title: CAF15 transfected with ASO TERRA

source_name: CAF15 transfected with ASO TERRA


title: Female, Cocaine, E2F3a antibody, Replicate 2

status: Public on Aug 10 2026

type: SRA

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

country: USA

institute: Mount Sinai School of Medicine

description: Library name: F-coc-2

library_source: genomic

data_processing:
The NGS-Data-Charmer pipeline was used for preprocessing, QC, and alignment of the dataset (https://github.com/shenlab-sinai/NGS-Data-Charmer). Peak calling was performed using MACS on deduplicated alignments (parameters: -f BAMPE -g mm -B -q 0.01), using IgG as background.
Assembly: mm10
Supplementary files format and content: Peak calls are provided as Narrowpeak files, generated by MACS.
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: Nucleus accumbens

extract_protocol:
Nuclei were equally split for IGG and E2F3a and Cut&Run was performed using IGG (CellSignaling #2729; 1:100) or E2F3a (MilliporeSigma #HPA065012, 1:50) antibodies. DNA fragments were eluted by incubating the samples at 37˚C for 30 min with 500 RPM mixing (Eppendorf, Thermomixer). The samples were centrifuged at 16,000 RCF for 5 min at 4˚C and the supernatant was reserved for DNA clean-up via phenol-chloroform precipitation.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) with modifications.

treatment_protocol: Female and male mice were injected (i.p.) with saline or cocaine (20 mg/kg) for 7 consecutive days in their home-cages before brain collection for CUT&RUNseq. Nuclei were isolated from frozen tissue of bilateral  12G punches of the Nucleus accumbens) .

tag: tissue

value: Nucleus accumbens

tag: antibody

tag: genotype

value: Wildtype C57BL/6J

tag: treatment

value: coc

tag: Sex

value: Female


title: NAM 0.5mM_T8 rep2

city: Lausanne

first: Aline

last: Roch

address: EPFL Innovation Park Building L

country: Switzerland

institute: DOPPL SA

description: Library name: S74

library_source: transcriptomic

data_processing:
Aligned to hg19 genome using bowtie2 in --sensitive-local mode
Peak calling using epic
Assembly: hg19
Supplementary files format and content: csv files include raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: small intestine

extract_protocol:
Each well of the Gri3D® platform was collected individually on day T-2 or day T-8. 4 wells of the same condition were collected separately and analyzed as quadruplicates for transcriptome profiling. Samples were lysed using LBE lysis buffer (C39467, Beckman Coulter) and vortexed for 1 min. Lysates were stored at –80°C before performing RNA extraction and subsequent analysis. Total RNA was extracted from human organoid tissues using the Agencourt RNAdvance Tissue Kit (A32649, Beckman Coulter), following the manufacturer’s protocol. Tissue disruption and lysis were carried out using the FastPrep-24™ instrument (MP Biomedicals) at a speed setting of 6.0 for two cycles of 1 minute each. A total of 400 µL of lysate was processed per sample, and RNA was eluted in 50 µL of nuclease-free water. RNA concentration was quantified using the Quant-iT™ RiboGreen RNA Assay Kit (R11490, Invitrogen) on a SpectraMax® F1 Microplate Reader (Molecular Devices). Integrity was assessed with the Fragment Analyzer 96-capillary system (Agilent Technologies) using the Standard Sensitivity RNA Analysis Kit (DNF-471-0500). We consistently obtained high-quality RNA from all organoid samples, with an average yield of 0.36 µg per sample. Notably, all samples achieved an RNA integrity number (RIN) value of 10, indicating excellent RNA integrity.
A total of 300 ng of RNA per sample was used to generate sequencing libraries with the Illumina Stranded mRNA Library Prep Kit, following the manufacturer's protocol. The workflow includes a bead-based mRNA capture, followed by fragmentation, first- and second-strand synthesis, end repair, 3’ adenylation, and indexed linker ligation steps. The adapter-ligated cDNA library fragments were next enriched by PCR using 13 cycles of amplification. From the extracted total RNA, 90 individual barcoded stranded mRNASeq libraries were successfully prepared with an average yield of 35.4 ng/µL. Two equimolar pools of 78 and 12 unique dual (UD) indexed libraries were sequenced paired-end (PE) with 59 bases each read on four individual P3 100 NextSeq 2000 flow cells. The first dark cycle was introduced to the sequencing run to improve the flow-cell cluster detection. 5.0 billion PE reads passing the chastity filter (>Q30) were generated, with an average of 46.2 million reads per sample with a standard deviation of 11.8 million reads (26%).

treatment_protocol: On day 4, cytokines were introduced to the organoids to initiate Phase 1 of epithelial barrier disruption (T-0). Organoids were stimulated with CytoMix, a pro-inflammatory cytokine cocktail comprising TNF-α (300-01A, Thermo Fisher Scientific), IL-1β (200-01B, Thermo Fisher Scientific), and IFN-γ (300-02, Thermo Fisher Scientific), each administered at final concentrations of 5, 10, 20, or 50 ng/mL. In parallel, IFN-γ was applied as a single agent at identical concentrations. Cytokines were reconstituted at 100 µg/mL in PBS (10010056, Thermo Fisher Scientific) supplemented with 0.1% bovine serum albumin (BSA; 15260-037, Thermo Fisher Scientific). CytoMix was removed, and the cultures were washed by performing two successive medium replacements, marking the onset of the Phase 2 post-treatment recovery period (T–2). As part of the prevention protocol, organoids cultured in Gri3D® platform for 72 hours (day 3) were supplemented with the bioactive compounds’ dexamethasone (DEX - 1 µM; D4902, Sigma-Aldrich), niacinamide (NAM - 0.5 mM; 0429449, DSM-Firmenich), and β-hydroxybutyrate (BHB - 1 mM; 3HB-Mg, Osaka Gas). Following cytokine withdrawal and medium washout, bioactives were reintroduced into the culture at the same concentration on day T-2 and subsequently replenished at identical concentrations on days T-4 and T-6.

value: small intestine

tag: cell line

tag: cell type

value: primary intestinal epithelial cells

value: Niacinamide 0.5 mM

tag: time

value: day 8 post cytokine treatment


title: BCL-CD8T-0h-IL7R-cKO_rep1

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Library name: BCL-CD8T-0h-IL7R-cKO1
BCL-0h-CKO1
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

data_processing:
Trim Galore (v0.6.7) and Trimmomatic (v0.39) was used to remove the low quality reads (parametrs- --quality 20 --stringency 3)
Bowtie2 (v2.5.1) was used to align reads to the mouse genome
Assembly: mm10
Supplementary files format and content: tab delimited text files includes FPKM values for each sample

source_name: spleen

growth_protocol: T cells were maintained in 1640 supplemented with 10% fetal bovine serum (BI), 10mM Hepes (Gibco), 1% NEAA (Gibco), 1% penicillin/streptomycin (Gibco), 50uM β-Mercaptoethanol (Gibco) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from 1 × 10⁶ naïve or activated T cells using TRIzol reagent (Invitrogen, 15596018).
RNA-seq libraries were constructed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770L) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with or without 2 µg/ml coated anti-CD3 antibody and 2 µg/ml soluble anti-CD28 antibody.

value: spleen

value: naive CD8 T cell

value: unstimulated


title: Female, Saline, E2F3a antibody, Replicate 1

description: Library name: F-sal-1

value: sal


title: NAM 0.5mM_T8 rep1

description: Library name: S73


title: CytoMix + NAM 0.5mM_T8 rep3

description: Library name: S85

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL, Niacinamide 0.5mM


title: CAF19 transfected with siCTRL

type: RNA

city: Charlestown

first: Gian Paolo

last: Dotto

state: MA

address: 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hsopital

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data were processed using Transcriptome Analysis Console v4.0.3.14 with siNONO and siCTR as comparison groups.

source_name: CAF19 transfected with siCTRL

label_protocol: RNA was not labeled.

growth_protocol: Cells are grown in DMEM with 10% FBS, 1% penicillin and 1% streptomycin in regular cell culture conditions.

extract_protocol: Total RNA was extracted using Zymo Direct-zol RNA Miniprep kit.

treatment_protocol: Cancer-associated fibroblasts (CAFs) were transfected with two independent siRNAs targeting NONO (siNONO#1(Mission siRNA  NM_007363 SASI_Hs02_00343477 and siNONO#2 (Mission siRNA  NM_007363 SASI_Hs02_00343479 or with a non-targeting control siRNA (MISSION siRNA Universal Negative Control #1 SIC001) at the concentration of 30nM using HiPerFect transfection reagent (Qiagen), according to the manufacturer’s instructions. Briefly, siRNAs and HiPerFect were mixed in serum-free medium and incubated for 10 minutes at room temperature to allow complex formation. The siRNA–HiPerFect complexes were then added dropwise to CAFs plated at 60–70% confluence in complete medium. Cells were harvested 72 hours post-transfection for downstream analyses.


title: mDG; K/+; H2BGFP (replicate 12; mouse 1LLR) [kmc12]

city: Quechee

first: Michael

middle: J

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

data_processing:
RNA sequencing read aligment was performed using bcbio-nextgen 1.0.2a0-a003647 (https://bcbio-nextgen.readthedocs.io/) against the GRCm38 / mm10 reference genome with transcript annotations corresponding to Ensembl release 84. Aligned counts generated by salmon 0.8.0 were used for downstream analysis.
Differential expression analysis was performed in R 3.4.0 / Bioconductor 3.5 using bcbioRNASeq 0.0.18 and DESeq2 1.16.1.
Assembly: mm10 / GRCm38; Ensembl 84
Supplementary files format and content: Raw salmon-derived count matrix used as input for DESeq2 analysis (CSV)
Supplementary files format and content: DESeq2 normalized count matrix (CSV)
Supplementary files format and content: STAR aligned count matrix (TSV)

molecule: polyA RNA

source_name: dentate gyrus

extract_protocol:
The dentate gyrus subregion was dissected from adult (3 months old) CaMKIIa rtTA; tetOKlf9/ tetO-Klf9 mice in which Klf9 expression was inducibly upregulated in the DG following two weeks of 9-tert-butyl-doxycycline (9TBD) treatment. 9TBD treated tetOKlf9/tetO-Klf9 mice were used as controls.
RNA extracted from dentate gyrus was subjected to polyA selection and library preps for next-generation Illumina HiSeq (50 bp, single-end reads, 25 million reads/sample).

value: dentate gyrus

tag: condition

value: expt

tag: replicate

tag: mouse

value: mDG; K/+; H2BGFP

tag: cage

tag: date of_birth

tag: age (weeks)


title: OXDAY7 cre+ CD45

city: Leuven

first: Gabriele

last: Bergers

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven-VIB CCB

description:
Library name: scrCCB125
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed using CellRanger (version 7.0.1) and aligned to the mouse reference genome mm10-2020-A.
Assembly: mm10-2020-A
Supplementary files format and content: Gene expression count matrices in 10X Genomics format: For each sample, three tab-delimited compressed files are provided: (1) *_barcodes.tsv.gz contains cell barcodes (one per line), (2) *_features.tsv.gz contains gene identifiers and symbols (tab-separated: gene_id, gene_symbol, feature_type), and (3) *_matrix.mtx.gz contains the sparse count matrix in Matrix Market format with rows corresponding to genes and columns to cell barcodes.

source_name: lymph node

growth_protocol: Mice were maintained in individually ventilated cages in a room with controlled temperature and humidity under a 12-h light/12-h dark cycle with ad libitum access to water and food. 7-10 week old C57BL/6 mice were used for experiments.

extract_protocol:
Lymph nodes were extracted and minced, then incubated at 37°C in serum-free RPMI containing 0.8mg/ml Dispase II, 0.2 mg/ml Collagenase P and 0.1mg/ml Dnase I for 15 minutes, refreshing twice with manual dissociation between each incubation. Remaining enzymes were quenched in MACs buffer and suspensions were passed through 70um strainers. For endothelial cell analysis, immune cells were depleted using positive selection mouse CD45 microbeads. The negative fraction containing endothelial cells and positive fraction containing immune cells were collected separately and washed with PBS before flow cytometry sorting.
Single cell suspensions were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3' Library, Gel Bead & Multiplex Kit, and Chip Kit (10x Genomics), aiming for 10,000 cells per library. Samples were processed using kits pertaining to V2 barcoding chemistry of 10x Genomics. Single samples were processed in a single well of a PCR plate, and all samples were processed in parallel in the same thermal cycler.

treatment_protocol: Mice were treated with tamoxifen 5 times according to the Jackson protocol for Cre recombination. For inflammation induction, mice were shaved with Veet on the abdomen and 50 ul of 4% Oxazolone (3:1 acetone:olive oil) was applied to each area. Mice were left for 3 to 7 days post-treatment. Vehicle control mice received acetone:olive oil without oxazolone.

value: lymph node

value: immune cells

value: ATG12 fl/fl x CDH5 CreER positive

value: oxazolone day 7


title: NCM460 cells co-cultured with IL-1β-high macrophages, independent replicate 3

city: Changsha

first: Qi

last: Sun

state: Hunan

address: 139 Renmin Middle Road

department: Department of Geriatric Surgery

institute: The Second Xiangya Hospital, Central South University

description:
Library name: NCM460_IL1Bpos_Mac_3
Independent parallel sample from the NCM460_IL1Bplus_Mac group.
A793

data_processing:
Raw sequencing reads were filtered using fastp v0.21.0 with the parameters -l 50 -n 5 -q 15.
Clean reads were aligned to the reference genome using STAR v2.7.2a with default parameters.
Gene-level read counts were generated using HTSeq v0.13.5.
Assembly: GRCh38
Supplementary files format and content: gene-level raw read counts for all samples.

growth_protocol: FHC and NCM460 human colonic epithelial cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2. THP-1 cells were cultured under standard conditions and differentiated into macrophage-like cells before co-culture experiments.

extract_protocol:
Total RNA was extracted using a universal RNA extraction kit according to the manufacturer's instructions. RNA concentration was measured using a Qubit 4 Fluorometer, and RNA integrity was assessed using the Agilent 4200 TapeStation system. Qualified RNA samples were used for RNA-seq library construction.
RNA-seq libraries were constructed using a commercial mRNA-seq library preparation kit according to the manufacturer's protocol. Library quality was assessed before sequencing, and qualified libraries were sequenced on the BGISEQ-500 platform with paired-end reads.

treatment_protocol: THP-1 cells were differentiated into macrophage-like cells and subjected to inflammatory stimulation. IL1B knockdown was performed using shRNA to generate IL-1β-low macrophages. Inflammatory stimulated THP-1-derived macrophages were used as IL-1β-high macrophages, whereas IL1B-knockdown macrophages receiving the same stimulation were used as IL-1β-low macrophages. FHC and NCM460 cells were co-cultured with IL-1β-low or IL-1β-high macrophages before RNA extraction.

value: human colonic epithelial cells

value: co-cultured with IL-1β-high THP-1-derived macrophages


title: DEX 1µM_T8 rep4

description: Library name: S68

value: small intestine

value: primary intestinal epithelial cells

value: Dexamethasone 1 µM


title: mDG; K/+; H2BGFP (replicate 11; mouse 1LLR) [kmc11]


title: OXDAY7 cre+ CD31

description:
Library name: scrCCB124
10X Genomics

value: endothelial cells


title: NCM460 cells co-cultured with IL-1β-high macrophages, independent replicate 2

description:
Library name: NCM460_IL1Bpos_Mac_2
Independent parallel sample from the NCM460_IL1Bplus_Mac group.
A158


title: BCL-CD8T-0h-IL7R-cKO_rep2

description:
Library name: BCL-CD8T-0h-IL7R-cKO2
BCL-0h-CKO2
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: spleen

value: naive CD8 T cell


title: DEX 1µM_T8 rep3

description: Library name: S67

value: day 8 post cytokine treatment


title: mDG; K/+; H2BGFP (replicate 10; mouse 4LLR) [kmc10]


title: BCL-CD8T-0h-WT_rep3

description:
Library name: BCL-CD8T-0h-WT3
BCL-0h-WT3
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: WT

value: unstimulated


title: NCM460 cells co-cultured with IL-1β-high macrophages, independent replicate 1

description:
Library name: NCM460_IL1Bpos_Mac_1
Independent parallel sample from the NCM460_IL1Bplus_Mac group.
A216


title: OXDAY7 cre- CD45

description:
Library name: scrCCB123
10X Genomics

value: ATG12 fl/fl x CDH5 CreER negative


title: DEX 1µM_T8 rep2

description: Library name: S66


title: CAF24 transfected with siNONO2

source_name: CAF24 transfected with siNONO2


title: mDG; K/+ (replicate 9; mouse 6LR) [kmc09]

value: dentate gyrus

value: expt

value: mDG; K/+


title: OXDAY7 cre- CD31

description:
Library name: scrCCB122
10X Genomics

value: lymph node


title: NCM460 cells co-cultured with IL-1β-low macrophages, independent replicate 3

description:
Library name: NCM460_IL1Bneg_Mac_3
Independent parallel sample from the NCM460_IL1Bminus_Mac group.
A543

value: co-cultured with IL-1β-low THP-1-derived macrophages


title: DEX 1µM_T8 rep1

description: Library name: S65


title: mDG; K/+; H2BGFP (replicate 8; mouse 132) [kmc08]

value: mDG; K/+; H2BGFP


title: Vehicle cre- CD45

description:
Library name: scrCCB121
10X Genomics

value: immune cells

value: vehicle control


title: NCM460 cells co-cultured with IL-1β-low macrophages, independent replicate 2

description:
Library name: NCM460_IL1Bneg_Mac_2
Independent parallel sample from the NCM460_IL1Bminus_Mac group.
A156

value: human colonic epithelial cells


title: CytoMix 10_T2 rep4

description: Library name: S64

value: small intestine

value: primary intestinal epithelial cells

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL

value: day 2 post cytokine treatment


title: CAF24 transfected with siNONO1

source_name: CAF24 transfected with siNONO1


title: Vehicle cre- CD31

description:
Library name: scrCCB120
10X Genomics

value: endothelial cells


title: mDG; K/+ (replicate 7; mouse 7LR) [kmc07]


title: CytoMix 10_T2 rep3

description: Library name: S63


title: BCL-CD8T-0h-WT_rep1

description:
Library name: BCL-CD8T-0h-WT1
BCL-0h-WT1
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: spleen

value: naive CD8 T cell

value: WT


title: NCM460 cells co-cultured with IL-1β-low macrophages, independent replicate 1

description:
Library name: NCM460_IL1Bneg_Mac_1
Independent parallel sample from the NCM460_IL1Bminus_Mac group.
A384


title: Vehicle cre+ CD45

description:
Library name: scrCCB119
10X Genomics

value: ATG12 fl/fl x CDH5 CreER positive


title: mDG; +/+ (replicate 6; mouse 1L) [kmc06]

value: dentate gyrus

value: control


title: FHC cells co-cultured with IL-1β-high macrophages, independent replicate 3

description:
Library name: FHC_IL1Bpos_Mac_3
Independent parallel sample from the FHC_IL1Bplus_Mac group.
A859

source_name: FHC

value: FHC

value: co-cultured with IL-1β-high THP-1-derived macrophages


title: CytoMix 10_T2 rep2

description: Library name: S62


title: FHC cells co-cultured with IL-1β-high macrophages, independent replicate 2

description:
Library name: FHC_IL1Bpos_Mac_2
Independent parallel sample from the FHC_IL1Bplus_Mac group.
A184


title: Vehicle cre+ CD31

description:
Library name: scrCCB118
10X Genomics

value: lymph node


title: mDG; +/+ (replicate 4; mouse 4L) [kmc04]


title: mDG; +/+ (replicate 5; mouse 1L) [kmc05]

value: expt


title: OXDAY3 cre- CD45

description:
Library name: scrCCB117
10X Genomics

value: immune cells

value: ATG12 fl/fl x CDH5 CreER negative

value: oxazolone day 3


title: FHC cells co-cultured with IL-1β-high macrophages, independent replicate 1

description:
Library name: FHC_IL1Bpos_Mac_1
Independent parallel sample from the FHC_IL1Bplus_Mac group.
A317

value: human colonic epithelial cells


title: CytoMix 10_T2 rep1

description: Library name: S61

value: small intestine

value: primary intestinal epithelial cells

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL


title: Control_T2 rep4

description: Library name: S60

value: Untreated

value: day 2 post cytokine treatment


title: mDG; +/+ (replicate 3; mouse 6L) [kmc03]


title: OXDAY3 cre- CD31

description:
Library name: scrCCB116
10X Genomics

value: endothelial cells


title: FHC cells co-cultured with IL-1β-low macrophages, independent replicate 3

description:
Library name: FHC_IL1Bneg_Mac_3
Independent parallel sample from the FHC_IL1Bminus_Mac group.
A461

value: co-cultured with IL-1β-low THP-1-derived macrophages


title: Control_T2 rep3

description: Library name: S59


title: OXDAY3 cre+ CD45

description:
Library name: scrCCB115
10X Genomics

value: ATG12 fl/fl x CDH5 CreER positive


title: FHC cells co-cultured with IL-1β-low macrophages, independent replicate 2

description:
Library name: FHC_IL1Bneg_Mac_2
Independent parallel sample from the FHC_IL1Bminus_Mac group.
A742


title: mDG; +/+ (replicate 1; mouse 129) [kmc01]

value: dentate gyrus

value: control


title: mDG; +/+; H2BGFP (replicate 2; mouse 141) [kmc02]

value: mDG; +/+; H2BGFP


title: OXDAY3 cre+ CD31

description:
Library name: scrCCB114
10X Genomics

value: lymph node


title: Control_T2 rep2

description: Library name: S58


title: FHC cells co-cultured with IL-1β-low macrophages, independent replicate 1

description:
Library name: FHC_IL1Bneg_Mac_1
Independent parallel sample from the FHC_IL1Bminus_Mac group.
A132

value: FHC


title: Control_T2 rep1

description: Library name: S57


title: BRB-seq Batch 7 Water Control

status: Public on Aug 09 2026

city: Boston

first: Juan

middle: Ignacio

last: Fuxman Bass

address: 5 Cummington mall

department: Biology

institute: Boston University

description: Library name: BRB_seq_Batch7_WaterControl

data_processing:
Reads were aligned to a custom GRCh38 reference genome augmented with viral transcriptional regulator (vTR) sequences using STARsolo. Gene-level UMI count matrices were generated using STARsolo with barcode and UMI correction enabled.
Samples were quality filtered based on sequencing depth and concordance between expected and observed vTR assignments.
Gene-level counts were normalized and differential expression analysis was performed using DESeq2.
Pathway enrichment analysis was performed using fgsea with Reactome gene sets obtained from MSigDB.
Assembly: GRCh38 primary assembly with GENCODE v46 annotations, augmented with viral transcriptional regulator (vTR) reference sequences.
Supplementary files format and content: *_raw_counts.tsv are tab-delimited raw gene-level count matrices generated from STARsolo
Supplementary files format and content: samples_metadata.tsv is a tab-delimited metadata file containing sample annotations, including batch, plate, well position, treatment condition, viral transcriptional regulator (vTR) assignment, barcode sequence, sample identifier, and quality-control filtering status.
Supplementary files format and content: VTRs_CDS.tsv is a tab-delimited file containing viral transcriptional regulator (vTR) identifiers and their corresponding coding DNA sequences (CDS).

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C with 5% CO2. Cells were seeded in 96-well plates at a density of 18,000 cells per well one day prior to transfection. For Batch 7 experiments, HEK293 cells were cultured under the same conditions.

extract_protocol:
Total RNA was obtained from cell lysates generated using the MERCURIUS DRUG-seq/BRB-seq protocol (Alithea Genomics). Cells were lysed directly in plate wells and lysates were processed according to the manufacturer’s instructions for reverse transcription and library preparation.
BRB-seq libraries were prepared using the MERCURIUS DRUG-seq kit (Alithea Genomics). RNA from individual samples was reverse transcribed using barcoded oligo-dT primers, enabling sample-specific indexing during first-strand cDNA synthesis. cDNA from all samples within a plate was pooled, purified, treated with exonuclease, converted to double-stranded cDNA, and quantified. Libraries were generated by tagmentation followed by PCR amplification with Illumina-compatible adapters and sequenced on an Illumina NovaSeq platform.

treatment_protocol: Cells were transfected with plasmids expressing individual viral transcriptional regulators (vTRs), empty vector controls, or left untransfected. Twenty-four hours after transfection, cells were either infected with Sendai virus, treated with Poly(dA:dT), treated with water control, or left untreated depending on the experimental condition. RNA was collected two days post-transfection.

value: WaterControl

tag: batch


title: BRB-seq Batch 7 Poly(dA:dT)

description: Library name: BRB_seq_Batch7_Poly_dAdT


title: BRB-seq Batch 6 Sendai

description: Library name: BRB_seq_Batch6_Sendai

value: Sendai


title: BRB-seq Batch 6 No Sendai Control

description: Library name: BRB_seq_Batch6_NoSendaiControl

value: NoSendaiControl


title: BRB-seq Batch 5 Sendai

description: Library name: BRB_seq_Batch5_Sendai


title: BRB-seq Batch 4 No Sendai Control

description: Library name: BRB_seq_Batch4_NoSendaiControl


title: BRB-seq Batch 5 No Sendai Control

description: Library name: BRB_seq_Batch5_NoSendaiControl


title: BRB-seq Batch 4 Sendai

description: Library name: BRB_seq_Batch4_Sendai


title: BRB-seq Batch 3 No Sendai Control

description: Library name: BRB_seq_Batch3_NoSendaiControl


title: BRB-seq Batch 3 Sendai

description: Library name: BRB_seq_Batch3_Sendai


title: BRB-seq Batch 2 Sendai

description: Library name: BRB_seq_Batch2_Sendai


title: BRB-seq Batch 2 No Sendai Control

description: Library name: BRB_seq_Batch2_NoSendaiControl


title: BRB-seq Batch 1 Sendai

description: Library name: BRB_seq_Batch1_Sendai


title: A549_het1_tumor_SAHA_rep6

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Library name: Sample 44

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq
Fastq files were mapped to hg38 human genome by HISAT2
Gene reads count tables were generated by HTSeq
Assembly: hg38
Supplementary files format and content: text files includes raw reads count

source_name: Tumor

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Plus Mini Kit according to the manufacturer’s instructions.
KAPA Stranded mRNA-Seq Kit

value: Tumor

value: SAHA


title: A549_het1_tumor_SAHA_rep3

description: Library name: Sample 43


title: BRB-seq Batch 1 No Sendai Control

description: Library name: BRB_seq_Batch1_NoSendaiControl


title: A549_het1_tumor_SAHA_rep2

description: Library name: Sample 42


title: A549_het1_tumor_SAHA_rep1

description: Library name: Sample 41


title: A549_het1_tumor_DMSO_rep5

description: Library name: Sample 40

value: DMSO


title: A549_het1_tumor_DMSO_rep4

description: Library name: Sample 39


title: A549_het1_tumor_DMSO_rep3

description: Library name: Sample 38


title: A549_het1_tumor_DMSO_rep2

description: Library name: Sample 37


title: A549_WT_tumor_SAHA_rep8

description: Library name: Sample 36

value: WT


title: A549_WT_tumor_SAHA_rep6

description: Library name: Sample 35


title: A549_WT_tumor_SAHA_rep4

description: Library name: Sample 34


title: A549_WT_tumor_DMSO_rep8

description: Library name: Sample 32


title: A549_WT_tumor_SAHA_rep3

description: Library name: Sample 33


title: A549_WT_tumor_DMSO_rep7

description: Library name: Sample 31


title: A549_WT_tumor_DMSO_rep2

description: Library name: Sample 29


title: A549_WT_tumor_DMSO_rep3

description: Library name: Sample 30


title: A549_homo_tumor_rep5

description: Library name: Sample 28

value: homo


title: hls1_air_section2_region3

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing: MERFISH images were processed according to the manufacturer's specifications (Vizgen). The resulting tables of spatial coordinates of single mRNA molecules are provided.

organism: Arabidopsis thaliana

source_name: 3d-old control treated hls1 etiolated seedlings

growth_protocol: Arabidopsis seedlings were grown in complete darkness for 72h prior to embedding and flash freezing

extract_protocol: Embedded tissue blocks were acclimated to -18C in a pre-cooled cryostat chamber (Leica) for 1 h. Tissue blocks were trimmed until the tissue was entered, after which 10 µm sections were visually inspected until the region of interest was exposed. Sample mounting and preparation were performed according to the MERSCOPE user guide.

treatment_protocol: Seedlings were grown in control (zero grade air) or ethylene treatment conditions at a flow rate of 30mL / min

tag: treatmet

value: air

tag: developmental stage

value: 3-day-old etiolated


title: A549_homo_tumor_rep1

description: Library name: Sample 26

tag: tissue


title: GFP TM Female1

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

department: Anatomy and Cell Biology

institute: uiowa

description: Library name: 394

data_processing:
To quantify transcript-level abundances, we performed the quality control for RNA-seq reads and used the Salmon tool with mapping-based mode again the mouse reference transcriptome (mm10). After transcript quantification, the differential gene expression analysis between different groups was conducted with the DESeq2 package. Differential expression was defined as log 2 fc > 0.58 and FDRadjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: csv files include FPKM files for each sample

source_name: Liver

extract_protocol:
For RNA-seq, Trizol-purified RNAs were re-purified using RNeasy (QIAgen) and RNA integrity validated using NanoDrop.
Briefly, 2 μg/sample of RNA was used for sequencing using Illumina HiSeq 4000/75PE Sequencer. 23 million reads were generated for each sample.

value: Liver


title: A549_homo_tumor_rep4

description: Library name: Sample 27


title: A549_het2_tumor_rep4

description: Library name: Sample 24


title: A549_het2_tumor_rep3

description: Library name: Sample 23


title: A549_het2_tumor_rep1

description: Library name: Sample 22


title: A549_homo_tumor_rep0

description: Library name: Sample 25


title: A549_het2_tumor_rep0

description: Library name: Sample 21


title: PAS79_3

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

description:
Library name: Sample 9
PAS57_vs_PAS96 and PAS57_vs_PAS87

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Assembly: Pseudomonas aeruginosa PAS57, PAS96, and PAS79
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: csv files include FPKM values for each sample

organism: Pseudomonas aeruginosa

source_name: native sample of PAS79 strain

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAS57, PAS96, and PAS79, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAS57, PAS96, and PAS79 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: None treatment.

value: native sample of PAS79 strain

tag: growth phase

value: exponential growth phase

value: native bacterial cells

tag: strain

value: control of PAS79


title: Col_ET_section2_region3

source_name: 3d-old ethylene treated WT etiolated seedlings

tag: genotype

value: Col

value: ethylene


title: N1E-115 EGFP vs EGPF-NaV1.2CT High Glucose 2

city: Tlalnepantla

first: Ana

middle: Victoria

last: Vega

state: Mexico

address: Avenida de los Barrios No. 1, Colonia Los Reyes Iztacala, C.P. 54090, Tlalnepantla de Baz, Estado de México

department: physiology

country: Mexico

institute: Universidad Nacional Autónoma de México

hyb_protocol: For pre-hybridization the slides were re-hydrated with water vapor at 60°C, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92°C, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42°C. The slides were washed and dried for further hybridization. Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the 22 thousand oligos mouse arrays for 14 h at 42°C.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Alexa555 and Alexa647 density mean value (Dty), background mean value (Bck) and Signal (Sig) cross channel loees normalization value (by subgrids) were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM. GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

source_name: neuroblastoma N1E-115

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Cells N1E-115 were plated at 21000 cell/cm^2 in DMEM (Low glucose DMEM Gibco) /10% FBS/4 mM Glutamine/1X streptomycin /1X pencillin.

extract_protocol: The total RNA was purified using the RNeasy mini kit (Qiagen, Hilden, Germany) according the instructions of manufacturer.

treatment_protocol: N1E-115 cells were transfected 24h after plating with PEI (4:1), and with 2 micrograms (0.98 pmol) of a plasmid pEGFP (control) or plasmid pEGFP-NaV1.2CT-Flag, encoding pEGFP and a fusion of 229 amino acids of the carboxi-terminus of mouse voltage gated sodium channel NaV1.2 (Scn2A). Total RNA was extracted 48h after transfection

value: neuroblastoma N1E-115

tag: transfected plasmid

value: pEGFP-C1 plasmid

tag: glucose


title: N1E-115 EGFP vs EGPF-NaV1.2CT High Glucose 1

tag: cell type


title: A549_het1_tumor_rep4

description: Library name: Sample 20

tag: cell line


title: PAS79_1

description:
Library name: Sample 7
PAS57_vs_PAS96 and PAS57_vs_PAS85

tag: treatment


title: PAS79_2

description:
Library name: Sample 8
PAS57_vs_PAS96 and PAS57_vs_PAS86


title: Control_PAS96_3

description:
Library name: Sample 6
PAS57_vs_PAS96 and PAS57_vs_PAS84

source_name: native sample of PAS96 strain

value: native sample of PAS96 strain

value: control of PAS96


title: A549_het1_tumor_rep3

description: Library name: Sample 19

value: Tumor


title: Control_PAS96_2

description:
Library name: Sample 5
PAS57_vs_PAS96 and PAS57_vs_PAS83


title: mESCs, EPR19847 ChIP, 400 μg usage

first: Xiaoyang

last: Guo

address: 5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: 400

data_processing:
Raw data was trimmed with Cutadapt v1.18 (-a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTC' -A 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT' -m 50 -q 20,20), and aligned against the mm10 reference genome using bowtie2 v2.2.5 with default settings. The resulting SAM alignment files were quality filtered and converted to BAM format using SAM tools v1.3 (-q 10). Picard tools v1.140 was applied to reorder and sort the files and remove duplicate reads. Peaks were called by MACS2 v 2.1.1.20160309 (-f BAMPE -g mm -q 0.001) , and peak distribution was analyzed using annotatePeaks.pl from HOMER v4.10.3. Peak summits within 1 kb of Refseq transcription start sites (TSSs) were annotated to the corresponding genes. For 50 µg EPR19847 and RL2 ChIP-seq, only peaks observed from at least 2 out of 3 replicates were denoted as high-confidence peaks, and target TSSs from at least 2 out of 3 replicates were considered as ChIP targets. Gene Ontology analysis was performed on DAVID. BAM files were indexed with SAM tools before normalized and converted to bigwig format by deepTools v3.1.3 (-bs 1 --normalizeUsing RPGC). Bigwig files were visualized in Integrative Genomics Viewer (IGV). ChIP-seq profile of EPR19847 was merged from 3 biological replicates before normalization and conversion. DeepTools was applied to the calculation of pairwise Pearson correlation (bs 100), and metaprofiles of ChIP-seq reads on RefSeq genes (gene body and +/-2kb) and super/typical enhancers. Reference genome and annotation files were downloaded from UCSC.
Assembly: mm10
Supplementary files format and content: bigwig files for peaks found in each sample

source_name: Embryonic stem cell

growth_protocol: Cells were cultured at 37°C with 5% CO2. R1 murine embryonic stem cells were cultured in dishes coated with 0.1% gelatin (Sigma-Aldrich).  Culture media for mESC contains KO-DMEM (Gibco), 15% fetal bovine serum (Hyclone), 1x GlutaMAX (Gibco), 1x nonessential amino acids (Gibco), 100 U/mL penicillin, 100 μg/mL streptomycin (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF) (Millipore), and 100 μM 2-mercaptoethanol (Sigma-Aldrich).

extract_protocol:
3x107 cells were digested from dishes with 0.25%Trypsin-EDTA (Gibco) at 80% clousure. 1% formaldhyde in PBS was added for crosslinkage at room temperature for 15 min. 2 M glycine was used to quench the reation until the final concentration reached 0.125 M. The cells were incubated for 5 min at temperature and centifuged for 5 min at 2,000 xg. Cells were washed with cold PBS twice and lysed with lysis buffer (150 mM NaCl,50 mM Tris,5 mM EDTA,0.5% Igepa CA-630,1% Triton X-100,pH 7.5). The pellets were collected by centifuge for 10 min at 4,000 xg and resuspended with hypersonic buffer (150 mM NaCl,50 mM Tris,1 mM EDTA,0.1% SDS,0.1% Sodium deoxycholate,1% Triton X-100,pH 7.5). Then the solution was sonificated at 4°C (30 cycles, halt 30 s per 30 s cycle). The pellets were collected by centifuge for 15 min at 20,000 xg.
The collected pellets were resuspended in immunoprecipitation buffer (10 mM Tris-HCl, pH 7.5,150 mM NaCl, 1% Igepal CA-630, 0.1%SDS) and supplemented with 50 μg normal rabbit IgG for 3 h preclear. Then 100 μL protein G agarose beads were added and incubated for 3 h at 4°C. The beads were removed by 900 xg centifuge for 5 min. Then the corresponding amount of antibodies was added to the supernatant and incubate at 4°C for 12 h. Then 100 μL  protein G agarose beads were added and incubated for 3 h at 4°C. The beads were collected and washed with the following buffer successively: ChIP low-salt buffer (150 mM NaCl,20 mM Tris,2 mM EDTA,0.1% SDS,1% Triton X-100,pH 8.1),ChIP high-salt buffer (500 mM NaCl,20 mM Tris,2 mM EDTA,0.1% SDS,1% Triton X-100,pH 8.1),LiCl buffer (250 mM LiCl,10 mM Tris,1 mM EDTA,1% Igepal CA-630,1% Sodium deoxycholate,pH 8.1), TE buffer and water. Then the beads were added with 90 μL 0.15% TFA and shaked for 5 min at room temperature. 4 μL 1 M Tris-HCl (pH 8.0) was added to neturalize the acid. The supernatant was supplemented with 1 μL 10% SDS and 1 μL 20 mg/mL protease K, and shaked at 68°C for 2 h on thermomixer. The DNA was purificated by trizol for high-throughput sequencing.

value: Embryonic stem cell

value: EPR19847 ChIP, 400 μg usage


title: N1E-115 EGFP vs EGFP-NaV1.2CT Low Glucose

description: Cells transfected with pEGFP-NaV1.2CT-flag plasmid cultured in DMEM low glucose

value: 5 mM


title: A549_het1_tumor_rep2

description: Library name: Sample 18


title: Control_PAS96_1

description:
Library name: Sample 4
PAS57_vs_PAS96 and PAS57_vs_PAS82


title: mESCs, EPR19847 ChIP, 100 μg usage

description: Library name: 100

value: WT

value: EPR19847 ChIP, 100 μg usage


title: Control_PAS57_2

description:
Library name: Sample 2
PAS57_vs_PAS96 and PAS57_vs_PAS80

source_name: native sample of PAS57 strain

value: native sample of PAS57 strain

value: control of PAS57


title: Control_PAS57_3

description:
Library name: Sample 3
PAS57_vs_PAS96 and PAS57_vs_PAS81

value: exponential growth phase


title: A549_het1_tumor_rep1

description: Library name: Sample 17


title: TED orbital fibroblast_1

city: Rochester

first: Collynn

last: Woeller

address: 601 Elmwood Avenue

institute: University of Rochester

description: Library name: TED_1

data_processing:
bcltofastq-2.19.0
Assembly: Human hg38, annotation H38
Supplementary files format and content: Supplementary files format and content: Tab delimited txt file contains raw count for each file

source_name: Orbital fibroblast

growth_protocol: Standard culture conditions

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion (RNase-Free DNase Set, Qiagen).
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina) at the University of Rochester Functional Genomics Core and sequenced on an Illumina NovaSeq 6000 (150-bp paired-end; ~30 million reads/sample).

treatment_protocol: Untreated

value: Orbital fibroblast

value: TED


title: mESCs, EPR19847 ChIP, 50 μg usage, replication 3

description: Library name: 50_rep3

value: EPR19847 ChIP, 50 μg usage


title: Control_ PAS57_1

description:
Library name: Sample 1
PAS57_vs_PAS96 and PAS57_vs_PAS79

value: native bacterial cells


title: A549_WT_tumor_rep4

description: Library name: Sample 16


title: mESCs, EPR19847 ChIP, 50 μg usage, replication 2

description: Library name: 50_rep2


title: Liver, 6-mo, Cisd2hKO, PZ19b, rep4

city: Taipei

first: Yi-Long

last: Huang

state: Not US or Canada

address: No.155, Sec.2, Linong Street, Peitou

department: Center for Healthy Longevity and Aging Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

description:
Library name: C775L
RNA input 1 ug

data_processing:
CLC Genomics Workbench 22.0.2
Reads were trimmed using quality scores with a quality limit of 0.01, ambiguous nucleotides were trimmed with a maximum of two ambiguities allowed, read-through adapters were automatically trimmed using the Illumina New trim adapter list, and the first 12 nucleotides at the 5' end were removed.
Trimmed reads were mapped to the Mus musculus GRCm38/mm10 reference genome and quantified using the RNA-Seq Analysis tool in CLC Genomics Workbench 22.0.2 with gene and mRNA annotation tracks. Mapping parameters were mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, and similarity fraction = 0.8.
Assembly: GRCm38, mm10
Supplementary files format and content: CSV file containing DESeq2-normalized gene-level counts used for PCA.
Supplementary files format and content: Tab-delimited text file including expected count for each gene (used for DESeq2 analysis)

extract_protocol:
Total RNA extraction from liver samples was performed through phenol/chloroform method using TRIzol (T9424, Sigma). 1 or 4 μg of total RNA was used for the construction of sequencing libraries
Stranded mRNA-seq libraries were prepared from total RNA using Illumina library preparation kits according to the manufacturer's instructions. The natural aging batch was prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit, whereas the Cisd2 hKO batch was prepared using the Illumina Stranded mRNA Prep, Ligation kit.

value: Liver

value: PZ19b for 3 mo


title: Liver, 6-mo, Cisd2hKO, PZ19b, rep3

description:
Library name: C774L
RNA input 1 ug


title: Liver, 6-mo, Cisd2hKO, PZ19b, rep2

description:
Library name: C773L
RNA input 1 ug


title: A549_WT_tumor_rep2

description: Library name: Sample 15


title: Liver, 6-mo, Cisd2hKO, PZ19b, rep1

description:
Library name: C771L
RNA input 1 ug


title: mESCs, EPR19847 ChIP, 50 μg usage, replication 1

description: Library name: 50_rep1


title: mESCs, RL2 ChIP benchmark

description: Library name: RL2

value: RL2 ChIP benchmark


title: A549_WT_tumor_rep1

description: Library name: Sample 14


title: Liver, 6-mo, Cisd2hKO, Veh, rep4

description:
Library name: C770L
RNA input 1 ug

value: Veh (10% PG) for 3 mo


title: Liver, 6-mo, Cisd2hKO, Veh, rep3

description:
Library name: C768L
RNA input 1 ug


title: A549_WT_tumor_rep0

description: Library name: Sample 13

value: Tumor


title: mESCs, IgG ChIP control

description: Library name: IgG

value: Embryonic stem cell

value: IgG ChIP control


title: Liver, 6-mo, Cisd2hKO, Veh, rep2

description:
Library name: C767L
RNA input 1 ug


title: Liver, 6-mo, Cisd2hKO, Veh, rep1

description:
Library name: C766L
RNA input 1 ug


title: A549_homo_cell_rep3

description: Library name: Sample 12

value: homo


title: Liver, 6-mo, Cisd2f/f, PZ19b, rep4

description:
Library name: C765L
RNA input 1 ug


title: Liver, 6-mo, Cisd2f/f, PZ19b, rep3

description:
Library name: C763L
RNA input 1 ug


title: mESCs, no antibody input control

description: Library name: Input

value: WT

value: no antibody input control


title: A549_homo_cell_rep2

description: Library name: Sample 11


title: Liver, 6-mo, Cisd2f/f, PZ19b, rep2

description:
Library name: C762L
RNA input 1 ug


title: Liver, 6-mo, Cisd2f/f, PZ19b, rep1

description:
Library name: C761L
RNA input 1 ug


title: WBC_RNA

first: Doga

middle: C.

last: Gulhan

address: 149 13th Street, Room 7.011

institute: Mass General Brigham

description:
Library name: WBC_RNA
SMART-SEQ2

data_processing:
Single-cell RNAseq processing - Raw paired-end FASTQ files were quality and adapter trimmed using Trim Galore. Cleaned reads were aligned to the mm10 reference genome using HISAT2 with transcript-aware settings. SAM files were converted to BAM format, sorted, and indexed using SAMtools. RNA-SeQC was used to assess alignment quality and generate sequencing QC metrics. Gene-level read counts were quantified using featureCounts based on a GTF annotation file (exonic regions), and individual sample counts were merged to produce a final gene expression count matrix for downstream analysis.
Single-cell DNAseq Processing - Raw paired-end FASTQ files were quality and adapter trimmed using Trim Galore. Cleaned reads were aligned to the mm10 reference genome using BWA-MEM. Alignments were filtered for mapping quality, sorted, and indexed using SAMtools. PCR duplicates were removed using Picard, and alignment quality metrics were generated. Processed BAM files were used to generate genome-wide coverage tracks and BED files, and downstream copy number variation analysis was performed using Ginkgo.
Assembly: mm10
Supplementary files format and content: RNA - Processed File - Raw Counts (rna_counts_raw.tsv)
Supplementary files format and content: DNA - Processed File - Segment normalized copy number profiles - Scaled - Ginkgo 500k bins (dna_ginkgo_seg_norm_scaled.tsv)

source_name: Control

growth_protocol: B16F10 melanoma cells (C57BL/6J background) were cultured under standard conditions in DMEM supplemented with 10% fetal bovine serum and 1× penicillin/streptomycin at 37 °C with 5% CO₂. Cells were maintained in adherent culture and routinely tested for mycoplasma contamination. For in vivo experiments, cells were expanded and injected into syngeneic mice as described in the study design. Blood and tissue samples were collected at defined time points for downstream single-cell analysis.

extract_protocol:
Single cells were isolated by fluorescence-activated cell sorting (FACS) based on tumor and host markers. Individual cells were subjected to parallel DNA and RNA extraction using protocols optimized for low-input material. DNA and RNA were processed separately to enable SNP-based identification of tumor versus host origin and transcriptomic profiling.
For transcriptome analysis, single-cell RNA sequencing libraries were generated using a low-input protocol suitable for individual cells after following SmartSeq2 protocol. For genomic analysis, DNA libraries were prepared to enable detection of predefined tumor-specific and WBC-specific SNPs after following MALBAC protocol. Libraries were indexed, amplified, and sequenced using high-throughput platforms. Downstream analysis quantified tumor and host SNP support per cell and generated gene expression profiles for classification and comparative analysis.

treatment_protocol: Mice were injected with fluorescently labeled B16F10 melanoma cells to enable tracking of tumor-derived material. No additional drug treatments were applied. Circulating cells and tissue-derived cells were isolated from blood and organs, including lung, at experimental endpoints. Samples were processed immediately for single-cell sorting and sequencing.

value: Control

value: WBC

tag: age

value: 6-8 weeks

tag: Sex

value: Female

value: Naive

tag: library type

value: RNA


title: Liver, 6-mo, Cisd2f/f, Veh, rep4

description:
Library name: C760L
RNA input 1 ug


title: PltLike_RNA

description:
Library name: PltLike_RNA
SMART-SEQ2

value: PltLike


title: A549_homo_cell_rep1

description: Library name: Sample 10


title: Liver, 6-mo, Cisd2f/f, Veh, rep3

description:
Library name: C759L
RNA input 1 ug

value: Liver


title: Caenorhabditis elegans with Jellyfish treatment_03

city: Shanghai

first: Zhou

last: Peng

address: 720 Xianxia Rd.

institute: Shanghai tongren hospital

description: Library name: I3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork(parameter-Qqality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLS genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM value for each sample
Supplementary files format and content: tab-delimited text files include Counts value for each sample

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: Caenorhabditis elegans grown in NGM with OP50

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd.(Shanghai, China).

treatment_protocol: T5 stock peptide solutions 50 mg/mL diluted with OP50 suspension were added as 100 μL per plate. L4-stage worms were transformed onto these plates 24 h later for exposure.

value: Whole organism

value: Jellyfish peptide treated


title: A549_het2_cell_rep3

description: Library name: Sample 9


title: Liver, 6-mo, Cisd2f/f, Veh, rep2

description:
Library name: C758L
RNA input 1 ug

value: Veh (10% PG) for 3 mo


title: P4_RNA

description:
Library name: P4_RNA
SMART-SEQ2

source_name: Blood

value: Blood

value: DP

value: Tumor


title: CD4T_0h-WT_rep1

description:
Library name: CD4T_0h-WT-1
24h-WT-1
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

source_name: spleen

value: spleen

value: naive CD4 T cell

value: unstimulated


title: PFBS_placenta6_Control_male

city: San Diego

first: Elana

last: Elkin

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

description: Library name: PFBS_placenta6_Control_male

data_processing:
Reads were aligned to the human genome using STAR.
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than 100 across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the DeSeq2 package (version 4.1) for R statistical computing.
Assembly: hg38
Supplementary files format and content: tabular files

source_name: placenta

growth_protocol: HTR-8/SVneo cells: Cells were cultured between passages 25-75 and maintained in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37 °C in a 5% CO2 humidified incubator. Cells were split and passaged at 70-90% confluence prior to use for experiments. Villous Explants: Term trimester placental tissues (N = 7, 4 male, 3 female) were obtained from full-term, non-laboring elective cesarean sections performed at UC San Diego Medical Center under Institutional Review Board approval with written informed consent. Tissues were collected in collaboration with UC San Diego Center for Perinatal Discovery. Following collection, tissues were transported back to the lab in ice-cold media. Tissues were repeatedly washed in PBS and blood clots removed. Chorionic villous tissue was carefully dissected out to form explants. Explants were further dissected into approximately 5 mg (wet) pieces. Four to six explants were placed in each experimental well, yielding a total of approximately 25 mg per well. Explants were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% P/S and placed in experimental conditions immediately after dissections.

extract_protocol:
RNeasy Mini Kit (cells) miRNeasy Mini Kit (tissues)
TruSeq mRNA Library Prep Kit with poly(A) enrichment (Illumina, San Diego, CA, USA)

treatment_protocol: Explant Tissues: Immediately prior to each experiment 1M PFBS stock was quickly thawed in a 37°C water bath and diluted in complete RPMI 1640 medium (supplemented with 10% FBS and 1% P/S) to prepare a 1 mM intermediate working solution. The working solution was further diluted in RPMI 1640 medium to final concentrations of 100 nM-100 µM, depending on experiments. Final concentrations for RNA transcriptomic experiments were 0 and 5µM in cells, and 0, 5, and 20 µM PFBS in tissue explants.

value: placenta

value: female

value: Explants-various cells

tag: exposure time

value: 24 hours

tag: placental donor

tag: sequencing batch

value: batch 2026


title: Liver, 6-mo, Cisd2f/f, Veh, rep1

description:
Library name: C756L
RNA input 1 ug


title: A549_het2_cell_rep2

description: Library name: Sample 8


title: FR0002FE34-1

first: Gagandeep

last: Kaur

address: 601 Elmwood Ave

department: Environmental Medicine

institute: University of Rochester Medical Center

hyb_protocol: Appropriate volume (200µl per slide)  of diluted detection antibody (Human IO Core Protein Panel plus Immune Activation Status, Immune Cell Typing, Cell Death, MAPK Signaling, PI3K/AKT Signaling and Drug Target panels)  and morphology marker (GeoMx Morphology Kit) mix was added to the staining surface of the slides and left in the humidity chamber at 4⁰C overnight. Following protein staining, the slides were washed in three washed of 1X TBST and fixed by adding 200 µL of 4% PFA for 30 minutes at room temperature. Next, the slides were washed and stained with apropriate amount of nuclear stain using the GeoMx Nuclear Stain Morphology Kit and incubated for 20 min. Finally the slides were washed and mounted using one drop (~50 µL) of Fluoromount G.

scan_protocol: Xenium samples - 5 µm FFPE sections were placed in the sample area of a Xenium slide (10X Genomics, PN-3000941). Following tissue placement slides were dried and placed in a desiccator at room temperature according to manufacturer’s instructions (10X Genomics, CG000578). Slides were deparaffinized, decrosslinked, and prepared for the Xenium Analyzer (10X Genomics, CG000580; 10X Genomics,  with segmentation: CG000749). Slide scanning was then performed on the Xenium Analyzer (10X Genomics, CG000584).

data_processing: Expression data was generated using the on-board Xenium Ranger workflow

label: Xenium probe set

source_name: Lung

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Formalin fixed parrafin embedded (FFPE) tissue sextions from normal and COPD patient lungs were sectioned in 5 µm thick sections and mounted on Superfrost Plus or BOND Plus slides onto the scan area. The slides were deparrafinized and place in staining jar with freshly prepared Citrate Buffer (pH = 6) at hish pressure and temperature at 15 minutes followined by cooling on bench for 25-30 min, for antigen retrieval. Thereafter the slides were washed and blocked with Buffer W for 1 hour in a humidity chamber.

value: Lung

tag: tissue preservation method

value: FFPE

tag: disease

value: Normal

value: male

tag: smoking status

value: Current Smoker


title: FR0002FE34-2

tag: tissue


title: P2_RNA

description:
Library name: P2_RNA
SMART-SEQ2

value: 6-8 weeks

value: Female

tag: batch

value: RNA


title: A549_het2_cell_rep1

description: Library name: Sample 7

tag: genotype


title: P1_RNA

description:
Library name: P1_RNA
SMART-SEQ2

source_name: Blood; Lung

value: Blood; Lung

value: DP

value: Tumor


title: FR00005239-2

value: COPD


title: FR00005239-1


title: Duplike_RNA

description:
Library name: Duplike_RNA
SMART-SEQ2

value: Control

value: Duplike

value: Naive


title: A549_het1_cell_rep2

description: Library name: Sample 5


title: FR00024897-2

value: Non Smoker


title: A549_het1_cell_rep3

description: Library name: Sample 6


title: FR00024897-1


title: CDP_RNA

description:
Library name: CDP_RNA
SMART-SEQ2

value: CDP


title: IR-RL-14-2

value: Lung

value: female


title: C3R_RNA

description:
Library name: C3R_RNA
SMART-SEQ2

value: Blood

value: CTC; DP; WBC


title: A549_het1_cell_rep1

description: Library name: Sample 4


title: IR-RL-21-23-1

value: FFPE

value: Normal

value: male


title: IR-RL-21-23-2


title: A549_WT_cell_rep3

description: Library name: Sample 3

value: WT


title: IR-RL-22-14-2


title: C2R_RNA

description:
Library name: C2R_RNA
SMART-SEQ2

value: Blood; Lung

value: 6-8 weeks

value: Female

value: RNA


title: A549_WT_cell_rep2

description: Library name: Sample 2


title: IR-RL-22-14-1


title: IR-RL-32-22-2

value: Former Smoker


title: IR-RL-32-22-1


title: IR-RL-29-19

value: COPD

value: Current Smoker


title: C2N_RNA

description:
Library name: C2N_RNA
SMART-SEQ2

source_name: Lung; Blood

value: Lung; Blood

value: DP; WBC

value: Tumor


title: IR-RL-16-8-02

value: Lung


title: A549_WT_cell_rep1

description: Library name: Sample 1


title: IR-RL-16-8-01


title: C1R_RNA

description:
Library name: C1R_RNA
SMART-SEQ2


title: Multiome,AMEpiC,TxSEC,ATAC

city: Taipei City

first: Ting-Han

last: Chang

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of Oral Biology, College of Dentistry

description: Library name: AMEpiC_CONV02_ATAC

library_source: genomic single cell

data_processing:
For miRNA data, adapter clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach. Low-quality bases were trimmed from the 3′ end of reads, and reads shorter than 18 nucleotides after trimming were discarded.
For single-nucleus multiome data, sequencing reads were processed using the 10x Genomics Cell Ranger ARC pipeline to generate gene expression and chromatin accessibility count matrices.
Assembly: Human reference genome GRCh38 (hg38) was used for read alignment and annotation.
Supplementary files format and content: Processed data files include a raw feature-barcode count matrix generated by the 10x Genomics Cell Ranger ARC pipeline in HDF5 format (raw_feature_bc_matrix.h5), containing gene expression and chromatin accessibility counts for all detected barcodes prior to cell filtering. In addition, ATAC fragment files (atac_fragments.tsv.gz) are provided, which contain genomic coordinates of ATAC-seq fragments for downstream reanalysis and custom peak calling.

source_name: Primary cells

growth_protocol: AM-1 cells were maintained in KGM Gold medium, while primary ameloblastoma-derived epithelial cells (AMEpiCs) were cultured in KGM Gold supplemented with 10 µM Y-27632 at 37 °C in a humidified atmosphere containing 5% CO₂. Primary mesenchymal stromal cells (MSCs) were cultured in complete α-MEM (α-MEM with 10% FBS and 1% penicillin/streptomycin/amphotericin B) until reaching approximately 80% conﬂuence. Then, cells were washed with PBS twice and cultured in serum-free α-MEM for 48 hours. The conditioned medium was subsequently collected and centrifuged at 4,400 rpm for 20 min to remove cellular debris. The supernatant was then concentrated using a 30 kDa molecular-weight-cutoff ultrafiltration unit (Cytiva, #GE28-9323-61) by centrifugation at 4,400 rpm for approximately 30 min, repeated twice, with one intermediate wash using PBS.

extract_protocol:
Multiome: Single nuclei were isolated according to the manufacturer’s protocol prior to downstream library preparation.
Single-nucleus multiome libraries (snRNA-seq and snATAC-seq) were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform according to the manufacturer’s instructions.

treatment_protocol: Cells were exposed to mesenchymal stromal cell–derived secretome or vehicle control and maintained in growth factor–free KBM Gold medium for 72 h prior to RNA or single-nucleus multiome profiling.

value: Primary cells

value: Epithelial cells

value: ATAC


title: C1N_RNA

description:
Library name: C1N_RNA
SMART-SEQ2

value: CTC; DP; WBC


title: IR-RL-23-23-01

value: FFPE

value: male


title: IR-RL-23-23-02


title: C1L_RNA

description:
Library name: C1L_RNA
SMART-SEQ2

value: Blood; Lung


title: Multiome,AMEpiC,TxSEC,GEX

description: Library name: AMEpiC_CONV02_RNA

value: mRNA


title: Liver, 32-mo, WT,PZ19b, rep3

description:
Library name: PZ19b-072L
RNA input 4 ug

source_name: Liver

value: Liver

value: WT

value: PZ-19b for 5 mo


title: Liver, 26-mo, WT,PZ19b, rep2

description:
Library name: PZ19b-050
RNA input 4 ug


title: B16F10_RNA

description:
Library name: B16F10_RNA
SMART-SEQ2

value: Control

value: CTC

value: RNA


title: IR-RL-029-07

type: other

hyb_protocol: Following protein staining, the slides were washed in three washed of 1X TBST and fixed by adding 200 µL of 4% PFA for 30 minutes at room temperature. Next, the slides were washed and stained with apropriate amount of nuclear stain using the GeoMx Nuclear Stain Morphology Kit and incubated for 20 min. Finally the slides were washed and mounted using one drop (~50 µL) of Fluoromount G.

molecule: other

label_protocol: Appropriate volume (200µl per slide)  of diluted detection antibody (Human IO Core Protein Panel plus Immune Activation Status, Immune Cell Typing, Cell Death, MAPK Signaling, PI3K/AKT Signaling and Drug Target panels)  and morphology marker (GeoMx Morphology Kit) mix was added to the staining surface of the slides and left in the humidity chanber at 4⁰C overnight

extract_protocol: Formalin fixed parrafin embedded (FFPE) tissue sextions from normal and COPD patient lungs were sectioned in 5 µm thick sections and mounted on Superfrost Plus or BOND Plus slides onto the scan area. The slides were deparrafinized and place in staining jar with freshly prepared Citrate Buffer (pH = 6) at hish pressure and temperature at 15 minutes followined by cooling on bench for 25-30 min, for antigen retrieval. Thereafter the slides were washed and blocked with Buffer W for 1 hour in a humidity chamber.

tag: disease state

value: COPD

value: female

value: Current Smoker


title: Secretome(SEC), GMSC01

description: Library name: GMSC01_SEC

data_processing:
For miRNA data, adapter clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach. Low-quality bases were trimmed from the 3′ end of reads, and reads shorter than 18 nucleotides after trimming were discarded.
Assembly: Human reference genome GRCh38 (hg38) was used for read alignment and annotation.
Supplementary files format and content: CSV files containing counts for each RNA-seq and miRNA-seq sample.

growth_protocol: Primary mesenchymal stromal cells (MSCs) were cultured in complete α-MEM (α-MEM with 10% FBS and 1% penicillin/streptomycin/amphotericin B) until reaching approximately 80% conﬂuence.

extract_protocol:
Total RNA was extracted using TRIzol reagent (for mRNA/RNA-seq) or TRIzol LS reagent (for microRNA profiling) according to the manufacturers’ instructions. RNA concentration and integrity were assessed before library preparation.
miRNA sequencing libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer’s instructions. Adapters were sequentially ligated to the 3′ and 5′ ends of miRNAs, followed by universal cDNA synthesis with unique molecular identifier (UMI) assignment, cDNA purification, library amplification, and final library cleanup.

treatment_protocol: Then, cells were washed with PBS twice and cultured in serum-free α-MEM for 48 hours. The conditioned medium was subsequently collected and centrifuged at 4,400 rpm for 20 min to remove cellular debris. The supernatant was then concentrated using a 30 kDa molecular-weight-cutoff ultrafiltration unit (Cytiva, #GE28-9323-61) by centrifugation at 4,400 rpm for approximately 30 min, repeated twice, with one intermediate wash using PBS.

value: Primary cells

value: Mesenchymal stromal cells

value: Female

value: SEC:concentrated conditioned medium (> 30 kDa)


title: Liver, 26-mo, WT,PZ19b, rep1

description:
Library name: PZ19b-049
RNA input 4 ug


title: Secretome(SEC), GMSC02

description: Library name: GMSC02_SEC

value: Male


title: WBC_DNA

description:
Library name: WBC_DNA
MALBAC

value: WBC

value: 6-8 weeks

value: Naive

value: DNA


title: IR-LL-14-011

value: Normal


title: IR-RL-17-026-2

value: Non Smoker


title: Secretome(SEC), AMMSC_CONV04

description: Library name: AMMSC_CONV04_SEC


title: Liver, 27-mo, WT, Veh, rep3

description:
Library name: PZ19b-069
RNA input 4 ug

value: Liver

value: WT

value: Veh (10% PG) for 5 mo


title: PltLike_DNA

description:
Library name: PltLike_DNA
MALBAC

value: Control

value: PltLike


title: IR-RL-17-026-1

value: female


title: Liver, 26-mo, WT, Veh, rep2

description:
Library name: PZ19b-046
RNA input 4 ug


title: P4_DNA

description:
Library name: P4_DNA
MALBAC

value: Blood

value: DP

value: Tumor


title: Secretome(SEC), AMMSC_CONV02

description: Library name: AMMSC_CONV02_SEC

value: Primary cells

value: Mesenchymal stromal cells

value: Female

value: SEC:concentrated conditioned medium (> 30 kDa)


title: 941-4

city: hefei

first: Xinwei

last: Zhao

state: anhui

address: changjiang strest

institute: anhui agricultural university

description: Library name: sample24

data_processing:
RNA extracted from Arabidopsis thaliana, Illumina PE150 library construction. Raw reads demultiplexed with Bcl2fastq v2.20.0.422, quality checked by FastQC v0.10.1, trimmed via Cutadapt v1.9.1. Clean reads mapped to TAIR10.51 with HISAT2 v2.2.1. Transcripts assembled with StringTie v1.3.3b, novel transcripts annotated with Cuffcompare v2.2.1. SNV/InDel called by samtools v0.1.19 and annotated by ANNOVAR v2013.02.11. Gene counts quantified with HTSeq v0.6.1; global RNA-seq QC via RSeQC. DEGs calculated by DESeq2 v1.26.0, GO/KEGG functional enrichment conducted. Alternative splicing analyzed with rMATS v4.1.0; DEXSeq v1.18.4 for DEU.
Assembly: Arabidopsis thaliana TAIR10.51
Supplementary files format and content: all.fpkm_anno.xls

source_name: Whole plant

extract_protocol:
Plant material preparation: Arabidopsis thaliana materials included wild-type Col-0, uap1-1 and uap1-2 mutant seedlings. Seeds were germinated and grown to 10-day-old seedlings under standard normal growth conditions; a subset of seedlings was treated at 4 °C for 24 h cold stress before tissue collection. Whole seedling tissues were harvested and immediately frozen in liquid nitrogen for RNA extraction. Total RNA isolation: Total RNA extraction, integrity detection and purity quantification were performed by Azenta Life Sciences (Suzhou, China) following their proprietary standard RNA extraction protocol for plant tissue. Briefly, high-quality intact total RNA was purified from frozen seedling tissues, followed by rigorous quality control to verify RNA integrity number (RIN), OD260/280 and OD260/230 ratios to exclude degraded or contaminated RNA samples.
Total RNA was isolated from Arabidopsis tissues and quality-checked for purity, concentration and integrity (RIN) via Nanodrop, agarose electrophoresis and Agilent 2100. Poly(A) mRNA was enriched with oligo(dT) beads to remove non-coding RNAs. Purified mRNA was randomly fragmented to 200–300 bp. First-strand cDNA was synthesized with random hexamers and M-MuLV reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. cDNA fragments were end-repaired, 3’-A-tailed, and ligated to Illumina barcoded PE adapters. Target-size fragments were purified by magnetic beads and amplified via 10–15 cycles of high-fidelity PCR. Libraries were quality-controlled by qPCR and Agilent 2100, then pooled and sequenced on Illumina platform with PE150 strategy.

value: Whole plant

value: uap1-2 homozygous T-DNA insertion mutant (Col-0 background)


title: P2_DNA

description:
Library name: P2_DNA
MALBAC

value: Lung

value: 6-8 weeks

value: DNA


title: Liver, 26-mo, WT, untreated, rep1

description:
Library name: Old040
RNA input 4 ug

value: Liver

value: WT

value: untreated


title: Secretome(SEC), AMMSC_CONV01

description: Library name: AMMSC_CONV01_SEC


title: AM-1 cells, AM_CONV03-SEC

description:
Library name: AM_CONV03-SEC
Column name in All_counts.csv: AM_CONV03-SEC

data_processing:
Raw sequencing data were converted to FASTQ format using Illumina bcl2fastq software.
Assembly: Human reference genome GRCh38 (hg38) was used for read alignment and annotation.
Supplementary files format and content: CSV files containing counts for each RNA-seq sample.

extract_protocol:
Total RNA was extracted using TRIzol reagent (for mRNA/RNA-seq) or TRIzol LS reagent (for microRNA profiling) according to the manufacturers’ instructions. RNA concentration and integrity were assessed before library preparation.
mRNA libraries were prepared from 1 µg of total RNA, with poly(A)+ RNA enrichment using oligo(dT) beads. Strand-specific libraries were generated by dUTP incorporation during second-strand synthesis, followed by adaptor ligation and PCR amplification.

value: Epithelial cells


title: P1_DNA

description:
Library name: P1_DNA
MALBAC

value: Blood; Lung


title: 941-2

description: Library name: sample22


title: AM-1 cells, AM_CONV02-SEC

description:
Library name: AM_CONV02-SEC
Column name in All_counts.csv: AM_CONV02-SEC


title: Liver, 3-mo, WT, untreated, rep2

description:
Library name: YM04
RNA input 4 ug


title: Duplike_DNA

description:
Library name: Duplike_DNA
MALBAC

value: Control

value: Duplike

value: Naive


title: 941-1

description: Library name: sample21


title: AM-1 cells, AM_CONV01-SEC

description:
Library name: AM_CONV01-SEC
Column name in All_counts.csv: AM_CONV01-SEC


title: 457-4

description: Library name: sample20

value: uap1-1 homozygous T-DNA insertion mutant (Col-0 background)


title: CDP_DNA

description:
Library name: CDP_DNA
MALBAC

value: CDP


title: Ptbp1 siRNA 2

city: hangzhou

first: Mengran

last: Zhang

state: zhejiang

address: shilongshan street

institute: westlake university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: astrocyte

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: astrocyte

value: Ptbp1 siRNA


title: C3R_DNA

city: Charlestown

description:
Library name: C3R_DNA
MALBAC

value: Blood

value: CTC; DP; WBC

value: Female

value: Tumor


title: Ptbp1 siRNA 1


title: AM-1 cells, GM_CONV02-SEC

description:
Library name: GM_CONV02-SEC
Column name in All_counts.csv: GM_CONV02-SEC


title: Liver, 3-mo, WT, untreated, rep1

description:
Library name: YM03
RNA input 4 ug


title: 457-2

description: Library name: sample18

value: Whole plant


title: AM-1 cells, C3

description:
Library name: AM-1_C-3
Column name in All_counts.csv: AM-1_C-3

value: Vehicle (PBS)


title: NC siRNA 1

value: NC siRNA


title: NC siRNA 2


title: 457-1

description: Library name: sample17


title: WT-4

description: Library name: sample16

value: Wild type (Col-0)


title: exo_shNFAT3_4_C

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Library name: exo_shNFAT3_4_C

library_source: other

data_processing:
Small RNA-Seq data were analyzed by GenoSplice using the CAP-miRSeq pipeline
Assembly: hg19
Supplementary files format and content: raw count matrix for all mature miRNA

source_name: luminal breast cancer

growth_protocol: T-47D-derived extracellular vesicles (EVs) were isolated by differential centrifugation and ultracentrifugation. Briefly, cells were cultured to ~70% confluence and incubated for 48 h in EV-depleted medium. Conditioned medium was sequentially centrifuged at 300 g, 2,000 g, and 10,000 g to remove cells and debris, followed by ultracentrifugation at 120,000 g for 90 min at 4°C. EV pellets were washed twice in PBS and re-pelleted under identical conditions. Final EVs preparations were resuspended in PBS, aliquoted, and stored at -80°C. Particle size distribution and concentration were assessed by nanoparticle tracking analysis (NTA) using ZetaView instruments (Particle Metrix). EV preparations were used within one freeze–thaw cycle

extract_protocol:
In order to control the efficacy of miRNA loading, RNA extraction and RT-qPCR was performed on EVs. QIAGEN miRNeasy Micro Kit (#217084) was used to retrieve miRNA loaded in extracellular vesicles as well as endogenous miRNAs
Small RNA Library Prep Kit NEB

value: luminal breast cancer

value: mammary

value: EVs production


title: AM-1 cells, C2

description:
Library name: AM-1_C-2
Column name in All_counts.csv: AM-1_C-2

value: Epithelial cells


title: C1N_DNA

description:
Library name: C1N_DNA
MALBAC

value: Blood; Lung

value: 6-8 weeks

value: DNA


title: WT-3

description: Library name: sample15


title: C1L_DNA

description:
Library name: C1L_DNA
MALBAC


title: AM-1 cells, C1

description:
Library name: AM-1_C-1
Column name in All_counts.csv: AM-1_C-1


title: exo_shNFAT3_4_B

description: Library name: exo_shNFAT3_4_B


title: exo_shNFAT3_4_A

description: Library name: exo_shNFAT3_4_A


title: 4_350

description:
Library name: 4_350
Fresh frozen Spatial transcriptomics

data_processing:
Samples RL_15, RL_16, and RL_17 - 10X provided cellranger mkfastq and count version 6.0.1 using standard parameters
Visium - 10X provided spaceranger mkfastq and count version 1.3.1 using standard parameters
All remaining scRNA-Seq samples - 10X provided cellranger mkfastq and count version 7.0.1 using standard parameters
Assembly: 10X provided GRCh38-2020-A transcriptome
Supplementary files format and content: scRNA-Seq - compressed filtered gene bc matrices output folder
Supplementary files format and content: Spatial Transcriptomics - whole compressed output folder excluding bams as generated by spaceranger version 1.3.1
Library strategy: Spatial Transcriptomics

extract_protocol:
We used three distinct lung sections (1”) –   parenchymal, peri-bronchial and sub-pleural regions-for each lung sample. The lung lobes were weighed and placed into Gentle MACS C-tube (Miltenyi, Gaithersburg, MD) with Liberase (Cat# 5401127001; Roche, Basel, Switzerland) enzymatic cocktail with 1% DNase. The tubes were then transferred to the gentleMACS dissociator (Miltenyi, Gaithersburg, MD) and the manufacturer’s protocol for human lung digestion was run.  The sample tubes were then transferred to the MACSmix rotator and incubated at 370C for 30 minutes with constant rotation. After incubation, the cell suspension was mixed with 5 mL of DMEM with 10% FBS and strained through a 100-micron MACS Smart Strainer. Thereafter, the suspension was centrifuged at 500g for 10 minutes at 40C, the supernatant was discarded, and 1 mL of RBC lysis buffer was added to the cell pellet to digest RBCs. The suspension was left on ice for 5 min in RBC lysis buffer and then 4 mL of ice-cold PBS with 10% FBS was added to stop the lysis. The suspension was again centrifuged at 500g for 10 minutes at 40C. The cell pellet was suspended in 5 mL PBS with 10% FBS, and cell number and viability were checked using AO/PI staining on a Nexcelom Cellometer Auto2000. This cell suspension was immediately used for C12FdG staining as described earlier [37] and submitted to the Genomics Research Core at URMC for library preparation for scRNA seq.
scRNA-seq -Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s NovaSeq 6000 at a mean sequence depth of 30,000 reads per cell. Read alignment was performed to GRCh38 genome. Spatial transriptomics - 5um sections were placed on the spatially barcoded capture areas of a 10X Genomics Visium Gene Expression Slide (10X Genomics, Pleasanton, CA). Following tissue placement, slide drying, and overnight incubation in a desiccator, the slide was deparaffinized, H&E stained, and imaged using a VS120 Slide Scanner (Olympic) at 20X magnification. Sequence ready libraries were then constructed according to the manufacturer’s instructions (10X Genomics, CG000407). Final libraries were sequenced on the NovaSeq6000 (Illumina, San Diego, CA) to obtain at least 50,000 reads per spot.

treatment_protocol: The human lung samples were procured through United Network for Organ Sharing facilitated by the International Institute for the Advancement of Medicine (IIAM). Few of the samples used for spatial transcriptomics/proteomics were obtained from commercial sources (Origene)

value: Lung

value: male

value: Current Smoker

value: COPD


title: WT-1

description: Library name: sample13


title: 3_350

description:
Library name: 3_350
Fresh frozen Spatial transcriptomics

value: Former Smoker


title: CM-4

city: MONROVIA

first: Yahuei

last: Kuo

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to mm10 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using in-house R scripts
Assembly: mm10
Supplementary files format and content: tab delimited text file gene expression counts

source_name: PBMC

extract_protocol:
The bone marrow mononuclear cells were collected from the femurs, tibias, and pelvic bones using a mortar and pestle of mice and subjected to RBC lysis. After RBC lysis, total RNA was isolated from BM mononuclear cells using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, 80224).
micriRNAseq: illumina microRNAseq protocol (Minor Modification by core). mRNAseq: KAPA mRNA HyperPrep Kit
lib pre of microRNAseq and mRNAseq were done respectively by microRNAseq protocol and mRNAseq protocol Using total RNA samples

value: PBMC

value: CM


title: 941-C4

description: Library name: sample12

value: Whole plant

value: uap1-2 homozygous T-DNA insertion mutant (Col-0 background)

value: Cold (4°C for 24-h)


title: 3_346

description:
Library name: 3_346
Fresh frozen Spatial transcriptomics


title: CM-3


title: exo_shNFAT3_3_B

description: Library name: exo_shNFAT3_3_B

value: luminal breast cancer


title: 941-3

description: Library name: sample23


title: Liver, 3-mo, WT, untreated, rep3

description:
Library name: YM08
RNA input 4 ug

value: Liver

value: WT

value: untreated


title: 2_350

description:
Library name: 2_350
Fresh frozen Spatial transcriptomics

value: Non Smoker

value: Normal


title: 941-C3

description: Library name: sample11


title: exo_shNFAT3_3_A

description: Library name: exo_shNFAT3_3_A

value: mammary

value: EVs production


title: CM-2


title: 2_346

description:
Library name: 2_346
Fresh frozen Spatial transcriptomics

value: Lung

value: female


title: 941-C2

description: Library name: sample10


title: 457-3

description: Library name: sample19

value: uap1-1 homozygous T-DNA insertion mutant (Col-0 background)


title: exo_shCtl_C

description: Library name: exo_shCtl_C


title: 1_350

description:
Library name: 1_350
Fresh frozen Spatial transcriptomics


title: 941-C1

description: Library name: sample9


title: AM-1 cells, GM_CONV03-SEC

description:
Library name: GM_CONV03-SEC
Column name in All_counts.csv: GM_CONV03-SEC

value: Epithelial cells

value: Female


title: CM-1

value: PBMC

value: CM


title: C2R_DNA

description:
Library name: C2R_DNA
MALBAC

value: Blood; Lung

value: CTC; DP; WBC

value: 6-8 weeks

value: Tumor

value: DNA


title: exo_shCtl_B

description: Library name: exo_shCtl_B

value: luminal breast cancer


title: Ctrl-6

value: Ctrl


title: AM-1 cells, GM_CONV01-SEC

description:
Library name: GM_CONV01-SEC
Column name in All_counts.csv: GM_CONV01-SEC


title: 1_346

description:
Library name: 1_346
Fresh frozen Spatial transcriptomics

value: male

value: Non Smoker

value: Normal


title: 457-C4

description: Library name: sample8

value: Whole plant

value: Cold (4°C for 24-h)


title: C2N_DNA

description:
Library name: C2N_DNA
MALBAC

value: Lung; Blood

value: DP; WBC


title: exo_shCtl_A

description: Library name: exo_shCtl_A

value: mammary

value: EVs production


title: 457-C3

description: Library name: sample7

value: uap1-1 homozygous T-DNA insertion mutant (Col-0 background)


title: Ctrl-5

value: PBMC


title: RL_17_Cells

description:
Library name: RL_17_Cells
10x Genomics

data_processing:
Samples RL_15, RL_16, and RL_17 - 10X provided cellranger mkfastq and count version 6.0.1 using standard parameters
Visium - 10X provided spaceranger mkfastq and count version 1.3.1 using standard parameters
All remaining scRNA-Seq samples - 10X provided cellranger mkfastq and count version 7.0.1 using standard parameters
Assembly: 10X provided GRCh38-2020-A transcriptome
Supplementary files format and content: scRNA-Seq - compressed filtered gene bc matrices output folder
Supplementary files format and content: Spatial Transcriptomics - whole compressed output folder excluding bams as generated by spaceranger version 1.3.1

value: Lung

value: female


title: C1R_DNA

description:
Library name: C1R_DNA
MALBAC

value: Blood; Lung

value: CTC; DP; WBC

value: 6-8 weeks

value: Female

value: Tumor


title: Ctrl-4

value: Ctrl


title: HD-04

city: New Orleans

first: Weiqiang

last: Lin

state: LA

address: 1324 Tulane Ave

institute: Tulane University

description: Library name: HD-04

data_processing:
Raw data were preprocessed and aligned using the 10x Genomics Space Ranger
Assembly: Human genome GRCh38
Supplementary files format and content: cytassist_image.tiff: cytassist image
Supplementary files format and content: filtered_feature_bc_matrix.h5: Transcript counts
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions.parquet: spatial barcodes and the coordinates
Supplementary files format and content: aligned_fiducials.jpg: aligned fiduciats of the tissue image
Supplementary files format and content: count.csv: normalized gene count
Supplementary files format and content: meta.csv: meta information
Supplementary files format and content: coords.csv: spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Human femoral head

extract_protocol:
Human femoral head specimens were collected during hip arthroplasty, stored temporarily in culture medium at 4 °C and transferred to Tulane University School of Medicine. Bone blocks were excised from the weight-bearing region under continuous cooling with sterile PBS, fixed in 10% formalin at 4 °C for 48 h, and decalcified sequentially in RNase-free 14% and 20% EDTA at 4 °C with regular solution changes. Samples were then dehydrated through graded ethanol, cleared in xylene and embedded in low-melting-point paraffin.
Spatial transcriptome sequencing libraries were prepared using the 10x Genomics Visium HD Spatial Gene Expression Slides & Reagent Kit according to the manufacturer’s instructions.

value: Human femoral head

tag: slide parameters


title: 457-C2

description: Library name: sample6

value: Whole plant


title: RL_16_Cells

description:
Library name: RL_16_Cells
10x Genomics

value: male

value: Current Smoker

value: COPD


title: Ctrl-3


title: 457-C1

description: Library name: sample5

value: Cold (4°C for 24-h)


title: RL_15_Cells

description:
Library name: RL_15_Cells
10x Genomics

value: Normal


title: HD-03

description: Library name: HD-03


title: HD-02

description: Library name: HD-02


title: exo_shNFAT3_3_C

description: Library name: exo_shNFAT3_3_C

value: luminal breast cancer

tag: cell type

value: mammary

value: EVs production


title: Ctrl-2

value: PBMC


title: WT-2

description: Library name: sample14

value: Wild type (Col-0)


title: Liberase_LUL

description:
Library name: Liberase_LUL
10x Genomics

value: Lung

value: female


title: WT-C4

description: Library name: sample4


title: Ctrl-1


title: HD-01

description: Library name: HD-01


title: IR_RL_034_2

description:
Library name: IR_RL_034_2
10x Genomics


title: B16F10_DNA

description:
Library name: B16F10_DNA
MALBAC

value: Control

value: CTC

value: DNA


title: WT-C3

description: Library name: sample3


title: Lck_Hashtag_Data

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: Library name: Lck-W1-CSP

data_processing:
Resulting cDNA libraries were sequenced on NextSeq 2000 (Illumina, NextSeq 1000/2000 Control Software 1.7.2.48444) with NextSeq 1000/2000 P3 XLEAP-SBS 100-cycle kit.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 109 and prepared using the mkref tool from 10x Cell Ranger v8.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from 10x Cell Ranger v8.0.1 using R2 sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm39 v109 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples and finalized results.
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Splenocytes were collected on day 5 post LM-OVA-immunization. Samples were enriched for CD8+ cells by using Dynabeads™ Untouched™ Mouse CD8 Cells Kit (Cat#11417D, Invitrogen) according to manufacturer’s instructions. The cells were resuspended in HBSS and stained with with LIVE/DEAD near-IR dye, anti-CD8a BV421, anti-CD45.1 PE, and anti-CD45.2 APC antibodies together with TotalSeq-C Hashtag antibodies for multiplexing (BioLegend; MH1: #155861, MH2: #155863, MH3: #155865, MH5: #155869, MH6: #155871, MH7: #155873, MH8: #155875, MH9: #155877, MH10: #155879). Viable CD8α+, CD45.2+OT-I cells were FACS sorted.
Cells were loaded onto a 10X Chromium X machine (10X Genomics). The sequencing libraries were prepared using the Chromium GEM-X Single Cell 5′ Reagent Kits v3 with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10x Genomics; #PN-1000263, #PN-1000286, #PN-1000541, #PN-1000190, #PN-1000215, #PN-1000250), following the manufacturer's protocol (#CG000736 Rev A).

value: spleen

tag: cell line

value: CD8+ T cells

value: WT/cLCK KO


title: WT-C2

description: Library name: sample2

value: Whole plant

tag: treatment