title: Blood,S21_W0

description:
Library name: S21_W0
S.mansoni Human challenge model


title: Blood,S18_W8

status: Public on Dec 16 2025

type: SRA

city: Lubbock

first: Aravindan

last: Kalyanasundaram

state: Texas

address: 3601 4th Street

department: Immunology and Molecular Microbiology

country: USA

institute: Texas Tech University Health Sciences Center

description:
Library name: S18_W8
S.mansoni Human challenge model

library_source: transcriptomic

data_processing:
A comprehensive transcriptomic analysis pipeline was implemented, beginning with stringent quality control of raw FASTQ sequencing reads using FastQC, Fastp, SortMeRNA, and Kraken2/Bracken to remove lowquality sequences and contaminants.
Cleaned reads were aligned to the CHM13 human reference genome using STAR, and gene expression was quantified with featureCounts, followed by normalization using edgeR.
Assembly: CHM13
Supplementary files format and content: raw.counts.tsv.gz

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was extracted and purified from whole blood collected in PAXgene Blood RNA tubes from 30 participants at six time points, including baseline (prior to exposure, Week 0) and every four weeks thereafter until Week 20 post-exposure (i.e., Weeks 0, 4, 8, 12, 16, and 20 using the Total RNA extraction kit (RNeasy kit, Qiagen).
The Ribo-Zero Gold kit and TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, Inc., San Diego, CA) were used to deplete rRNA from total RNA and to prepare stranded RNA libraries. Paired-end whole-transcriptome sequencing (100 base pairs) was performed on the NovaSeq 6000 platform (Illumina, Inc., San Diego, CA) at the Clinical Genomics Core Facility in Gothenburg, Sweden.

treatment_protocol: The two controlled human Schistosoma infection dose escalation trials at Leiden University Medical Center. A total of 30 volunteers (designated S1 to S30) were recruited. In the first CHI trial (NCT02755324), 17 volunteers were exposed with either 10 (n = 3), 20 (n =11), or 30 (n = 3) male S. mansoni cercariae.  In the second CHI trial (NCT04269915), 13 volunteers (5 male and 8 female adult volunteers) were challenged with 10 (n = 3) or 20 (n = 10) female S. mansoni cercariae. Participants exposed with male cercariae received PZQ at Week 12, while those exposed with female cercariae were treated at both Week 8 and Week 12.

tag: tissue

value: Blood

tag: treatment

value: Cercarial challenge

tag: time

value: Week 8

tag: Sex

value: female

tag: batch


title: Blood,S20_W12

description:
Library name: S20_W12
S.mansoni Human challenge model

value: Week 12

value: male


title: Blood,S22_W12

description:
Library name: S22_W12
S.mansoni Human challenge model


title: Blood,S19_W12

description:
Library name: S19_W12
S.mansoni Human challenge model


title: Blood,S22_W8

description:
Library name: S22_W8
S.mansoni Human challenge model


title: Blood,S23_W20

description:
Library name: S23_W20
S.mansoni Human challenge model

value: Week 20


title: Blood,S18_W4

description:
Library name: S18_W4
S.mansoni Human challenge model

value: Week 4


title: Blood,S17_W20

description:
Library name: S17_W20
S.mansoni Human challenge model


title: Blood,S18_W16

description:
Library name: S18_W16
S.mansoni Human challenge model

value: Week 16


title: Blood,S17_W16

description:
Library name: S17_W16
S.mansoni Human challenge model


title: Blood,S18_W0

description:
Library name: S18_W0
S.mansoni Human challenge model

value: Week 0


title: Blood,S17_W8

description:
Library name: S17_W8
S.mansoni Human challenge model


title: Blood,S18_W20

description:
Library name: S18_W20
S.mansoni Human challenge model


title: Blood,S18_W12

description:
Library name: S18_W12
S.mansoni Human challenge model


title: Blood,S17_W4

description:
Library name: S17_W4
S.mansoni Human challenge model


title: Blood,S17_W0

description:
Library name: S17_W0
S.mansoni Human challenge model


title: Blood,S17_W12

description:
Library name: S17_W12
S.mansoni Human challenge model


title: Blood,S20_W20

description:
Library name: S20_W20
S.mansoni Human challenge model


title: Blood,S15_W20

description:
Library name: S15_W20
S.mansoni Human challenge model


title: Blood,S15_W16

description:
Library name: S15_W16
S.mansoni Human challenge model


title: Blood,S14_W8

description:
Library name: S14_W8
S.mansoni Human challenge model


title: Blood,S15_W0

description:
Library name: S15_W0
S.mansoni Human challenge model


title: Blood,S14_W4

description:
Library name: S14_W4
S.mansoni Human challenge model


title: Blood,S16_W0

description:
Library name: S16_W0
S.mansoni Human challenge model


title: Blood,S14_W12

description:
Library name: S14_W12
S.mansoni Human challenge model


title: Blood,S13_W20

description:
Library name: S13_W20
S.mansoni Human challenge model


title: Blood,S14_W16

description:
Library name: S14_W16
S.mansoni Human challenge model


title: Blood,S13_W0

description:
Library name: S13_W0
S.mansoni Human challenge model


title: Blood,S13_W4

description:
Library name: S13_W4
S.mansoni Human challenge model


title: Blood,S15_W8

description:
Library name: S15_W8
S.mansoni Human challenge model


title: Blood,S14_W0

description:
Library name: S14_W0
S.mansoni Human challenge model


title: Blood,S13_W8

description:
Library name: S13_W8
S.mansoni Human challenge model


title: Blood,S12_W8

description:
Library name: S12_W8
S.mansoni Human challenge model


title: Blood,S12_W4

description:
Library name: S12_W4
S.mansoni Human challenge model


title: Blood,S12_W16

description:
Library name: S12_W16
S.mansoni Human challenge model


title: Blood,S16_W16

description:
Library name: S16_W16
S.mansoni Human challenge model


title: Blood,S11_W4

description:
Library name: S11_W4
S.mansoni Human challenge model


title: Blood,S12_W12

description:
Library name: S12_W12
S.mansoni Human challenge model


title: Blood,S11_W8

description:
Library name: S11_W8
S.mansoni Human challenge model


title: Blood,S10_W8

description:
Library name: S10_W8
S.mansoni Human challenge model


title: Blood,S10_W20

description:
Library name: S10_W20
S.mansoni Human challenge model


title: Blood,S12_W0

description:
Library name: S12_W0
S.mansoni Human challenge model


title: Blood,S11_W12

description:
Library name: S11_W12
S.mansoni Human challenge model


title: Blood,S11_W0

description:
Library name: S11_W0
S.mansoni Human challenge model


title: Blood,S10_W4

description:
Library name: S10_W4
S.mansoni Human challenge model


title: Blood,S10_W16

description:
Library name: S10_W16
S.mansoni Human challenge model


title: Blood,S09_W8

description:
Library name: S09_W8
S.mansoni Human challenge model


title: Blood,S10_W0

description:
Library name: S10_W0
S.mansoni Human challenge model


title: Blood,S10_W12

description:
Library name: S10_W12
S.mansoni Human challenge model


title: Blood,S09_W20

description:
Library name: S09_W20
S.mansoni Human challenge model


title: Blood,S09_W12

description:
Library name: S09_W12
S.mansoni Human challenge model


title: Blood,S09_W16

description:
Library name: S09_W16
S.mansoni Human challenge model


title: Blood,S11_W20

description:
Library name: S11_W20
S.mansoni Human challenge model


title: Blood,S07_W8

description:
Library name: S07_W8
S.mansoni Human challenge model


title: Blood,S08_W8

description:
Library name: S08_W8
S.mansoni Human challenge model


title: Blood,S09_W0

description:
Library name: S09_W0
S.mansoni Human challenge model


title: Blood,S08_W4

description:
Library name: S08_W4
S.mansoni Human challenge model


title: Blood,S08_W0

description:
Library name: S08_W0
S.mansoni Human challenge model


title: Blood,S08_W12

description:
Library name: S08_W12
S.mansoni Human challenge model


title: Blood,S08_W16

description:
Library name: S08_W16
S.mansoni Human challenge model


title: Blood,S07_W4

description:
Library name: S07_W4
S.mansoni Human challenge model


title: Blood,S07_W12

description:
Library name: S07_W12
S.mansoni Human challenge model


title: Blood,S07_W0

description:
Library name: S07_W0
S.mansoni Human challenge model


title: Blood,S06_W8

description:
Library name: S06_W8
S.mansoni Human challenge model


title: Blood,S06_W4

description:
Library name: S06_W4
S.mansoni Human challenge model


title: Blood,S09_W4

description:
Library name: S09_W4
S.mansoni Human challenge model


title: Blood,S05_W8

description:
Library name: S05_W8
S.mansoni Human challenge model


title: Blood,S05_W12

description:
Library name: S05_W12
S.mansoni Human challenge model


title: Blood,S05_W4

description:
Library name: S05_W4
S.mansoni Human challenge model


title: Blood,S05_W20

description:
Library name: S05_W20
S.mansoni Human challenge model


title: Blood,S05_W0

description:
Library name: S05_W0
S.mansoni Human challenge model


title: Blood,S04_W4

description:
Library name: S04_W4
S.mansoni Human challenge model


title: Blood,S04_W0

description:
Library name: S04_W0
S.mansoni Human challenge model


title: Blood,S04_W8

description:
Library name: S04_W8
S.mansoni Human challenge model


title: Blood,S04_W12

description:
Library name: S04_W12
S.mansoni Human challenge model


title: Blood,S03_W8

description:
Library name: S03_W8
S.mansoni Human challenge model


title: Blood,S04_W16

description:
Library name: S04_W16
S.mansoni Human challenge model


title: Blood,S03_W4

description:
Library name: S03_W4
S.mansoni Human challenge model


title: Blood,S02_W8

description:
Library name: S02_W8
S.mansoni Human challenge model


title: Blood,S07_W16

description:
Library name: S07_W16
S.mansoni Human challenge model


title: Blood,S02_W0

description:
Library name: S02_W0
S.mansoni Human challenge model


title: Blood,S02_W16

description:
Library name: S02_W16
S.mansoni Human challenge model


title: Blood,S01_W20

description:
Library name: S01_W20
S.mansoni Human challenge model


title: Blood,S01_W8

description:
Library name: S01_W8
S.mansoni Human challenge model


title: Blood,S01_W4

description:
Library name: S01_W4
S.mansoni Human challenge model


title: Blood,S02_W20

description:
Library name: S02_W20
S.mansoni Human challenge model


title: Blood,S01_W16

description:
Library name: S01_W16
S.mansoni Human challenge model


title: Blood,S01_W12

description:
Library name: S01_W12
S.mansoni Human challenge model


title: Blood,S06_W20

description:
Library name: S06_W20
S.mansoni Human challenge model


title: Blood,S06_W0

description:
Library name: S06_W0
S.mansoni Human challenge model


title: Blood,S06_W12

description:
Library name: S06_W12
S.mansoni Human challenge model


title: Blood,S01_W0

description:
Library name: S01_W0
S.mansoni Human challenge model


title: DOGMAseq, HTO, Sample 102

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

description:
Library name: 102___HTO
HTO library

library_source: other

data_processing:
Raw BCL files from sequencing for ADT/HTO modalities were demultiplexed using bcl2fastq2 (Illumina) or cellranger-arc (10X Genomics) mkfastq. ATAC fastq files were filtered for index hopping using index-hopping-filter (10X Genomics). ATAC and GEX fastq files were then aligned to a chimeric hg38-HIV (HXB2 sequence) genome and count matrices were generated using cellranger-arc count. ADT and HTO fastq files were aligned to the TotalSeqA cocktail catalog using kallisto and bustools which includes barcode correction and counting to create cell by feature matrices. A Snakemake pipeline for kallisto and bustools is found here: https://github.com/betts-lab/scc-proc.
Assembly: hg38 + HXB2
Supplementary files format and content: For ATAC files, standard cellranger-arc count output files for fragments with cell barcodes. For GEX files, standard cellranger-arc count output files for filtered matrix output. For ADT/HTO, matrix/feature/cell files that are outputted from kallisto bustools.

molecule: protein

source_name: lymph node

extract_protocol:
Buffer and cell preparation were performed as previously published (Mimitou et al.) following the LLL permeabilization protocol. All subsequent cell preparation and antibody staining steps, including centrifugation, were performed at 10°C or on ice unless specified. 5 x 105 - 1 x 106 sorted CD3+, CD8- non-naive T cells were pelleted at 500g for 5 minutes. Cell pellet was resuspended in 22.5uL of Staining Buffer (PBS, 1% BSA, 0.2U/uL RNAse Inhibitor (Roche)) and incubated with 2.5uL of TruStain FcX (Biolegend) for 10 minutes. One vial of TotalSeq-A Human Universal Cocktail, v1.0 (Biolegend) was resuspended according to the Biolegend protocol with Staining Buffer. 25uL of prepared antibody cocktail was added to the cells and incubated for 30 minutes. Cells were washed three times with 1 mL of Staining Buffer at 400g for 5 minutes. After the final wash cells were resuspended in 450uL of PBS.  Following the LLL permeabilization protocol cells were fixed with 0.1% paraformaldehyde for 10 minutes at room temperature and quenched with 0.125M final glycine solution. Fixed cells were washed two times with Staining Buffer at 400g for 5 minutes. Cells were lysed with 100uL of LLL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 1% BSA, 1 mM DTT, 2 U/μl RNAse inhibitor) for 3 minutes. Cells were washed with 1mL of cold LLL wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 1 U/μl RNAse inhibitor) and the tube inverted before pelleting the cells at 500g for 5 minutes. Cell pellet was resuspended with 10X Genomics Multiome 1x Nuclei Buffer, and complete cell permeabilization was confirmed using Trypan blue staining. If aggregates were detected in the cell count, cells were filtered using a 40um FlowMi strainer (Sigma) and re-counted. Cells were diluted as needed according to the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (Version CG000338 RevF).  Samples were processed using the Chromium X platform (10X Genomics).
Single-cell sequencing library preparations for the ATAC and GEX libraries were made following the 10X Genomics User Guide Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (Version CG000338 RevF), with the following modifications as previously published and outlined below. Step 4.1, during the preamplification PCR spike in 1 μL of 0.2 μM ADT/HTO additive primer (ADT additive primer sequence: 5’CCTTGGCACCCGAGAATT*C*C, HTOv2 additive primer sequence:5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGAT*C*T) was added to each individual sample preparation. Step 4.3k, during the SPRI clean-up, elute the pre-amplification sample in 100uL of EB buffer. Use 25uL of pre-amplification sample +15uL of EB (Qiagen) as input for the ATAC library indexing, and use 35uL of pre-amplification sample as input for the cDNA amplification reaction. Use 5uL of pre-amplification sample as input for the ADT and HTO libraries.  ADT/HTO dual index single-cell sequencing library preparation followed the antibody manufacturer’s protocol (BioLegend). Briefly, 5uL of the pre-amplification sample was mixed with 40uL of H20. The antibody-derived oligomers were amplified and indexed with 50 μL of KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and 5 μL of forward/reverse indexing primers.  Post-amplification, ADT/HTO libraries were purified with 120 μL SPRIselect (Beckman) cleanup and eluted with 30 μL of EB buffer. All final libraries were quantified using a Qubit dsDNA HS Assay Kit (Invitrogen) and analyzed using a High Sensitivity D1000 DNA tape (Agilent) on a TapeStation D4200 (Agilent).

value: lymph node

tag: cell type

value: sorted cd3+ cd8- non-naive cells

tag: disease state

value: viremic


title: DOGMAseq, HTO, Sample 103

description:
Library name: 103___HTO
HTO library


title: DOGMAseq, HTO, Sample 101

description:
Library name: 101___HTO
HTO library


title: DOGMAseq, HTO, Sample 105

description:
Library name: 105___HTO
HTO library


title: DOGMAseq, HTO, Sample 104

description:
Library name: 104___HTO
HTO library


title: DOGMAseq, HTO, Sample 99

description:
Library name: 99___HTO
HTO library


title: Blood,S03_W16

description:
Library name: S03_W16
S.mansoni Human challenge model


title: DOGMAseq, HTO, Sample 100

description:
Library name: 100___HTO
HTO library


title: DOGMAseq, HTO, Sample 95

description:
Library name: 95___HTO
HTO library

value: hiv-


title: DOGMAseq, HTO, Sample 96

description:
Library name: 96___HTO
HTO library


title: DOGMAseq, HTO, Sample 94

description:
Library name: 94___HTO
HTO library


title: DOGMAseq, HTO, Sample 93

description:
Library name: 93___HTO
HTO library


title: Blood,S03_W0

description:
Library name: S03_W0
S.mansoni Human challenge model


title: DOGMAseq, HTO, Sample 98

description:
Library name: 98___HTO
HTO library


title: DOGMAseq, HTO, Sample 92

description:
Library name: 92___HTO
HTO library


title: DOGMAseq, HTO, Sample 90

description:
Library name: 90___HTO
HTO library


title: DOGMAseq, HTO, Sample 87

description:
Library name: 87___HTO
HTO library


title: DOGMAseq, HTO, Sample 85

description:
Library name: 85___HTO
HTO library


title: DOGMAseq, HTO, Sample 84

description:
Library name: 84___HTO
HTO library


title: DOGMAseq, HTO, Sample 88

description:
Library name: 88___HTO
HTO library


title: DOGMAseq, HTO, Sample 89

description:
Library name: 89___HTO
HTO library


title: DOGMAseq, HTO, Sample 83

description:
Library name: 83___HTO
HTO library


title: DOGMAseq, HTO, Sample 82

description:
Library name: 82___HTO
HTO library


title: DOGMAseq, HTO, Sample 81

description:
Library name: 81___HTO
HTO library


title: DOGMAseq, HTO, Sample 80

description:
Library name: 80___HTO
HTO library

value: ART-treated


title: DOGMAseq, HTO, Sample 74

description:
Library name: 74___HTO
HTO library


title: DOGMAseq, HTO, Sample 76

description:
Library name: 76___HTO
HTO library


title: DOGMAseq, HTO, Sample 75

description:
Library name: 75___HTO
HTO library


title: DOGMAseq, HTO, Sample 97

description:
Library name: 97___HTO
HTO library


title: DOGMAseq, HTO, Sample 78

description:
Library name: 78___HTO
HTO library


title: DOGMAseq, HTO, Sample 79

description:
Library name: 79___HTO
HTO library


title: DOGMAseq, HTO, Sample 77

description:
Library name: 77___HTO
HTO library


title: DOGMAseq, HTO, Sample 70

description:
Library name: 70___HTO
HTO library


title: DOGMAseq, HTO, Sample 69

description:
Library name: 69___HTO
HTO library


title: DOGMAseq, HTO, Sample 66

description:
Library name: 66___HTO
HTO library


title: DOGMAseq, HTO, Sample 71

description:
Library name: 71___HTO
HTO library


title: DOGMAseq, HTO, Sample 73

description:
Library name: 73___HTO
HTO library


title: DOGMAseq, HTO, Sample 72

description:
Library name: 72___HTO
HTO library


title: DOGMAseq, HTO, Sample 67

description:
Library name: 67___HTO
HTO library


title: DOGMAseq, HTO, Sample 68

description:
Library name: 68___HTO
HTO library


title: DOGMAseq, HTO, Sample 63

description:
Library name: 63___HTO
HTO library


title: DOGMAseq, HTO, Sample 65

description:
Library name: 65___HTO
HTO library


title: DOGMAseq, HTO, Sample 64

description:
Library name: 64___HTO
HTO library


title: DOGMAseq, HTO, Sample 86

description:
Library name: 86___HTO
HTO library


title: DOGMAseq, HTO, Sample 91

description:
Library name: 91___HTO
HTO library


title: DOGMAseq, HTO, Sample 61

description:
Library name: 61___HTO
HTO library


title: DOGMAseq, HTO, Sample 62

description:
Library name: 62___HTO
HTO library


title: DOGMAseq, HTO, Sample 57

description:
Library name: 57___HTO
HTO library


title: DOGMAseq, HTO, Sample 54

description:
Library name: 54___HTO
HTO library


title: DOGMAseq, HTO, Sample 55

description:
Library name: 55___HTO
HTO library


title: DOGMAseq, HTO, Sample 56

description:
Library name: 56___HTO
HTO library


title: DOGMAseq, HTO, Sample 52

description:
Library name: 52___HTO
HTO library


title: DOGMAseq, HTO, Sample 53

description:
Library name: 53___HTO
HTO library


title: DOGMAseq, HTO, Sample 51

description:
Library name: 51___HTO
HTO library


title: DOGMAseq, HTO, Sample 50

description:
Library name: 50___HTO
HTO library


title: DOGMAseq, HTO, Sample 49

description:
Library name: 49___HTO
HTO library


title: DOGMAseq, HTO, Sample 47

description:
Library name: 47___HTO
HTO library


title: DOGMAseq, HTO, Sample 48

description:
Library name: 48___HTO
HTO library


title: DOGMAseq, HTO, Sample 42

description:
Library name: 42___HTO
HTO library


title: DOGMAseq, HTO, Sample 43

description:
Library name: 43___HTO
HTO library


title: DOGMAseq, HTO, Sample 40

description:
Library name: 40___HTO
HTO library


title: DOGMAseq, HTO, Sample 41

description:
Library name: 41___HTO
HTO library


title: DOGMAseq, HTO, Sample 44

description:
Library name: 44___HTO
HTO library


title: DOGMAseq, HTO, Sample 60

description:
Library name: 60___HTO
HTO library


title: DOGMAseq, HTO, Sample 36

description:
Library name: 36___HTO
HTO library


title: DOGMAseq, HTO, Sample 37

description:
Library name: 37___HTO
HTO library


title: DOGMAseq, HTO, Sample 59

description:
Library name: 59___HTO
HTO library


title: DOGMAseq, HTO, Sample 39

description:
Library name: 39___HTO
HTO library


title: DOGMAseq, HTO, Sample 38

description:
Library name: 38___HTO
HTO library


title: DOGMAseq, HTO, Sample 34

description:
Library name: 34___HTO
HTO library


title: DOGMAseq, HTO, Sample 35

description:
Library name: 35___HTO
HTO library


title: cpxR D51E Y. pseudotuberculosis replicate 2

city: Santa Cruz

first: Victoria

last: Auerbuch

state: CA

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California Santa Cruz

description: Library name: CpxR_D51E_3

data_processing:
demultiplexing, quality control, and adapter trimming was performed with bcI-convert (v4.2.4)
Read mapping was performed with HISAT2
Read qualification was performed using Subread's featureCounts functionality
Read counds were normalized using edgeR's Trimmed Mean of M values algorithm and subsequent values were converted to counts per million
Differential expression analysis was performed using edgeR's glmQLFTest
Assembly: RNA sequences were mapped to Y. pseudotuberculosis strain IP2666pIB1 GenBank annotations under accession numbers CP032566.1 (chromosome) and CP032567.1 (pYV virulence plasmid)
Supplementary files format and content: Hug_et_al_RNAseq_processed_data.xlsx contains TMM values of all genes for both WT vs ΔcpxA and WT vs cpxRD51E comparisons as well as lists of differentially expressed genes called for each comparison

organism: Yersinia pseudotuberculosis

source_name: bacterial culture

growth_protocol: Bacterial strains were grown overnight in 2ml of LB shaking at 26°C and then subcultured to an OD600 of 0.2 in fresh low calcium LB (made by supplementing LB with 20mM sodium oxalate and 20mM magnesium chloride). Cultures were grown shaking for 1.5 hours at 26°C and then moved to 37°C shaking for an additional 1.5 hours. Cultures were then spun down at 4000rpm (~200xg) for 5 minutes to pellet cells.

extract_protocol:
Supernatants were removed and pellets were resuspended in 1mL Qiagen RNA Protect Bacterial Reagent. Total RNA was isolated using the Qiagen RNeasy Mini kit and DNA was removed from samples using the Thermo Fisher TURBO DNA-free Kit. RNA quality was then assessed using an Agilent 2000 Bioanalyzer. Samples were DNAse treated with Invitrogen DNAse (RNAse free).
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices

treatment_protocol: no treatment

value: bacterial culture

tag: cell line

value: strain IP2666pIB1

value: LB media

tag: genotype

value: cpxR D51E

value: 1.5 hours shaking at 26°C, then 1.5 hours shaking at 37°C


title: delta cpxA Y. pseudotuberculosis replicate 3

description: Library name: dcpxA_4

value: delta cpxA


title: DOGMAseq, HTO, Sample 58

description:
Library name: 58___HTO
HTO library


title: cpxR D51E Y. pseudotuberculosis replicate 1

description: Library name: CpxR_D51E_1


title: delta cpxA Y. pseudotuberculosis replicate 1

description: Library name: dcpxA_2


title: DOGMAseq, HTO, Sample 33

description:
Library name: 33___HTO
HTO library


title: cpxR D51E Y. pseudotuberculosis replicate 3

description: Library name: CpxR_D51E_4


title: delta cpxA Y. pseudotuberculosis replicate 2

description: Library name: dcpxA_3


title: DOGMAseq, HTO, Sample 46

description:
Library name: 46___HTO
HTO library


title: wildtype Y. pseudotuberculosis replicate 3

description: Library name: WT_4

value: wildtype


title: wildtype Y. pseudotuberculosis replicate 2

description: Library name: WT_3


title: DOGMAseq, HTO, Sample 32

description:
Library name: 32___HTO
HTO library


title: DOGMAseq, HTO, Sample 45

description:
Library name: 45___HTO
HTO library


title: wildtype Y. pseudotuberculosis replicate 1

description: Library name: WT_1


title: DOGMAseq, HTO, Sample 30

description:
Library name: 30___HTO
HTO library


title: DOGMAseq, HTO, Sample 29

description:
Library name: 29___HTO
HTO library


title: DOGMAseq, HTO, Sample 28

description:
Library name: 28___HTO
HTO library


title: Patient200-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

type: RNA

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: BRCA wild-type

data_processing: Cq values were background-filtered, assays must have been detected with at least 5 Cq less than the negative control, and with Cq<37 to be included in the data analysis. Then, duplicates were averaged; if one of the replicated contained non-detect, the second one was used in place of the mean. Data was normalized by subtracting each Cq value from the mean of Cq values of miRNAs detected in all samples in a set so that later higher normalized value means higher expression.

label: SYBR green

source_name: Serum

label_protocol: Total RNA was reverse transcribed using the miRCURY LNA RT Kit (QIAGEN). The resulting cDNA was diluted and used for qPCR reactions following the miRCURY LNA protocol. Each miRNA was analyzed in duplicate using the SYBR Green master mix and a Custom Ready-to-Use PCR panel. Negative controls without RNA template were included and processed alongside the samples. Amplification was carried out using a LightCycler 480 Real-Time PCR System (Roche) on 384-well plates. Amplification and melting curves were analyzed with Roche LC software using the second derivative method for Cq determination.

extract_protocol: RNA extraction was performed using QIAGEN reagents for miRNA isolation, according to manufacturer procedures. UniSp3, UniSP6, UniSp100 and UniSp101 spike-ins were added for quality control.

tag: age

tag: menopausal status

value: Premenopausal


title: DOGMAseq, HTO, Sample 27

description:
Library name: 27___HTO
HTO library


title: DOGMAseq, HTO, Sample 26

description:
Library name: 26___HTO
HTO library


title: DOGMAseq, HTO, Sample 25

description:
Library name: 25___HTO
HTO library


title: DOGMAseq, HTO, Sample 24

description:
Library name: 24___HTO
HTO library


title: Patient195-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient192-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient194-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, HTO, Sample 21

description:
Library name: 21___HTO
HTO library


title: DOGMAseq, HTO, Sample 19

description:
Library name: 19___HTO
HTO library


title: Patient189-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient187-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, HTO, Sample 20

description:
Library name: 20___HTO
HTO library


title: Patient184-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation

value: Postmenopausal


title: Patient185-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient181-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: DOGMAseq, HTO, Sample 18

description:
Library name: 18___HTO
HTO library


title: DOGMAseq, HTO, Sample 23

description:
Library name: 23___HTO
HTO library


title: DOGMAseq, HTO, Sample 17

description:
Library name: 17___HTO
HTO library


title: DOGMAseq, HTO, Sample 31

description:
Library name: 31___HTO
HTO library


title: DOGMAseq, HTO, Sample 16

description:
Library name: 16___HTO
HTO library


title: Patient176-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: Patient173-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, HTO, Sample 15

description:
Library name: 15___HTO
HTO library


title: Patient175-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, HTO, Sample 14

description:
Library name: 14___HTO
HTO library


title: Patient171-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient191-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: Patient170-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient169-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, HTO, Sample 13

description:
Library name: 13___HTO
HTO library


title: DOGMAseq, HTO, Sample 22

description:
Library name: 22___HTO
HTO library


title: DOGMAseq, HTO, Sample 12

description:
Library name: 12___HTO
HTO library


title: Patient167-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient178-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, HTO, Sample 11

description:
Library name: 11___HTO
HTO library


title: Patient161-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, HTO, Sample 10

description:
Library name: 10___HTO
HTO library


title: Patient162-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: DOGMAseq, HTO, Sample 8

description:
Library name: 8___HTO
HTO library


title: DOGMAseq, HTO, Sample 7

description:
Library name: 7___HTO
HTO library


title: DOGMAseq, HTO, Sample 6

description:
Library name: 6___HTO
HTO library


title: DOGMAseq, HTO, Sample 5

description:
Library name: 5___HTO
HTO library


title: DOGMAseq, HTO, Sample 4

description:
Library name: 4___HTO
HTO library


title: Patient155-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient145-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: Patient151-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: Patient149-Serum-Healthy-BRCA2_mutation-Female-Postmenopausal

description: BRCA2 mutation


title: DOGMAseq, HTO, Sample 3

description:
Library name: 3___HTO
HTO library


title: DOGMAseq, HTO, Sample 1

description:
Library name: 1___HTO
HTO library


title: Patient142-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient141-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient147-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 104

description:
Library name: 104___ADT
ADT library


title: Patient137-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient130-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: Patient160-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 101

description:
Library name: 101___ADT
ADT library


title: DOGMAseq, HTO, Sample 9

description:
Library name: 9___HTO
HTO library


title: Patient128-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 102

description:
Library name: 102___ADT
ADT library


title: Patient127-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 100

description:
Library name: 100___ADT
ADT library


title: Patient136-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: Patient126-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: Patient125-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 99

description:
Library name: 99___ADT
ADT library


title: Patient119-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 98

description:
Library name: 98___ADT
ADT library


title: DOGMAseq, ADT, Sample 97

description:
Library name: 97___ADT
ADT library


title: Patient117-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, HTO, Sample 2

description:
Library name: 2___HTO
HTO library


title: DOGMAseq, ADT, Sample 96

description:
Library name: 96___ADT
ADT library


title: Patient116-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 105

description:
Library name: 105___ADT
ADT library


title: Patient115-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 95

description:
Library name: 95___ADT
ADT library


title: DOGMAseq, ADT, Sample 94

description:
Library name: 94___ADT
ADT library


title: DOGMAseq, ADT, Sample 103

description:
Library name: 103___ADT
ADT library


title: Patient114-Serum-Healthy-BRCA_status_unknown-Female-Postmenopausal

description: BRCA status unknown


title: DOGMAseq, ADT, Sample 93

description:
Library name: 93___ADT
ADT library


title: DOGMAseq, ADT, Sample 92

description:
Library name: 92___ADT
ADT library


title: Patient110-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient106-Serum-Healthy-BRCA2_mutation-Female-Postmenopausal

description: BRCA2 mutation


title: Patient103-Serum-Healthy-BRCA_status_unknown-Female-Unknown

description: BRCA status unknown

value: Unknown


title: Patient101-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 89

description:
Library name: 89___ADT
ADT library


title: DOGMAseq, ADT, Sample 90

description:
Library name: 90___ADT
ADT library


title: DOGMAseq, ADT, Sample 91

description:
Library name: 91___ADT
ADT library


title: Patient099-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 88

description:
Library name: 88___ADT
ADT library


title: DOGMAseq, ADT, Sample 87

description:
Library name: 87___ADT
ADT library


title: Patient100-Serum-Healthy-BRCA_status_unknown-Female-Unknown

description: BRCA status unknown


title: Patient098-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 86

description:
Library name: 86___ADT
ADT library


title: Patient096-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: Patient095-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 85

description:
Library name: 85___ADT
ADT library


title: Patient094-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 82

description:
Library name: 82___ADT
ADT library


title: Patient093-Serum-Healthy-BRCA_status_unknown-Female-Premenopausal

description: BRCA status unknown


title: DOGMAseq, ADT, Sample 83

description:
Library name: 83___ADT
ADT library


title: DOGMAseq, ADT, Sample 81

description:
Library name: 81___ADT
ADT library


title: Patient085-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 78

description:
Library name: 78___ADT
ADT library


title: Patient090-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 80

description:
Library name: 80___ADT
ADT library


title: Patient072-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: Patient081-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient078-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 79

description:
Library name: 79___ADT
ADT library


title: DOGMAseq, ADT, Sample 76

description:
Library name: 76___ADT
ADT library


title: Patient083-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: Patient071-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 75

description:
Library name: 75___ADT
ADT library


title: DOGMAseq, ADT, Sample 77

description:
Library name: 77___ADT
ADT library


title: Patient070-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 84

description:
Library name: 84___ADT
ADT library


title: Patient074-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 73

description:
Library name: 73___ADT
ADT library


title: Patient069-Serum-Healthy-BRCA2_mutation-Female-Postmenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 72

description:
Library name: 72___ADT
ADT library


title: Patient066-Serum-Healthy-BRCA_status_unknown-Female-Premenopausal

description: BRCA status unknown


title: Patient067-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient064-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 71

description:
Library name: 71___ADT
ADT library


title: DOGMAseq, ADT, Sample 69

description:
Library name: 69___ADT
ADT library


title: Patient063-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: Patient062-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 68

description:
Library name: 68___ADT
ADT library


title: Patient061-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient059-Serum-Healthy-BRCA2_mutation-Female-Postmenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 67

description:
Library name: 67___ADT
ADT library


title: DOGMAseq, ADT, Sample 74

description:
Library name: 74___ADT
ADT library


title: DOGMAseq, ADT, Sample 64

description:
Library name: 64___ADT
ADT library


title: DOGMAseq, ADT, Sample 65

description:
Library name: 65___ADT
ADT library


title: DOGMAseq, ADT, Sample 66

description:
Library name: 66___ADT
ADT library


title: Patient058-Serum-Healthy-BRCA2_mutation-Female-Postmenopausal

description: BRCA2 mutation


title: Patient057-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 61

description:
Library name: 61___ADT
ADT library


title: DOGMAseq, ADT, Sample 63

description:
Library name: 63___ADT
ADT library


title: Patient053-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 60

description:
Library name: 60___ADT
ADT library


title: DOGMAseq, ADT, Sample 70

description:
Library name: 70___ADT
ADT library


title: Patient047-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: Patient048-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 62

description:
Library name: 62___ADT
ADT library


title: Patient046-Serum-Healthy-BRCA_wild-type-Female-Premenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 58

description:
Library name: 58___ADT
ADT library


title: DOGMAseq, ADT, Sample 57

description:
Library name: 57___ADT
ADT library


title: Patient042-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 56

description:
Library name: 56___ADT
ADT library


title: DOGMAseq, ADT, Sample 55

description:
Library name: 55___ADT
ADT library


title: Patient043-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 59

description:
Library name: 59___ADT
ADT library


title: Patient039-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 54

description:
Library name: 54___ADT
ADT library


title: Patient037-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: Patient034-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: DOGMAseq, ADT, Sample 53

description:
Library name: 53___ADT
ADT library


title: Patient033-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient055-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 52

description:
Library name: 52___ADT
ADT library


title: DOGMAseq, ADT, Sample 51

description:
Library name: 51___ADT
ADT library


title: DOGMAseq, ADT, Sample 50

description:
Library name: 50___ADT
ADT library


title: Patient030-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: Patient032-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient026-Serum-Healthy-BRCA_status_unknown-Female-Premenopausal

description: BRCA status unknown


title: DOGMAseq, ADT, Sample 49

description:
Library name: 49___ADT
ADT library


title: Patient049-Serum-Healthy-BRCA_wild-type-Female-Unknown

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 47

description:
Library name: 47___ADT
ADT library


title: DOGMAseq, ADT, Sample 46

description:
Library name: 46___ADT
ADT library


title: Patient024-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient018-Serum-Healthy-BRCA_wild-type-Female-Unknown

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 45

description:
Library name: 45___ADT
ADT library


title: DOGMAseq, ADT, Sample 44

description:
Library name: 44___ADT
ADT library


title: DOGMAseq, ADT, Sample 43

description:
Library name: 43___ADT
ADT library


title: Patient016-Serum-Healthy-BRCA2_mutation-Female-Premenopausal

description: BRCA2 mutation


title: Patient014-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 41

description:
Library name: 41___ADT
ADT library


title: DOGMAseq, ADT, Sample 42

description:
Library name: 42___ADT
ADT library


title: Patient011-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: Patient023-Serum-Healthy-BRCA1_mutation-Female-Postmenopausal

description: BRCA1 mutation


title: Patient002-Serum-Healthy-BRCA_wild-type-Female-Postmenopausal

description: BRCA wild-type


title: DOGMAseq, ADT, Sample 40

description:
Library name: 40___ADT
ADT library


title: Patient001-Serum-Healthy-BRCA_status_unknown-Female-Postmenopausal

description: BRCA status unknown


title: Patient004-Serum-Healthy-BRCA1_mutation-Female-Premenopausal

description: BRCA1 mutation


title: DOGMAseq, ADT, Sample 39

description:
Library name: 39___ADT
ADT library


title: DOGMAseq, ADT, Sample 38

description:
Library name: 38___ADT
ADT library


title: Patient 29-Plasma-Healthy-BRCA wild-type-Female

data_processing:
Cq values were background-filtered, assays must have been detected with at least 5 Cq less than the negative control, and with Cq<37 to be included in the data analysis. Then, duplicates were averaged; if one of the replicated contained non-detect, the second one was used in place of the mean. Data was normalized by subtracting each Cq value from the mean of Cq values of miRNAs detected in all samples in a set so that later higher normalized value means higher expression
In non-normalized data, lower value indicates higher miRNA expression. In normalized data, higher value indicates higher miRNA expression.

source_name: Plasma

tag: sample group

value: BRCA wild-type

value: Plasma

tag: gender

value: female

tag: subject id

value: Patient 29

tag: molecule subtype

value: miRNA


title: Patient 29-Serum-Healthy-BRCA wild-type-Female

value: Serum


title: DOGMAseq, ADT, Sample 48

description:
Library name: 48___ADT
ADT library

value: lymph node

value: sorted cd3+ cd8- non-naive cells

value: ART-treated


title: DOGMAseq, ADT, Sample 36

description:
Library name: 36___ADT
ADT library


title: Patient 27-Serum-Healthy-BRCA wild-type-Female

value: Patient 27


title: DOGMAseq, ADT, Sample 35

description:
Library name: 35___ADT
ADT library


title: DOGMAseq, ADT, Sample 37

description:
Library name: 37___ADT
ADT library


title: Patient 26-Serum-Healthy-BRCA wild-type-Female

value: Patient 26


title: Patient 26-Plasma-Healthy-BRCA wild-type-Female


title: DOGMAseq, ADT, Sample 34

description:
Library name: 34___ADT
ADT library


title: Patient 27-Plasma-Healthy-BRCA wild-type-Female


title: DOGMAseq, ADT, Sample 33

description:
Library name: 33___ADT
ADT library


title: DOGMAseq, ADT, Sample 32

description:
Library name: 32___ADT
ADT library


title: Patient 23-Plasma-Healthy-BRCA wild-type-Female

value: Patient 23


title: Patient 23-Serum-Healthy-BRCA wild-type-Female


title: DOGMAseq, ADT, Sample 31

description:
Library name: 31___ADT
ADT library


title: Patient 22-Serum-Healthy-BRCA wild-type-Female

value: Patient 22


title: Patient 22-Plasma-Healthy-BRCA wild-type-Female


title: DOGMAseq, ADT, Sample 29

description:
Library name: 29___ADT
ADT library


title: DOGMAseq, ADT, Sample 27

description:
Library name: 27___ADT
ADT library


title: DOGMAseq, ADT, Sample 28

description:
Library name: 28___ADT
ADT library


title: Patient 21-Plasma-Healthy-BRCA wild-type-Female

value: Patient 21


title: Patient 20-Serum-Healthy-BRCA mutation-Female

value: BRCA mutation

value: Patient 20


title: Patient 21-Serum-Healthy-BRCA wild-type-Female


title: Patient 18-Serum-Healthy-BRCA mutation-Female

value: Patient 18


title: Patient 18-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 21

description:
Library name: 21___ADT
ADT library

value: viremic


title: DOGMAseq, ADT, Sample 22

description:
Library name: 22___ADT
ADT library


title: DOGMAseq, ADT, Sample 23

description:
Library name: 23___ADT
ADT library


title: DOGMAseq, ADT, Sample 20

description:
Library name: 20___ADT
ADT library


title: Patient 20-Plasma-Healthy-BRCA mutation-Female

value: Plasma


title: Patient 17-Plasma-Healthy-BRCA mutation-Female

value: female

value: Patient 17


title: Patient 16-Serum-Healthy-BRCA mutation-Female

value: Patient 16

value: miRNA


title: Patient 15-Serum-Healthy-BRCA mutation-Female

value: Serum

value: Patient 15


title: Patient 15-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 30

description:
Library name: 30___ADT
ADT library

value: lymph node

value: sorted cd3+ cd8- non-naive cells

value: ART-treated


title: DOGMAseq, ADT, Sample 19

description:
Library name: 19___ADT
ADT library


title: DOGMAseq, ADT, Sample 17

description:
Library name: 17___ADT
ADT library


title: Patient 14-Serum-Healthy-BRCA mutation-Female

value: Patient 14


title: DOGMAseq, ADT, Sample 16

description:
Library name: 16___ADT
ADT library


title: DOGMAseq, ADT, Sample 18

description:
Library name: 18___ADT
ADT library


title: Patient 13-Serum-Healthy-BRCA mutation-Female

value: Patient 13


title: Patient 14-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 26

description:
Library name: 26___ADT
ADT library


title: DOGMAseq, ADT, Sample 25

description:
Library name: 25___ADT
ADT library


title: DOGMAseq, ADT, Sample 15

description:
Library name: 15___ADT
ADT library


title: DOGMAseq, ADT, Sample 24

description:
Library name: 24___ADT
ADT library


title: DOGMAseq, ADT, Sample 14

description:
Library name: 14___ADT
ADT library


title: Patient 13-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 13

description:
Library name: 13___ADT
ADT library


title: Patient 12-Plasma-Healthy-BRCA mutation-Female

value: Patient 12


title: Patient 17-Serum-Healthy-BRCA mutation-Female

value: BRCA mutation


title: Patient 12-Serum-Healthy-BRCA mutation-Female


title: Patient 11-Serum-Healthy-BRCA mutation-Female

value: Patient 11


title: DOGMAseq, ADT, Sample 10

description:
Library name: 10___ADT
ADT library


title: DOGMAseq, ADT, Sample 11

description:
Library name: 11___ADT
ADT library


title: Patient 10-Serum-Healthy-BRCA mutation-Female

value: Patient 10


title: Patient 11-Plasma-Healthy-BRCA mutation-Female


title: Patient 16-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 7

description:
Library name: 7___ADT
ADT library

value: viremic


title: DOGMAseq, ADT, Sample 8

description:
Library name: 8___ADT
ADT library


title: Patient 7-Serum-Healthy-BRCA mutation-Female

value: Patient 7


title: Patient 8-Plasma-Healthy-BRCA mutation-Female

value: Plasma

value: female

value: Patient 8


title: DOGMAseq, ADT, Sample 9

description:
Library name: 9___ADT
ADT library


title: DOGMAseq, ADT, Sample 5

description:
Library name: 5___ADT
ADT library


title: DOGMAseq, ADT, Sample 6

description:
Library name: 6___ADT
ADT library


title: Patient 6-Serum-Healthy-BRCA mutation-Female

value: Patient 6

value: miRNA


title: Patient 6-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 3

description:
Library name: 3___ADT
ADT library


title: Patient 7-Plasma-Healthy-BRCA mutation-Female


title: Patient 5-Serum-Healthy-BRCA mutation-Female

value: Serum

value: Patient 5


title: DOGMAseq, ADT, Sample 4

description:
Library name: 4___ADT
ADT library

value: lymph node

value: sorted cd3+ cd8- non-naive cells


title: Patient 8-Serum-Healthy-BRCA mutation-Female


title: DOGMAseq, ADT, Sample 12

description:
Library name: 12___ADT
ADT library


title: DOGMAseq, ADT, Sample 2

description:
Library name: 2___ADT
ADT library


title: DOGMAseq, ADT, Sample 1

description:
Library name: 1___ADT
ADT library


title: Patient 4-Plasma-Healthy-BRCA mutation-Female

value: Patient 4


title: DOGMAseq, GEX, Sample 104

description:
Library name: 104___GEX
GEX library

library_source: transcriptomic single cell

molecule: polyA RNA


title: Patient 5-Plasma-Healthy-BRCA mutation-Female


title: Patient 3-Serum-Healthy-BRCA mutation-Female

value: Patient 3


title: Patient 4-Serum-Healthy-BRCA mutation-Female


title: Patient 10-Plasma-Healthy-BRCA mutation-Female


title: DOGMAseq, GEX, Sample 102

description:
Library name: 102___GEX
GEX library


title: Patient 3-Plasma-Healthy-BRCA mutation-Female


title: Patient 2-Serum-Healthy-BRCA mutation-Female

value: Patient 2


title: Patient 2-Plasma-Healthy-BRCA mutation-Female

value: BRCA mutation


title: DOGMAseq, GEX, Sample 100

description:
Library name: 100___GEX
GEX library


title: DOGMAseq, GEX, Sample 98

description:
Library name: 98___GEX
GEX library


title: DOGMAseq, GEX, Sample 99

description:
Library name: 99___GEX
GEX library


title: Cerebellum synaptosome PreRNA, replicate 9 (Cseq)

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

description:
Library name: cseq36 Syn_Pre_nb
Neuronal barcode (NB)
cseq36_Spre_barcodes.tsv.gz
cseq36_Spre_features.tsv.gz
cseq36_Spre_matrix.mtx.gz

data_processing:
Raw sequencing data was processed using Cell Ranger (v7.1.0) with custom genome references including SynBar and Cre genes. Nuclear libraries were processed using force-cells parameter of actual loaded amount, while synaptosomal libraries used expect-cells parameter of actual loaded amount. Barcode sequences were extracted from filtered nuclear and unfiltered synaptosomal BAM files using custom Python scripts. Sequences were collapsed using Hamming distance 1 within samples to account for sequencing errors.
Assembly: mm10
Supplementary files format and content: CellRanger output files: *barcodes.tsv.gz, *features.tsv.gz, *matriz.mtx.gz (* represents different samples)

molecule: other

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
After perfusion with ice-cold PBS, target brain regions (right one-third cerebellum or bilateral pons) were dissected, homogenized in SET buffer (sucrose, Tris-HCl, EDTA, protease and RNase inhibitors), and centrifuged to separate nuclear (P1) and synaptosomal (S1) fractions. Nuclei were isolated from P1 by brief rinsing and resuspension in nuclear lysis buffer, followed by homogenization (cerebellum) or gentle mixing (pons), dilution, incubation on ice, filtration, centrifugation, washing, and staining with SiR-DNA in washing and staining buffer prior to flow cytometry. Synaptosomes were isolated from S1 by centrifugation to obtain synaptosomal pellet (P2), which was resuspended in washing and staining buffer, blocked with Fc receptor blocker, stained with anti-V5-Alexa Fluor 647 and anti-HA-PE antibodies, washed, and incubated with CellBrite 405 membrane dye. Nuclei were sorted by DNA content (SiR-DNA) and GFP expression, while synaptosomes were sorted based on scatter profiles, membrane integrity (CellBrite 405), and double-positivity for V5 and HA, and all sorted samples were collected into tubes containing appropriate collection buffers for downstream processing.
Libraries were generated using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G, and 10x Chromium Controller (10x Genomics) according to manufacturer's protocol with modifications. For each experiment, approximately 20,000-30,000 individually sorted GFP-positive nuclei or double-positive synaptosomes were loaded into each channel of the chip. For nuclear libraries, cDNA was amplified, size-selected using SPRIselect beads to separate transcriptome and barcode components, and independently constructed into mRNA libraries and barcode libraries. Synaptosome libraries were constructed using barcode-specific amplification without template switching oligonucleotides.

value: Cerebellum

tag: library type

value: NB


title: Cerebellum synaptosome PostRNA, replicate 9 (Cseq)

description:
Library name: cseq36 Syn_Post_nb
Neuronal barcode (NB)
cseq36_Spost_barcodes.tsv.gz
cseq36_Spost_features.tsv.gz
cseq36_Spost_matrix.mtx.gz


title: Pons nucleus mRNA, replicate 7 (Cseq)

description:
Library name: cseq36 PN_mRNA
polyA RNA
cseq36_PN_barcodes.tsv.gz
cseq36_PN_features.tsv.gz
cseq36_PN_matrix.mtx.gz

source_name: Pons

value: Pons

value: mRNA


title: DOGMAseq, GEX, Sample 105

description:
Library name: 105___GEX
GEX library

value: viremic


title: DOGMAseq, GEX, Sample 97

description:
Library name: 97___GEX
GEX library


title: Cerebellum nucleus PostRNA, replicate 7 (Cseq)

description:
Library name: cseq36 CN_Post_nb
Neuronal barcode (NB)
cseq36_CN_barcodes.tsv.gz
cseq36_CN_features.tsv.gz
cseq36_CN_matrix.mtx.gz


title: DOGMAseq, GEX, Sample 96

description:
Library name: 96___GEX
GEX library

value: hiv-


title: DOGMAseq, GEX, Sample 103

description:
Library name: 103___GEX
GEX library


title: Cerebellum nucleus mRNA, replicate 7 (Cseq)

description:
Library name: cseq36 CN_mRNA
polyA RNA
cseq36_CN_barcodes.tsv.gz
cseq36_CN_features.tsv.gz
cseq36_CN_matrix.mtx.gz


title: DOGMAseq, GEX, Sample 94

description:
Library name: 94___GEX
GEX library


title: control sample rep5

city: Guangzhou

first: Haifeng

last: Cui

state: Guangdong

address: jinsui

country: China

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

description:
Library name: CTRL-vehicle-5
/

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include genecount values for each Sample

source_name: retina

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: retina

value: retina cells

value: control sample rep5


title: control sample rep3

description:
Library name: CTRL-vehicle-3
/

value: control sample rep3


title: control sample rep2

description:
Library name: CTRL-vehicle-2
/

value: control sample rep2


title: DOGMAseq, GEX, Sample 91

description:
Library name: 91___GEX
GEX library

value: lymph node


title: DOGMAseq, GEX, Sample 93

description:
Library name: 93___GEX
GEX library

value: sorted cd3+ cd8- non-naive cells


title: DOGMAseq, GEX, Sample 101

description:
Library name: 101___GEX
GEX library


title: control sample rep1

description:
Library name: CTRL-vehicle-1
/

value: control sample rep1


title: DOGMAseq, GEX, Sample 90

description:
Library name: 90___GEX
GEX library


title: DOGMAseq, GEX, Sample 89

description:
Library name: 89___GEX
GEX library


title: Sample for establishing the light damage model rep5

description:
Library name: LD-vehicle-5
/


title: Sample for establishing the light damage model rep4

description:
Library name: LD-vehicle-4
/


title: DOGMAseq, GEX, Sample 88

description:
Library name: 88___GEX
GEX library


title: DOGMAseq, GEX, Sample 87

description:
Library name: 87___GEX
GEX library


title: Sample for establishing the light damage model rep3

description:
Library name: LD-vehicle-3
/


title: Pons nucleus PreRNA, replicate 7 (Cseq)

description:
Library name: cseq36 PN_Pre_nb
Neuronal barcode (NB)
cseq36_PN_barcodes.tsv.gz
cseq36_PN_features.tsv.gz
cseq36_PN_matrix.mtx.gz


title: Sample for establishing the light damage model rep2

description:
Library name: LD-vehicle-2
/


title: DOGMAseq, GEX, Sample 86

description:
Library name: 86___GEX
GEX library


title: Sample for establishing the light damage model rep1

description:
Library name: LD-vehicle-1
/


title: DOGMAseq, GEX, Sample 85

description:
Library name: 85___GEX
GEX library


title: DOGMAseq, GEX, Sample 95

description:
Library name: 95___GEX
GEX library


title: DOGMAseq, GEX, Sample 83

description:
Library name: 83___GEX
GEX library


title: DOGMAseq, GEX, Sample 84

description:
Library name: 84___GEX
GEX library


title: control sample rep4

description:
Library name: CTRL-vehicle-4
/

value: control sample rep4


title: DOGMAseq, GEX, Sample 82

description:
Library name: 82___GEX
GEX library


title: A74 Sample for establishing the light damage model rep2

description:
Library name: LD_A74_5
/


title: A74 Sample for establishing the light damage model rep3

description:
Library name: LD_A74_6
/


title: DOGMAseq, GEX, Sample 81

description:
Library name: 81___GEX
GEX library


title: DOGMAseq, GEX, Sample 92

description:
Library name: 92___GEX
GEX library


title: DOGMAseq, GEX, Sample 80

description:
Library name: 80___GEX
GEX library

value: ART-treated


description:
Library name: LD_4
/

value: Sample for establishing the light damage model rep3


description:
Library name: LD_3
/

value: Sample for establishing the light damage model rep2


title: A74 Sample for establishing the light damage model rep1

description:
Library name: LD_A74_2
/


title: DOGMAseq, GEX, Sample 78

description:
Library name: 78___GEX
GEX library


title: DOGMAseq, GEX, Sample 79

description:
Library name: 79___GEX
GEX library


title: DOGMAseq, GEX, Sample 77

description:
Library name: 77___GEX
GEX library


title: control sample rep2

description:
Library name: CTRL_2
/


description:
Library name: LD_2
/

value: Sample for establishing the light damage model rep1


title: DOGMAseq, GEX, Sample 76

description:
Library name: 76___GEX
GEX library


title: MC38, CKO1

city: Beijing

first: Qile

last: Guo

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

description: Library name: MC38_CKO1

data_processing:
Fastq files were processed with Cell Ranger (v 7.0.1), using default parameters.
Assembly: mm10
Supplementary files format and content: cell ranger gene expression count matrix for single cells

source_name: MC38 tumours

extract_protocol:
MC38 tissues were enzymatically digested with a solution containing Collagenase D (Roche) and DNase I (Roche) in RPMI 1640 for 45 min at 37 °C. B16 tissues were enzymatically digested with a solution containing Collagenase IV (Yuanye Biology), Dispase II (Sigma-Aldrich), and Dnase I (Roche) in RPMI 1640 for 30 min at 37 °C. KPC tumours were treated with a mixture of dispase (Life Technologies), collagenase P (Sigma Aldrich), and DNase I (Roche) in RPMI 1640 for 45 min at 37 °C. The obtained single cells suspensions were filtered on 100-µm cell strainers, incubated with RBC lysis buffer for 10 minutes on ice and resuspended in the appropriate buffer for cell counting and down-stream application. Live cells negative for CD45 and CD31 were isolated via FACS for scRNA sequencing.
Single-cell libraries were prepared using the Chromium GEM-X Single Cell 3' Reagent Kits (v4, 10x Genomics), according to the manufacturers’ instructions.

value: Day 11

value: CD45-CD31- cells

value: MC38 tumours

tag: strain


title: MC38, CKO2

description: Library name: MC38_CKO2

tag: tissue


title: DOGMAseq, GEX, Sample 74

description:
Library name: 74___GEX
GEX library


title: DOGMAseq, GEX, Sample 75

description:
Library name: 75___GEX
GEX library


title: DOGMAseq, GEX, Sample 73

description:
Library name: 73___GEX
GEX library


title: MC38, ctrl3

description: Library name: MC38_ctrl3


title: MC38, ctrl2

description: Library name: MC38_ctrl2


title: DOGMAseq, GEX, Sample 72

description:
Library name: 72___GEX
GEX library


title: B16, CKO2

description: Library name: B16_CKO2

source_name: B16 tumours

value: B16 tumours


title: DOGMAseq, GEX, Sample 71

description:
Library name: 71___GEX
GEX library


title: MC38, ctrl1

description: Library name: MC38_ctrl1


title: DOGMAseq, GEX, Sample 69

description:
Library name: 69___GEX
GEX library


title: DOGMAseq, GEX, Sample 70

description:
Library name: 70___GEX
GEX library


title: B16, ctrl2

description: Library name: B16_ctrl2


title: B16, CKO1

description: Library name: B16_CKO1


title: DOGMAseq, GEX, Sample 67

description:
Library name: 67___GEX
GEX library


title: DOGMAseq, GEX, Sample 66

description:
Library name: 66___GEX
GEX library


title: DOGMAseq, GEX, Sample 68

description:
Library name: 68___GEX
GEX library


title: B16, ctrl1

description: Library name: B16_ctrl1


title: KPC, ctrl

description: Library name: KPC_ctrl

source_name: KPC tumours

value: KPC tumours


title: KPC, CKO

description: Library name: KPC_CKO


title: control sample rep1

description:
Library name: CTRL_1
/

value: retina

value: retina cells

tag: treatment


title: control sample rep3

description:
Library name: CTRL_3
/

value: control sample rep3


title: DOGMAseq, GEX, Sample 64

description:
Library name: 64___GEX
GEX library


title: NS_triplicate_3

city: Stanford

first: Yang

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

description: Library name: NS_C

data_processing:
FastQC was used to check the quality of fastq files. Sequences were mapped to theGRCm38/mm10 reference genome with RSubread, and gene features were quantified with feature Counts.
Assembly: mm10
Supplementary files format and content: Feature counts

source_name: primary cells

growth_protocol: Pimary mouse T cells

extract_protocol:
Total RNA was extracted from 1-2.5million cells per condition using a RNeasy Micro Kit (Qiagen) followed by mRNA library preparation (poly-A enrichment) according to manufacturer instructions.
polyA enrichment

treatment_protocol: cytokines

value: spleen

value: Mouse T cells

value: Wildtype

value: Untreated


title: DOGMAseq, GEX, Sample 62

description:
Library name: 62___GEX
GEX library

value: lymph node

value: sorted cd3+ cd8- non-naive cells


title: NS_triplicate_1

description: Library name: NS_A


title: GERcombo_triplicate_2

description: Library name: GERcombo_B


title: DOGMAseq, GEX, Sample 61

description:
Library name: 61___GEX
GEX library

value: ART-treated


title: DOGMAseq, GEX, Sample 60

description:
Library name: 60___GEX
GEX library


title: GERcombo_triplicate_3

description: Library name: GERcombo_C


title: DOGMAseq, GEX, Sample 59

description:
Library name: 59___GEX
GEX library


title: DOGMAseq, GEX, Sample 58

description:
Library name: 58___GEX
GEX library


title: GER119_triplicate_3

description: Library name: GER119_C


title: GER119_triplicate_1

description: Library name: GER119_A


title: DOGMAseq, GEX, Sample 65

description:
Library name: 65___GEX
GEX library


title: DOGMAseq, GEX, Sample 56

description:
Library name: 56___GEX
GEX library


title: GER112_triplicate_3

description: Library name: GER112_C


title: GER112_triplicate_2

description: Library name: GER112_B


title: GER112_triplicate_1

description: Library name: GER112_A


title: DOGMAseq, GEX, Sample 53

description:
Library name: 53___GEX
GEX library


title: DOGMAseq, GEX, Sample 51

description:
Library name: 51___GEX
GEX library


title: DOGMAseq, GEX, Sample 52

description:
Library name: 52___GEX
GEX library


title: GER110_triplicate_3

description: Library name: GER110_C


title: DOGMAseq, GEX, Sample 50

description:
Library name: 50___GEX
GEX library


title: GER110_triplicate_1

description: Library name: GER110_A


city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Library name: SIA17C2_Hetz_5dpmi_GFP_Negative_DAPI_Negative

data_processing:
Data Formatting - bcl-convert 4.1.7
Data Cleaning - fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification - subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
Assembly: GRCm39 + M31
Supplementary files format and content: Unormalized gene counts for each sample within the submission

source_name: heart

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA). RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols.

value: heart

value: GFP- Remote zone cardiomyocyte

value: Myocardial Infarction


title: DOGMAseq, GEX, Sample 49

description:
Library name: 49___GEX
GEX library


title: GER119_triplicate_2

description: Library name: GER119_B


title: SIA_Hetz_21A7_5dpmi_DAPI_Neg_GFP_Neg

description: Library name: SIA_Hetz_21A7_5dpmi_DAPI_Neg_GFP_Neg


description: Library name: SIA17C1_Hetz_5dpmi_GFP_Negative_DAPI_Negative


title: DOGMAseq, GEX, Sample 48

description:
Library name: 48___GEX
GEX library


title: DOGMAseq, GEX, Sample 46

description:
Library name: 46___GEX
GEX library


title: DOGMAseq, GEX, Sample 47

description:
Library name: 47___GEX
GEX library


title: GERcombo_triplicate_1

description: Library name: GERcombo_A


title: NS_triplicate_2

description: Library name: NS_B


title: DOGMAseq, GEX, Sample 54

description:
Library name: 54___GEX
GEX library


title: SIA_Hetz_21A5_5dpmi_DAPI_Neg_GFP_Neg

description: Library name: SIA_Hetz_21A5_5dpmi_DAPI_Neg_GFP_Neg


title: DOGMAseq, GEX, Sample 63

description:
Library name: 63___GEX
GEX library


title: GER110_triplicate_2

description: Library name: GER110_B


title: SIA_Hetz_21A4_5dpmi_DAPI_Neg_GFP_Neg

description: Library name: SIA_Hetz_21A4_5dpmi_DAPI_Neg_GFP_Neg


title: DOGMAseq, GEX, Sample 55

description:
Library name: 55___GEX
GEX library


title: DOGMAseq, GEX, Sample 57

description:
Library name: 57___GEX
GEX library


title: DOGMAseq, GEX, Sample 44

description:
Library name: 44___GEX
GEX library


title: DOGMAseq, GEX, Sample 43

description:
Library name: 43___GEX
GEX library


description: Library name: _SIA17C2_Hetz_5dpmi_GFP_Positive_DAPI_Negative__SIA17C2_Hetz_5dpmi_GFP_Positive_DAPI_Positive_

value: GFP+ Border zone cardiomyocyte


description: Library name: _SIA17C1_Hetz_5dpmi_GFP_Positive_DAPI_Negative__SIA17C1_Hetz_5dpmi_GFP_Positive_DAPI_Positive_


description: Library name: _SIA_Hetz_21A7_5dpmi_DAPI_Neg_GFP_Pos__SIA_Hetz_21A7_5dpmi_DAPI_Pos_GFP_Pos_


title: DOGMAseq, GEX, Sample 42

description:
Library name: 42___GEX
GEX library


description: Library name: _SIA_Hetz_21A5_5dpmi_DAPI_Neg_GFP_Pos__SIA_Hetz_21A5_5dpmi_DAPI_Pos_GFP_Pos_


title: DOGMAseq, GEX, Sample 41

description:
Library name: 41___GEX
GEX library


title: DOGMAseq, GEX, Sample 40

description:
Library name: 40___GEX
GEX library


description: Library name: _SIA_Hetz_21A4_5dpmi_DAPI_Neg_GFP_Pos__SIA_Hetz_21A4_5dpmi_DAPI_Pos_GFP_Pos_


title: DOGMAseq, GEX, Sample 39

description:
Library name: 39___GEX
GEX library


title: DOGMAseq, GEX, Sample 38

description:
Library name: 38___GEX
GEX library


title: GAS6_2

city: hangzhou

first: Yan

last: He

state: 浙江省

address: hangzhou

institute: 浙江大学医学院附属第二医院

description: Library name: L1EIA2903507-GAS6_2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp [1] with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 [2] software. The mapped reads of each sample were assembled by StringTie [3] in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM[4] was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 [5] or DEGseq [6]. DEGs with |log2FC|≧1 and FDR＜ 0.05(DESeq2 ) or FDR ＜ 0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ＜ 0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and Python scipy software, respectively.
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS [7]. Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events
Assembly: GRCm39 (mm39)
Supplementary files format and content: (.csv)

source_name: skin

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample [OD260/280=1.8~2.2,OD260/230≥2.0,RQN≥6.5, 28S:18S≥1.0, >1μg（常量）OR OD260/280=1.8~2.2, RIN>6.5,＞10ng（微量）]was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The XX RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.（NovaSeq 测序平台）OR the sequencing library was performed on DNBSEQ-T7 platform(PE150) using DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.（T7 测序平台）.

value: skin

value: Male

value: hydrogel + GAS6 mRNA-LNP


title: GAS6_3

institute: 浙江大学医学院附属第二医院

description: Library name: L1EIA2903508-GAS6_3


title: GAS6_1

institute: 浙江大学医学院附属第二医院

description: Library name: L1EIA2903506-GAS6_1


title: DOGMAseq, GEX, Sample 36

description:
Library name: 36___GEX
GEX library


title: DOGMAseq, GEX, Sample 45

description:
Library name: 45___GEX
GEX library


title: Ctr_3

institute: 浙江大学医学院附属第二医院

description: Library name: L1EIA2903504-Ctr_3

value: hydrogel + LNP


title: KPC, ctrl, R4

data_processing:
Fastq files were processed with Cell Ranger (v 7.0.1), using default parameters.
Assembly: mm10
Supplementary files format and content: cell ranger gene expression and cell multiplexing oligos count matrix for single cells

source_name: tissue: KPC tumours strain: C57BL/6 genotype: Adam12flox/flox ,PdgfraCreERT2 and WT(littermate controls ) time: Day 17

extract_protocol:
KPC tumours were treated with a mixture of dispase (Life Technologies), collagenase P (Sigma Aldrich), and DNase I (Roche) in RPMI 1640 for 45 min at 37 °C. The obtained single cells suspensions were filtered on 100-µm cell strainers, incubated with RBC lysis buffer for 10 minutes on ice and resuspended in the appropriate buffer for cell counting and down-stream application. Live cells negative for CD326 and CD24 were isolated via FACS for scRNA sequencing.
Libraries of cells from KPC tumours were prepared using the Chromium Next GEM Single Cell 3’ HT kit with Feature Barcode technology (v.3.1, 10x Genomics), according to th manufacter's instruction.

value: KPC tumours

value: WT(littermate controls )

tag: time

value: Day 17


title: DOGMAseq, GEX, Sample 33

description:
Library name: 33___GEX
GEX library


title: KPC, ctrl, R3


title: Ctr_2

institute: 浙江大学医学院附属第二医院

description: Library name: L1EIA2903503-Ctr_2

tag: Sex


title: DOGMAseq, GEX, Sample 34

description:
Library name: 34___GEX
GEX library


title: DOGMAseq, GEX, Sample 32

description:
Library name: 32___GEX
GEX library


title: DOGMAseq, GEX, Sample 31

description:
Library name: 31___GEX
GEX library


title: DOGMAseq, GEX, Sample 30

description:
Library name: 30___GEX
GEX library


title: Ctr_1

institute: 浙江大学医学院附属第二医院

description: Library name: L1EIA2903502-Ctr_1


title: KPC, ctrl, R1


title: KPC, Adam12pCKO, R4

value: Adam12flox/flox ,PdgfraCreERT2


title: DOGMAseq, GEX, Sample 29

description:
Library name: 29___GEX
GEX library


title: KPC, Adam12pCKO, R2


title: DOGMAseq, GEX, Sample 28

description:
Library name: 28___GEX
GEX library


title: KPC, Adam12pCKO, R3


title: DOGMAseq, GEX, Sample 25

description:
Library name: 25___GEX
GEX library


title: DOGMAseq, GEX, Sample 26

description:
Library name: 26___GEX
GEX library


title: KPC, Adam12pCKO, R1


title: DOGMAseq, GEX, Sample 37

description:
Library name: 37___GEX
GEX library


title: DOGMAseq, GEX, Sample 27

description:
Library name: 27___GEX
GEX library


title: C57BL/6, Adam12pCKO, Adrenal gland, R2

data_processing:
Quality control and preprocessing of fastq files were conducted with fastp (v 0.23.4) using default parameters. Reads were mapped to the mouse genome mm10 using STAR aligner (v.2.7.10a) with default settings. FeatureCounts (v. 2.0.6) was then applied to count reads overlapping genes.
Assembly: mm10
Supplementary files format and content: Tab-separated counts file (gzipped format)

source_name: tissue: Adrenal gland strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

extract_protocol:
Total RNA was extracted from isolated tissues using the RNA isolation Total RNA Extraction Reagent (Vazyme). 100ng of total RNA was used for the construction of sequencing libraries
RNA sequencing libraries were prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme)

value: Adrenal gland

value: Female

value: Adam12flox/flox , PdgfraCreERT2

value: Week 8-10


title: DOGMAseq, GEX, Sample 24

description:
Library name: 24___GEX
GEX library

value: lymph node

value: sorted cd3+ cd8- non-naive cells

value: viremic


title: DOGMAseq, GEX, Sample 35

description:
Library name: 35___GEX
GEX library

value: ART-treated


title: KPC, ctrl, R2


title: DOGMAseq, GEX, Sample 23

description:
Library name: 23___GEX
GEX library


title: C57BL/6, ctrl, Adrenal gland, R1

source_name: tissue: Adrenal gland strain: C57BL/6 Sex: M genotype: WT time: Week 8-10

value: WT


title: C57BL/6, Adam12pCKO, Adrenal gland, R1

source_name: tissue: Adrenal gland strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: C57BL/6, ctrl, Stomach, R2

source_name: tissue: Stomach strain: C57BL/6 Sex: F genotype: WT time: Week 8-10

value: Stomach


title: C57BL/6, ctrl, Adrenal gland, R2

source_name: tissue: Adrenal gland strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: C57BL/6, ctrl, Stomach, R1

source_name: tissue: Stomach strain: C57BL/6 Sex: M genotype: WT time: Week 8-10

value: Male


title: DOGMAseq, GEX, Sample 21

description:
Library name: 21___GEX
GEX library

source_name: lymph node


title: DOGMAseq, GEX, Sample 18

description:
Library name: 18___GEX
GEX library


title: DOGMAseq, GEX, Sample 19

description:
Library name: 19___GEX
GEX library


title: DOGMAseq, GEX, Sample 20

description:
Library name: 20___GEX
GEX library


title: C57BL/6, Adam12pCKO, Stomach, R2

source_name: tissue: Stomach strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: C57BL/6, Adam12pCKO, Stomach, R1

source_name: tissue: Stomach strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: C57BL/6, Adam12pCKO, Kidney, R2

source_name: tissue: Kidney strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

value: Kidney


title: DOGMAseq, GEX, Sample 17

description:
Library name: 17___GEX
GEX library


title: C57BL/6, ctrl, Kidney, R2

source_name: tissue: Kidney strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: DOGMAseq, GEX, Sample 16

description:
Library name: 16___GEX
GEX library


title: C57BL/6, Adam12pCKO, Kidney, R1

source_name: tissue: Kidney strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: DOGMAseq, GEX, Sample 15

description:
Library name: 15___GEX
GEX library


title: DOGMAseq, GEX, Sample 14

description:
Library name: 14___GEX
GEX library


title: C57BL/6, Adam12pCKO, Luminal, R2

source_name: tissue: Luminal strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

value: Luminal


title: DOGMAseq, GEX, Sample 12

description:
Library name: 12___GEX
GEX library


title: C57BL/6, ctrl, Luminal, R2

source_name: tissue: Luminal strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: DOGMAseq, GEX, Sample 13

description:
Library name: 13___GEX
GEX library


title: DOGMAseq, GEX, Sample 11

description:
Library name: 11___GEX
GEX library


title: C57BL/6, ctrl, Luminal, R1

source_name: tissue: Luminal strain: C57BL/6 Sex: M genotype: WT time: Week 8-10


title: DOGMAseq, GEX, Sample 10

description:
Library name: 10___GEX
GEX library


title: DOGMAseq, GEX, Sample 22

description:
Library name: 22___GEX
GEX library


title: C57BL/6, Adam12pCKO, Heart, R2

source_name: tissue: Heart strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

value: Heart


title: C57BL/6, Adam12pCKO, Luminal, R1

source_name: tissue: Luminal strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: DOGMAseq, GEX, Sample 9

description:
Library name: 9___GEX
GEX library


title: C57BL/6, ctrl, Heart, R2

source_name: tissue: Heart strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: C57BL/6, ctrl, Heart, R1

source_name: tissue: Heart strain: C57BL/6 Sex: M genotype: WT time: Week 8-10


title: C57BL/6, Adam12pCKO, Heart, R1

source_name: tissue: Heart strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: DOGMAseq, GEX, Sample 7

description:
Library name: 7___GEX
GEX library


title: DOGMAseq, GEX, Sample 8

description:
Library name: 8___GEX
GEX library


title: DOGMAseq, GEX, Sample 6

description:
Library name: 6___GEX
GEX library


title: C57BL/6, Adam12pCKO, Breast, R2

source_name: tissue: Breast strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

value: Breast


title: C57BL/6, ctrl, Breast, R2

source_name: tissue: Breast strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: DOGMAseq, GEX, Sample 4

description:
Library name: 4___GEX
GEX library


title: DOGMAseq, GEX, Sample 3

description:
Library name: 3___GEX
GEX library


title: DOGMAseq, GEX, Sample 2

description:
Library name: 2___GEX
GEX library


title: DOGMAseq, GEX, Sample 5

description:
Library name: 5___GEX
GEX library


title: C57BL/6, ctrl, Breast, R1

source_name: tissue: Breast strain: C57BL/6 Sex: M genotype: WT time: Week 8-10


title: C57BL/6, Adam12pCKO, Breast, R1

source_name: tissue: Breast strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: C57BL/6, Adam12pCKO, Spleen, R2

source_name: tissue: Spleen strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

value: Spleen


title: C57BL/6, ctrl, Spleen, R2

source_name: tissue: Spleen strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: DOGMAseq, ATAC, Sample 105

description:
Library name: 105___ATAC
ATAC library

library_source: genomic single cell

molecule: genomic DNA

source_name: lymph node


title: DOGMAseq, GEX, Sample 1

description:
Library name: 1___GEX
GEX library


title: C57BL/6, ctrl, Spleen, R1

source_name: tissue: Spleen strain: C57BL/6 Sex: M genotype: WT time: Week 8-10


title: DOGMAseq, ATAC, Sample 103

description:
Library name: 103___ATAC
ATAC library


title: C57BL/6, Adam12pCKO, Spleen, R1

source_name: tissue: Spleen strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: C57BL/6, Adam12pCKO, Small intestine, R2

source_name: tissue: Small intestine strain: C57BL/6 Sex: F genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10

value: Small intestine


title: DOGMAseq, ATAC, Sample 102

description:
Library name: 102___ATAC
ATAC library


title: C57BL/6, ctrl, Small intestine, R2

source_name: tissue: Small intestine strain: C57BL/6 Sex: F genotype: WT time: Week 8-10


title: DOGMAseq, ATAC, Sample 101

description:
Library name: 101___ATAC
ATAC library


title: C57BL/6, ctrl, Small intestine, R1

source_name: tissue: Small intestine strain: C57BL/6 Sex: M genotype: WT time: Week 8-10


title: DOGMAseq, ATAC, Sample 100

description:
Library name: 100___ATAC
ATAC library


title: C57BL/6, Adam12pCKO, Small intestine, R1

source_name: tissue: Small intestine strain: C57BL/6 Sex: M genotype: Adam12flox/flox , PdgfraCreERT2 time: Week 8-10


title: DOGMAseq, ATAC, Sample 99

description:
Library name: 99___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 97

description:
Library name: 97___ATAC
ATAC library


title: Co-injection, Ctrl, D21, R2

source_name: tissue: Tumour strain: C57BL/6 genotype: WT time: Day 12 and 21

extract_protocol:
Co-injection tumour tissues were enzymatically digested with a solution containing Collagenase D (Roche) and DNase I (Roche) in RPMI 1640 for 45 min at 37 °C. The obtained single cells suspensions were filtered on 100-µm cell strainers, incubated with RBC lysis buffer for 10 minutes on ice and resuspended in the appropriate buffer for cell counting and down-stream application. Live cells were isolated via FACS for scRNA sequencing.
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3’ Library & Gel Bead kit (v.3.1, 10x Genomics), according to the manufacturers’ instructions.

value: Tumour

value: Day 12 and 21


title: Co-injection, Ctrl, D21, R1


title: DOGMAseq, ATAC, Sample 96

description:
Library name: 96___ATAC
ATAC library

value: hiv-


title: Co-injection, sgAdam12pCKO, D21, R2


title: DOGMAseq, ATAC, Sample 98

description:
Library name: 98___ATAC
ATAC library


title: Co-injection, Ctrl, D12, R2


title: Co-injection, Ctrl, D12, R1


title: DOGMAseq, ATAC, Sample 95

description:
Library name: 95___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 93

description:
Library name: 93___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 92

description:
Library name: 92___ATAC
ATAC library


title: C57BL/6, ctrl, Kidney, R1

source_name: tissue: Kidney strain: C57BL/6 Sex: M genotype: WT time: Week 8-10

value: Week 8-10


title: Co-injection, sgAdam12pCKO, D12, R2


title: DOGMAseq, ATAC, Sample 91

description:
Library name: 91___ATAC
ATAC library

value: lymph node


title: DOGMAseq, ATAC, Sample 104

description:
Library name: 104___ATAC
ATAC library

value: sorted cd3+ cd8- non-naive cells


title: Co-injection, sgAdam12pCKO, D12, R1


title: B16F10, ctrl, fibroblast, R4

source_name: Lung

extract_protocol:
Lung tissues containing metastases were excised and isolated for dissociation. Tissues were dissociated using gentleMACS C tubes with an enzymatic digestion solution composed of collagenase A (Sigma Aldrich), dispase II (Sigma Aldrich), and DNase I (Roche) in RPMI 1640. The obtained single cells suspensions were filtered on 100-µm cell strainers, incubated with RBC lysis buffer for 10 minutes on ice and resuspended in the appropriate buffer for cell counting and down-stream application. Endothelial cells were enriched as CD45-CD326-CD24-CD31+ live cells via FACS. Fibroblasts were enriched as CD45-CD326-CD24-CD31- via FACS. Total RNA was extracted from the isolated cells using the RNA isolation Total RNA Extraction Reagent (Vazyme). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme)

value: Lung

value: fibroblast

value: Day 18


title: DOGMAseq, ATAC, Sample 90

description:
Library name: 90___ATAC
ATAC library


title: B16F10, ctrl, fibroblast, R3

value: WT


title: B16F10, ctrl, fibroblast, R2


title: DOGMAseq, ATAC, Sample 88

description:
Library name: 88___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 89

description:
Library name: 89___ATAC
ATAC library


title: B16F10, Adam12pCKO, fibroblast, R3

value: Adam12flox/flox ,PdgfraCreERT2


title: DOGMAseq, ATAC, Sample 87

description:
Library name: 87___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 85

description:
Library name: 85___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 86

description:
Library name: 86___ATAC
ATAC library


title: B16F10, Adam12pCKO, fibroblast, R2


title: B16F10, Adam12pCKO, fibroblast, R1


title: DOGMAseq, ATAC, Sample 84

description:
Library name: 84___ATAC
ATAC library


title: B16F10, ctrl, endothelial, R4

value: endothelial cell


title: DOGMAseq, ATAC, Sample 83

description:
Library name: 83___ATAC
ATAC library


title: B16F10, ctrl, endothelial, R3


title: DOGMAseq, ATAC, Sample 94

description:
Library name: 94___ATAC
ATAC library


title: B16F10, ctrl, endothelial, R2


title: DOGMAseq, ATAC, Sample 81

description:
Library name: 81___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 79

description:
Library name: 79___ATAC
ATAC library

value: ART-treated


title: B16F10, ctrl, endothelial, R1


title: B16F10, Adam12pCKO, endothelial, R1


title: B16F10, Adam12pCKO, endothelial, R2


title: B16F10, ctrl, fibroblast, R1


title: Co-injection, sgAdam12pCKO, D21, R1


title: DOGMAseq, ATAC, Sample 77

description:
Library name: 77___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 75

description:
Library name: 75___ATAC
ATAC library


title: wsberry, rep 3

city: Cambridge

first: Erin

middle: E

last: Reynolds

state: MA

address: 455 Main St

institute: Whitehead Institute

description: Library name: wsberry_3

data_processing:
RNA-seq read alignment to the W. somnifera genome was performed using STAR (v 2.7.1a) 2-pass mapping, starting with a genome index generated with gene models and the option "--sjdbOverhang 100" and then re-mapping with a genome index using splice junctions from the initial mapping and the option "--limitOutSJcollapsed 2000000".
Gene counts were generated by featureCounts (v 2.0.1) with the options "-p -s 2 -M --fraction".
Assembly: unpublished
Supplementary files format and content: tab-delimited text file including raw counts for each sample

organism: Withania somnifera

source_name: berry

growth_protocol: W. somnifera seeds were acquired from “All good things organic seeds” on Amazon.com in March 2017. Seeds were sown on potting mix with added vermiculite and vernalized for three to five days at 4 °C under a humidified lid. They were then grown on in-door growth shelves installed with full-spectrum LED growth lights (80–120 μmol photons m−2 s−1) under a 16 h light/8 h dark photoperiod at 22 °C. RNA was extracted from four different tissue types of W. somnifera (young leaves, old leaves, berry, and root) with three biological replicates per tissue. Young leaves were defined as leaves smaller than 2 cm and were plucked from the top of the plant, near the budding region. Young leaves, old leaves, and root tissue were harvested from ~6-week-old plants and berry tissue was harvested from ~6-month-old plants.

extract_protocol:
100 mg wet weight of old leaf and berry tissue was harvested, 30 mg wet weight young leaf tissue, and 150-200 mg wet weight of root tissue was harvested. Harvested tissues were flash frozen in liquid nitrogen and ground to a fine powder in liquid nitrogen using a mortar and pestle. RNA was extracted using the Qiagen RNeasy Plant Mini Kit. Extracted RNA samples were flash frozen in liquid nitrogen and submitted to the Genome Technology Core at Whitehead Institute for Illumina paired-end RNA sequencing.
Libraries were prepared for RNA-Seq using IDT’s Swift Rapid RNA Library Prep Kit, according to manufacturer’s directions.

value: berry


title: DOGMAseq, ATAC, Sample 76

description:
Library name: 76___ATAC
ATAC library


title: wsberry, rep 1

description: Library name: wsberry_1


title: DOGMAseq, ATAC, Sample 73

description:
Library name: 73___ATAC
ATAC library


title: wsroot, rep 3

description: Library name: wsroot_3

source_name: root

value: root


title: DOGMAseq, ATAC, Sample 74

description:
Library name: 74___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 72

description:
Library name: 72___ATAC
ATAC library


title: wsroot, rep 2

description: Library name: wsroot_2


title: DOGMAseq, ATAC, Sample 71

description:
Library name: 71___ATAC
ATAC library


title: wsroot, rep 1

description: Library name: wsroot_1


title: wsyoungleaf, rep 3

description: Library name: wsyoungleaf_3

source_name: young leaf

value: young leaf


title: DOGMAseq, ATAC, Sample 70

description:
Library name: 70___ATAC
ATAC library


title: DOGMAseq, ATAC, Sample 82

description:
Library name: 82___ATAC
ATAC library


title: Huh7 cells/ DMSO treatment/control/Rep2

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description:
Library name: Ctr2
Ctr2

data_processing:
RNA-Seq reads were mapped on hg38 transcriptome using the ENSEMBL GRCh38 annotation with the STAR aligner and further processed using RSEM.
Supplementary files format and content: comma-separated file includes Human ensembl_gene_id as rows and log2 transformed TPM and raw read count values for each sample as columns.
Assembly: Assembly: hg38
Supplementary files format and content: The processed data files are comma-separated files including Human ensembl_gene_id as rows and log2 transformed TPM and raw gene count values for each sample as columns.

source_name: Huh7 xenograft

growth_protocol: Subcutaneous Huh7 xenograft mouse model was constructed in 6 to 10 weeks old male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice (Strain #:005557, RRID:IMSR_JAX:005557).

extract_protocol:
The tumor tissues were resected. Total RNA was extracted from tumor tissues using RNeasy Plus Mini Kit (cat# 74136, Qiagen).
RNA libraries for RNA-seq were prepared using by the Genomics Core at the Van Andel Institute using total RNA

treatment_protocol: 1 ug compound  PB56874852 (dissolved in DMSO, 20ug/ml) was administrated via intratumor injection every 3 days for two weeks.

value: Huh7 xenograft

tag: disease

value: HCC

value: DMSO

tag: dose

tag: batch


title: DOGMAseq, ATAC, Sample 78

description:
Library name: 78___ATAC
ATAC library

tag: cell type

tag: disease state


title: wsyoungleaf, rep 1

description: Library name: wsyoungleaf_1


title: wsleaf, rep 3

description: Library name: wsleaf_3

source_name: leaf

value: leaf


title: Huh7 cells/ DMSO treatment/control/Rep1

description:
Library name: Ctr1
Ctr1


title: Huh7 cells/ PB56874852 treatment/4uM/Rep3

description:
Library name: C4_3
C4_3

value: Compound PB56874852


title: wsleaf, rep 2

description: Library name: wsleaf_2


title: Huh7 cells/ PB56874852 treatment/4uM/Rep2

description:
Library name: C4_2
C4_2