title: hevg2-nhp3-dpi07


title: hevg2-nhp5-dpi00

status: Public on Oct 06 2025

type: RNA

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

country: USA

institute: University of Texas Medical Branch

hyb_protocol: Purified RNA samples were hybridized with the NHP_Immunology_V2 reporter and capture codesets containing ~779 targets (Nanostring Technologies) for ~24h at 65˚C.

scan_protocol: Hybridized samples were loaded onto a nCounter SPRINT microfluidics cartridge that was immediately run on a Nanostring nCounter SPRINT Profiler to determine fluorescent counts for each target.

data_processing: Raw RCC files were processed in nSolver v4.0 to generate background-thresholded counts matrices. Count matrices were analysed in R using the limma package.

molecule: total RNA

organism: Chlorocebus aethiops

source_name: Circulating whole blood

growth_protocol: None; samples from in vivo model

extract_protocol: Samples inactivated in AVL were extracted with the QIAGEN RNeasy Kit according to the manufacturer's protocol. Samples inactivated in TRIzol LS were extracted according to the manufacturer's protocol.

treatment_protocol: Each animal was challenged with 5e5 PFU HeV

tag: nhp

tag: dpi

tag: timepoint

value: Baseline

tag: agent


title: sperm-2

type: SRA

city: Haining

first: Xinyu

last: Xiang

state: Zhejiang

address: 718 East Haizhou Road

country: China

institute: Zhejiang University

description: Library name: sperm-2

library_source: genomic

data_processing:
sRNA-seq data processing: FastQC v0.11.8 was applied for raw reads quality control. The NEB adapter sequence (AGATCGGAAGA) was trimmed from the 3′ ends of raw FASTQ files using Cutadapt v2.9. Reads shorter than 16 bases after trimming were discarded (-m 16), as well as those lacking adaptors (--trimmed-only). Small RNA sequences with a minimum length of 23 bases were defined as piRNAs for downstream analysis to exclude miRNAs and siRNAs. For alignment, reads were mapped to the axolotl genome or transposon consensus sequences with STAR v2.7.0e with the following parameters: up to 1000 multimapped reads permitted (--outFilterMultimapNmax 1000), a maximum of three mismatches allowed (--outFilterMismatchNmax 3), and minimum of 15 matched bases required (--outFilterMatchNmin 15). All multimapped reads were exported (--outSAMmultNmax -1) were included for quantification over genes or transposons, with each read contributing 1/n to the counts.
EM-seq data processing: Raw sequencing reads were quality-checked with FastQC v0.11.8 and processed using Trim Galore v0.6.7 with Cutadapt v3.4 to remove low-quality bases and adapter sequences (--quality 20 --length 25 --trim-n --clip_R2 5). To increase sequencing coverage and depth, the three replicates were merged for downstream analysis. Trimmed paired-end reads were aligned to the axolotl genome with standard pipeline from Bismark v0.24.0 with Bowtie2 v2.4.2, allowing up to 1 bp mismatch and permitting multimapping, with a random alignment reported for ambiguous mappings (-N 1 --ambig_bam). The mapped reads were deduplicated by deduplicate_bismark. CpG methylation data were then extracted using bismark_methylation_extractor with default parameters. The methylation coverage data generated by Bismark v0.24.0 was imported into SeqMonk v1.48.1 for quantification and visualization.
Assembly: AmexG_v6.0-DD from https://www.axolotl-omics.org
Supplementary files format and content: For sRNA-seq, transposon counts normalized by RPKM are included. For EM-seq, bismark deduplicated and methylation coverage extracted data are included.
Library strategy: EM-seq

molecule: genomic DNA

organism: Ambystoma mexicanum

source_name: spermatozoa

growth_protocol: All lines were bred and maintained at the Research Institute of Molecular Pathology (IMP) facilities.

extract_protocol:
For sRNA-seq, RNA was extracted from two testis and two oocyte samples of the white axolotl strain using lysis reagent (QIAzol, 79306), following the manufacturer’s protocol. For EM-seq, DNA was extracted from three sperm samples of the white axolotl strain using Monarch HMW DNA Extraction Kit (NEB, T3050L) and solubilized in 10mM Tris, pH 9.0, 0.5 mM EDTA.
For sRNA-seq, total RNA was size-selected for 15-40 nt fragments using 15% Novex TBE-urea gel (Invitrogen, EC68855BOX). RNA fragments were purified from the gel and resuspended in 10 μl nuclease-free water. Library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7330L) according to the manufacturer’s protocol. Sequencing was performed on an Illumina HiSeq2500 platform in 50-bp single-end read mode. For EM-seq, libraries were prepared using the NEBnext Enzymatic Methyl-seq kit (NEB, E7120L) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq2000 platform in 150-bp paired-end read mode.

treatment_protocol: Handling and surgical procedures adhered to local ethics committee guidelines, and animal experiments were conducted with approval from the Magistrate of Vienna.

tag: tissue

value: spermatozoa


title: CRSwNP_4, CD45+ ROI1

city: Boston

first: Guanrui

last: Liao

state: Massachusetts

address: 3 Blackfan Circle

institute: BIDMC

description: CRS Q3 Normalization.xlsx

library_source: transcriptomic

data_processing:
Probes from the Nanostring CTA panel were mapped and counted using the Nanostring GeoMx Data Analysis software pipeline. Thereafter, the data underwent quality control and normalization steps with the ‘Geomx-Tools' software from Nanostring
Assembly: GRCh38-3.0.0
Supplementary files format and content: Comma-separated values files including normalized gene counts for each sample

organism: Homo sapiens

source_name: Nasal poylps

extract_protocol:
Samples collected for Nanostring GeoMx-Digital Spatial Profiling were fixed in 10% neutral buffered formalin at room temperature for 24-48 hours at a volume 10 times greater than the tissue volume. The specimens were then washed in 1xPBS, dehydrated, and paraffin-embedded at the Stanford Histology Core, and sectioned onto Fisher Superfrost Plus microscope slides (Fisher, 12-500-15) at 5um. Slides were deparaffinized and prepared according to the official Nanostring GeoMx-NGS RNA Manual Slide Preparation protocol.
The Nanostring DSP Human CTA detection probe cocktail was then applied to the slides and incubated overnight (~18 hrs) at 37°C. Each ROI was uniquely indexed using Illumina’s i5 x  i7 dual-indexing system. In total, 4 µL of collected sample was used in a PCR reaction with 1 µM of i5 primer, 1 µM i7 primer, and 1 x Nanostring library prep PCR Master Mix. PCR reaction conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min, 18 cycles of 95 °C for 15 s, 65 °C for 60 s, 68 °C for 30 s, and final extension of 68 °C for 5 min. Then the product was purified with two rounds of AMPure XP beads (Beckman Coulter) at 1.2 x bead-to-sample ratio

value: Nasal poylps

tag: disease state

value: Chronic rhinosinusitis


title: sperm-1

description: Library name: sperm-1


title: CRSwNP_5, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp3-dpi04

value: 4 DPI


title: hevg2-nhp3-dpi14

value: >10 DPI


title: sperm-3

description: Library name: sperm-3


title: hevg2-nhp3-dpi21


title: CRSwNP_9, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_8, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp2-dpi10

value: Terminal


title: hevg2-nhp3-dpi00


title: hevg2-nhp2-dpi00


title: hevg2-nhp2-dpi04


title: hevg2-nhp2-dpi07

value: 7 DPI


title: H358 cells, AMG-resistant pool, AMG510 treated, biological replicate 3

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

description: Library name: AMG_pool_A3

data_processing:
Reads were aligned to the mouse transcriptome (hg38) using STAR, and gene expression was quantified with the PartekE/M annotation model, then normalized to counts per million (CPM).
Assembly: hg38
Supplementary files format and content: text file includes Medium ratio (DESeq2) for each sample

growth_protocol: NCI-H358 cells (treatment-naïve and drug-treatment) were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from cells (approximately 1×106 cells each sample) using the RNeasy Plus Kit (Qiagen, Inc).
RNA-Seq libraries were prepared with NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: Three resistant clones, their treatment-naïve counterparts, and the parental pool were treated with AMG510 (2 μM) or vehicle for 3 days.

tag: cell line

tag: cell type

value: Lung cancer Epithelial cell

tag: genotype

value: KRAS G12C mutant; TP53 null

tag: treatment

value: AMG510 (2 μM) 3 days


title: H358 cells, AMG-resistant pool, AMG510 treated, biological replicate 1

description: Library name: AMG_pool_A1


title: H358 cells, AMG-resistant pool, AMG510 treated, biological replicate 2

description: Library name: AMG_pool_A2


title: hevg2-nhp3-dpi10

value: 10 DPI


title: hevg2-nhp1-dpi35


title: H358 cells, AMG-resistant pool, Vehicle treated, biological replicate 2

description: Library name: AMG_pool_C2

value: vehicle 3 days


title: H358 cells, AMG-resistant pool, Vehicle treated, biological replicate 3

description: Library name: AMG_pool_C3


title: H358 cells, AMG-resistant pool, Vehicle treated, biological replicate 1

description: Library name: AMG_pool_C1


title: hevg2-nhp1-dpi28


title: H358 cells, treatment-naïve pool, AMG510 treated, biological replicate 3

description: Library name: Cont_pool__A3


title: hevg2-nhp1-dpi14


title: hevg2-nhp1-dpi07


title: hevg2-nhp1-dpi10


title: H358 cells, treatment-naïve pool, AMG510 treated, biological replicate 2

description: Library name: Cont_pool__A2


title: H358 cells, treatment-naïve pool, AMG510 treated, biological replicate 1

description: Library name: Cont_pool__A1


title: hevg2-nhp1-dpi04


title: H358 cells, treatment-naïve pool, Vehicle treated, biological replicate 3

description: Library name: Cont_pool__C3


title: H358 cells, treatment-naïve pool, Vehicle treated, biological replicate 2

description: Library name: Cont_pool__C2


title: H358 cells, Clone#3, AMG-resistant, AMG510 treated, biological replicate 3

description: Library name: AMG_106_125_A3


title: hevg2-nhp1-dpi00


title: H358 cells, treatment-naïve pool, Vehicle treated, biological replicate 1

description: Library name: Cont_pool__C1


title: H358 cells, Clone#3, AMG-resistant, AMG510 treated, biological replicate 1

description: Library name: AMG_106_125_A1


title: hevredlands-nhp5-dpi07

value: HeV-R


title: hevredlands-nhp5-dpi04


title: hevredlands-nhp5-dpi08


title: hevredlands-nhp5-dpi00


title: H358 cells, Clone#3, AMG-resistant, AMG510 treated, biological replicate 2

description: Library name: AMG_106_125_A2


title: hevredlands-nhp4-dpi06


title: H358 cells, Clone#3, AMG-resistant, Vehicle treated, biological replicate 3

description: Library name: AMG_106_125_C3


title: H358 cells, Clone#3, AMG-resistant, Vehicle treated, biological replicate 2

description: Library name: AMG_106_125_C2


title: H358 cells, Clone#3, AMG-resistant, Vehicle treated, biological replicate 1

description: Library name: AMG_106_125_C1


title: hevredlands-nhp3-dpi07


title: hevredlands-nhp4-dpi00


title: H358 cells, Clone#3, treatment-naïve, AMG510 treated, biological replicate 3

description: Library name: Cont_106_125_A3


title: hevredlands-nhp4-dpi04


title: H358 cells, Clone#3, treatment-naïve, AMG510 treated, biological replicate 2

description: Library name: Cont_106_125_A2


title: H358 cells, Clone#3, treatment-naïve, AMG510 treated, biological replicate 1

description: Library name: Cont_106_125_A1


title: ap1_stagemix-flower_sm-wt_chip_r2

city: Berlin

first: Manuel

last: Neumann

address: Philippstr. 13

country: Germany

institute: HU Berlin

description:
ap1_stagemix-flower_sm-wt_chip_r2
ap1_stagemix-flower_sm-wt_chip.bw
ap1_stagemix-flower_sm-wt_chip_peaks.narrowPeak

data_processing:
Quality of raw reads was assesed with FastQC (version 0.11.9)
Raw read were timmed with Trimmomatic v0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Trimmed Reads were mapped to the Arabidopsis genome using bowtie2 (version 2.4.4) with default parameters
Peak calling on aligend reads was done using MACS3 (version 3.0.0b1) with defaults parameters except: -g 101274395 -q 0.1 --mfold 1 50
bigWig files were generated using DeepTools with the command “bamCoverage” (version 3.5.1) with parameters -bs 1 --skipNonCoveredRegions
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for mock and background samples)

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: AP1 inducible transgenic seedlings were grown on ½ MS medium for 10 days and then treated with dex or mock solutions. Tissues were collected 2, 8, 24 and 48 hours after treatment. Plants were grown at 22℃ and 60% humidity and under long-day conditions (16hr light, 8hr dark)

extract_protocol:
2.5 to 3 g of seedlings and around 1g inflorescence were collected for ChIP-seq. Plant tissues were fixed in formaldehyde, and ChIP-seq was done according to the published protocol (Kaufmann, K., Muiño, J.M., Østerås, M., Farinelli, L., Krajewski, P., and Angenent, G.C. (2010a). Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5: 457–472.). Nuclei lysate was incubated with native SEP3 antibody for 1 hour, and 50 µl Dynabeads protein A (Thermo Fisher) was then added for immunoprecipitation.
Libraries were prepared suing the ThruPlex DNA-Seq kit (TaKaRa).

treatment_protocol: Treatment was done by spraying an equal amount of dex or mock solution on seedlings. Dex solution is prepared by mixing 25 μl 20 mM dexamethasone dissolved in DMSO and 8 μl Silwet in 50 ml water, and the mock solution is prepared by mixing 25 μl DMSO and 8 μl Silwet in 50 ml water. After treatment, seedlings were transferred back to their normal growth condition.

value: inflorescence

value: floral cells

tag: chip antibody

value: GFP antibody


title: H358 cells, Clone#3, treatment-naïve, vehicle treated, biological replicate 3

description: Library name: Cont_106_125_C3


title: hevredlands-nhp2-dpi07


title: hevredlands-nhp2-dpi00

value: Baseline


title: hevredlands-nhp2-dpi04


title: hevg2-nhp1-dpi21


description:
ap1_stagemix-flower_sm-background_chip_r1
ap1_stagemix-flower_sm-background_chip.bw


title: H358 cells, Clone#3, treatment-naïve, vehicle treated, biological replicate 2

description: Library name: Cont_106_125_C2


description:
ap1_stagemix-flower_tet-mut_cirspr_chip_r1
ap1_stagemix-flower_tet-mut_cirspr_chip.bw
ap1_stagemix-flower_tet-mut_cirspr_chip_peaks.narrowPeak

value: AP1 native antibody


title: hevredlands-nhp1-dpi07


title: hevredlands-nhp1-dpi04


title: H358 cells, Clone#2, AMG-resistant, AMG510 treated, biological replicate 2

description: Library name: AMG_103_117_A2


title: H358 cells, Clone#3, treatment-naïve, vehicle treated, biological replicate 1

description: Library name: Cont_106_125_C1


title: THP-1 cells infected with Francisella tularensis, treated with vehicle control, replicate 5

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description: Library name: infected-untreated-24hr-5

data_processing:
Reads were trimmed to remove adapter content and low-quality base calls using Trimmomatic v 0.38.0
Trimmed reads were aligned to the reference human genome GRCh38 using HISAT2 version 2.1.0
Read counts were generated from bam files using the bioconductor package GenomicAlignments version 1.16.0
Differentially expressed genes were identified using DESeq2 version 1.20.0 and a statistical model that identified statistically significant interactions between infection and treatment
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv contains read counts per gene per sample, as determined by GenomicAlignments (R/Bioconductor)
Supplementary files format and content: normalized_counts.csv contains counts per gene per sample, normalized by library size, as implemented in DESeq2 version 1.20.0

growth_protocol: THP-1 cells (ATCC TIB-202) were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gemini Bio-Products), 25 mM HEPES (Corning), 1 mM sodium pyruvate (Gibco), and 1% glutamine dipeptide (Gibco).

extract_protocol:
After incubation, cells were transferred to 15 ml conical tubes and collected by centrifugation. After removing the supernatant, the pellets were resuspended in Trizol and incubated at room temperature for 5 minutes. Chloroform was then added and vigorously mixed for 15 seconds until the sample turned milky pink. The mixture was then transferred to an organic matrix tube and centrifuged at max speed for 15 minutes. After centrifugation, the clear liquid layer was transferred to a new tube and 70% ethanol was added at a 1:1 ratio. The resulting mixture was then transferred to a spin column (Invitrogen PureLinkTM RNA Mini Kit) and spun at max speed for 15 seconds. The flow through was discarded and PureLink Dnase (Invitrogen) was added directly to the column and incubated for 15 minutes are room temperature. Following Dnase treatment, Wash Buffer 1 was added to the columns and centrifuged for 15 seconds. The columns were then washed with Wash Buffer 2 twice each time being spun for 15 seconds followed by a final 2 minute spin to ensure the column was dry. Spin columns were transferred to recovery tubes and total RNA was eluted with Rnase-free water. The columns were incubated at room temperature for 2 minutes before centrifuging for 1 minute. RNA concentrations were determined using a NanoDrop spectrophotometer and then stored at -80°C.
For RNA-Seq analysis of THP-1 cells (+ dillapiole), total RNA was extracted from five replicate samples in each experimental group. RNA was quantitated with Qubit RNA fluorimetric assays (ThermoFisher Scientific). RNA Integrity Numbers (RINs), assessed using 2100 Bioanalyzer RNA microfluidic chips, were greater than 8.5 for all samples. Illumina-compatible libraries were prepared using TruSeq Stranded mRNA kit (Illumina, San Diego CA). RNA libraries were sequenced on an Illumina HiSeq1500 sequencer.

treatment_protocol: . Uninfected and infected THP-1 cells were treated with dillapiole (8 mg/ml) or hexane 1 hour post infection. Plates were incubated for 24 hours at 37°C, 5% CO2.

tag: infection

value: Infected with Francisella tularensis

value: Control


title: H358 cells, Clone#2, AMG-resistant, AMG510 treated, biological replicate 1

description: Library name: AMG_103_117_A1


title: THP-1 cells infected with Francisella tularensis, treated with Dillapiole, replicate 4

description: Library name: infected-treated-24hr-4

value: Dillapiole


title: ap1_stagemix-flower_cispr-wt_chip_r1

description:
ap1_stagemix-flower_cispr-wt_chip_r1
ap1_stagemix-flower_cispr-wt_chip.bw
ap1_stagemix-flower_cispr-wt_chip_peaks.narrowPeak


title: BSA-vascular-cells-SB07-09

city: San Francisco

first: Henry

last: Rodriguez

address: 1322 3rd avenue

institute: University of California San Francisco

description:
Library name: BSA-vascular-cells-5
BSA_vasculature_cells_07

data_processing:
Adaptors and low-quality sequences were removed with TrimGalore software (https://github.com/FelixKrueger/TrimGalore). Mapping to FF, FcoR and ITAM/ITIM genes was performed with Kallisto and RSEM methods.
To quantify the expression of fester and FcoR genes, raw reads from B. schlosseri transcriptomes were mapped to the full-length of the fester and FcoR genes using Kallisto and RSEM. Expression levels were quantified using the Trimmed Mean of M-values (TMM).
Assembly: Transcriptomes were assembled using Trinity software with default parameters.
Supplementary files format and content: all.isoform.TMM.EXPR_FF_FcoR_Kallisto.txt
Supplementary files format and content: all.isoform.TMM.EXPR_FF_FcoR_RSEM.txt
Supplementary files format and content: all.isoform.TMM.EXPR_NK_genes_Ampullae_Kallisto.txt

organism: Botryllus schlosseri

source_name: Vasculature

extract_protocol:
Total RNA was isolated for whole colonies, blood cells, vasculature, and Integrin alpha-6-, BSA-, or ALDH-positive cells -sorted by FACS with the Monarch® Total RNA Miniprep Kit (NEB) or NucleoSpin RNA, Mini kit for RNA purification (MACHEREY-NAGEL) following the manufacturer’s protocols.
RNA samples were sequenced (poly-A library prep, 150 bp insert size, paired-end, 20 million reads per sample) at the UC Davis Genome Center or the Novogene company.

value: Vasculature

value: BSA vascular cells


title: THP-1 cells infected with Francisella tularensis, treated with Dillapiole replicate 5

description: Library name: infected-treated-24hr-5


title: H358 cells, Clone#2, AMG-resistant, AMG510 treated, biological replicate 3

description: Library name: AMG_103_117_A3


title: THP-1 cells infected with Francisella tularensis, treated with vehicle control, replicate 4

description: Library name: infected-untreated-24hr-4


title: THP-1 cells infected with Francisella tularensis, treated with Dillapiole, replicate 2

description: Library name: infected-treated-24hr-2


title: H358 cells, Clone#2, AMG-resistant, Vehicle treated, biological replicate 3

description: Library name: AMG_103_117_C3


description:
ap1_stagemix-flower_cirspr-background_chip_r1
ap1_stagemix-flower_cirspr-background_chip.bw


title: THP-1 cells infected with Francisella tularensis, treated with Dillapiole replicate 3

description: Library name: infected-treated-24hr-3


title: BSA-vascular-cells-SB06

description:
Library name: BSA-vascular-cells-4
BSA_vasculature_cells_06


title: BSA-vascular-cells-SB10-11

description:
Library name: BSA-vascular-cells-6
BSA_vasculature_cells_10


title: hevredlands-nhp3-dpi04

value: 4 DPI


title: hevredlands-nhp1-dpi00


title: hevredlands-nhp3-dpi00


title: THP-1 cells infected with Francisella tularensis, treated with vehicle control, replicate 2

description: Library name: infected-untreated-24hr-2


title: ap1_stagemix-flower_tet-mut_sm_chip_r1

description:
ap1_stagemix-flower_tet-mut_sm_chip_r1
ap1_stagemix-flower_tet-mut_sm_chip.bw
ap1_stagemix-flower_tet-mut_sm_chip_peaks.narrowPeak


title: H358 cells, Clone#2, AMG-resistant, Vehicle treated, biological replicate 2

description: Library name: AMG_103_117_C2

value: Lung cancer Epithelial cell


title: THP-1 cells infected with Francisella tularensis, treated with vehicle control, replicate 1

description: Library name: infected-untreated-24hr-1


title: ap1_stagemix-flower_sm-wt_chip_r1

description:
ap1_stagemix-flower_sm-wt_chip_r1
ap1_stagemix-flower_sm-wt_chip.bw
ap1_stagemix-flower_sm-wt_chip_peaks.narrowPeak


title: Uninfected THP-1 cells, treated with Dillapiole, replicate 5

description: Library name: uninfected-treated-24hr-5

value: Uninfected


title: BSA-vascular-cells-SB04

description:
Library name: BSA-vascular-cells-2
BSA_vasculature_cells_04


title: THP-1 cells infected with Francisella tularensis, treated with Dillapiole, replicate 1

description: Library name: infected-treated-24hr-1


title: H358 cells, Clone#2, AMG-resistant, Vehicle treated, biological replicate 1

description: Library name: AMG_103_117_C1

value: KRAS G12C mutant; TP53 null


title: BSA-vascular-cells-SB01-03

description:
Library name: BSA-vascular-cells-1
Removed from the processed data


title: Uninfected THP-1 cells, treated with Dillapiole, replicate 4

description: Library name: uninfected-treated-24hr-4


title: THP-1 cells infected with Francisella tularensis, treated with vehicle control, replicate 3

description: Library name: infected-untreated-24hr-3


title: H358 cells, Clone#2, treatment-naïve, AMG510 treated, biological replicate 3

description: Library name: Cont_103_117_A3

value: AMG510 (2 μM) 3 days


title: BSA-vascular-cells-SB05

description:
Library name: BSA-vascular-cells-3
BSA_vasculature_cells_05


title: Uninfected THP-1 cells, treated with Dillapiole, replicate 3

description: Library name: uninfected-treated-24hr-3


title: Uninfected THP-1 cells, treated with Dillapiole, replicate 2

description: Library name: uninfected-treated-24hr-2


title: Uninfected THP-1 cells, treated with Dillapiole, replicate 1

description: Library name: uninfected-treated-24hr-1


title: Uninfected THP-1 cells, treated with vehicle control, replicate 5

description: Library name: uninfected-untreated-24hr-5


title: H358 cells, Clone#2, treatment-naïve, AMG510 treated, biological replicate 1

description: Library name: Cont_103_117_A1


title: Uninfected THP-1 cells, treated with vehicle control, replicate 4

description: Library name: uninfected-untreated-24hr-4


title: Whole-body-SMH-replicate-3

description:
Library name: Whole body-12
WB_SMH_802

source_name: Whole colony (WB)

value: Whole colony (WB)

value: All cells


title: Uninfected THP-1 cells, treated with vehicle control, replicate 1

description: Library name: uninfected-untreated-24hr-1


title: H358 cells, Clone#2, treatment-naïve, AMG510 treated, biological replicate 2

description: Library name: Cont_103_117_A2


title: RNA, treatment 2

city: Wenzhou

first: Chenghao

last: Li

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

description: Library name: RNA_treatment_2

data_processing:
Clean reads were aligned to the reference genome (hg38) using STAR (v2.7.9a) in end-to-end mode.
The BAM files were converted to BigWig format using deepTools
Assembly: hg38
Supplementary files format and content: bigwig

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed with the Agilent 2100 Bioanalyzer, and only samples with RIN ≥ 7 were used for library preparation.
RNA-seq libraries were prepared using a 3′ mRNA-seq library preparation kit (e.g., QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina, Lexogen) according to the manufacturer’s instructions. Briefly, libraries were generated from poly(A)+ RNA using oligo(dT) priming, followed by reverse transcription and second-strand cDNA synthesis from the 3′ end of transcripts.


title: Uninfected THP-1 cells, treated with vehicle control, replicate 2

description: Library name: uninfected-untreated-24hr-2


title: H358 cells, Clone#2, treatment-naïve, vehicle treated, biological replicate 2

description: Library name: Cont_103_117_C2

value: vehicle 3 days


title: Whole-body-SMH-replicate-2

description:
Library name: Whole body-11
WB_SMH_rep2


title: H358 cells, Clone#2, treatment-naïve, vehicle treated, biological replicate 3

description: Library name: Cont_103_117_C3


title: Uninfected THP-1 cells, treated with vehicle control, replicate 3

description: Library name: uninfected-untreated-24hr-3


title: Whole-body-SMH-replicate-1

description:
Library name: Whole body-10
WB_SMH_rep1


title: Whole-body-SMGO-replicate-3

description:
Library name: Whole body-9
WB_SMGO_rep3


title: RNA, NC 2

description: Library name: RNA_NC_2


title: H358 cells, Clone#2, treatment-naïve, vehicle treated, biological replicate 1

description: Library name: Cont_103_117_C1


title: RNA, treatment 1

description: Library name: RNA_treatment_1


title: Whole-body-SMGO-replicate-1

description:
Library name: Whole body-7
WB_SMGO_rep1


title: RNA, NC 1

description: Library name: RNA_NC_1


title: H2AZac, treatment 2, ChIP

description:
Library name: H2AZac_treatment_2
paired-end

data_processing:
chip-seq reads were alioned to the UCSC hg38 genome using Bowtie version 1.12.0nly uniquely mapping reads with at most two mismatches were retained.
ChIP-seq data were marked for duplicates using Picard (v1.128) and filtered for mapping quality using SAMtools
MACS2 (Version 2.1.1) with genomic DNA as input to define background, following all default parameters except -p 1e-9.
The BAM files were converted to BigWig format using deepTools
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Crosslinked with 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, and chromatin was sheared to 100–600 bp using a Covaris M220 ultrasonicator.
DNA was subjected to library preparation with NEBNext ChIP-seq Library Pre Reagent (NEB #E7370S, USA)


title: H358 cells, Clone#1, AMG-resistant, AMG510 treated, biological replicate 3

description: Library name: AMG_102_130_A3


title: H2AZac, treatment 1, ChIP

description:
Library name: H2AZac_treatment_1
paired-end


title: H2AZac, NC 2, ChIP

description:
Library name: H2AZac_NC_2
paired-end


title: Whole-body-SKI-replicate-2

description:
Library name: Whole body-5
WB_SKI_rep2


title: H358 cells, Clone#1, AMG-resistant, AMG510 treated, biological replicate 2

description: Library name: AMG_102_130_A2


title: H358 cells, Clone#1, AMG-resistant, AMG510 treated, biological replicate 1

description: Library name: AMG_102_130_A1


title: Whole-body-SKI-replicate-3

description:
Library name: Whole body-6
WB_SKI_rep3


title: Whole-body-SB825-replicate-3

description:
Library name: Whole body-3
WB_825_rep3


title: Whole-body-SMGO-replicate-2

description:
Library name: Whole body-8
WB_SMGO_rep2


title: SARS-CoV-2 infected human ES cell-derived aggregates, 11 dpi

city: Kyoto

first: Eiraku

last: Mototsugu

state: Kyoto

address: 53, Kawahara-cho

department: Institute for Life and Medical Sciences

country: Japan

institute: Kyoto University

description:
Library name: hESC_SARSCoV2_day11.csv.gz
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequence reads were aligned to the human genome (GRCh38) and a count matrix of unique molecular identifiers (UMIs) was generated using CellRanger (version 4.0.0)
Assembly: GRCh38

source_name: hESC-derived nasal organoids

extract_protocol:
KhES1-derived organoids were dissociated into single cells by TrypLE Select. The cells were suspended in 0.04% bovine serum albumin-containing phosphate-buffered saline, diluted to an optimal concentration, and applied to a chromium controller (10x Genomics).
The Chromium Single Cell 3’ Library & Gel Beads Kit v3 (10x Genomics) was used to generate oligo-dT-primed cDNA libraries, following the manufacturer’s protocol. The cDNA library for each sample was prepared separately and sequenced on an Illumina NovaSeq6000 (Illumina). The sequence reads were aligned against the reference which had built with GRCh38 genome assembly and the SARS-CoV-2 genome (GenBank: LC528233.1) using the cellranger count command in Cell Ranger (version 4.0.0) to generate a count matrix of unique molecular identifiers for each gene per cell.

value: hESC-derived nasal organoids

value: infected


title: Whole-body-SKI-replicate-1

description:
Library name: Whole body-4
WB_SKI_rep1


title: SARS-CoV-2 infected human ES cell-derived aggregates, 1 dpi

description:
Library name: hESC_SARSCoV2_day1.csv.gz
10x Genomics


title: H358 cells, Clone#1, AMG-resistant, Vehicle treated, biological replicate 1

description: Library name: AMG_102_130_C1


title: SARS-CoV-2 infected human ES cell-derived aggregates, 7 dpi

description:
Library name: hESC_SARSCoV2_day7.csv.gz
10x Genomics


title: Whole-body-SB825-replicate-1

description:
Library name: Whole body-1
WB_825_rep1


title: Whole-body-SB825-replicate-2

description:
Library name: Whole body-2
WB_825_rep2


title: mock infection human ES cell-derived aggregate 3

description:
Library name: hESC_3.csv.gz
10x Genomics

value: uninfected


title: H358 cells, Clone#1, treatment-naïve, AMG510 treated, biological replicate 3

description: Library name: Cont_102_130_A3


title: mock infection human ES cell-derived aggregate 2

description:
Library name: hESC_2.csv.gz
10x Genomics


title: H358 cells, Clone#1, AMG-resistant, Vehicle treated, biological replicate 3

description: Library name: AMG_102_130_C3


title: postInfusion_ADT1

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Universitätsklinikum Erlangen

description:
Library name: postInfusion_ADT1
10x Genomics

data_processing:
The sequencing sample was processed via the cellranger (version 6.0.2, 10x Genomics) `multi`-command using the gene expression reference GRCh38 (version 2020A, 10x Genomics) with added CAR-Gene-Sequence, the VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics), and custom feature barcodes (barcodes.csv).
Assembly: GRCh38 (version 2020A, 10x Genomics), vdj-GRCh38 (version 5.0.0, 10x Genomics), barcodes.csv
Supplementary files format and content: comma-separated value files and matrix files
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
Cyropreserved post-infusion CAR-T cells were thawed and rested overnight at 2x10^6 cells/mL in cRPMI (RPMI 1640 Medium + 10% heat-inactivated FCS, 0.05 mM β-mercaptoethanol, 0.05 mg/mL gentamicin, 1.1915 g/L HEPES, 0.2 g/L L-glutamine, 100 U/mL Penicillin-Streptomycin). After manual counting, all cells (1.35x106 C14, 3.55x106 C16 and 3.1x106 C20 cells) were collected and washed twice in 200 µL sterile-filtrated Wash buffer (PBS, pH 7.4, with 1% filtered FCS) and then resuspended in the 50 µL (C14) or 100 µL (C16, C20) sterile-filtrated Stain buffer (PBS, pH 7.4 containing 1% FSC, 0.1 g/L Herring sperm DNA). 4.4 µL (for C14) or 8.8 µL (for C16, C20) of dCODE reagent mastermix (2.0 μL of CD19-dCODE® Dextramer (Immudex, DS005), 2.0 μL of control-dCODE® Dextramer (Immudex, WI03233), and 0.4 μL 100 μM d-Biotin for C14. For C16 and C20 these volumes were doubled.) were added and incubated for 15 min in the dark at room temperature. Mastermixes comprising a unique DNA-barcoded hashtag antibody (0.5 µL per 1x106 PBMCs of TotalSeq-C anti-human hashtag antibodies 1–3 (BioLegend: for C14: 394661, for C16: 394663, for C20: 394665)), a CITEseq-antibody mix of DNA-barcoded CITE-Seq TotalSeq C antibodies (0.25 µg per 5x10^6 PBMCs of anti-human CD4 (BioLegend, 300567), 0.25 µg per 5x106 PBMCs of anti-human CD8 (BioLegend, 344753), 0.078 µg per 5x106 PBMCs of anti-human CD45RA (BioLegend, 304163), 0.078 µg per 5x10^6 PBMCs of anti-human CD62L (BioLegend, 304851), 0.3125 µg per 5x10^6 PBMCs of anti-human CD95 (BioLegend, 305651), 0.277 µg per 5x10^6 PBMCs of anti-human CCR7 (BioLegend, 353251) in Stain buffer (PBS, pH 7.4, with 1% FCS and 0.1 g/L Herring sperm DNA) and a mix surface markers and viability dye (anti-CD56-FITC (1:200, Invitrogen, 11-0566-42), anti-CD19-FITC (1:200, BioLegend, 302205), anti-CD4-BV711 (1:400, BD Horizon, 568371), anti-CD3-PE/Cy7 (1:200, Beckman Coulter, 737657), anti-CD8a-APC (1:400, BioLegend, 301014), anti-CD14-APC/Cy7 (1:200, BD Pharmingen, 557831) and ZombieAqua (1:500, BioLegend, 423102) in Stain buffer) was centrifuged (14,000 xg, 10 min, room temperature) and then added to the respective cells suspension. After 20 min incubation in the dark on ice, samples were washed 4 times with Wash buffer (300 xg, 5 min, 4°C) and then resuspended in 500 µL sterile-filtered FACS buffer (PBS, 0.5% BSA). Sort enrichment was performed for single, live, CD56-, CD19-, CD14-, CD3+ dCODE-Dextramer+ cells on a MoFlo Astrios EQ sorter (Beckman). In total, 5,670 C14 cells, 69,925 C16 cells and 11,560 C20 cells were sorted into pre-coated 1.5 mL tubes containing FACS-buffer. Immediately after sorting, cells were loaded onto a Chromium Next GEM Chip K (10X Genomics) and Chromium Next GEM Single-Cell 5′ kits v.2 to generate gene expression (GEX), T cell receptor (VDJ) and cell surface (CITEseq) libraries according to the manufacturer’s instructions (10X Genomics, 1000263, 1000256, 1000252, 1000286, 1000250, 1000215, 1000190). Libraries were sequenced at Novogene (Cambridge, UK) on an Illumina NovaSeq platform with PE150 strategy.
Library construction was performed according to manufacturer's instructions (10x Genomics) for 5' GEX, VDJ and CITEseq, V2 chemistry dual index

value: PBMC

value: T cells

value: CAR-T cell infusion (Kymriah, Novartis)


title: postInfusion_VDJ3

description:
Library name: postInfusion_VDJ3
10x Genomics

data_processing:
The sequencing sample was processed via the cellranger (version 6.0.2, 10x Genomics) `multi`-command using the gene expression reference GRCh38 (version 2020A, 10x Genomics) with added CAR-Gene-Sequence, the VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics), and custom feature barcodes (barcodes.csv).
Assembly: GRCh38 (version 2020A, 10x Genomics), vdj-GRCh38 (version 5.0.0, 10x Genomics), barcodes.csv
Supplementary files format and content: comma-separated value files and matrix files


title: Blastogenetic cycle-Male-MDR-D

description:
Library name: Blastogenetic cycle-Male-21
Male_MDR_D

source_name: Whole colony

value: Whole colony


title: mock infection human ES cell-derived aggregate 1

description:
Library name: hESC_1.csv.gz
10x Genomics


title: postInfusion_ADT3

description:
Library name: postInfusion_ADT3
10x Genomics


title: H358 cells, Clone#1, treatment-naïve, AMG510 treated, biological replicate 2

description: Library name: Cont_102_130_A2


title: H2AZac, NC 1, ChIP

description:
Library name: H2AZac_NC_1
paired-end


title: Blastogenetic cycle-Male-MDR-C2

description:
Library name: Blastogenetic cycle-Male-20
Male_MDR_C2


title: postInfusion_VDJ2

description:
Library name: postInfusion_VDJ2
10x Genomics


title: H358 cells, Clone#1, treatment-naïve, AMG510 treated, biological replicate 1

description: Library name: Cont_102_130_A1


title: SARS-CoV-2 infected human ES cell-derived aggregates, 2 dpi

description:
Library name: hESC_SARSCoV2_day2.csv.gz
10x Genomics


title: postInfusion_GEX3

description:
Library name: postInfusion_GEX3
10x Genomics


title: H358 cells, Clone#1, AMG-resistant, Vehicle treated, biological replicate 2

description: Library name: AMG_102_130_C2


title: postInfusion_GEX2

description:
Library name: postInfusion_GEX2
10x Genomics


title: H358 cells, Clone#1, treatment-naïve, vehicle treated, biological replicate 2

description: Library name: Cont_102_130_C2


title: preInfusion, VDJ, 2

description:
Library name: preInfusion_VDJ2
10x Genomics

data_processing:
The sequencing sample was processed via the cellranger (version 6.0.2, 10x Genomics) `multi`-command using the gene expression reference GRCh38 (version 2020A, 10x Genomics) with added CAR-Gene-Sequence and the VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics).
Assembly: GRCh38 (version 2020A, 10x Genomics), vdj-GRCh38 (version 5.0.0, 10x Genomics), barcodes.csv
Supplementary files format and content: comma-separated value files and matrix files

extract_protocol:
Leftover clinical anti-CD19 CAR T cells (Kymriah, Novartis) of three donors were rinsed from the infusion bag and tubes and peripheral blood mononuclear cell (PBMC) were isolated and then cryopreserved. Without rest, thawed CAR-T cells and Nalm6 cells were washed in medium (in RPMI 1640 + 10% FCS + 2 mM L-glutamine + 25 mM HEPES + 20 IU/mL IL-2). After manual counting, 2 mL CAR T cells of each donor (5x10^5 cells/mL) were either co-cultured with 0.5 mL Nalm6 (1x10^6 cells/mL) (=stimulated) or 0.5 mL of additional medium(=unstimulated), respectively, in 6-well plates at 37°C, 5% CO2 for 24 h. These stimulated and unstimulated pre-infusion CAR-T cells were subjected to flow-based cell sorting. After an initial washing step with PBS (300 xg for 6 min at 21°C), samples were incubated with ZombieAqua (1:100, BioLegend) for 10 min in the dark at room temperature. Samples were washed once with 1 mL PBA (PBS + 0.25% BSA + 0.02% NaN3) and human CD19 CAR Detection Reagent (1:50, Milentyi biotec, 130-129-550) were added, mixed and incubated for 10 min at room temperature in the dark. After washing twice with 2 mL PBA at room temperature, an antibody mastermix comprising anti-CD19-PE antibody (1:50, clone 4G7, BioLegend), anti-CD3-APC (1:33, UCHT1, BioLegend) and anti-Streptavidin-PE/TexasRed (1:200, ThermoFischer, SA1017) was added and incubated for 20 min at room temperature in the dark, followed by two final washing steps in sorting buffer (PBA + 1 mM EDTA). Single, live CD19- CD3+ lymphocytes (8333 cells per donor and condition) were sorted on a MoFlo XDP (Beckman Coulter) sorter. Immediately after sorting, cells were pooled into one 10X sample according to their stimulation condition and loaded to a Chromium Next GEM Chip K (10X Genomics) and Chromium Next GEM Single-Cell 5′ kits v.2 were used to generate GEX and VDJ libraries according to the manufacturer’s instructions (10X Genomics, 1000266, 1000196, 1000256, 1000252, 1000287, 3000431, 3000510). Libraries were sent to Novogene and sequenced on an Illumina NovaSeq platform with PE150 strategy.
Library construction was performed according to manufacturer's instructions (10x Genomics) for 5' GEX and VDJ, V2 chemistry dual index


title: preInfusion, VDJ, 1

description:
Library name: preInfusion_VDJ1
10x Genomics


title: H358 cells, Clone#1, treatment-naïve, vehicle treated, biological replicate 3

description: Library name: Cont_102_130_C3


title: postInfusion_ADT2

description:
Library name: postInfusion_ADT2
10x Genomics


title: Blastogenetic cycle-Male-MDR-A2

description:
Library name: Blastogenetic cycle-Male-16
Male_MDR_A2


title: preInfusion, GEX, 2

description:
Library name: preInfusion_GEX2
10x Genomics


title: postInfusion_GEX1

description:
Library name: postInfusion_GEX1
10x Genomics


title: preInfusion, GEX, 1

description:
Library name: preInfusion_GEX1
10x Genomics


title: Blastogenetic cycle-Male-MDR-B2

description:
Library name: Blastogenetic cycle-Male-18
Male_MDR_B2


title: H358 cells labeled by Lib3b +AMG510

description:
Library name: X4
10x Genomics

data_processing:
scRNA-seq and barcode data were processed using both 10x Genomics Cloud Analysis and Partek Flow (Partek Inc.). Barcode identification was performed by using 14-base reference sequences—“GACGTGCTAGTACG” for BC1 and “TCGATACAGCTGAC” for BC2—located immediately downstream of the barcode. The raw transcriptomic and barcode reads were aligned and normalized against the human reference genome (hg38) via 10x Cloud Analysis, generating single-cell count matrices.
Assembly: hg38
Supplementary files format and content: h5 files for gene expression (transcriptome) of single cells and *f.h5 file for feature barcode reads of single cells

growth_protocol: in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 1% penicillin-streptomycin.

extract_protocol:
Single-cell suspensions were prepared and assessed for viability (>90%) using trypan blue staining by TC20 Automated Cell Counter (BioRad, Inc). Viable cells were processed with a modified protocol of Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics , Inc). (incorporating Feature Barcoding technology for CRISPR)
Gel beads-in-emulsion (GEMs) were created to capture ~8,000 cells per channel. After GEM reverse transcription and cDNA amplification, a 0.6× size selection was used to collect larger cDNA fragments for gene expression library construction. In contrast, a 0.6–1.2× fraction containing shorter cDNAs was dedicated to generating gRNA barcode libraries. Targeted PCR amplification further enriched gRNA barcode transcripts with primers specific to gRNA sequences. To ensure sufficient coverage and minimize amplification bias, each cDNA sample underwent 3 parallel amplification reactions for both BC1 and BC2. Libraries were indexed using the Dual Index Kit TT Set A (10x Genomics, Inc) and sequenced on an Illumina NovaSeq X Plus system

treatment_protocol: Cells were treated with vehicle or AMG510 (2uM) for 2 weeks. During the treatment, medium was replenished every 3 days, and cells were sub-cultured at 80% confluence to maintain exponential growth.

value: Lung cancer epithelial cells

value: KRAS G12C Mutant; TP53 Null

value: AMG510 2uM for 2 weeks


title: PF50

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description:
Library name: Sample 11
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis, was used to identify distinct cell populations and visualize cell clusters in graphs. Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content. Hashtags were demultiplexed based on the Seurat package, https://satijalab.org/seurat/articles/hashing_vignette.html
Assembly: GrCh38A genome
Supplementary files format and content: H5 files for gene expression, CSV files for TCR outputs

source_name: PBMCs

extract_protocol:
PBMCs were acquired from whole blood samples using Ficoll. Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit (10x Genomics).
Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit +V(D)J Enrichment Kit, Human T Cell (10x Genomics).

value: PBMCs

tag: health status

value: healthy control

tag: chemistry


title: PF48

description:
Library name: Sample 9
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: H358 cells, Clone#1, treatment-naïve, vehicle treated, biological replicate 1

description: Library name: Cont_102_130_C1

value: Lung cancer Epithelial cell

value: KRAS G12C mutant; TP53 null


title: PF46

description:
Library name: Sample 7
Treatments hashed together, HTO5-ctr,HTO6-regn,HTO7-aIL13,HTO8-aIL4,HTO9-aIL13ra1,HTO10-aIL13ra2


title: PF47

description:
Library name: Sample 8
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: F. tularensis LVS treated with Dillapiole, replicate 8

description: Library name: LVS-Dillapiole-8

data_processing:
Raw reads were trimmed to remove adapter content and low-confidence base calls using Trimmomatic version 0.38
Trimmed reads were quantified using salmon version 0.12.0 and coding sequences for ASM924v1 obtained from NCBI GenBank
Differentially expressed genes were identified using DESeq2 version 1.24.0 with a Benjamini-Hochberg adjusted p-value threshold of 0.1
Assembly: ASM924v1
Supplementary files format and content: raw_counts.csv contains raw counts as reported by DESeq2 after import from salmon quantification using the tximport biodconductor library
Supplementary files format and content: noramlized_counts.csv contains gene counts normalized by library size, as implemented in DESeq2
Supplementary files format and content: fpkm.csv contains FPKM values for gene counts, as implemented by DESeq2

organism: Francisella tularensis

source_name: Whole bacteria

growth_protocol: F. tularensis LVS was provided by Dr. Karen Elkins (U.S. Food and Drug Administration). Frozen stock cultures were streaked onto chocolate II agar plates and incubated at 37°C, 5% CO2 for three days. Bacteria from agar plates were used to inoculate sterile filtered TSBc broth [Tryptic Soy Broth (Difco) supplemented with 0.1% L-Cysteine hydrochloride (Fisher)]; these bacteria were then grown at 37°C with shaking for 14-18 hours.

extract_protocol:
Broth cultures of F. tularensis LVS treated with vehicle, dillapiole (8 mg/ml), or no treatment were grown to stationary phase and normalized to the lowest OD600 and pelleted. After removing the supernatant, the pellets were resuspended in Trizol and incubated at room temperature for 5 minutes. Chloroform was then added and vigorously mixed for 15 seconds until the sample turned milky pink. The mixture was then transferred to an organic matrix tube and centrifuged at max speed for 15 minutes. After centrifugation, the aqueous phase was transferred to a new tube and 70% ethanol was added at a 1:1 ratio. The resulting mixture was then transferred to a spin column (Invitrogen PureLinkTM RNA Mini Kit) and spun at max speed for 15 seconds. After the flow through was discarded, PureLink Dnase (Invitrogen) was added directly to the column and incubated for 15 minutes are room temperature. Following Dnase treatment, Wash Buffer 1 was added to the columns and centrifuged for 15 seconds. The columns were then washed with Wash Buffer 2 twice; for each wash, the columns were centrifuged for 15 seconds followed by a final 2 minute spin to ensure the column was dry. Spin columns were transferred to recovery tubes and Rnase free water was added to elute RNA. The columns incubated at room temperature for 2 minutes before centrifuging for 1 minute. The RNA concentrations were determined using a NanoDrop spectrophotometer and then stored at -80°C
For RNA-Seq analysis of Francisella cells (hexane vs dillapiole treated), total RNA was extracted from eight replicate samples in each experimental group. RNA Integrity Number (RIN) values as determined by Bioanalyzer electrophoresis were all above 9. RNA samples (2 mg) were dissolved in 15 ml TE buffer (10mM Tris HCL pH 8.0, 1mM EDTA). 16S and 23S ribosomal RNA (rRNA) were removed using the MICROBExpress Bacterial mRNA Enrichment kit (Life Technologies). rRNA-depleted RNA samples were then resuspended in Rnase-free water and quantitated by fluorescence-based Qubit RNA HS Assay kit (ThermoFisher Scientific) and fragmented for 4 minutes at 94ºC to be used as input for RNA library preparation. Illumina-compatible RNA libraries were prepared using KAPA RNA HyperPrep Kit (KAPA Biosystems, Inc). Library quality and insert size were assessed by electrophoresis on Agilent DNA High Sensitivity DNA chips; average library size was ~ 370 bp. Libraries were quantitated using fluorescence-based Qubit dsDNA HS Assay (ThermoFisher Scientific). Purified libraries were clustered and sequenced on an Illumina HiSeq1500 in a 2 x50 paired end Rapid Run at the Marshall University Genomics Core Facility.

value: Whole bacteria

value: Dillapiole


title: H358 cells labeled by Lib3 + Vehicle (DMSO)

description:
Library name: X2
10x Genomics

value: Vehicle for 2 weeks


title: H358 cells labeled by Lib3b +Vehicle(DMSO)

description:
Library name: X3
10x Genomics


title: Blastogenetic cycle-Male-MDR-C1

description:
Library name: Blastogenetic cycle-Male-19
Male_MDR_C1

value: All cells


title: Blastogenetic cycle-Male-MADM-D

description:
Library name: Blastogenetic cycle-Male-14
Male_MADM_D


title: PF49

description:
Library name: Sample 10
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: Blastogenetic cycle-Male-MADM-C2

description:
Library name: Blastogenetic cycle-Male-13
Male_MADM_C2


title: SZ33

description:
Library name: Sample 6
Treatments hashed together, HTO5-ctr,HTO6-regn,HTO7-aIL13,HTO8-aIL4,HTO9-aIL13ra1,HTO10-aIL13ra2

value: Sezary Syndrome


title: Blastogenetic cycle-Male-MADM-C1

description:
Library name: Blastogenetic cycle-Male-12
Male_MADM_C1


title: F. tularensis LVS treated with Dillapiole, replicate 7

description: Library name: LVS-Dillapiole-7


title: Blastogenetic cycle-Male-MDR-B1

description:
Library name: Blastogenetic cycle-Male-17
Male_MDR_B1


title: SZ32

description:
Library name: Sample 5
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: Blastogenetic cycle-Male-MDR-A1

description:
Library name: Blastogenetic cycle-Male-15
Male_MDR_A1


title: KPdSPHK1#5

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

data_processing:
Reads in fastq format were aligned to the mouse reference genome version GRCh38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Reads per gene were counted by STAR.
Assembly: Reads in fastq format were aligned to the mouse reference genome version GRCh38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Reads per gene were counted by STAR.
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was harvested using Rneasy Mini kit (QIAGEN)
Sequencing libraries were be prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs).

value: lung


title: F. tularensis LVS treated with Dillapiole, replicate 6

description: Library name: LVS-Dillapiole-6


title: SZ39

description:
Library name: Sample 4
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: KPdSPHK1#4


title: Blastogenetic cycle-Male-MADM-B1

description:
Library name: Blastogenetic cycle-Male-10
Male_MADM_B1


title: F. tularensis LVS treated with Dillapiole, replicate 5

description: Library name: LVS-Dillapiole-5


title: Blastogenetic cycle-Male-MADM-B2

description:
Library name: Blastogenetic cycle-Male-11
Male_MADM_B2


title: SZ38

description:
Library name: Sample 3
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: F. tularensis LVS treated with Dillapiole, replicate 4

description: Library name: LVS-Dillapiole-4


title: KPdSPHK1#3


title: Blastogenetic cycle-Male-MADM-A2

description:
Library name: Blastogenetic cycle-Male-9
Male_MADM_A2


title: SZ5

description:
Library name: Sample 2
Treatments hashed together, HTO1-ctr,HTO2-regn,HTO3-aIL13,HTO4-aIL4,HTO5-aIL13ra1,HTO6-aIL13ra2


title: postInfusion_VDJ1

description:
Library name: postInfusion_VDJ1
10x Genomics

value: PBMC


title: KPdSPHK1#1


title: Blastogenetic cycle-Male-M001-D

description:
Library name: Blastogenetic cycle-Male-7
Male_M001_D


title: KPdSPHK1#2


title: F. tularensis LVS treated with Dillapiole, replicate 2

description: Library name: LVS-Dillapiole-2


title: F. tularensis LVS treated with Dillapiole, replicate 3

description: Library name: LVS-Dillapiole-3


title: Blastogenetic cycle-Male-MADM-A1

description:
Library name: Blastogenetic cycle-Male-8
Male_MADM_A1


title: Donor 2, IL-10 ChCR transduced, unstimulated

city: Zurich

first: Sabrina

last: Traxel

address: Raemistrasse 100

department: Department of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital Zurich

data_processing:
Reads were trimmed with fastp v0.23.4. Non-default trimming options were --trim_poly_x --trim_front1 1 --trim_poly_x --poly_x_min_len 10 --length_required 18
Alignment with STAR v2.7.10b with the options --sjdbOverhang 150 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 100000 --alignMatesGapMax 100000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 3 ConcordantPair
Expression quantification using the R and the method Rsubread::featureCounts
Assembly: GRCh38.p13 with using Ensembl gene annotation Release_102 downlaode on 2024-03-14
Supplementary files format and content: Txt files holding gene expression counts

source_name: Primary human macrophages

growth_protocol: Monocytes were differentiated to macrophages for 7 days in RPMI supplemented with 10% human AB serum and Penicillin-Streptmycin

extract_protocol:
RNA extraction using Qiagen RNeasy Mini with oncolumn DNase digestion
Illumina Stranded mRNA Prep, Ligation; https://emea.illumina.com/products/by-type/sequencing-kits/library-prep-kits/stranded-mrna-prep.html

tag: donor id

value: Donor 2

tag: construct

value: IL-10 ChCR

tag: stimulation

value: unstimulated

value: Primary human macrophages


title: KP#5


title: Blastogenetic cycle-Male-M001-C2

description:
Library name: Blastogenetic cycle-Male-6
Male_M001_C2

value: Whole colony


title: F. tularensis LVS treated with Dillapiole, replicate 1

description: Library name: LVS-Dillapiole-1


title: H358 cells labeled by Lib3 + AMG510

description:
Library name: X1
10x Genomics

value: Lung cancer epithelial cells

value: KRAS G12C Mutant; TP53 Null

value: AMG510 2uM for 2 weeks


title: Blastogenetic cycle-Male-M001-C1

description:
Library name: Blastogenetic cycle-Male-5
Male_M001_C1


title: F. tularensis LVS treated with vehicle control, replicate 7

description: Library name: LVS-Hexane-7

value: Hexane (vehicle control)


title: KP#4


title: Blastogenetic cycle-Male-M001-B2

description:
Library name: Blastogenetic cycle-Male-4
Male_M001_B2


title: Donor 1, mock transduced, 100ng/ml IL-10

value: Donor 1

value: mock


title: Donor 1, mock transduced, 10ng/ml IFNγ

value: 10ng/ml IFNγ


title: F. tularensis LVS treated with vehicle control, replicate 8

description: Library name: LVS-Hexane-8

value: Whole bacteria


title: F. tularensis LVS treated with vehicle control, replicate 6

description: Library name: LVS-Hexane-6


title: KP#2


title: Donor 1, mock transduced, unstimulated


title: Blastogenetic cycle-Male-M001-B1

description:
Library name: Blastogenetic cycle-Male-3
Male_M001_B1

value: All cells


title: SZ30

description:
Library name: Sample 1
Treatments hashed together, HTO6-ctr,HTO7-regn,HTO8-aIL13,HTO9-aIL4,HTO10-aIL13ra1

value: PBMCs

value: Sezary Syndrome


title: F. tularensis LVS treated with vehicle control, replicate 5

description: Library name: LVS-Hexane-5


title: KP#1

value: lung


title: Donor 3, TGFb ChCR transduced, 100ng/ml TGFβ

value: Donor 3

value: TGFb ChCR

value: 100ng/ml TGFβ


title: CD45+, OX40 agonist treated, scRNAseq

city: Tel Aviv

first: Tomer

last: Weiss

state: Tel-Aviv-Jaffa

address: Klachkin 9

country: Israel

institute: Tel Aviv University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Melanoma

extract_protocol:
Tumors were mechanically and enzymatically digested using mouse Tumor Dissociation Kit, from Miltenyi Biotech (cat 130-096-730). Tumor-infiltrating leukocytes were isolated from tumor cells using Ficoll (Ficoll premium 1.084, from Cytiva, cat 17544602). Cells were washed and resuspended in 100 μL FACS buffer (PBS with 2 mM EDTA, 25 mM Hepes, and 1% Bovine Serum Albumin), and stained with antibody against CD45 conjugated with APC-Cy7 (clone 30F11, from Biolegend, cat 103116) for 30 min on ice in the dark. DAPI viability dye (from Sigma-Aldrich, cat D9542) was added before the read and to enable dead cells exclusion. All data were collected on a BD Aria Sorted (BD Biosciences) and analyzed with FlowJo software (Tree Star). Live leukocytes, defined as DAPI- CD45+ cells were sorted into sorting medium (PBS with 0.5% Bovine Serum Albumin).
Sorted cells were then centrifuged at 300 G for 5 min, resuspended into a sorting medium at a concentration of 1000 cells/ μL. Cells were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 30 Reagent Kits v3 according to manufacturer’s protocol (10× Genomics). The generated single-cell RNA-seq libraries were sequenced using NextSeq 500/550 High Output Kit v2.5 (75 Cycles)

treatment_protocol: B16-F10 Mouse Melanoma cells were incubated at 37°C with 5% CO2 and preserved within Dulbecco’s Modified Eagle Medium (DMEM) (Biological Industry, Israel) with 10% fetal bovine serum (FBS) (Gibco, USA), 1% penicillin/streptomycin (Biological Industry, Israel) and 1% L-glutamine (Biological Industry, Israel). Tumor cells were detached using 0.25% Trypsin-0.05% EDTA (Biological Industries) and washed with PBS before injection.2×105 cells were resuspended in saline (100 uL) and subcutaneously implanted in the right flank of  ten-week immunocompetent female C57BL/6 wild-type mice.

value: Melanoma

value: B16-F10 tumor

value: Leukocytes

tag: Sex

value: Female

value: OX40 agonist


title: CD45+, control, scRNAseq

description: 10x Genomics

value: control


title: Ampullae-SMH-replicate-3

description:
Library name: Ampullae-16
Ampullae_SMH_Rep3

source_name: Ampullae tissue

value: Ampullae tissue

value: Vasculature cells


title: Donor 1, mock transduced, 100ng/ml TGFβ

value: Donor 1

value: mock

value: Primary human macrophages


title: F. tularensis LVS treated with vehicle control, replicate 3

description: Library name: LVS-Hexane-3

value: Whole bacteria

value: Hexane (vehicle control)


title: F. tularensis LVS treated with vehicle control, replicate 4

description: Library name: LVS-Hexane-4


title: Donor 3, TGFb ChCR transduced, 10ng/ml IFNγ

value: 10ng/ml IFNγ


title: Blastogenetic cycle-Male-M001-A1

description:
Library name: Blastogenetic cycle-Male-1
Male_M001_A1

value: Whole colony

value: All cells


title: OE_LGALS1_2

city: changchun

first: Zanhui

last: Jia

address: The Second Hospital of Jilin University, 2nd Building, 218 Pingzhi Street, Changchun

institute: Second Hospital of Jilin University

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13).; http://hannonlab.cshl.edu/fastx toolkit/).
The short reads less than 16nt were also dropped. After that, clean reads were aligned to the GRch38 genome by tophat2 (Kim, Pertea et al. 2013) allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) (Trapnell, Williams et al. 2010).
The R Bioconductor package edgeR (Robinson, McCarthy et al. 2010) was utilized to screen out the differentially expressed genes (DEGs). A false discovery rate <0.05 and fold change>2 or < 0.5were set as the cut-off criteria for identifying DEGs.
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include reads counts, FPKM values for each Sample

source_name: Hela cells

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted with TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and   fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products   corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's  instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

value: Hela cells

value: LGALS1 overexpressed  in Hela cell


title: Ampullae-SMH-replicate-2

description:
Library name: Ampullae-15
Ampullae_SMH_Rep2


title: Donor 3, IL-10 ChCR transduced, 100ng/ml IL-10

value: Donor 3

value: IL-10 ChCR


title: Donor 3, TGFb ChCR transduced, unstimulated

value: TGFb ChCR

value: unstimulated


title: F. tularensis LVS treated with vehicle control, replicate 2

description: Library name: LVS-Hexane-2


title: OE_LGALS1_1


title: F. tularensis LVS treated with vehicle control, replicate 1

description: Library name: LVS-Hexane-1


title: Ampullae-SMH-replicate-1

description:
Library name: Ampullae-14
Ampullae_SMH_Rep1


title: NC_2

value: Hela  cell (control plasmid)


title: Donor 3, IL-10 ChCR transduced, 10ng/ml IFNγ


title: 13M 5xFAD

city: Laramie

first: Yun

state: WY

address: 1000 E University Ave

department: Zoology and Physiology

institute: University of Wyoming

description:
Library name: 5xFAD
10x Genomics

data_processing:
After sequencing, clean reads were analysed with mouse reference genome mm10 with the addition transgenes (Cre and GCaMP6f) using Cell Ranger 6.0.1. Introns were included in the analysis. https://www.10xgenomics.com/support/software/cell-ranger/latest
Assembly: Mouse mm 10
Supplementary files format and content: Matrix files,Tab-separated values files

molecule: nuclear RNA

source_name: medial prefrontal cortex

extract_protocol:
To collect the fresh tissues for snRNA-seq, mice were euthanized in CO2 chamber and mice brains were immediately dissected out. Using a vibratome, mice brains were freshly sliced into 200-400 µm thickness and the mPFC region was dissected out utilizing fine forceps under microscope. Four to six mPFC tissues (40-60 mg) were combined and immediately snap-frozen in liquid nitrogen and shipped to SingulOmics with dry ice for snRNA-sequencing.
Nuclei were isolated and 3' single cell gene expression libraries(Next GEM v3.1) were constructed using 10x Chromium system. The libraries were sequenced with 200 million PE 150 reads per sample in Illumina NovaSeq.

value: medial prefrontal cortex

value: Neurons and Glia

tag: strain

tag: age

value: 12-13 month old

tag: developmental stage

value: Adult

tag: collection date


title: NC_1


title: Ampullae-SMGO-replicate-3

description:
Library name: Ampullae-13
Ampullae_SMGO_Rep3

tag: tissue

value: Ampullae tissue

value: Vasculature cells


title: Blastogenetic cycle-Male-M001-A2

description:
Library name: Blastogenetic cycle-Male-2
Male_M001_A2

tag: cell line


title: Ampullae-SMGO-replicate-2

description:
Library name: Ampullae-12
Ampullae_SMGO_Rep2

tag: cell type


title: 13M WT

description:
Library name: WT2
10x Genomics


title: KP#3

value: lung


title: Donor 3, mock transduced, 100ng/ml TGFβ

value: mock

value: 100ng/ml TGFβ

value: Primary human macrophages


title: DMSO-6h rep3

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: DMSO-6h-3_S52_R1_001.fastq.gz

data_processing:
Sequencing reads were de-multiplexed using bcl2fastq (v2.17.1.14)
Low quality reads (Q < 30) removed and trimmed using cutadapt (v1.14).
Reads were mapped to the human (hg19) reference genomes using HISAT2 (v2.0.4)
Reads were counted using featureCounts (-O) from subread (v 2.0.0).
Counts were filtered using filterByExpr from edgeR (v 3.38.1) with default parameters, quantile normalised using voom and differential gene expression performed using Limma (v 3.52.1).
Assembly: hg19
Supplementary files format and content: raw counts

extract_protocol:
RNA was extracted with the Direct-zol RNA Microprep kit (Zymo Research) according to manufacturer’s instructions.
QuantSeq 3’mRNA-seq Library Prep Kit for Illumina

value: DMSO

tag: time


title: Ampullae-SMGO-replicate-2-technical

description:
Library name: Ampullae-11
Ampullae_SMGO_Technical_Rep2


title: 6M TDP KO

description:
Library name: KO
10x Genomics

value: Tdp43 F/F


title: Donor 3, mock transduced, 100ng/ml IL-10

value: Donor 3


title: DMSO-6h rep1

description: Library name: DMSO-6h-1_S50_R1_001.fastq.gz

tag: treatment


title: Ampullae-SMGO-replicate-1-technical

description:
Library name: Ampullae-10
Ampullae_SMGO_Technical_Rep1


title: Donor 3, mock transduced, 10ng/ml IFNγ

value: 10ng/ml IFNγ


title: 2M TDP KO-2

description:
Library name: KO2
10x Genomics

value: 5-6month old


title: Ampullae-SB825-FDA-replicate-3

description:
Library name: Ampullae-9
Ampullae_SB825FDA_Rep3


title: Donor 3, mock transduced, unstimulated

value: unstimulated


title: 2M TDP KO-1

description:
Library name: KO1
10x Genomics


title: Ampullae-SB825-FDA-replicate-2

description:
Library name: Ampullae-8
Ampullae_SB825FDA_Rep2


title: Donor 1, TGFb ChCR transduced, 100ng/ml TGFβ

value: Donor 1

value: TGFb ChCR


title: VPR8-6h rep2

description: Library name: VPR8-6h-2_S48_R1_001.fastq.gz


title: Ampullae-SB825-FDA-replicate-1

description:
Library name: Ampullae-7
Ampullae_SB825FDA_Rep1


title: VPR8-6h rep1

description: Library name: VPR8-6h-1_S47_R1_001.fastq.gz


title: Donor 1, TGFb ChCR transduced, 10ng/ml IFNγ


title: Donor 3, IL-10 ChCR transduced, unstimulated

value: IL-10 ChCR


title: 2M TDP Ctrl

description:
Library name: WT1
10x Genomics

value: medial prefrontal cortex

value: Neurons and Glia


title: VPR8-24h rep3

description: Library name: VPR8-24h-3_S31_R1_001.fastq.gz


title: Ampullae-SB825-FEA-replicate-3

description:
Library name: Ampullae-6
Ampullae_SB825FEA_Rep3

value: Ampullae tissue


title: Donor 1, TGFb ChCR transduced, unstimulated


title: Donor 1, IL-10 ChCR transduced, 100ng/ml IL-10


title: KC-Tie2 3

city: Nashville

first: Matthew

last: Alexander

state: TN

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

description:
Library name: Sample 6
Library name: 9239-ZC-0012

data_processing:
Partek Flow v 12.5.0
Read alignment was performed using a STAR based aligner
After filtering gene counts <30 and normalization, differential gene expression was determined using DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited file of p values, fold change, FDR, and group means for individual genes

source_name: kidney

extract_protocol:
RNA extraction was performed with Trizol reagent followed by RNEasy MinElute Cleanup kit (Qiagen) per manufacturer’s instructions
cDNA library preparation was performed using a polyA-selected library preparation kit (New England Biolabs)

value: kidney

tag: genotype


title: Ampullae-SB825-FEA-replicate-2

description:
Library name: Ampullae-5
Ampullae_SB825FEA_Rep2

data_processing:
Adaptors and low-quality sequences were removed with TrimGalore software (https://github.com/FelixKrueger/TrimGalore). Mapping to FF, FcoR and ITAM/ITIM genes was performed with Kallisto and RSEM methods.
To quantify the expression of fester and FcoR genes, raw reads from B. schlosseri transcriptomes were mapped to the full-length of the fester and FcoR genes using Kallisto and RSEM. Expression levels were quantified using the Trimmed Mean of M-values (TMM).
Assembly: Transcriptomes were assembled using Trinity software with default parameters.
Supplementary files format and content: all.isoform.TMM.EXPR_FF_FcoR_Kallisto.txt
Supplementary files format and content: all.isoform.TMM.EXPR_FF_FcoR_RSEM.txt
Supplementary files format and content: all.isoform.TMM.EXPR_NK_genes_Ampullae_Kallisto.txt

value: Vasculature cells


title: Ampullae-SB825-FEA-replicate-1

description:
Library name: Ampullae-4
Ampullae_SB825FEA_Rep1


title: DMSO-6h rep2

description: Library name: DMSO-6h-2_S51_R1_001.fastq.gz


title: VPR8-24h rep2

description: Library name: VPR8-24h-2_S30_R1_001.fastq.gz


title: 6M TDP Ctrl

description:
Library name: Control
10x Genomics

value: 12-13 month old

value: Adult


title: Donor 1, IL-10 ChCR transduced, 10ng/ml IFNγ

value: Primary human macrophages


title: VPR8-24h rep1

description: Library name: VPR8-24h-1_S29_R1_001.fastq.gz


title: Donor 1, IL-10 ChCR transduced, unstimulated


title: VPR8-6h rep3

description: Library name: VPR8-6h-3_S49_R1_001.fastq.gz


title: Ampullae-SB825-FX-replicate-3

description:
Library name: Ampullae-3
Ampullae_SB825FX_Rep3


title: DMSO-24h rep3

description: Library name: DMSO-24h-3_S34_R1_001.fastq.gz

value: DMSO


title: DMSO-24h rep2

description: Library name: DMSO-24h-2_S33_R1_001.fastq.gz


title: Donor 2, mock transduced, 100ng/ml TGFβ

value: Donor 2

value: mock

value: 100ng/ml TGFβ


title: Control 3

description:
Library name: Sample 3
Library name: 9239-ZC-0009

value: Control


title: Control 2

description:
Library name: Sample 2
Library name: 9239-ZC-0008


title: Ampullae-SB825-FX-replicate-1

description:
Library name: Ampullae-1
Ampullae_SB825FX_Rep1


title: Ampullae-SB825-FX-replicate-2

description:
Library name: Ampullae-2
Ampullae_SB825FX_Rep2


title: 2M C57 Ctrl

description:
Library name: TDP
10x Genomics

value: 5-6month old


title: DMSO-24h rep1

description: Library name: DMSO-24h-1_S32_R1_001.fastq.gz


title: Donor 2, mock transduced, 100ng/ml IL-10


title: ALDH-Individual-7-plus

description:
Library name: ALDH cells-8
ALDH_Loser_7_plus

source_name: whole-colony-ALDH-cells

value: whole-colony-ALDH-cells

value: ALDH positive cells


title: Control 1

description:
Library name: Sample 1
Library name: 9239-ZC-0007


title: Donor 2, mock transduced, 10ng/ml IFNγ

value: 10ng/ml IFNγ


title: ALDH-Individual-7-minus

description:
Library name: ALDH cells-7
ALDH_Loser_7_minus

value: ALDH negative cells


title: scRNAseq_SPAS1neg_PD1neg_IFNgneg_CD8_TRAMPC2_D30_Tumor_TCR

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

description:
Library name: Sample 12
10x Genomics TCR

library_source: other

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: scTCR: filtered_contig_annotations.csv

molecule: other

source_name: Tumor

extract_protocol:
CD8 T cells were sorted from the lung or the tumor.
We used Chromium Single Cell V(D)J Reagent Kits (v1.1 Chemistry)(10x Genomics) to generate scRNA-Seq libraries according to the manufacturer’s protocol.

value: Tumor

value: ex vivo

value: GREAT

tag: batch


title: B2B3-6h rep3

description: Library name: B2B3-6h-3_S46_R1_001.fastq.gz


title: Donor 2, mock transduced, unstimulated

value: unstimulated


title: scRNAseq_SPAS1neg_PD1neg_IFNgneg_CD8_TRAMPC2_D30_Tumor_HTO

description:
Library name: Sample 11
10x Genomics HTO

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: scTCR: filtered_contig_annotations.csv
Library strategy: CITE-seq


title: KC-Tie2 2

description:
Library name: Sample 5
Library name: 9239-ZC-0011

value: kidney


title: B2B3-6h rep1

description: Library name: B2B3-6h-1_S44_R1_001.fastq.gz


title: scRNAseq_SPAS1neg_PD1pos_IFNgpos_CD8_TRAMPC2_D30_Tumor_TCR

description:
Library name: Sample 9
10x Genomics TCR


title: Donor 2, TGFb ChCR transduced, 100ng/ml TGFβ

value: TGFb ChCR


title: scRNAseq_SPAS1neg_PD1neg_IFNgneg_CD8_TRAMPC2_D30_Tumor_GEX

description:
Library name: Sample 10
10x Genomics GEX


title: B2B3-24h rep2

description: Library name: B2B3-24h-2_S27_R1_001.fastq.gz


title: KC-Tie2 1

description:
Library name: Sample 4
Library name: 9239-ZC-0010


title: ALDH-Individual-2B-minus

description:
Library name: ALDH cells-3
ALDH_Winner_2B_minus

extract_protocol:
Total RNA was isolated for whole colonies, blood cells, vasculature, and Integrin alpha-6-, BSA-, or ALDH-positive cells -sorted by FACS with the Monarch® Total RNA Miniprep Kit (NEB) or NucleoSpin RNA, Mini kit for RNA purification (MACHEREY-NAGEL) following the manufacturer’s protocols.
RNA samples were sequenced (poly-A library prep, 150 bp insert size, paired-end, 20 million reads per sample) at the UC Davis Genome Center or the Novogene company.


title: ALDH-Individual-1-plus

description:
Library name: ALDH cells-2
ALDH_Loser_1_plus


title: B2B3-24h rep1

description: Library name: B2B3-24h-1_S26_R1_001.fastq.gz


title: scRNAseq_SPAS1neg_PD1pos_IFNgpos_CD8_TRAMPC2_D30_Tumor_GEX

description:
Library name: Sample 7
10x Genomics GEX


title: Donor 2, IL-10 ChCR transduced, 10ng/ml IFNγ

value: IL-10 ChCR

value: Primary human macrophages


title: Donor 2, IL-10 ChCR transduced, 100ng/ml IL-10

value: Donor 2


title: 12h amp treated rep3

city: Brookings

first: Xuan

last: Butzin

state: SD

address: 1451 Stadium Rd

department: Biology and Microbiology

institute: South Dakota State University

data_processing:
bowtie2 (version 2.5.2) was used to align pair-end sequencing reads (fastq files) to NC_000913.3, CP025268.1:815706-816329 (tetR cds) and the plasmid p24KmNB82
samtools (version 1.19) was used to convert the sam file to bam, to sort by cooordinates and to create index for the sorted bam file
featureCounts (version 2.0.6) was used to count the number of reads mapped to cds
Assembly: NC_000913.3
Supplementary files format and content: Table with raw read counts for every gene and sample; comma separated values

organism: Escherichia coli

growth_protocol: Cultures were grown in modified MMB+ media, which consists of the following: K2HPO4 (10.5 mg/ml), KH2PO4 (4.5 mg/ml), (NH4)2SO4 (2.0 mg/ml), C6H5Na3O7 (0.5 mg/ml), NaCl (1.0 mg/ml), 2 mM MgSO4 x 7H2O, 100 µM CaCl2, thiamine (10 µg/ml), 0.5% glycerol, amino acids (40 µg/ml) and kanamycin (25 µg/ml)

extract_protocol:
Samples were treated with Tween (0.2%) and chloramphenicol (5 µg/ml) then immediately filtered out of solution and resuspended in lysis buffer containing 25 mM Tris pH 8.0, 25 mM NH4Cl, 10 mM MgOAc, 0.8 % Triton X-100, 0.1 U/µL RNase-free DNase I, 1 U/μL. Then immediately frozen in liquid nitrogen and stored at -80 C.  Frozen pellets were thawed on ice and centrifuged for 20 minutes at 16,000 x g at 4 °C with 0.3% Sodium Deoxychorate to pellet particulate matter. The supernatant was then removed and RNA was column purified (Qiagen miRNeasy cat. No. 217004) before removing rRNA (Invitrogen RiboMinus cat no. K155004) Superase-In, ~60 U/µl ReadyLyse Lysozyme, 1.55 mM Chloramphenicol, and 17 μΜ 5′-guanylyl imidodiphosphate (GMPPNP).
cDNA libraries were prepared and multiplexed according to manufacturer's protocols: NEBNext Ultra II cat no. E7103S. Libraries were then pooled and sequenced by Illumina HiSeq paired-end sequencing.

treatment_protocol: Cultures were grown to mid log phase (OD ~0.5) in MMB+ media and treated with lethal concentrations of ampicillin (0.1 mg/ml). Samples were collected after 3 hours, 6 hours, and 24 hours. 0h treatment was the mid log phase culture right before the ampicillin treatment.

tag: plasmid

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA12

value: ampcillin 24h


title: VDJ seq - lane C

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

description: TCR-C

data_processing:
Single cell reads for RNA and CITE-seq antibodies are mapped to the human transcriptome and counted using cellranger (version 6.1.2)
TCR-seq reads are mapped and assembled using cellranger
Assembly: hg38
Supplementary files format and content: h5 files forGEX/CITE assays
Supplementary files format and content: csv of mapped and assembled VDJ reads for TCR assay

source_name: breast/blood

growth_protocol: ex vivo

extract_protocol:
CD3 positive cells were sorted from fresh breast tissue sections
Sample preparation followed by 10x Genomics scRNA-seq v3 chemistry protocol. Samples were processed as described on the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

value: breast/blood

value: CD3 pos cells

value: WT


title: ALDH-Individual-6-minus

description:
Library name: ALDH cells-5
ALDH_Winner_6_minus

value: whole-colony-ALDH-cells


title: Donor 2, TGFb ChCR transduced, 10ng/ml IFNγ

value: 10ng/ml IFNγ


title: B2B3-24h rep3

description: Library name: B2B3-24h-3_S28_R1_001.fastq.gz


title: IA6-Individual-81C-positive-replicate-2

description:
Library name: Integrin alpha-6 (IA6) cells-12
IA6_81C_plus_rep2

value: IA6 positive cells


title: scRNAseq_SPAS1neg_PD1pos_IFNgpos_CD8_TRAMPC2_D30_Tumor_HTO

description:
Library name: Sample 8
10x Genomics HTO

value: Tumor


title: ALDH-Individual-2B-plus

description:
Library name: ALDH cells-4
ALDH_Winner_2B_plus

value: ALDH positive cells


title: VDJ seq - lane B

description: TCR-B


title: scRNAseq_SPAS1pos_CD8_TRAMPC2_D30_Tumor_TCR

description:
Library name: Sample 6
10x Genomics TCR

value: ex vivo

value: SPAS1 Tetramer+ CD8

value: GREAT


title: B2B3-6h rep2

description: Library name: B2B3-6h-2_S45_R1_001.fastq.gz


title: VDJ seq - lane A

description: TCR-A


title: scRNAseq_SPAS1pos_CD8_TRAMPC2_D30_Tumor_GEX

description:
Library name: Sample 4
10x Genomics GEX


title: 6h amp treated rep3

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA9

value: ampcillin 6h


title: 12h amp treated rep1

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA10


title: ALDH-Individual-6-plus

description:
Library name: ALDH cells-6
ALDH_Winner_6_plus


title: scRNAseq_SPAS1pos_CD8_TRAMPC2_D30_LN_TCR

description:
Library name: Sample 3
10x Genomics TCR

source_name: Lymph Node

value: Lymph Node


title: 12h amp treated rep2

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA11


title: IA6-Individual-81C-negative-replicate-2

description:
Library name: Integrin alpha-6 (IA6) cells-10
IA6_81C_minu_rep2

value: IA6 negative cells


title: ALDH-Individual-1-minus

description:
Library name: ALDH cells-1
ALDH_Loser_1_minus

value: ALDH negative cells


title: Donor 2, TGFb ChCR transduced, unstimulated

value: Donor 2

value: TGFb ChCR

value: unstimulated

value: Primary human macrophages


title: scRNAseq_SPAS1pos_CD8_TRAMPC2_D30_LN_HTO

description:
Library name: Sample 2
10x Genomics HTO


title: scRNAseq_SPAS1pos_CD8_TRAMPC2_D30_Tumor_HTO

description:
Library name: Sample 5
10x Genomics HTO


title: CITE seq - lane C

description: CITE-C

molecule: protein

value: breast/blood

value: CD3 pos cells

value: WT


title: 6h amp treated rep1

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA7


title: scRNAseq_SPAS1pos_CD8_TRAMPC2_D30_LN_GEX

description:
Library name: Sample 1
10x Genomics GEX

value: ex vivo

value: SPAS1 Tetramer+ CD8


title: IA6-Individual-81C-positive-replicate-1

description:
Library name: Integrin alpha-6 (IA6) cells-11
IA6_81C_plus_rep1

value: IA6 positive cells


title: IA6-Individual-81A-positive-replicate-1

description:
Library name: Integrin alpha-6 (IA6) cells-7
IA6_81A_plus_rep1


title: IA6-Individual-81A-positive-replicate-2

description:
Library name: Integrin alpha-6 (IA6) cells-8
IA6_81A_plus_rep2


title: IA6-Individual-81C-negative-replicate-1

description:
Library name: Integrin alpha-6 (IA6) cells-9
IA6_81C_minu_rep1


title: CITE seq - lane B

description: CITE-B


title: RNA seq - lane C

description: GEX-C


title: 6h amp treated rep2

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA8

value: ampcillin 6h


title: Doxo

city: St. Louis

first: Ganesh

middle: Kumar

last: Raut

address: Euclid Ave

institute: Washington University School of Medicine

description:
Library name: Sample 2
10X Genomics

data_processing:
The Cell Ranger Software Suite from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. The Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10). For data analysis, the filtered feature barcode matrices were loaded into Partek Flow.
Assembly: GRCm38 (mm10)
Supplementary files format and content: *filtered_feature_bc_matrix.txt
Supplementary files format and content: Processed data GSA.xlsx

source_name: Bone

extract_protocol:
Bones (femurs and tibias) were harvested from euthanized mice and placed in cold DMEM/F12. Muscle and connective tissues were removed. Bones were gently ground and then cut into small fragments. Fragments were transferred and digested with fresh 2 mg/ml collagenase in DMEM/F12 on a rotating water bath at 37°C for 30 min. Following the first digestion, the released cell suspension was filtered through a 70-μm nylon mesh into a collection tube and placed on ice. A second digestion of the remaining fragments was performed and the cell suspension was filtered into the same collection tube. Reactions were quenched with FACS buffer (PBS plus 0.5% BSA) with 2mM EDTA. Following FACS buffer wash and RBC lysis, dissociated cells were labeled with anti-CD45 magnet microbeads and enriched into a CD45+ fraction and CD45- fraction by MACS (magnetic-activated cell sorting, Miltenyi Biotech). Cells were stained with fluorochrome antibodies for 20 min on ice for cell sorting. We used CD45, CD71, Ter119 and CD31 to deplete CD45+ CD71+, Ter119+, CD31+ populations using a BD FACS Aria III Cell Sorter
Cells were delivered for library construction using 10X Genomics Chromium 3′ GEM Single-Cell Library v3 kit (10X Genomics). Sequencing was performed according to a standard pipeline at The Genome Technology Access Center at Washington University, St. Louis.

treatment_protocol: Vehicle and Chemotherapy

value: Bone

value: Bone resident cells

value: 12 weeks

value: Doxorubicin

value: Female


title: 3h amp treated rep2

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA5

value: ampcillin 3h


title: CITE seq - lane A

description: CITE-A


title: Vehicle

description:
Library name: Sample 1
10X Genomics

value: Vehicle


title: IA6-Individual-81A-negative-replicate-2

description:
Library name: Integrin alpha-6 (IA6) cells-6
IA6_81A_minu_rep2

value: IA6 negative cells


title: 3h amp treated rep3

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA6


title: 3h amp treated rep1

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA4


title: IA6-Individual-81A-negative-replicate-1

description:
Library name: Integrin alpha-6 (IA6) cells-5
IA6_81A_minu_rep1


title: 0h untreated log rep3

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA3

value: no treatment


title: RNA seq - lane A

description: GEX-A

value: breast/blood

value: CD3 pos cells

value: WT


title: scRNAseq_GEX_B16_CD8_CAR_T_D7_Spleen_Bach2iKO

description:
Library name: Sample 7
10x Genomics GEX

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Multiome: Cell versus gene matrix of UMI counts for gene expression assay and cell versus fragment matrix for ATAC assay were generated from fastq files aligned to mm10 using cellranger-arc (v 2.0.0).
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: SCATAC-Seq: tab-separated values files

source_name: Spleen

extract_protocol:
CAR T cells isolated from spleen were sorted for scRNA-Seq or multiome anallysis.
We used Chromium Next GEM Single Cell 5' Kit (10x Genomics) to generate scRNA-Seq libraries according to the manufacturer’s protocol. We used Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics) to generate scRNA-Seq and scATAC-Seq libraries according to the manufacturer’s protocol.

value: Spleen

value: ex vivo

value: CD8+ CAR T cells

value: Bach2 iKO


title: IA6-Individual-79G-positive-replicate-2

description:
Library name: Integrin alpha-6 (IA6) cells-4
IA6_79G_plus_rep2

value: IA6 positive cells


title: RC brain organoids, hiPSC line 2, day 90

city: Lausanne

first: Giuseppe

last: Aiello

address: Rue du Bugnon,9

institute: University of Lausanne

description: Library name: RC-Line2

data_processing:
We aligned reads to GRCh38 human reference genome with Cell Ranger 7.2 (10x Genomics) using default parameters to produce the cell-by-gene, Unique Molecular Identifier (UMI) count matrix. UMI counts were analysed using the Seurat R package v.5. Cells were filtered for a min. 1000 genes, maximal mitochondrial content of 10%. Resulting high quality cells were normalized ("LogNormalize") for scaled for each cell to a total expression of 10K UMI. Doublets were removed using DoubletFinder, while unlabeled negative cells were retained as their distribution was similar to that of singlets. All analyses were conducted using doublet-free datasets.
Assembly: GRCh38 human reference genome
Supplementary files format and content: These files contain Seurat objects of single-cell RNA-seq data from the RCLine1 and RCLine2 samples after quality control and preprocessing. Cells with low counts, high mitochondrial content, or predicted doublets were removed. Each object includes log-normalized counts, cell metadata (QC metrics, clustering, and doublet classification), and dimensionality reduction (PCA/UMAP) results.

source_name: Brain organoids

extract_protocol:
Organoids were cultured in Neurobasal A-Plus medium supplemented with B-27 Plus (2%) and Glutamax (1%) until harvesting at day 90. Pool of three organoids were separately incubated in Trypsin (Sigma Aldrich)/Accutase (StemCell Technologies) (1:1) containing 10 U/ml DNaseI (Thermo Fisher Scientific) in the gentleMACS™ Dissociator (Miltenyi Biotec) set at program NTDK1. After digestion the cell suspension was passed through a 70μm strainer. Samples were loaded to recover 16.000 cells onto a Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000127) and processed through the Chromium controller to generate single-cell GEMs (Gel Beads in Emulsion).
scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, PN-1000269). Organoids libraries were pooled and sequenced using the Element Biosciences AVITI. A total of 166 million reads were requested per library to ensure sufficient coverage for downstream analysis.

value: Brain organoids

value: Line 2

value: Brain


title: 0h untreated log rep2

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA2


title: scRNAseq_HTO_B16_CD8_CAR_T_D7_Spleen_Control

description:
Library name: Sample 6
10x Genomics HTO

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Multiome: Cell versus gene matrix of UMI counts for gene expression assay and cell versus fragment matrix for ATAC assay were generated from fastq files aligned to mm10 using cellranger-arc (v 2.0.0).
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: SCATAC-Seq: tab-separated values files
Library strategy: CITE-seq


title: scRNAseq_HTO_B16_CD8_CAR_T_D7_Spleen_Bach2iKO

description:
Library name: Sample 8
10x GenomicsHTO


title: IA6-Individual-79G-positive-replicate-1

city: San Francisco

first: Henry

address: 1322 3rd avenue

institute: University of California San Francisco

description:
Library name: Integrin alpha-6 (IA6) cells-3
IA6_79G_plus_rep1


title: RC brain organoids, hiPSC line 1, day 90

description: Library name: RC-Line1

value: Line 1


title: 0h untreated log rep1

value: laciq, PN25-tetR, SpR, deoR, supE44, Delta(lacZYA-argFV169), Phi80 lacZDeltaM15, hsdR17(rK- mK+), recA1, endA1, gyrA96, thi-1, relA1


title: scRNAseq_GEX_B16_CD8_CAR_T_D7_Spleen_Control

description:
Library name: Sample 5
10x Genomics GEX


title: IA6-Individual-79C-positive-replicate-2

description:
Library name: Integrin alpha-6 (IA6) cells-2
IA6_79C_plus_rep2


title: Gene expression in liver of Usp21 KO mice 3

city: Nagasaki

first: Takashi

last: Ito

address: 1-12-4, Sakamoto, Nagasaki

department: Biomedical Sciences

institute: Nagasaki University

description: Library name: USP21KO-3_S6

data_processing:
Transcriptome-Based Pipeline: Raw RNA-seq reads underwent initial QC using rabbitQCplus. Quantification was conducted using Salmon against a full selective-alignment (SA) index (salmon_sa_index). Transcript-level quantification results were summarized to gene-level TPM values using tximport. Final outputs included raw TPM values (*_salmon_TPM.csv) and log-transformed TPM (*_salmon_logTPM.csv). Genome-based visualization files (e.g., bigWig) were not generated for this pipeline.
Genome-Based Pipeline: Reads were aligned to the mm10 reference genome using Partek® Genomics Suite. Gene-level read counts were obtained using HTSeq with the annotation file gencode.vM23.basic.annotation.gtf.Normalization was performed using edgeR, applying TMM normalization, and outputting:
Assembly: Reads were aligned to the mm10 genome using Partek® Genomics Suite.
Supplementary files format and content: Raw CPM: *_from_bam_norm_TMM_CPM.csv
Supplementary files format and content: Log-transformed CPM: *_from_bam_norm_TMM_logCPM.csv.
Supplementary files format and content: For visualization, bigWig files were generated from BAMs using deepTools bamCoverage, scaled by CPM.

source_name: Liver

extract_protocol:
The total RNA was extracted using the ISOGEN Ⅱ reagent (NIPPON GENE, Japan). cDNA was synthesized using 0.5 μg total RNA as a template with oligo (dT) primer (Life Technologies, CA), random hexamers (Takara Bio, Japan), and M-MuLV reverse tran-scriptase (New England Biolabs, MA).
RNA libraries for RNA-seq were prepared using ILLumina seq library prep kit using the manufacturers protocol

value: Liver

value: Usp21 KO


title: RNA seq - lane B

description: GEX-B


title: Gene expression in liver of Usp21 KO mice 1

description: Library name: USP21KO-1_S4


title: scATACseq_Multiome_E2APBX1_CAR_T_D20_Spleen

description:
Library name: Sample 4
10x Genomics ATAC


title: C1SAN/CSB/WT cell line biological rep 4

city: Durham

first: Hana

middle: Isadora

last: Wasserman

state: NC

address: 3308 Old Chapel Hill Road

institute: Duke University

description: Library name: C1SAN/CSB/WT G2947 bio rep 4

data_processing:
Raw ATAC-seq reads were processed using the ENCODE ATAC-seq-pipeline (v2.2.3) and hg19 reference genome for irreproducibility detection rate (IDR) analysis of the four biological replicates. Per ENCODE pipeline recommendations, conservative IDR peakspeaks were called with MACS2 narrowPeak settings using a threshold p-value<0.01 and subsequent IDR threshold of 0.05.
Assembly: hg19
Supplementary files format and content: narrowPeak files containing IDR conservative peak calls from the four biological replicates

growth_protocol: Human skin fibroblast cells were grown in DMEM/F-12 (Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12) containing 10% fetal bovine serum (FBS) at 37 °C and 5% CO2. Prior to processing, cells were resuspended in growth media (containing 10% DMSO) and frozen for −1°C/min for 24 hours.

extract_protocol:
Four biological replicates of the human skin fibroblasts CS1AN/CSB/WT cell line were prepared with the Omni ATAC-seq protocol, using approximately 50,000 cells per library. Omni ATAC-seq protocol was performed as described in Corces et al. Nature Methods 2017.Oct;14(10):959-962 "An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues".
ATAC-seq

value: Skin fibroblast


title: C1SAN/CSB/WT cell line biological rep 1

description: Library name: C1SAN/CSB/WT G2944 bio rep 1


title: Gene expression in liver of WT mice 3

description: Library name: WT-3_S3


title: Blood-Individual-FLLC2

last: Rodriguez

description:
Library name: Blood-2
Blood_FLLC2

source_name: Blood

value: Blood

value: All blood cells


title: Blood-Individual-LFC4

description:
Library name: Blood-3
Blood_LFC4


title: IA6-Individual-79C-positive-replicate-1

description:
Library name: Integrin alpha-6 (IA6) cells-1
IA6_79C_plus_rep1


title: scRNAseq_Multiome_E2APBX1_CAR_T_D20_Spleen

description:
Library name: Sample 3
10x Genomics GEX

value: WT


title: C1SAN/CSB/WT cell line biological rep 2

description: Library name: C1SAN/CSB/WT G2945 bio rep 2


title: scRNAseq_Multiome_CAR_T_in_vitro

description:
Library name: Sample 1
10x Genomics GEX

value: Spleen

value: in vitro


title: Gene expression in liver of WT mice 2

description: Library name: WT-2_S2


title: Blood-Individual-FL3

description:
Library name: Blood-1
Blood_FL3