FTY_11

description: Library name: Sample 35


title: ExT28_day14_Tumor_Ly108_FTY_9

description: Library name: Sample 33


title: ExT28_day14_Tumor_Ly108_cont_3

description: Library name: Sample 27


title: ExT28_day14_Tumor_Ly108_cont_5

description: Library name: Sample 29


title: ExT28_day14_Tumor_Ly108_cont_2

description: Library name: Sample 26


title: ExT28_day14_Tumor_Ly108_FTY_8

description: Library name: Sample 32


title: ExT28_day14_Tumor_Ly108_cont_6

description: Library name: Sample 30


title: ExT28_day14_Tumor_Ly108_FTY_10

description: Library name: Sample 34


title: ExT28_day14_Tumor_Ly108_cont_4

description: Library name: Sample 28


title: ExT28_day14_Tumor_Ly108_cont_1

description: Library name: Sample 25


title: ExT28_day14_Tumor_DP_FTY_12

description: Library name: Sample 24


title: ExT28_day14_Tumor_DP_FTY_11

description: Library name: Sample 23


title: ExT28_day14_Tumor_DP_FTY_7

description: Library name: Sample 19


title: ExT28_day14_Tumor_DP_FTY_10

description: Library name: Sample 22


title: ExT28_day14_Tumor_DP_FTY_8

description: Library name: Sample 20


title: ExT28_day14_Tumor_DP_cont_6

description: Library name: Sample 18


title: ExT28_day14_Tumor_DP_FTY_9

description: Library name: Sample 21


title: ExT28_day14_Tumor_DP_cont_5

description: Library name: Sample 17


title: ExT28_day14_Tumor_DP_cont_4

description: Library name: Sample 16


title: ExT28_day14_Tumor_DP_cont_3

description: Library name: Sample 15


title: ExT28_day14_Tumor_Ly108_FTY_7

description: Library name: Sample 31


title: ExT28_day14_Tumor_CD8_FTY_12

description: Library name: Sample 12


title: ExT28_day14_Tumor_CD8_FTY_11

description: Library name: Sample 11


title: ExT28_day14_Tumor_CD8_FTY_10

description: Library name: Sample 10


title: ExT28_day14_Tumor_DP_cont_1

description: Library name: Sample 13


title: Proximal colon, GFP-intermediate, Replicate 1

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: Library name: COLP_Int1

data_processing:
The reads were then mapped to the mouse genome build mm10 using STAR based on GENCODE M22 annotations. Gene counts were counted using featureCounts (part of the Subread package) based on GENCODE M22 annotations. The gene counts were then used in edgeR for a differential expression of genes (DEG) analysis with multiple testing correction done using the method of Benjamini and Hochberg.
Assembly: mm10
Supplementary files format and content: Genes counts, TPM and RPKM in long format for all samples as a tab delimited file.

source_name: Proximal colon

growth_protocol: Mouse 8 weeks old

extract_protocol:
Chelation buffer crypt dissociation with TrypLE single cell dissociation. GFP-sorting by FACS in RLTplus + b-mercaptoethanol. Rneasy microkit (qiagen) RNA extraction. A minimum of 30,000 cells for colon and 50,000 cells for small intestine were collected from each GFP fraction.
FASTQ files containing the RNA-Seq reads were checked for quality control issues using FASTQC and MultiQC for which no issues were found.

value: Proximal colon

value: Epithelial cells


title: ExT28_day14_Tumor_CD8_FTY_9

description: Library name: Sample 9


title: ExT28_day14_Tumor_CD8_FTY_7

description: Library name: Sample 7


title: ExT28_day14_Tumor_CD8_FTY_8

description: Library name: Sample 8


title: ExT28_day14_Tumor_CD8_cont_4

description: Library name: Sample 4


title: ExT28_day14_Tumor_CD8_cont_2

description: Library name: Sample 2


title: ExT28_day14_Tumor_CD8_cont_5

description: Library name: Sample 5


title: ExT28_day14_Tumor_CD8_cont_3

description: Library name: Sample 3


title: ExT28_day14_Tumor_CD8_cont_6

description: Library name: Sample 6


title: ExT2.4_day21_Tim3_23

description: Library name: Sample 70


title: ExT28_day14_Tumor_DP_cont_2

description: Library name: Sample 14


title: ExT2.4_day21_Tim3_20

description: Library name: Sample 68


title: ExT2.4_day21_Tim3_19

description: Library name: Sample 67


title: ExT2.4_day21_PD1nega_22

description: Library name: Sample 62


title: ExT2.4_day21_Tim3_15

description: Library name: Sample 65


title: ExT2.4_day21_Tim3_13

description: Library name: Sample 64


title: ExT2.4_day21_PD1nega_23

description: Library name: Sample 63


title: ExT2.4_day21_Tim3_17

description: Library name: Sample 66


title: ExT2.4_day21_PD1nega_19

description: Library name: Sample 60


title: ExT28_day14_Tumor_CD8_cont_1

description: Library name: Sample 1


title: ExT2.4_day21_PD1nega_20

description: Library name: Sample 61


title: ExT2.4_day21_PD1nega_15

description: Library name: Sample 58


title: ExT2.4_day21_PD1nega_17

description: Library name: Sample 59


title: ExT2.4_day21_PD1nega_13

description: Library name: Sample 57


title: ExT2.4_day21_Tim3_22

description: Library name: Sample 69


title: ExT2.4_day21_Ly108_20

description: Library name: Sample 54


title: ExT2.4_day21_Ly108_17

description: Library name: Sample 52


title: ExT2.4_day21_Ly108_23

description: Library name: Sample 56


title: ExT2.4_day21_Ly108_15

description: Library name: Sample 51


title: ExT28_day21_Tumor_DP_cont_2

description: Library name: Sample 74


title: ExT2.4_day21_Ly108_19

description: Library name: Sample 53


title: ExT2.4_day21_double_19

description: Library name: Sample 46


title: ExT2.4_day21_double_20

description: Library name: Sample 47


title: ExT2.4_day21_Ly108_22

description: Library name: Sample 55


title: ExT2.4_day21_double_17

description: Library name: Sample 45


title: ExT2.4_day21_double_15

description: Library name: Sample 44


title: ExT2.4_day21_Ly108_13

description: Library name: Sample 50


title: ExT2.4_day14_Tim3_23

description: Library name: Sample 42


title: ExT2.4_day21_double_13

description: Library name: Sample 43


title: ExT2.4_day14_Tim3_22

description: Library name: Sample 41


title: ExT2.4_day21_double_22

description: Library name: Sample 48


title: ExT2.4_day14_Tim3_20

description: Library name: Sample 40


title: ExT2.4_day14_Tim3_17

description: Library name: Sample 38


title: ExT2.4_day14_Tim3_13

description: Library name: Sample 36


title: ExT2.4_day14_PD1nega_20

description: Library name: Sample 33


title: ExT2.4_day14_PD1nega_23

description: Library name: Sample 35


title: ExT2.4_day14_Tim3_15

description: Library name: Sample 37


title: ExT2.4_day21_double_23

description: Library name: Sample 49


title: ExT2.4_day14_PD1nega_19

description: Library name: Sample 32


title: ExT2.4_day14_PD1nega_15

description: Library name: Sample 30


title: ExT2.4_day14_PD1nega_17

description: Library name: Sample 31


title: ExT2.4_day14_Ly108_19

description: Library name: Sample 25


title: ExT2.4_day14_Ly108_23

description: Library name: Sample 28


title: ExT2.4_day14_PD1nega_22

description: Library name: Sample 34


title: ExT2.4_day14_Ly108_20

description: Library name: Sample 26


title: ExT2.4_day14_Ly108_15

description: Library name: Sample 23


title: ExT2.4_day14_double_20

description: Library name: Sample 19


title: ExT2.4_day14_double_19

description: Library name: Sample 18


title: ExT2.4_day14_double_22

description: Library name: Sample 20


title: ExT2.4_day14_Ly108_13

description: Library name: Sample 22


title: ExT2.4_day14_PD1nega_13

description: Library name: Sample 29


title: ExT2.4_day14_double_23

description: Library name: Sample 21


title: ExT2.4_day14_double_15

description: Library name: Sample 16


title: ExT28_day21_Tumor_DP_cont_4

description: Library name: Sample 76


title: ExT2.4_day14_Tim3_19

description: Library name: Sample 39


title: ExT2_3_day21_Tumor_CD8_23

description: Library name: Sample 14


title: ExT2.4_day14_Ly108_17

description: Library name: Sample 24


title: ExT2.4_day14_double_13

description: Library name: Sample 15


title: ExT2_3_day21_Tumor_CD8_22

description: Library name: Sample 13


title: ExT2_3_day21_Tumor_CD8_20

description: Library name: Sample 12


title: ExT2_3_day21_Tumor_CD8_19

description: Library name: Sample 11


title: ExT2.4_day14_Ly108_22

description: Library name: Sample 27


title: ExT2_3_day21_Tumor_CD8_13

description: Library name: Sample 8


title: ExT2_3_day14_Tumor_CD8_23

description: Library name: Sample 7


title: ExT2_3_day21_Tumor_CD8_17

description: Library name: Sample 10


title: ExT2_3_day14_Tumor_CD8_22

description: Library name: Sample 6


title: ExT2_3_day14_Tumor_CD8_20

description: Library name: Sample 5


title: ExT2_3_day14_Tumor_CD8_17

description: Library name: Sample 3


title: ExT2.4_day14_double_17

description: Library name: Sample 17


title: ExT2_3_day14_Tumor_CD8_19

description: Library name: Sample 4


title: ExT2_3_day14_Tumor_CD8_13

description: Library name: Sample 1


title: IgG_CUTTag of shInts7 E14TG2a cells repeat 2

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

country: China

institute: central south university

description: Library name: shInts7_IgG_CUTTag_rep2

library_source: genomic

data_processing:
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
For RNA-seq analysis, the RNA-seq data underwent initial quality assessment and adapter trimming utilizing Trim Galore (version 0.6.4_dev). Subsequently, the trimmed reads were aligned to the mm10 reference genome using STAR (version 2.7.2d). For the quantification of reads corresponding to genomic features, featureCounts (version 2.0.0) was employed.
For ATAC-seq analysis, clean fragments were aligned to the mm10 genome using Bowtie2 (v2.2.5) with parameters --local --very-sensitive --no-mixed --phred33 -I 30 -X 2000. MACS2 (v2.2.6) was used for peak calling with the settings '-f BAMPE -g mm --nomodel --shift -100 --extsize 200 -p 1e-3'. Differential accessibility analysis was performed using MACS2 (v2.2.6) 'macs2 bdgdiff', while peak annotation was conducted with ChIPseeker (v1.38.0). Bigwig files were generated following the same procedure as CUT&Tag data processing.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using bamCoverage, from both replicates and linked to the corresponding rep1 sample records
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: Mouse E14TG2a ESCs were cultured on gelatin-coated dishes in DMEM (High Glucose, with Sodium Pyruvate, with L-Alanyl-L-Glutamine) (Vivacell) supplemented with 15% fetal bovine serum (Vistech), 1× non-essential amino acids (Gibco), 100 μM β-mercaptoethanol (Sigma), and 1000 U/mL of leukemia inhibitory factor (LIF) (Millipore). The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag was performed following the protocol provided by the Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen). A total of 50,000 cells were harvested and subjected to two rounds of washing using washing buffer (composed of 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Protease inhibitor cocktail). Subsequently, the cells were incubated with activated Concanavalin A coated magnetic beads. To this, 0.5 μg of HA antibody was added and allowed to incubate on a rotating platform at 4 °C for a duration of 16 hours. Following this, 0.5 μL of Goat anti-Rabbit secondary antibody was introduced and incubated for an additional hour. After a thorough washing step, the cells were treated with pA/G-Tn5 transposase at 37°C for 1 hour. Subsequently, DNA extraction was carried out by DNA selection beads.
ATAC-seq experiments were conducted using the Hieff NGS® ATAC-Seq Library Prep Kit (Yeasen, 12208ES12). 100,000 cells were harvested and washed with PBS before resuspension in 50 μl of lysis buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. The cells were incubated on ice for 5 min to facilitate lysis. Nuclei were then treated with the Tn5 transposome in tagmentation buffer at 37°C for 30 min. To terminate the reaction, stop buffer was directly added.
Total RNA was harvested using Trizol reagent from 5*106 ESCs.
To amplify libraries, 16 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, 7 μL ddH2O, and 25 μL 2× Ultima Amplification Mix, and run the following cycling conditions with lid heat on: 72 °C for 3 min; 95 °C for 30 s; 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 30 s; final extension at 72 °C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.2× volume of DNA selection beads (60 μL), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer.
For ATAC-seq, DNA purification was carried out using 2.4× DNA Extract Beads, followed by PCR amplification to generate sequencing libraries. The purified libraries underwent quality assessment prior to high-throughput sequencing. Two independent replicates were performed to ensure reproducibility.

treatment_protocol: Cells were infected with a lentivirus carrying shNT or shInts7 for 24 hours and then collected

value: mouse embryonic stem cell

tag: treatment


title: IgG_CUTTag of control E14TG2a cells repeat 2

description: Library name: shNT_IgG_CUTTag_rep2

value: shNT


title: Kap1S824p_CUTTag of shInts7 E14TG2a cells repeat 2

description:
Library name: shInts7_Kap1S824p_CUTTag_rep2
shInts7_Kap1S824p.compareInput.rpm.bw


title: Kap1S824p_CUTTag of control E14TG2a cells repeat 2

description:
Library name: shNT_Kap1S824p_CUTTag_rep2
shNT_Kap1S824p.compareInput.rpm.bw


title: ExT2_3_day21_Tumor_CD8_15

description: Library name: Sample 9


title: Kap1S824p_CUTTag of control E14TG2a cells repeat 1

description:
Library name: shNT_Kap1S824p_CUTTag_rep1
shNT_Kap1S824p.compareInput.rpm.bw


title: RNA-seq of shInts7 E14TG2a cells repeat 2

description:
Library name: shInts7_RNAseq_rep2
shInts7_RNAseq.bw

data_processing:
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
For RNA-seq analysis, the RNA-seq data underwent initial quality assessment and adapter trimming utilizing Trim Galore (version 0.6.4_dev). Subsequently, the trimmed reads were aligned to the mm10 reference genome using STAR (version 2.7.2d). For the quantification of reads corresponding to genomic features, featureCounts (version 2.0.0) was employed.
For ATAC-seq analysis, clean fragments were aligned to the mm10 genome using Bowtie2 (v2.2.5) with parameters --local --very-sensitive --no-mixed --phred33 -I 30 -X 2000. MACS2 (v2.2.6) was used for peak calling with the settings '-f BAMPE -g mm --nomodel --shift -100 --extsize 200 -p 1e-3'. Differential accessibility analysis was performed using MACS2 (v2.2.6) 'macs2 bdgdiff', while peak annotation was conducted with ChIPseeker (v1.38.0). Bigwig files were generated following the same procedure as CUT&Tag data processing.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using bamCoverage, from both replicates and linked to the corresponding rep1 sample records

molecule: total RNA


title: RNA-seq of shInts7 E14TG2a cells repeat 1

description:
Library name: shInts7_RNAseq_rep1
shInts7_RNAseq.bw


title: RNA-seq of control E14TG2a cells repeat 2

description:
Library name: shNT_RNAseq_rep2
shNT_RNAseq.bw


title: ExT2_3_day14_Tumor_CD8_15

description: Library name: Sample 2


title: LysoPS_OVA_1ug

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

country: USA

institute: University at Buffalo

description:
Library name: LysoPS_OVA_1ug
10x Genomics

library_source: transcriptomic single cell

data_processing:
Preliminary filtered data generated from 10× CellRanger v7.2.0 were used for downstream filtering and analysis. Alignment and quantification were performed using Cellranger v.7.2.0 against the 10x supplied v7 mm10-2020-A reference set.
Assembly: mm10
Supplementary files format and content: 10x genomics filtered feature matrix files

source_name: Mesenteric lymph nodes

extract_protocol:
Each group consisted of six animals and collected mesenteric lymph node (MLN) at the end of the study. We obtained MLN cells suspension using enzymatic digestion and cells were removed using dead cell removal
Samples with >70% cell viability were confirmed for single-cell RNA sequencing. The assays were conducted at the University at Buffalo Genomics and Bioinformatics Core. According to the Chromium Next GEM Single Cell 3’ Reagent Kit v.3.1 (Dual Index) manual, samples were prepared and loaded with 10,000 cells per sample onto 10× Chromium chips (10× Genomics, Pleasanton CA). The 10× Chromium libraries were prepared and sequenced with dual barcoding, paired-end reads (28x,10i,10i,90x) on the NovaSeq 6000 platform using an SP flowcell (Illumina, San Diego, CA).

value: Mesenteric lymph nodes

value: intestinal cells

value: LysoPS-OVA


title: RNA-seq of control E14TG2a cells repeat 1

description:
Library name: shNT_RNAseq_rep1
shNT_RNAseq.bw


title: IgG_CUTTag of shInts7 E14TG2a cells repeat 1

description: Library name: shInts7_IgG_CUTTag_rep1


title: ATAC-seq of shInts7 E14TG2a cells repeat 2

description:
Library name: shInts7_ATACseq_rep2
shInts7-ATAC.bw


title: IgG_CUTTag of control E14TG2a cells repeat 1

description: Library name: shNT_IgG_CUTTag_rep1


title: Kap1S824p_CUTTag of shInts7 E14TG2a cells repeat 1

description:
Library name: shInts7_Kap1S824p_CUTTag_rep1
shInts7_Kap1S824p.compareInput.rpm.bw


title: ATAC-seq of shInts7 E14TG2a cells repeat 1

description:
Library name: shInts7_ATACseq_rep1
shInts7-ATAC.bw


title: ATAC-seq of control E14TG2a cells repeat 2

description:
Library name: shNT_ATACseq_rep2
shNT-ATAC.bw


title: Ascending adventitial fibroblasts 10ng/ml TGFb, rep 3

city: Stanford

first: Chad

middle: S

last: Weldy

state: CA

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

description: Library name: C12

data_processing:
RNAseq data were processed using a workflow starting from fastq files and code is available on github (https://github.com/zhaoshuoxp/Pipelines-Wrappers/blob/master/RNAseq.sh). In brief, the quality control was performed using FastQC, mapping to the human genome mm10 was performed using STAR second pass mapping to increase the percentage of mapped reads, and counting was done with featureCounts using GENCODE gtf annotation. Next, differential analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: CSV file including raw featureCounts for each sample

source_name: Primary mouse adventitial fibroblast

growth_protocol: Adventitia was cut into small pieces with microscissors and plated into 12 well plates with DMEM media with 5% FBS. Following cell attachment to the plate, cells were cultured at 37C and expanded for 48 hours. Cells were washed with PBS and passaged 1x and plated into a 12 well plate at 65,000 cells/mL.

extract_protocol:
RNA was isolated from disrupted primary adventitial fibroblast cells using standard RNeasy mini kit protocol (Qiagen).
Isolated RNA underwent quality assessment, cDNA conversion, and library construction by Novogene (San Jose, CA).

treatment_protocol: Upon cell culture reaching ~80% confluence, cells were treated with either solute control or mouse TGFb (invitae) (10ng/mL) for 48 hours.

value: Primary mouse adventitial fibroblast

value: mouse fibroblast

tag: strain

tag: age

value: 14 weeks

tag: batch


title: Ascending adventitial fibroblasts 10ng/ml TGFb, rep 2

description: Library name: C11


title: ATAC-seq of control E14TG2a cells repeat 1

description:
Library name: shNT_ATACseq_rep1
shNT-ATAC.bw


title: Ascending adventitial fibroblasts 10ng/ml TGFb, rep 1

description: Library name: C10


title: DES2_ATAC

description:
Library name: DES2_ATAC
10X Genomics, scATACseq

library_source: genomic single cell

data_processing:
Demultiplexed Fastq files and matrix files were generated with Cellranger for RNA and Cellranger-atac for ATAC datasets.
Assembly: mm10 genome used for reference
Supplementary files format and content: filtered sequence read with matrix.h5 files are reported and ultimately used in Seurat and SIgnac for data analysis.

source_name: descending thoracic aorta from subclavian artery to renal artery

extract_protocol:
Aortic tissue was dissected from the aortic root to the brachiocephalic artery (Ascending), from the brachiocephalic artery up including the carotid artery (carotid), and descending thoracic aorta from subclavian artery to renal arter (descending). Protocol follows as such:1) Prepare the Enzyme Solution (on ice):     Final (working) concentration of Liberase is 2 units/mL    Final (working) concentration of Elastase is 2 units/mL     For 1mL of enzyme solution:     Liberase TM (26 units/mL)  77  uL     Elastase (125 units/mL)   16  uL     HBSS      907 uL     Total      1   mL  2) Place enzyme mixture on ice while aorta is being harvested  3) Perfuse mouse with ~10mL PBS via LV puncture  4) Harvest aortic root and open longitudinally. Wash with PBS x3 in 12-well dish. Keep on ice while collecting from multiple mice.  5) Move root to 12-well dish with 1mL of enzyme mixture.  6) Incubate in 37C incubator for ~30-45 minutes (adjust time based on age and extent of calcification e.g. if Apoe w/ 16wk HFD incubate for 45 minutes). At the end of the incubation, mince thoroughly with scissors for a few minutes (<5min) until tissue is mostly dissolved.  7) Pipet up and down ~20-30 times to thoroughly disrupt tissue. Confirm full digestion under the microscope (single cells w/o clumps). If the tissue is not fully digested after pipetting incubate at 37C for an additional 10-15 minutes (may lead to increased cell lysis).   8) Transfer cell suspension into 1.5mL Eppendorf and centrifuge at 500xg for 5 minutes.  9) Carefully remove supernatant (confirm that the cell pellet is still present).  10) Resuspend the cells in 200uL HBSS (adjust volume as needed). Cell solution was then sorted for live cells on FACS and then proceeded to 10X capture following 10X protocol.  11) Immediately prior to FACS and/or staining, pass cells through a 35um strainer. Note: Coating collection tubes in BSA solution may improve cell survival. 1) Coat the 1.5mL eppendorf tubes used to store the cells prior to FACS, and the FACS collection eppendorf tubes, with 10% BSA in PBS (i.e. fill up tube, and pipette out all volume - then wait a few minutes and then pipet out the rest that gradually slid to the bottom).  2) Wash Buffer: 10mM Tris pH 7.4 (CATALOGUE NUMBER) 10mM NaCl (CATALOGUE NUMBER) 3mM MgCl2 (CATALOGUE NUMBER) 1% BSA (1:10 dilution from 10% BSA stock (CATALOGUE NUMBER)) 0.1% Tween-20 (1:100 dilution from 10% stock (CATALOGUE NUMBER))  NOTE: Wash buffer can be prepared ahead of time and kept at 4C without adding BSA. Add all reagents, except for BSA, to a new 500mL bottle of ultra-pure water and keep at 4C until needed.  3) 0.1X lysis buffer: 196uL wash buffer + 2uL 1X Promega digitonin and 2uL NP-40, followed by 1:10 (200uL + 1800uL) dilution with wash buffer.   After FACS (all centrifugation steps at 4C):  4) Spin cells at 500g x 10 min, gently pipet off all supernatant (with P1000 and P100).  5) Add 45uL 0.1X lysis buffer, mix x3, and incubate for 15 minutes on ice.  6) Add 50uL chilled wash buffer WITHOUT mixing.  7) Spin at 500g x10 min, remove 95uL supernatant with P100.  8) Add 45uL 1X diluted nuclei buffer (diluted 1:20 with H2O), WITHOUT mixing.  9) Spin at 500g x10 min. Remove supernatant with P100 (set to 40uL) and P10 (set to 10uL).  10) Resuspend in 7uL 1X diluted nuclei buffer.  11) Mix 25uL nuclei buffer and 25uL Trypan blue. Mix 1 uL nuclei suspension with 9uL od Trypan blue dilution (1:10 dilution). Load into hemacytometer and examine with Zeiss in microscope room (not TC scope). Count the average number of nuclei in the large boxes and calculate nuclei/uL. Remember to account for 10x dilution factor.  12) Dilute nuclei with more nuclei buffer, if desired.  13) Aim for 8000-9000 nuclei per capture
scRNA and scATAC libraries were prepared following 10X protocol.

value: cells of the vessel wall

value: 16 weeks of age

value: wildtype

value: ATAC Batch 2


title: CAR2_ATAC

description:
Library name: CAR2_ATAC
10X Genomics, scATACseq

source_name: brachiocephalic artery take off up to common carotid artery into skull insertion


title: DES1_ATAC

description:
Library name: DES1_ATAC
10X Genomics, scATACseq

value: descending thoracic aorta from subclavian artery to renal artery

value: ATAC Batch 1


title: ASC2_ATAC

description:
Library name: ASC2_ATAC
10X Genomics, scATACseq

source_name: aortic root, ascending aorta to brachiocephalic artery take off


title: DES1_RNA

description:
Library name: DES1_RNA
10X Genomics, scRNAseq

value: RNA Batch 1


title: CAR1_RNA

description:
Library name: CAR1_RNA
10X Genomics, scRNAseq

value: brachiocephalic artery take off up to common carotid artery into skull insertion


title: ASC1_ATAC

description:
Library name: ASC1_ATAC
10X Genomics, scATACseq

value: aortic root, ascending aorta to brachiocephalic artery take off


title: ASC2_RNA

description:
Library name: ASC2_RNA
10X Genomics, scRNAseq

value: RNA Batch 2


title: Ascending adventitial fibroblasts 0ng/ml TGFb, rep 3

description: Library name: C9

value: WT


title: CAR2_RNA

description:
Library name: CAR2_RNA
10X Genomics, scRNAseq


title: CAR1_ATAC

description:
Library name: CAR1_ATAC
10X Genomics, scATACseq


title: ASC1_RNA

description:
Library name: ASC1_RNA
10X Genomics, scRNAseq


title: DES2_RNA

description:
Library name: DES2_RNA
10X Genomics, scRNAseq


title: Ascending adventitial fibroblasts 0ng/ml TGFb, rep 2

description: Library name: C8


title: Descending adventitial fibroblasts 10ng/ml TGFb, rep 3

description: Library name: C6


title: Descending adventitial fibroblasts 10ng/ml TGFb, rep 2

description: Library name: C5


title: Descending adventitial fibroblasts 10ng/ml TGFb, rep 1

description: Library name: C4


title: Descending adventitial fibroblasts 0ng/ml TGFb, rep 3

description: Library name: C3


title: Descending adventitial fibroblasts 0ng/ml TGFb, rep 2

description: Library name: C2


title: Descending adventitial fibroblasts 0ng/ml TGFb, rep 1

description: Library name: C1


title: Tumour Passage Balb/c-2 (YUMM1.7 cells) tumour C rep2

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: Library name: Balb_c2_C_EKRN230042263-1A_HKMHTDSX7_L3

data_processing:
HiSat2 v2.0.5, assembled into transcripts with Stringtie v1.3.3b, and summarised into gene counts with featureCounts v1.5.0-p3.
Assembly: mm10
Supplementary files format and content: GEO, Transposable element normalised counts.csv: CSV file containing normalised counts (FPKM) for each sample for the set of human transposable elements

source_name: Dissociated tumour

growth_protocol: YUMM1.7 were obtained from the American Tissue Culture Collection. YUMM1.7 and dissociated tumour cells were grown in DMEM F-12 media (Gibco) supplemented with 10% FBS (Labtech), 1% non-essential amino acids (Gibco), and 1% penicillin/streptomycin (Gibco). Cells were passaged every 2-3 days at 70-80% confluency

extract_protocol:
Total RNA was extracted using the RNAeasy kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification for the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Dissociated tumour

value: Melanoma


title: Tumour Passage CBA (YUMM1.7 cells) tumour A

description: Library name: CBA_A_EKRN230042264-1A_HKMHTDSX7_L3


title: Ascending adventitial fibroblasts 0ng/ml TGFb, rep 1

description: Library name: C7


title: Tumour Passage CBA (YUMM1.7 cells) tumour B

description: Library name: CBA_B_EKRN230042265-1A_HKMHTDSX7_L3


title: Tumour Passage CBA (YUMM1.7 cells) tumour C

description: Library name: CBA_C_EKRN230042266-1A_HKMHTDSX7_L3


title: Tumour Passage Balb/c-2 (YUMM1.7 cells) tumour A rep2

description: Library name: Balb_c2_A_EKRN230042261-1A_HKMHTDSX7_L3


title: Tumour Passage Balb/c-2 (YUMM1.7 cells) tumour B rep2

description: Library name: Balb_c2_B_EKRN230042262-1A_HKMGWDSX7_L1


title: Tumour Passage Balb/c-2 (YUMM1.7 cells) tumour C

description: Library name: BALBc_2C


title: Tumour Passage Balb/c-2 (YUMM1.7 cells) tumour B

description: Library name: BALBc_2B


title: Tumour Passage Balb/c-1 (YUMM1.7 cells) tumour B

description: Library name: BALBc_1B


title: Tumour Passage Balb/c-1 (YUMM1.7 cells) tumour A

description: Library name: BALBc_1A


title: Tumour Passage Balb/c-1 (YUMM1.7 cells) tumour D

description: Library name: BALBc_1D


title: TNBC3_D0_CD8

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Library name: TNBC3_D0_CD8

data_processing:
FASTQ files were aligned and assembled using MiXCR v3.0.13 with default parameters on human TCR sequences.
Assembly: GRCh38
Supplementary files format and content: Excel file includes clonotype information and relative frequencies for each sample
Library strategy: TCR-Seq

organism: Homo sapiens

source_name: primary

extract_protocol:
Total RNA was extracted from sorted CD8+ T cells or regulatory T cells from peripheral blood.
Sequencing libraries were prepared using the SMARTer Human TCR a/b Profiling Kit

value: PBMC

value: CD8+ T cell


title: TNBC1_D0_Treg

description: Library name: TNBC1_D0_Treg

value: Treg cell


title: Lum1_D0_CD8

description: Library name: Lum1_D0_CD8


title: TNBC1_D0_CD8

description: Library name: TNBC1_D0_CD8


title: TNBC1_D7_Treg

description: Library name: TNBC1_D7_Treg


title: TNBC2_D7_Treg

description: Library name: TNBC2_D7_Treg


title: TNBC2_D0_Treg

description: Library name: TNBC2_D0_Treg


title: Lum2_D7_Treg

description: Library name: Lum2_D7_Treg


title: TNBC2_D0_CD8

description: Library name: TNBC2_D0_CD8


title: Lum1_D0_Treg

description: Library name: Lum1_D0_Treg


title: TNBC4_D0_Treg

description: Library name: TNBC4_D0_Treg


title: Lum2_D0_Treg

description: Library name: Lum2_D0_Treg


title: Lum1_D7_CD8

description: Library name: Lum1_D7_CD8


title: TNBC4_D7_Treg

description: Library name: TNBC4_D7_Treg


title: TNBC3_D7_CD8

description: Library name: TNBC3_D7_CD8


title: TNBC1_D7_CD8

description: Library name: TNBC1_D7_CD8


title: Tumour Passage Balb/c-1 (YUMM1.7 cells) tumour C

description: Library name: BALBc_1C


title: Lum1_D7_Treg

description: Library name: Lum1_D7_Treg


title: Bone, FibrousDysplasia3, GNAS locus

city: San Francisco

first: Edward

last: Hsiao

address: 505 Parnassus Ave

institute: UCSF

description:
Library name: FD28_gnas
Amplified GNAS locus from 10x Genomics library run on Illumina Miseq

data_processing:
Barcode processing of 10x full-library generated FASTQ files and gene counting were performed using Cell Ranger version 3.1.0 (10x Genomics, https://www.10xgenomics.com/support/software/cell-ranger/latest).
Reads from GNAS-amplified 10x libraries were run at or trimmed to 120 base-pairs in length (from 250bp).  FASTQs from multiple runs were merged for each sample and then processed using Cell Ranger, as described above.  GNAS reads whose barcodes intersected with those of the filtered 10x full-library datasets were retained and assigned a GNAS genotype according to their nucleotide sequence at coding positions c.601 or c.602.
Assembly: Human reference, GRCh38 (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#grch38_3.0.0)
Supplementary files format and content: Tab-separated values (tsv) files and matrix (mtx) files are output generated by the 'cellranger count' command (https://www.10xgenomics.com/support/software/cell-ranger/latest/resources/cr-command-line-arguments).
Supplementary files format and content: Comma-separated values (csv) files contain the number of reads per GNAS genotype per cell barcode.

source_name: Right proximal femur

extract_protocol:
Surgical bone was collected in 80% Dulbecco’s Modified Eagle media (DMEM, Gibco) and 20% fetal bovine serum (FBS, Avantor, Seradigm) and transported on ice directly from the operating room to the laboratory for processing within 2–3 hours of surgical resection. Approximately 1 cubic centimeter of FD or WT bone was mechanically dissociated using a mortar and pestle for at least one minute until the bone fragments were white in color. Bone fragments were then enzymatically digested by incubating with type II collagenase (Gibco, 3000 U/ml) at 37⁰ C for 20 minutes with continuous gentle agitation and briefly vortexed every 5 minutes. The digested fragments were passed through a 70-μm prefilter, followed by a 40-μm filter, to collect the cells and strain the debris. Red blood cell lysis buffer (Biolegend) was added to the cells for 10 minutes in the dark, quenched with 1x PBS (Gibco), and followed by centrifugation at 600 x g for 5 minutes. Non-viable cells were removed using magnetic activated cell sorting (MACS) with a dead cell removal kit (Miltenyi Biotec). The resulting live cell fraction was enriched for CD45- cells using a MACS CD45 depletion kit (Miltenyi Biotec), following the manufacturer’s instructions. Cells isolated after CD45 depletion were resuspended in PBS containing 0.04% bovine serum albumin (BSA) at a final concentration of 1,000 cells/μL.
Library construction of 10x Genomics Single-cell libraries: Single-cell libraries were generated by the UC Davis Gene Expression Core according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Library construction of GNAS amplified libraries: The remainder of the amplified 10x full-length cDNA library that was not used for 10X library generation was further amplified using standard Illumina sequencing primers (FOR-Illumina R1: 5′ CTA CAC GAC GCT CTT CCG ATC T-3′ and REV-Illumina template switch oligo primer: 5′-AAG CAG TGG TAT CAA CGC AGA GTA CAT-3′, Integrated DNA Technologies (IDT)). The amplified cDNA library contains full-length gene transcripts that are labeled with a 10X cell barcode (CB) and a unique molecular identifier (UMI). The GNAS transcripts were selectively amplified by PCR using the standard Read 1 Illumina sequencing primer (see above) and a second primer targeting exon 8 of GNAS (REV: 5′-CAA GAT CGA CGT GAT CAA GCA-3′). A customized partial Illumina Read 2 sequence was added to the 5′ end of exon 8 of GNAS via PCR (FOR Illumina R1, REV: 5′ GTT CAG ACG TGT GCT CTT CCG ATC TCA AGC AGG CTG ACT ATG TGC-3′), followed by the addition of P5 and P7 sample index (SI) Illumina adaptors (FOR-P5: 5′ REV-Partial Read 2-Sample Index – P7: 5′-CAA GCA GAA GAC GGC ATA CGA GAT N TGA CTG GAG TTC AGA CGT GT-3′ (where N= an eight–base pair individual sample index).

value: Right proximal femur

tag: disease state

value: Stromal, Endothelial, Perivascular cells


title: Bone, FibrousDysplasia2, GNAS locus

description:
Library name: FD21_gnas
Amplified GNAS locus from 10x Genomics library run on Illumina Miseq or NovaSeq

source_name: Left femur

value: Left femur

value: Fibrous Dysplasia


title: TNBC2_D7_CD8

description: Library name: TNBC2_D7_CD8


title: Bone, FibrousDysplasia1, GNAS locus

description:
Library name: FD16_gnas
Amplified GNAS locus from 10x Genomics library run on Illumina Miseq or NovaSeq


title: Bone, FibrousDysplasia4, GNAS locus

description:
Library name: FD716_gnas
Amplified GNAS locus from 10x Genomics library run on Illumina Miseq or NovaSeq


title: Tumour Passage Balb/c-2 (YUMM1.7 cells) tumour A

description: Library name: BALBc_2A


title: Tumour passage N2.3 (YUMM1.7 cells) tumour C

description: Library name: N2_3C


title: Tumour passage N2.3 (YUMM1.7 cells) tumour B

description: Library name: N2_3B


title: CTCF-C8_dTAG_4hr_HiC

city: La Jolla

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

description: Library name: MB124

data_processing:
HiC data was first aligned to the hg38 reference genome using BWA-MEM and processed with in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Aligned data was de-duplicated using Picard MarkDuplicates.
Contact files were generated from bam files using in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Juicer was used to create .hic files from contact files, while cooler was used to create multi-resolution cool (mcool) files.
Assembly: hg38
Supplementary files format and content: Multi-resolution cool file
Supplementary files format and content: hic file

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin, and grown at 37°C with 5% CO2. Prior to differentiation, WTC11 iNgn2 hiPSC cells  were maintained on Cultrex-coated plates in either Essential 8 Flex Medium (Gibco #A2858501) or mTeSR Plus (StemCell Technologies #100-0276). WTC11 iNgn2 hiPSC cells were differentiated into neurons using SMAD inhibition or into cardiomyocytes using STEMdiff Ventricular Cardiomyocyte Differentiation Kit (StemCell Technologies #05010).

extract_protocol:
Cells were fixed and processed according to the Arima Genomics HiC+ Kit protocol.
Proximity-ligated DNA was first sonicated to ~400 bp using a Covaris M220 with 50 W power, 10% duty factor and 200 cycles per burst for 78 seconds, and then size-selected using AMPure beads. Lbrary preparation was performed using KAPA HyperPrep (Roche #KK8502) according to instructions provided with the Arima Genomics HiC+ Kit, with library preparation done on streptavidin beads.

treatment_protocol: Asynchronous hTERT RPE-1 cells or post-mitotic hiPSC-derived cells were treated with DMSO or dTAGV-1 for the stated times.

value: hTERT RPE-1

value: dTAG 4hr


title: CTCF-C8_dTAG_24hr_HiC

description: Library name: MB123

value: dTAG 24hr


title: Tumour passage N2.2 (YUMM1.7 cells) tumour C

description: Library name: N2_2C


title: Tumour passage N2.3 (YUMM1.7 cells) tumour A

description: Library name: N2_3A


title: CTCF-C1_DMSO_HiC

description: Library name: MB117

value: DMSO


title: Tumour passage N2.2 (YUMM1.7 cells) tumour B

description: Library name: N2_2B


title: CTCF-C8_DMSO_HiC

description: Library name: MB121


title: Tumour passage N2.1 (YUMM1.7 cells) tumour B

description: Library name: N2_1B


title: Tumour passage N2.1 (YUMM1.7 cells) tumour D

description: Library name: N2_1D


title: Tumour passage F2 (YUMM1.7 cells) tumour D

description: Library name: F2_D


title: Tumour passage N2.1 (YUMM1.7 cells) tumour E

description: Library name: N2_1E


title: R2

city: Houston

first: Jiemiao

last: Hu

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Library name: sample 2

data_processing:
After total RNA was extracted, mRNA was purified from 5 μg total RNA using Dynabeads Oligo (dT) (Thermo Fisher) with 2 rounds of purification. The 2 × 150-bp paired-end sequencing (PE150) was performed on an Illumina Novaseq 6000 system following the vendor's recommended protocol.
Assembly: All samples were aligned to the human reference genome using the HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package.
Supplementary files format and content: txt

source_name: PDX tumor

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher) following the manufacturer's procedure. The total RNA quantity and purity were analyzed using a Bioanalyzer 2100 system and RNA 6000 Nano LabChip.
High-quality RNA samples with RNA integrity number (RIN)  >7.0 were used to construct the sequencing library.

value: PDX tumor

value: osteosarcoma


title: CTCF-C1_dTAG_4hr_HiC

description: Library name: MB120


title: NR3

description: Library name: sample 6


title: NR2

description: Library name: sample 5


title: Bone, FibrousDysplasia4

description:
Library name: FD716
10x Genomics


title: Tumour passage N2.1 (YUMM1.7 cells) tumour C

description: Library name: N2_1C


title: Tumour passage F2 (YUMM1.7 cells) tumour C

description: Library name: F2_C


title: R3

description: Library name: sample 3


title: Tumour passage N2.2 (YUMM1.7 cells) tumour A

description: Library name: N2_2A


title: NR1

description: Library name: sample 4


title: Tumour passage F2 (YUMM1.7 cells) tumour E

description: Library name: F2_E


title: R1

description: Library name: sample 1


title: Bone, FibrousDysplasia2

description:
Library name: FD21
10x Genomics


title: Tumour passage N2.1 (YUMM1.7 cells) tumour A

description: Library name: N2_1A


title: Bone, FibrousDysplasia3

description:
Library name: FD28
10x Genomics


title: Untreated_Control

description:
Library name: Untreated_Control
10x Genomics

value: Mesenteric lymph nodes

value: intestinal cells

value: 5mM Citrate buffer


title: Tumour passage F2 (YUMM1.7 cells) tumour B

description: Library name: F2_B

value: Dissociated tumour

value: Melanoma


title: CTCF-C1_dTAG_24hr_HiC

description: Library name: MB119


title: Tumour passage F2 (YUMM1.7 cells) tumour A

description: Library name: F2_A


title: Bone, control4, osteoarthritis

description:
Library name: WT153
10x Genomics

source_name: Right femoral head

value: Right femoral head

value: Osteoarthritis

value: GNAS-WT


title: Tumour passage F1 (YUMM1.7 cells) tumour E

description: Library name: F1_E


title: Bone, FibrousDysplasia1

description:
Library name: FD16
10x Genomics

value: Right proximal femur

value: Stromal, Endothelial, Perivascular cells


title: Tumour passage F1 (YUMM1.7 cells) tumour D

description: Library name: F1_D


title: Tumour passage F1 (YUMM1.7 cells) tumour A

description: Library name: F1_A


title: Multiome, Subject 14, PBMC, vaccinated, ATAC

city: Gent

first: Valentino

last: D'Onofrio

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

description: Library name: Subject_14_ATAC

data_processing:
Fastq files were processed 10x Genomics Cell Ranger v5.0.1 using 10x Genomics Cloud Analysis
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5, atac_fragments.tsv, atac_fragments.tsv.gz.tbi, aggregation.csv

source_name: PBMC

extract_protocol:
Single cell multiome (RNA+ATAC) sequencing (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, Document Number GC000338 Rev F, 10X Genomics) was done using PBMCs collected at day 7. Nuclei were prepared from thawed PBMCs according to 10X Genomics demonstrated protocol (Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing, Document Number CG000365 Rev C, 10x Genomics). Single Cell Multiome ATAC and Gene Expression (GEX) libraries were prepared using the Chromium Single Cell Multiome ATAC + Gene Expression platform (10X Genomics, Pleasanton, CA). 10,000 nuclei were targeted for each sample. Isolated nuclei were transposed and partitioned into Gel Beads-in-emulsion (GEMs) using the 10x Chromium Controller and Next GEM Chip J.
ATAC and GEX libraries were generated from the same pool of pre-amplified transposed DNA/cDNA. Representative traces and quantitation of both libraries were determined using Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA). Sequencing was done on Illumina NovaSeq S4 targeting 20,000 reads per nucleus for gene expression and 25,000 reads per nucleus ATAC-seq.

value: PBMC

value: Primary

value: Gardasil


title: Tumour Passage F0 (YUMM1.7 cells) tumour D

description: Library name: F0_D


title: Bone, control3, osteoarthritis

description:
Library name: WT152
10x Genomics

source_name: Right knee

value: Right knee


title: Bone, control2, osteoarthritis

description:
Library name: WT151
10x Genomics

source_name: Left femoral head

value: Left femoral head


title: Tumour passage F1 (YUMM1.7 cells) tumour B

description: Library name: F1_B


title: Tumour Passage F0 (YUMM1.7 cells) tumour C

description: Library name: F0_C


title: Tumour Passage F0 (YUMM1.7 cells) tumour A

description: Library name: F0_A


title: Multiome, Subject 9, PBMC, vaccinated, ATAC

description: Library name: Subject_9_ATAC


title: Multiome, Subject 10, PBMC, vaccinated, ATAC

description: Library name: Subject_10_ATAC

value: Cervarix


title: Tumour Passage F0 (YUMM1.7 cells) tumour B

description: Library name: F0_B


title: YUMM1.7 cells rep 3

description: Library name: YUMM17_C


title: Multiome, Subject 13, PBMC, vaccinated, ATAC

description: Library name: Subject_13_ATAC


title: Multiome, Subject 14, PBMC, vaccinated, GEX

description: Library name: Subject_14_GEX

molecule: nuclear RNA


title: YUMM1.7 cells rep 1

description: Library name: YUMM17_A


title: Multiome, Subject 9, PBMC, vaccinated, GEX

description: Library name: Subject_9_GEX


title: Multiome, Subject 10, PBMC, vaccinated, GEX

description: Library name: Subject_10_GEX


title: CBA tumour C

description:
Library name: CBA_B3
CBA_B3_EKRN230042278-1A_HKMHGDSX7_L1

data_processing:
HiSat2 v2.0.5, assembled into transcripts with Stringtie v1.3.3b, and summarised into gene counts with featureCounts v1.5.0-p3.
Assembly: mm10
Supplementary files format and content: Biopsies normalized_TEandGene_counts_round3dp.xlsx: Excel file containing normalised counts (FPKM) for genes and transposable elements

source_name: tumour biopsy

growth_protocol: 1 million YUMM1.7 cells were injected into syngeneic mice (F0) passage then grown tumours were collected, dissociated and the resulting cells were injected into the next mouse passage (F1, F2, N2.1, N2.2, N2.3, Balb-c1, Balb/c-2 and CBA). Tumours from passages F0, N2.1, Balb/c-2 and CBA were collected and analysed by RNAseq

value: tumour biopsy


title: Multiome, Subject 8, PBMC, vaccinated, ATAC

description: Library name: Subject_8_ATAC


title: Bone, control1, osteoarthritis

description:
Library name: WT150
10x Genomics

source_name: Right femural head

value: Right femural head


title: Multiome, Subject 8, PBMC, vaccinated, GEX

description: Library name: Subject_8_GEX


title: YUMM1.7 cells rep 2

description: Library name: YUMM17_B


title: Multiome, Subject 7, PBMC, vaccinated, ATAC

description: Library name: Subject_7_ATAC


title: Balb/c-2 tumour C

description:
Library name: Balb_c2_B3
Balb_c2_B3_EKRN230042275-1A_HKMHGDSX7_L1


title: CBA tumour A

description:
Library name: CBA_B1
CBA_B1_EKRN230042276-1A_HKMHGDSX7_L1


title: Multiome, Subject 7, PBMC, vaccinated, GEX

description: Library name: Subject_7_GEX


title: Balb/c-2 tumour B

description:
Library name: Balb_c2_B2
Balb_c2_B2_EKRN230042274-1A_HKMHGDSX7_L1


title: N2.1 tumour C

description:
Library name: N21_B3
N21_B3_EKRN230042272-1A_HKNVWDSX7_L2


title: Multiome, Subject 5, PBMC, vaccinated, GEX

description: Library name: Subject_5_GEX


title: Multiome, Subject 6, PBMC, vaccinated, GEX

description: Library name: Subject_6_GEX


title: HPAEC, stretch group, pulsatile 10% stretch 1 Hz, cell line 2, rep 3

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

description:
Library name: Sample 33
Column name in raw counts: HPAEC_R_2stretch10_3

data_processing:
Initial quality control was performed using FastQC v0.11.8 and multiqc v1.7.
Fastq files were imported and trimmed for adapter sequences followed by quality trimming using CLC Genomics Workbench (CLC Bio, v21.0.2).
RNA-Seq Analysis tool v2.6 (CLC Genomics Workbench), only matches to the reverse strand of the genes were accepted (using the strand-specific reverse option)
Differential gene expression analysis between the sample groups was done using the Differential Expression for RNA-seq tool v2.7, where the normalization method was set as TMM.
Assembly: GRCh37
Supplementary files format and content: xlsx file contains raw counts, TPM, and CPM values for each sample

source_name: HPAEC

growth_protocol: HPAECs purchased from Lonza and grown with Lonza EGM2 media with 5% CO2 were used for RNAseq

extract_protocol:
mRNA was isolated by pooling cells from 3 Luer I slides for each condition using the RNAeasy mini kit (Qiagen), quantified using Nanodrop and evaluated for quality with a bioanalyzer by the UTSW Genomics Core. All samples had a RIN score of 10. 1.5 µg of RNA was used for library construction.
Illumina TruSeq® Stranded mRNA Library Preparation Kit (Catalog #20020594) was used for RNA-seq library construction.

treatment_protocol: cells were exposed to 48 hours of static conditions, pulsatile force, or non-pulsatile force. Pulsatility frequency was 1 Hz in all pulsatility condtions. Flow was 0 to 15 dyn/cm2, pressure was 5 to 25 mm Hg, and stretch was 0 to 10% of baseline. Flow and pressure was applied using the Ibidi system in u-Slide I Luer slides, 0.4 mm height, coated with ibitreat for cell adhesion. Stretch was applied using the Flexcell system, with uniflex plates coated with gelatin for cell adhesion.

value: HPAEC

value: primary endothelial cells

value: WT

value: Stretch Group:pulsatile stretch


title: F0 tumour B

description:
Library name: F0_B2
F0_B2_EKRN230042268-1A_HKNVWDSX7_L2

value: Melanoma


title: HPAEC, stretch group, pulsatile 10% stretch 1 Hz, cell line 2, rep 2

description:
Library name: Sample 32
Column name in raw counts: HPAEC_R_2stretch10_2


title: CBA tumour B

description:
Library name: CBA_B2
CBA_B2_EKRN230042277-1A_HKMHGDSX7_L1


title: Multiome, Subject 6, PBMC, vaccinated, ATAC

description: Library name: Subject_6_ATAC


title: N2.1 tumour B

description:
Library name: N21_B2
N21_B2_EKRN230042271-1A_HKNVWDSX7_L2


title: FAT1_LPSgp100_rep3

city: Bethesda

first: Katherine

last: Goldfarbmuren

state: MD

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

description:
Library name: Sample18
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 23_429_LPS_GP100

data_processing:
https://github.com/CCBR/RENEE
per RENEE pipeline: adapter trimming, aligment, RSEM gene/isoform counting
Assembly: mm10_M21
Supplementary files format and content: RSEM.genes.expected_count.all_samples.txt contains raw count matrix
Supplementary files format and content: RSEM.genes.TPM.all_samples.txt contains TPM normalized count matrix

source_name: BMDCs

extract_protocol: Zymo Research RNA extraction kit

value: BMDCs

tag: time

value: mature


title: F0 tumour C

description:
Library name: F0_B3
F0_B3_EKRN230042269-1A_HKNVWDSX7_L2


title: Multiome, Subject 5, PBMC, vaccinated, ATAC

description: Library name: Subject_5_ATAC


title: HPAEC, stretch group, pulsatile 10% stretch 1 Hz, cell line 2, rep 1

description:
Library name: Sample 31
Column name in raw counts: HPAEC_R_2stretch10_1


title: F0 tumour A

description:
Library name: F0_B1
F0_B1_EKRN230042267-1A_HKNVWDSX7_L2


title: HPAEC, stretch group, absent stretch, cell line 2, rep 3

description:
Library name: Sample 30
Column name in raw counts: HPAEC_R_2static_3

value: Stretch Group:absent stretch


title: Balb/c-2 tumour A

description:
Library name: Balb_c2_B1
Balb_c2_B1_EKRN230042273-1A_HKNVWDSX7_L2


title: N2.1 tumour A

description:
Library name: N21_B1
N21_B1_EKRN230042270-1A_HKNVWDSX7_L2


title: Oral_Free_OVA_1ug

description:
Library name: Oral_Free_OVA_1ug
10x Genomics

source_name: Mesenteric lymph nodes

value: Mesenteric lymph nodes

value: intestinal cells

value: Free OVA


title: HPAEC, stretch group, absent stretch, cell line 2, rep 1

description:
Library name: Sample 28
Column name in raw counts: HPAEC_R_2static_1


title: HPAEC, stretch group, absent stretch, cell line 2, rep 2

description:
Library name: Sample 29
Column name in raw counts: HPAEC_R_2static_2


title: FAT1_LPSgp100_rep2

description:
Library name: Sample17
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 22_415_LPS_GP100


title: HPAEC, stretch group, pulsatile 10% stretch 1 Hz, cell line 1, rep 3

description:
Library name: Sample 27
Column name in raw counts: HPAEC_R_1stretch10_3


title: WT_LPSgp100_rep3

description:
Library name: Sample15
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 12_WT_LPS_GP100_3

value: C57BL/6 WT


title: WT_LPSgp100_rep2

description:
Library name: Sample14
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 11_WT_LPS_GP100_2


title: WT_LPSgp100_rep1

description:
Library name: Sample13
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 10_WT_LPS_GP100_1


title: HPAEC, stretch group, absent stretch, cell line 1, rep 3

description:
Library name: Sample 24
Column name in raw counts: HPAEC_R_1static_3


title: FAT1_NT_rep2

description:
Library name: Sample11
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 17_415_NT

value: immature


title: HPAEC, stretch group, pulsatile 10% stretch 1 Hz, cell line 1, rep 1

description:
Library name: Sample 25
Column name in raw counts: HPAEC_R_1stretch10_1


title: HPAEC, stretch group, pulsatile 10% stretch 1 Hz, cell line 1, rep 2

description:
Library name: Sample 26
Column name in raw counts: HPAEC_R_1stretch10_2


title: FAT1_NT_rep3

description:
Library name: Sample12
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 18_429_NT


title: HPAEC, stretch group, absent stretch, cell line 1, rep 1

description:
Library name: Sample 22
Column name in raw counts: HPAEC_R_1static_1


title: WT_NT_rep3

description:
Library name: Sample9
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 7_WT_NT3


title: FAT1_NT_rep1

description:
Library name: Sample10
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 16_414_NT


title: HPAEC, flow group, 15 dyn/cm2 pulsatile 1 Hz, rep 3

description:
Library name: Sample 21
Column name in raw counts: Pulsatile_3

value: Flow Group:pulsatile flow


title: HPAEC, stretch group, absent stretch, cell line 1, rep 2

description:
Library name: Sample 23
Column name in raw counts: HPAEC_R_1static_2


title: WT_NT_rep1

description:
Library name: Sample7
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 5_WT_NT1


title: HPAEC, flow group, 15 dyn/cm2 continuous, rep 3

description:
Library name: Sample 18
Column name in raw counts: Continuous_3

value: Flow Group:continuous flow


title: WT_NT_rep2

description:
Library name: Sample8
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 6_WT_NT2


title: Multiome, Subject 13, PBMC, vaccinated, GEX

description: Library name: Subject_13_GEX

value: PBMC

value: Primary

value: Cervarix


title: HPAEC, flow group, 15 dyn/cm2 pulsatile 1 Hz, rep 1

description:
Library name: Sample 19
Column name in raw counts: Pulsatile_1

value: HPAEC

value: primary endothelial cells


title: HPAEC, flow group, 15 dyn/cm2 continuous, rep 2

description:
Library name: Sample 17
Column name in raw counts: Continuous_2

value: WT


title: FAT1_D0_rep1

description:
Library name: Sample4
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 24_414_D0


title: HPAEC, flow group, 15 dyn/cm2 continuous, rep 1

description:
Library name: Sample 16
Column name in raw counts: Continuous_1


title: FAT1_LPSgp100_rep1

description:
Library name: Sample16
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 21_414_LPS_GP100


title: FAT1_D0_rep2

description:
Library name: Sample5
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 25_415_D0


title: HPAEC, flow group, absent flow, rep 3

description:
Library name: Sample 15
Column name in raw counts: Static_3

value: Flow Group:absent flow


title: WT_D0_rep3

description:
Library name: Sample3
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 15_WT_D0_3

value: BMDCs


title: HPAEC, flow group, absent flow, rep 2

description:
Library name: Sample 14
Column name in raw counts: Static_2


title: WT_D0_rep2

description:
Library name: Sample2
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 14_WT_D0_2


title: HPAEC, flow group, absent flow, rep 1

description:
Library name: Sample 13
Column name in raw counts: Static_1


title: WT_D0_rep1

description:
Library name: Sample1
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 13_WT_D0_1


title: HPAEC, pressure group, 5-25 mmHg pressure, rep 3

description:
Library name: Sample 12
Column name in raw counts: Pulse_P_3

value: Pressure Group:pulsatile


title: HPAEC, flow group, 15 dyn/cm2 pulsatile 1 Hz, rep 2

description:
Library name: Sample 20
Column name in raw counts: Pulsatile_2


title: HPAEC, pressure group, 5-25 mmHg pressure, rep 1

description:
Library name: Sample 10
Column name in raw counts: Pulse_P_1


title: FAT1_D0_rep3

description:
Library name: Sample6
column name in RSEM.genes.expected_count.all_samples.txt/RSEM.genes.TPM.all_samples.txt: 26_429_D0


title: HPAEC, pressure group, 25 mmHg pressure, rep 2

description:
Library name: Sample 8
Column name in raw counts: High_P_2

value: Pressure Group:high


title: HPAEC, pressure group, 25 mmHg pressure, rep 3

description:
Library name: Sample 9
Column name in raw counts: High_P_3


title: RB6935_55

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

description: APOE4, 15 months, acyclic menstrual cycles

data_processing:
Salmon v 0.15.0 was used to map the reads to Mouse cDNA library to get the quants
Tximport was used to get the unnormalized gene counts
DESeq2 was used to get the normalized gene counts for each sample
Assembly: Mus musculus Emsembl Release 95
Supplementary files format and content: Each processed file (.sf) contains the counts of each mapped transcript
Supplementary files format and content: unormalized counts,deseq2_p3apoe_unNormalizedCounts.csv
Supplementary files format and content: normalized counts,deseq2_p3apoe_NormalizedCounts.csv

source_name: Hippocampus

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: 15 months

tag: menstrual cycle

value: acyclic menstrual cycles


title: RB6935_58


title: HPAEC, pressure group, 5 mmHg pressure, rep 3

description:
Library name: Sample 6
Column name in raw counts: Low_P_3

value: Pressure Group:low


title: HPAEC, pressure group, 5 mmHg pressure, rep 2

description:
Library name: Sample 5
Column name in raw counts: Low_P_2


title: HPAEC, pressure group, absent pressure, rep 3

description:
Library name: Sample 3
Column name in raw counts: Static_P_3

value: Pressure Group:absent pressure


title: RB6935_52

description: APOE4, 15 months, Irregular menstrual cycles

value: Irregular menstrual cycles


title: HPAEC, pressure group, 5 mmHg pressure, rep 1

description:
Library name: Sample 4
Column name in raw counts: Low_P_1


title: HPAEC, pressure group, absent pressure, rep 2

description:
Library name: Sample 2
Column name in raw counts: Static_P_2


title: HPAEC, pressure group, absent pressure, rep 1

description:
Library name: Sample 1
Column name in raw counts: Static_P_1


title: RB6935_50


title: RB6935_49


title: RB6935_48


title: RB6935_47

description: APOE4, 9 months, Irregular menstrual cycles

value: 9 months


title: HPAEC, pressure group, 25 mmHg pressure, rep 1

description:
Library name: Sample 7
Column name in raw counts: High_P_1


title: RB6935_60


first: Alessandro

last: Sette

address: 9420 Athena Cir

department: Center for Infectious Disease and Vaccine Research

institute: La Jolla Institute for Immunology

description:
Library name: BOOST20_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST20_Hu_3_CD8_9D

data_processing:
Processing of scRNA-seq libraries: Data from scRNA-seq libraries were preprocessed by employing the 10x’s cellranger suite (v7.1.0) and the pre-built GRCh38 human genome reference (2020-A) as previously described (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020). Gene expression data from individual libraries were merged into one aggregated set for CD4+ T cells and another for CD8+ T cells. Metric reports for all single-cell transcriptome libraries and aggregated datasets indicate good-quality data. As detailed before (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020), the Seurat toolkit (v3.2.3) (Stuart et al., Cell, 2019) was employed in R to perform quality control (QC), unbiased clustering, dimensionality reduction and cluster annotation on each aggregated dataset. The following QC criteria were enforced to minimize doublets and eliminate low-quality transcriptomes: 1,500 unique molecular identifier (UMI) count 20,000; 800 gene count 4,400; and mitochondrial UMI percentage 10%. For dimensionality reduction and unbiased clustering, only the most variable genes accounting for 30% of the total standardized variance and the 30 principal components (PCs) were considered as arguments in the workflow described previously (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020). The final set of clusters identified at resolutions 0.4 and 0.2, respectively, for CD4+ and CD8+ T cells, were considered for in-depth annotation on the basis of their markers and gene set enrichment analysis (GSEA), as well as for downstream analyses. For comparisons involving early and late time points, samples collected at 1, 3, 6 and 9 months following the second vaccine dose were altogether considered as early time points, whereas samples collected at 3, 6, 9 and 12 months following the fourth vaccine dose were grouped and designated as late time points.
Processing of hashtag oligonucleotide (HTO)-seq libraries: Hashtag oligonucleotide (HTO) data were leveraged to perform sample deconvolution and further identify and remove multiplets, with the HTO data processed with the cellranger suite (v7.1.0) and deconvolution performed with the function MULTIseqDemux function from Seurat (v3.2.3) as detailed before (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020).
Assembly: GRCh38 (2020-A reference prebuilt and provided by 10x cellranger).
Supplementary files format and content: BOOST-1-CD4_processed_data_umi_counts.RDS: RDS file storing a numeric dgcMatrix object with raw UMI counts (seurat object slot "counts") for the aggregated dataset of CD4+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD4_processed_data_normalized_counts.RDS: RDS file storing a numeric dgcMatrix object with non-scaled normalized UMI counts (seurat object slot "data") for the aggregated dataset of CD4+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD4_processed_data_annotations.txt: The metadata including custom annotations made for the aggregated dataset of CD4+ T cells. Data are provided as tab-separated values; each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant Hashtag Oligo (HTO) data-related annotations have been provided in this file as well, including sample- and donor-related annotations.
Supplementary files format and content: BOOST-1-CD8_processed_data_umi_counts.RDS: RDS file storing a numeric dgcMatrix object with raw UMI counts (seurat object slot "counts") for the aggregated dataset of CD8+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD8_processed_data_normalized_counts.RDS: RDS file storing a numeric dgcMatrix object with non-scaled normalized UMI counts (seurat object slot "data") for the aggregated dataset of CD8+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD8_processed_data_annotations.txt: The metadata including custom annotations made for the aggregated dataset of CD8+ T cells. Data are provided as tab-separated values; each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant Hashtag Oligo (HTO) data-related annotations have been provided in this file as well, including sample- and donor-related annotations.
Supplementary files format and content: feature_README.txt: File alike the feature_reference.csv file used as input for cellranger feature count. However, 1) it is in tsv format and 2) it lists the information for all HTO/ADT libraries included in this project, which are specified under column "sample_id".

source_name: Blood

growth_protocol: The blood samples from multiple visits (time-points) from 54 donors were collected in heparin-coated blood bags. Peripheral blood mononuclear cells (PBMCs) were isolated using the same methodology as in previous studies (Dan et al., Science, 2021; Grifoni et al., Cell, 2020; Zhang et al., Cell, 2022), employing Ficoll-Paque (Lymphoprep, Nycomed Pharma, Oslo, Norway). In brief, whole blood was centrifuged for 15 minutes at 400g to separate the cellular fraction and plasma. Plasma was collected and stored at -20°C. PBMCs were separated by density-gradient sedimentation with Ficoll-Paque® PLUS. Isolated PBMCs were washed twice with RPMI 1640 to remove any residual Ficoll-Paque® PLUS. Subsequently, the PBMCs were resuspended in freezing media containing 90% fetal bovine serum (FBS; Hyclone Laboratories, Logan, UT) and 10% dimethyl sulfoxide (DMSO; Gibco, Waltham, MA) before time and temperature-controlled cryopreservation in liquid nitrogen until used for experiments.

extract_protocol:
To detect T cell-specific responses to SARS-CoV-2 Spike (S) antigens, we employed an activation-induced marker (AIM) assay methodology in combination with peptide megapool (MP) stimulation using the dual activation marker expression of OX40+4-1BB+ or CD69+4-1BB+ to detected antigen-specific CD4+ and CD8+ T cells, respectively (da Silva Antunes et al., Curr Protoc, 2023; Dan et al., J Immunol, 2016). Briefly, PBMC vials were thawed with subsequent determination of cell number. PBMCs were then plated in 96-well U-bottom plates at a concentration of 1-2×10^6 cells per well and immediately cultured together with peptide MPs (1 µg/mL), or phytohemagglutinin-L (PHA) (10 µg /mL; Roche, San Diego, CA) and DMSO as positive and negative controls, respectively, in 5% human serum (Gemini Bio-Products) for 18-24 h. After culture, cells were collected, washed and stained with the following antibody cocktail: CD8 BUV496 (1:50; BioLegend, clone RPA-T8, Cat# 612942), CD3 BUV805 (1:50; BioLegend, clone UCHT1, Cat# 612895), CD14 V500 (1:50; BioLegend, clone M5E2, Cat# 561391), CD19 V500 (1:50; BioLegend, clone HIB19, Cat# 561121), CD4 BV605 (1:100; BioLegend, clone RPA-T4, Cat# 562658), CD69 PE (1:50; BioLegend, clone FN50, Cat# 555531), OX40 PE-Cy7 (1:50; BioLegend, clone Ber-ACT35, Cat# 350012), 4-1BB APC (1:25; BioLegend, clone 4B4-1, Cat# 309810), Live/Dead Viability dye eFLuor506 (0.1:100; Invitrogen, Cat# 65-0866-14), brilliant staining buffer and PBS before being refrigerated for 30 minutes at 4°C, protected from light. TotalSeqTM-C oligonucleotide-conjugated antibodies (BioLegend) were also added at this step at 0.01mg/mL final concentration (one distinct antibody per sample). After two washes in PBS, cells were resuspended into 500 μl of MACS buffer (PBS containing 2mM EDTA (pH 8.0) and 0.5% BSA) and stored at 4ºC until flow cytometry acquisition. Activated CD4+ (OX40+4-1BB+) and CD8+ (4-1BB+CD69+) AIM+ cells were subsequently sorted using a BD FACSAria Fusion cell sorter (Becton Dickinson), and by employing the gating strategy represented in Fig S5 of the manuscript associated to these data. After sorting, ice-cold PBS was added, cells spun down, and single-cell libraries prepared.
For single-cell RNA-seq assays (10x Genomics, Pleasantown), in average 20,000- 50,000 AIM+ T cells per subject were sorted directly into low-retention, sterile 1.5 mL collection tubes (Thermo-fisher) pre-chilled on ice and containing 500 µl of PBS:FBS solution (1:1, vol:vol) supplemented with RNAse inhibitor (1:100, Takara Bio). 5 to 6 different samples were multiplexed using the TotalSeq-C DNA-oligo barcoded cell-surface housekeeping molecule antibodies (Biolegend) totaling approximately 60,000 cells per 10x lane (equivalent to one well of the 10x chip). Multiplexed samples were centrifuged at 600 ×g for 10 minutes at 4°C, and the supernatant was carefully removed, leaving behind 10-12 µL of residual volume. Cell pellets were resuspended in 25 µL of 10x Genomics-compatible resuspension buffer (0.22 µm filtered PBS containing 0.04 % ultrapure bovine serum albumin, Sigma-Aldrich). A 33 µL aliquot of the resuspended cells was transferred to an 8-strip PCR tube for downstream processing as per the 10x Genomics protocol. Left-over was used as cell-counting quality control check. Following the manufacturer's recommendations, single-cell RNA libraries were generated using the 10x Genomics standard 5’TAG v2 chemistry. Both cDNA amplification and library preparation were carried out using 13 PCR cycles. Barcoded cDNA products were collected, quantified, and pooled at equimolar concentrations. The libraries were sequenced on the Illumina Novaseq6000 (NIH, S10) platform with paired-end sequencing (S4 100x100cycle, Illumina) configured as follows: read length: read 1, 100 cycles; read 2, 100 cycles; i7 index, 10 cycles and i5 index 10 cycles. Size and quantity quality controls were performed throughout the procedure by capillary DNA high sensitivity electrophoresis (HS NGS Fragment Kit ,1-6000bp, Fragment Analyzer, Agilent) and Picogreen assay (Quant-iT™ PicoGreen™ dsDNA Assay Kits and dsDNA Reagents). Sequencing depth was aimed to reach 30,000 reads per cell for gene expressions, 8,000 reads/ cell for TCR, and antibody-feature sequencing (multiplexing analysis).

value: Blood

value: SARS-CoV-2 Spike (S) AIM+ CD8 T cells:CD3+ CD8+ CD69+ 4-1BB+

value: Activation-induced marker (AIM) assay


title: RB6935_59


description:
Library name: BOOST20_Hu_4_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST20_Hu_4_CD8_9D


title: RB6935_56


description:
Library name: BOOST20_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST20_Hu_2_CD4_9D

value: SARS-CoV-2 Spike (S) AIM+ CD4 T cells:CD3+ CD4+ OX40+ 4-1BB+


title: RB6935_57


description:
Library name: BOOST20_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST20_Hu_1_CD4_9D


title: RB6935_46


title: RB6935_44


title: RB6935_54


title: RB6935_53


description:
Library name: BOOST19_Hu_2_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST19_Hu_2_CD8_9D


title: RB6935_42


description:
Library name: BOOST19_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST19_Hu_3_CD8_9D


title: RB6935_41


title: RB6935_43


description:
Library name: BOOST19_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST19_Hu_1_CD4_9D


description:
Library name: BOOST029_Hu_CD8_2_6D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST029_Hu_CD8_2_6D


description:
Library name: BOOST029_Hu_CD4_1_6D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST029_Hu_CD4_1_6D


title: RB6935_39

description: APOE4, 9 months, regular menstrual cycles

value: regular menstrual cycles


title: RB6935_40


description:
Library name: BOOST028_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST028_Hu_2_CD4_9D


description:
Library name: BOOST028_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST028_Hu_1_CD4_9D


title: RB6935_38


title: RB6935_37


description:
Library name: BOOST027_Hu_4_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST027_Hu_4_CD8_9D


title: RB6935_36


title: RB6935_35

description: APOE4, 6 months, regular menstrual cycles

value: 6 months


description:
Library name: BOOST027_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST027_Hu_3_CD8_9D


description:
Library name: BOOST027_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST027_Hu_1_CD4_9D


description:
Library name: BOOST027_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST027_Hu_2_CD4_9D


title: RB6935_34


title: RB6935_33


title: RB6935_32


title: RB6935_31


description:
Library name: BOOST026_Hu_1_CD4_8D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST026_Hu_1_CD4_8D


description:
Library name: BOOST026_Hu_2_CD4_8D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST026_Hu_2_CD4_8D


description:
Library name: BOOST026_Hu_4_CD8_8D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST026_Hu_4_CD8_8D


description:
Library name: BOOST026_Hu_3_CD8_8D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST026_Hu_3_CD8_8D


title: RB6935_28

description: APOE3, 15 months, acyclic menstrual cycles


title: RB6935_30


title: RB6935_29


description:
Library name: BOOST025_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST025_Hu_3_CD8_9D


description:
Library name: BOOST025_Hu_4_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST025_Hu_4_CD8_9D


title: RB6935_26

description: APOE3, 15 months, Irregular menstrual cycles


description:
Library name: BOOST025_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST025_Hu_2_CD4_9D


title: RB6935_27


description:
Library name: BOOST024_Hu_4_CD8_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST024_Hu_4_CD8_10D


title: RB6935_25


description:
Library name: BOOST024_Hu_3_CD8_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST024_Hu_3_CD8_10D


title: RB6935_24


title: RB6935_23


description:
Library name: BOOST024_Hu_1_CD4_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST024_Hu_1_CD4_10D


title: RB6935_22


title: RB6935_21


title: RB6935_20


description:
Library name: BOOST023_Hu_4_CD8_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST023_Hu_4_CD8_10D


description:
Library name: BOOST023_Hu_3_CD8_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST023_Hu_3_CD8_10D


description:
Library name: BOOST023_Hu_2_CD4_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST023_Hu_2_CD4_10D


title: RB6935_19

description: APOE3, 9 months, Irregular menstrual cycles


description:
Library name: BOOST022_Hu_4_CD8_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST022_Hu_4_CD8_10D


title: RB6935_18


description:
Library name: BOOST022_Hu_3_CD8_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST022_Hu_3_CD8_10D


title: RB6935_17


title: RB6935_16


description:
Library name: BOOST022_Hu_2_CD4_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST022_Hu_2_CD4_10D


description:
Library name: BOOST024_Hu_2_CD4_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST024_Hu_2_CD4_10D


title: RB6935_15


description:
Library name: BOOST022_Hu_1_CD4_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST022_Hu_1_CD4_10D


title: RB6935_13

description: APOE3, 9 months, regular menstrual cycles


title: RB6935_12


description:
Library name: BOOST021_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST021_Hu_2_CD4_9D


title: RB6935_14


description:
Library name: BOOST021_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST021_Hu_3_CD8_9D


title: RB6935_9


title: RB6935_10


description:
Library name: BOOST018_Hu_3_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST018_Hu_3_9D


description:
Library name: BOOST018_Hu_4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST018_Hu_4_9D


description:
Library name: BOOST023_Hu_1_CD4_10D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST023_Hu_1_CD4_10D


title: RB6935_8


description:
Library name: BOOST018_Hu_2_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST018_Hu_2_9D


title: RB6935_7


description:
Library name: BOOST018_Hu_1_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST018_Hu_1_9D


description:
Library name: BOOST021_Hu_4_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST021_Hu_4_CD8_9D


description:
Library name: BOOST017_Hu_4_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST017_Hu_4_CD8_9D


title: RB6935_5

description: APOE3, 6 months, regular menstrual cycles


title: RB6935_6


description:
Library name: BOOST017_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST017_Hu_3_CD8_9D


title: HPAEC, pressure group, 5-25 mmHg pressure, rep 2

description:
Library name: Sample 11
Column name in raw counts: Pulse_P_2

value: HPAEC

value: primary endothelial cells

value: WT


title: RB6935_11


title: RB6935_4


description:
Library name: BOOST021_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST021_Hu_1_CD4_9D


description:
Library name: BOOST016_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST016_Hu_3_CD8_9D


title: RB6935_3


title: RB6935_2


description:
Library name: BOOST016_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST016_Hu_2_CD4_9D


title: RB6935_1


title: ADARhet_MDA5het_Tdt_3

description: 10X Genomics, tdT positive cells only

data_processing:
Demultiplexed Fastq files and matrix files were generated with Cellranger.
Assembly: mm10 genome used for reference
Supplementary files format and content: filtered sequence read with matrix.h5 files are reported and ultimately used in Seurat for data analysis.

source_name: aortic root, ascending aorta to brachiocephalic artery take off

extract_protocol:
readme_extract_protocol.txt
scRNA libraries were prepared following 10X protocol.
cDNA libraries were then sequenced to at least 50K reads per cell.

value: tdT positive cells only

value: Adar1 fl/WT, Ifih1-/+, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 24 weeks of age with atherosclerosis


description:
Library name: BOOST016_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST016_Hu_1_CD4_9D


description:
Library name: BOOST015_Hu_2_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST015_Hu_2_CD8_9D


title: ADARhet_MDA5het_nTdt_2

description: 10X Genomics, tdT negative cells only

value: aortic root, ascending aorta to brachiocephalic artery take off

value: tdT negative cells only


description:
Library name: BOOST014_Hu_4_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST014_Hu_4_CD8_9D


title: ADARhet_MDA5het_Tdt_2

description: 10X Genomics, tdT positive cells only


title: ADARhet_MDA5het_nTdt_1

description: 10X Genomics, tdT negative cells only