title: AdrD9292_BC, AdrD9292_PBMC; STB5, STP5 [TCR]

description:
Library name: A9292BCTCR
10x Genomics 5'


title: AdrD9292_BC, AdrD9292_PBMC; STB5, STP5 [GEX]

status: Public on Jun 25 2026

type: SRA

city: Taoyuan

first: Chuang-Wei

last: Wang

address: No. 5, Fusing St

country: Taiwan

institute: cgmh

description:
Library name: A9292BCGEX
10x Genomics 5'

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cell Ranger (10x Genomics) and Space Ranger (10x Genomics). Downstream analyses were performed using Seurat. For scRNA-seq quality control, cells with >20% mitochondrial gene content, fewer than 200 detected genes, or a number of detected genes greater than the upper quartile plus 1.5 × interquartile range (UQ + 1.5 × IQR) were excluded. For spatial analysis, spots located outside the tissue were removed.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98); GRCh38-2020-A
Supplementary files format and content: For scRNA-seq, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz were provided. For the TCR library, filtered_contig_annotations.csv.gz was also provided.
Supplementary files format and content: For Visium, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, as well as spatial information generated by Space Ranger, were provided.

molecule: total RNA

organism: Homo sapiens

source_name: Blister cell, PBMC

extract_protocol:
scRNA-seq: Lesional blister fluid collected from acute-stage patients was centrifuged at 750 × g for 10 minutes to isolate lesional blister cells (BC). Peripheral blood mononuclear cells (PBMCs) were isolated from ethylenediaminetetraacetic acid (EDTA)–anticoagulated blood by Ficoll density-gradient centrifugation (Cytiva).  Visium: FFPE skin sections (5 µm) were cut using a microtome and processed according to the Visium protocol.
scRNA-seq: Library preparation, including cDNA synthesis and library construction, was performed according to the manufacturer's Single Cell 5' v2 protocol (10x Genomics). Library quality was assessed using the Agilent 2200 TapeStation system, and sequencing was performed on the Illumina NovaSeq 6000 platform with a 150-bp read length. Abbreviations: GEX — gene expression library; TCR — T cell receptor library; CSP — multiplexed sample library.  Visium: Spatial transcriptome sequencing libraries were prepared using the 10x Genomics Visium Spatial Gene Expression for FFPE kit (v1 and v2), following the manufacturer's protocol.

tag: cell type

value: Blister cell, PBMC

tag: disease

value: SJS/TEN


title: AdrD9712_BC; STB7 [TCR]

description:
Library name: A9712BCTCR
10x Genomics 5'

source_name: Blister cell

value: Blister cell


title: AdrD9712_BC; STB7 [GEX]

description:
Library name: A9712BCGEX
10x Genomics 5'


title: AdrD8172_BC; STB3 [TCR]

description:
Library name: AD8172CT
10x Genomics 5'


title: AdrD5833_BC; STB2 [GEX]

description:
Library name: AD5833G
10x Genomics 5'


title: ENT_Set6_E2

city: NEW YORK

first: Panos

last: Roussos

state: NY

address: 1411 Madison Ave Apt 4E

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: ENT_Set6_E2
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.

library_source: transcriptomic

data_processing:
Paired-end snRNA-seq library reads were aligned to the hg38 reference genome using STARsolo59 and sample pools were demultiplexed using genotype matching via vireoSNP60. Donor identity for demultiplexed samples was assigned through comparison with SNP-array genotypes using the mbv module in QTLtools61.Preprocessing and cell clustering were performed with Scanpy (v1.9.8)62. First, we filtered cells with low quality and kept cells with: cell counts in each tissue from each donor (>150 cells), mitochondrial content (< 5%), total counts (< 50,000), and gene counts (1,000-10,000). Candidate doublets were detected using Scrublet63, and cells with a doublet score > 0.15, or clusters expressing markers of multiple cell types, were removed. Then, the gene counts were normalized to median total counts and logarithmized. The top 5,000 highly variable protein-coding genes (HVGs) on autosomal chromosomes were selected. PCA dimension reduction based on HVGs was performed. The batch effects (identity of donors and tissue sites) were corrected with Harmony64. We then computed the neighborhood graph and embedded it into two dimensions for visualization with UMAP26. Finally, the Leiden graph-clustering65 method was applied to cluster the neighborhood graph of cells (resolution = 1.5). Cell-type annotations were performed based on marker genes
Note: Although HTOs were included during library preparation, they were not used for demultiplexing within each pooled set, so the HTOs are not required to interpret the raw fastq data.  Instead, we relied entirely on genotype-based demultiplexing using genotype data.
Assembly: GRCh38
Supplementary files format and content: h5ad file with raw  count matrix and cell annotation

molecule: nuclear RNA

source_name: Olfactory Epithelium

extract_protocol:
Frozen nasal tissue was homogenized in a cold lysis buffer (0.32 M Sucrose, 5 mM CaCl2, 3 mM Magnesium acetate, 0.1 mM, EDTA, 10 mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) with RNAse inhibitors (Takara). The homogenate was filtered through a 40 µm cell strainer, and the flow-through was underlaid with sucrose solution before centrifugation at 107,000 xg for 1 hour at 4 ˚C. The resulting pellets were resuspended in PBS with 0.5% bovine serum albumin (BSA). Six samples were processed simultaneously, with up to 2 million nuclei per sample pelleted at 500 xg for 5 minutes at 4 ˚C. The nuclei were then resuspended in 100 µl staining buffer (2% BSA, 0.02% Tween-20, 10 mM Tris, 146 mM NaCl, 1 mM CaCl2 and 21 mM MgCl2) and incubated with 1 µg of a unique TotalSeq-A nuclear hashing antibody (BioLegend) for 30 minutes at 4 ˚C. Prior to fluorescence-activated nucleus sorting (FANS), volumes were adjusted to 250 µl with staining buffer, and 7-Aminoactinomycin D (7-AAD) was added according to the manufacturer’s instructions. 7-AAD positive nuclei were sorted into tubes pre-coated with 5% BSA using a FACSAria flow cytometer (BD Biosciences).
After FANS, the nuclei were washed twice with 200 µl of staining buffer, resuspended in PBS and quantified (Countess II, Life Technologies). Equal numbers of differentially hash-tagged nuclei were combined. Using 10x Genomics single cell 3’ v3.1 reagents, 60,000 nuclei (10,000 per donor) were processed in each of two Chromium G chip lanes (10x Genomics) lanes to create technical replicates. During cDNA amplification for library preparation, 1 µl of a 2 µm HTO cDNA PCR additive primer was included58. Both cDNA and HTO libraries were prepared according to manufacturer’s instructions (10x Genomics and BioLegend, respectively). Libraries were sequenced using the Novaseq platform (Illumina).

tag: tissue

value: Olfactory Epithelium

tag: developmental stage

value: adult


title: AdrD9316_BC; STB4 [TCR]

description:
Library name: A9316BCTCR
10x Genomics 5'


title: AdrD5833_BC; STB2 [TCR]

description:
Library name: AD5833T
10x Genomics 5'


title: HD43_PBMC; HD4 [GEX]

description:
Library name: AC18352G
10x Genomics 5'

source_name: PBMC

value: PBMC

value: HD


title: HD43_PBMC; HD4 [TCR]

description:
Library name: AC18352T
10x Genomics 5'


title: AdrD9292_BC, AdrD9292_PBMC; STB5, STP5 [CSP]

description:
Library name: A9292BCCSP
10x Genomics 5'


title: ENT_Set6_E1

description:
Library name: ENT_Set6_E1
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set5_C1

description:
Library name: ENT_Set5_C1
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set4_C2

description:
Library name: ENT_Set4_C2
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set3_C2

description:
Library name: ENT_Set3_C2
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set3_C1

description:
Library name: ENT_Set3_C1
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set4_C1

description:
Library name: ENT_Set4_C1
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set2_C2

description:
Library name: ENT_Set2_C2
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set2_C1

description:
Library name: ENT_Set2_C1
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set1_C1

description:
Library name: ENT_Set1_C1
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: ENT_Set1_C2

description:
Library name: ENT_Set1_C2
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: CTRL-WM_P07_E12

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: LigandScreen-P07-20230914-093_S285

data_processing:
Sequence reads were aligned using STAR (version 2.7.9a)
Counts matrix was generated using RSEM (version 1.3.1)
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: RSEM_Counts_Cardiopedia-Ligand.xlsx file includes raw counts for each sample

extract_protocol:
Total RNA was isolated using the NuceloMag RNA kit (Macherey-Nagel) on the EpMotion 5075t
RNA libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit (polyA RNA selection) on the EpMotion 5075t

treatment_protocol: hCO were stimulated with a library of 90 ligands (n = 2-5 hCO per ligand in final RNA-seq dataset after passing all quality control). After 24 hours, media was aspirated and hCO were washed with ice cold PBS- and lysed for RNAseq.

tag: cell line


title: Nif_P07_C12

description: Library name: LigandScreen-P07-20230914-091_S283


title: Nif_P07_B12

description: Library name: LigandScreen-P07-20230914-090_S282


title: Nif_P07_E11

description: Library name: LigandScreen-P07-20230914-085_S277


title: Nif_P07_A12

description: Library name: LigandScreen-P07-20230914-089_S281


title: Mav_P07_D11

description: Library name: LigandScreen-P07-20230914-084_S276


title: Mav_P07_C11

description: Library name: LigandScreen-P07-20230914-083_S275


title: Mav_P07_B11

description: Library name: LigandScreen-P07-20230914-082_S274


title: NECA_P07_F10

description: Library name: LigandScreen-P07-20230914-078_S270


title: Mav_P07_A11

description: Library name: LigandScreen-P07-20230914-081_S273


title: NECA_P07_G10

description: Library name: LigandScreen-P07-20230914-079_S271


title: NECA_P07_D10

description: Library name: LigandScreen-P07-20230914-076_S268


title: NECA_P07_C10

description: Library name: LigandScreen-P07-20230914-075_S267


title: NECA_P07_E10

description: Library name: LigandScreen-P07-20230914-077_S269


title: Iloprost_P07_A10

description: Library name: LigandScreen-P07-20230914-073_S265


title: Iloprost_P07_G09

description: Library name: LigandScreen-P07-20230914-071_S263


title: Iloprost_P07_E09

description: Library name: LigandScreen-P07-20230914-069_S261


title: Iloprost_P07_F09

description: Library name: LigandScreen-P07-20230914-070_S262


title: Ozanimod_P07_D09

description: Library name: LigandScreen-P07-20230914-068_S260


title: Ozanimod_P07_C09

description: Library name: LigandScreen-P07-20230914-067_S259


title: MRS2365_P07_D08

description: Library name: LigandScreen-P07-20230914-060_S252


title: Ozanimod_P07_G08

description: Library name: LigandScreen-P07-20230914-063_S255


title: MRS2365_P07_E08

description: Library name: LigandScreen-P07-20230914-061_S253


title: Ozanimod_P07_B09

description: Library name: LigandScreen-P07-20230914-066_S258


title: MRS2365_P07_C08

description: Library name: LigandScreen-P07-20230914-059_S251


title: MRS2365_P07_B08

description: Library name: LigandScreen-P07-20230914-058_S250


title: Fenoldopam_P07_E07

description: Library name: LigandScreen-P07-20230914-053_S245


title: CTRL-DMSO_P07_E06

description: Library name: LigandScreen-P07-20230914-045_S237


title: Fenoldopam_P07_B07

description: Library name: LigandScreen-P07-20230914-050_S242


title: CTRL-DMSO_P07_A07

description: Library name: LigandScreen-P07-20230914-049_S241


title: Fenoldopam_P07_D07

description: Library name: LigandScreen-P07-20230914-052_S244


title: CTRL-DMSO_P07_D06

description: Library name: LigandScreen-P07-20230914-044_S236


title: CTRL-WM_P07_C06

description: Library name: LigandScreen-P07-20230914-043_S235


title: CTRL-WM_P07_B06

description: Library name: LigandScreen-P07-20230914-042_S234


title: CTRL-WM_P07_A06

description: Library name: LigandScreen-P07-20230914-041_S233


title: CCh_P07_G05

description: Library name: LigandScreen-P07-20230914-039_S231


title: CCh_P07_E05

description: Library name: LigandScreen-P07-20230914-037_S229


title: CCh_P07_H05

description: Library name: LigandScreen-P07-20230914-040_S232


title: CCh_P07_F05

description: Library name: LigandScreen-P07-20230914-038_S230


title: Phenylephrine_P07_H04

description: Library name: LigandScreen-P07-20230914-032_S224


title: Phenylephrine_P07_A05

description: Library name: LigandScreen-P07-20230914-033_S225


title: Phenylephrine_P07_G04

description: Library name: LigandScreen-P07-20230914-031_S223


title: Isoprenaline_P07_F04

description: Library name: LigandScreen-P07-20230914-030_S222


title: Isoprenaline_P07_D04

description: Library name: LigandScreen-P07-20230914-028_S220


title: AdrD10022_BC, AdrD10022_PBMC; STB6, STP6 [GEX]

description:
Library name: A10022PBGEX
10x Genomics 5'


title: Isoprenaline_P07_C04

description: Library name: LigandScreen-P07-20230914-027_S219


title: CTRL-DMSO_P07_H03

description: Library name: LigandScreen-P07-20230914-024_S216


title: CTRL-DMSO_P07_G03

description: Library name: LigandScreen-P07-20230914-023_S215


title: CTRL-DMSO_P07_F03

description: Library name: LigandScreen-P07-20230914-022_S214


title: CTRL-WM_P07_E03

description: Library name: LigandScreen-P07-20230914-021_S213


title: Phenylephrine_P07_B05

description: Library name: LigandScreen-P07-20230914-034_S226


title: Phenylephrine_P07_C05

description: Library name: LigandScreen-P07-20230914-035_S227


title: CCh_P07_D05

description: Library name: LigandScreen-P07-20230914-036_S228


title: CTRL-WM_P07_D03

description: Library name: LigandScreen-P07-20230914-020_S212


title: CTRL-WM_P07_C03

description: Library name: LigandScreen-P07-20230914-019_S211


title: DKK-1_P07_E02

description: Library name: LigandScreen-P07-20230914-013_S205


title: DKK-1_P07_D02

description: Library name: LigandScreen-P07-20230914-012_S204


title: DKK-1_P07_C02

description: Library name: LigandScreen-P07-20230914-011_S203


title: Isoprenaline_P07_E04

description: Library name: LigandScreen-P07-20230914-029_S221


title: DKK-1_P07_E01

description: Library name: LigandScreen-P07-20230914-005_S197


title: DKK-1_P07_D01

description: Library name: LigandScreen-P07-20230914-004_S196


title: DKK-1_P07_C01

description: Library name: LigandScreen-P07-20230914-003_S195


title: VEGF-A165_P06_F12

description: Library name: LigandScreen-P06-20230914-094_S190


title: VEGF-A121_P06_E12

description: Library name: LigandScreen-P06-20230914-093_S189


title: AdrD1150_BC; STB1 [TCR]

description:
Library name: AdrD1150_TCR
10x Genomics 5'


title: TGF-β1_P06_D12

description: Library name: LigandScreen-P06-20230914-092_S188


title: Isoprenaline_P07_A04

description: Library name: LigandScreen-P07-20230914-025_S217


title: TRAIL_P06_C12

description: Library name: LigandScreen-P06-20230914-091_S187


title: TNF-a_P06_B12

description: Library name: LigandScreen-P06-20230914-090_S186


title: Thrombin_P06_A12

description: Library name: LigandScreen-P06-20230914-089_S185


title: ENT_Set5_C2

description:
Library name: ENT_Set5_C2
The labels "_C"  and "_E" in the sample titles do not represent any biological condition, experimental group, or technical variable. These are internal lab sample ids. All samples were processed using the same experimental protocols and conditions.


title: Apelin_P06_E11

description: Library name: LigandScreen-P06-20230914-085_S181


title: PGE2_P06_B11

description: Library name: LigandScreen-P06-20230914-082_S178


title: RSPO-1_P06_F11

description: Library name: LigandScreen-P06-20230914-086_S182


title: Pleiotrophin_P06_A11

description: Library name: LigandScreen-P06-20230914-081_S177


title: PLG_P06_H10

description: Library name: LigandScreen-P06-20230914-080_S176


title: PEDF_P06_G10

description: Library name: LigandScreen-P06-20230914-079_S175


title: PDGF-BB_P06_F10

description: Library name: LigandScreen-P06-20230914-078_S174


title: Nif_P07_D12

description: Library name: LigandScreen-P07-20230914-092_S284


title: PTH_P06_D10

description: Library name: LigandScreen-P06-20230914-076_S172


title: PDGF-AA_P06_E10

description: Library name: LigandScreen-P06-20230914-077_S173


title: OXT_P06_A10

description: Library name: LigandScreen-P06-20230914-073_S169


title: Noradrenaline_P06_H09

description: Library name: LigandScreen-P06-20230914-072_S168


title: GE30_0Gy_d2, CT, batch_2

city: Mannheim

first: Ahmad

last: Sami

state: Baden-Württemberg

address: Theodor-Kutzer-Ufer 1-3

department: Department of Radiation Oncology

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

description: Library name: GE30_0Gy_d2

data_processing:
Cleaned raw data after index sequences removal were provided by BGI Genomics
Gene raw read counts from the RNA-seq data were calculated with the Kallisto (pseudoalignment) program
Low count reads were removed with the filterByExpr function, followed by TMM normalisation with EdgeR library
Normalised log2 CPM values were obtained with the voomWithQualityWeights function from the limma pacage
Assembly: Homo_sapiens GRCh38 cdna collection
Supplementary files format and content: Raw counts and log2 CMP normalised data are saved as .csv files, containing data for all samples

source_name: in-vitro fibroblasts

growth_protocol: Early-passage fibroblast cultures were grown in AmnioMAXTM C-100 medium (Thermo Fisher, Darmstadt, Germany), supplemented with 7.5% AmnioMAXTM C-100 supplement, 7.5% fetal bovine serum (HyClone, Fisher Scientific GmbH, Schwerte, Germany, 2 mM glutamin and penicillin/streptomycin.

extract_protocol:
Total cellular RNA was extracted on day 0 from non-irradiated fibroblasts and on day 2 from irradiated and non-irradiated fibroblasts using Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.
Libraries were prepared by the BGI Genomics company as a commercial service

treatment_protocol: At passage 6, cell irradiation was performed with 4 Gy (6 MV) X-rays from a clinical therapy machine.

value: in-vitro fibroblasts

value: primary dermal fibroblast strain

tag: genotype

value: CT

tag: treatment

tag: batch

tag: time point


title: GE19_4Gy_d2, CC, batch_1

description: Library name: GE19_4Gy_d2

value: CC


title: NPY_P06_G09

description: Library name: LigandScreen-P06-20230914-071_S167


title: MDK_P06_E09

description: Library name: LigandScreen-P06-20230914-069_S165


title: NRG-1_P06_F09

description: Library name: LigandScreen-P06-20230914-070_S166


title: Mav_P07_H10

description: Library name: LigandScreen-P07-20230914-080_S272


title: LPA_P06_D09

description: Library name: LigandScreen-P06-20230914-068_S164


title: LTB4_P06_C09

description: Library name: LigandScreen-P06-20230914-067_S163


title: LIF_P06_B09

description: Library name: LigandScreen-P06-20230914-066_S162


title: Leptin_P06_A09

description: Library name: LigandScreen-P06-20230914-065_S161


title: 319 STING 2

city: Lausanne

first: Andrea

last: Ablasser

address: Rte Cantonale

country: Switzerland

institute: EPFL

description: Library name: 319 STING 2

data_processing:
The analysis of the RNA-seq was performed in the Galaxy server (https://usegalaxy.eu/). Briefly, RNA was mapped to human genome assembly GRCh38 using STAR aligner (Version 2.7.11b) and the counts were generated with featureCounts (Version 2.1.1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containg raw counts for each sample

extract_protocol:
RNA was isolated with RNeasy micro kit (Qiagen, 74004)
Samples were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760L) with ribodepletion starting from 750 ng of RNAs.

treatment_protocol: THP-1 SKO cells reconstituted with EGFP tagged WT or mutant STING were treated with doxycycline for 24h

value: Human monocytic leukemia cells (monocyte-like)

value: THP-1 STING1-knockout

value: D319K/D310K STING overexpression


title: Iloprost_P07_B10

description: Library name: LigandScreen-P07-20230914-074_S266


title: 119 STING 3

description: Library name: 119 STING 3

value: W119K/M120K STING overexpression


title: 119 STING 2

description: Library name: 119 STING 2


title: IL-4_P06_G08

description: Library name: LigandScreen-P06-20230914-063_S159


title: IL-6_P06_H08

description: Library name: LigandScreen-P06-20230914-064_S160


title: IL-17A_P06_F08

description: Library name: LigandScreen-P06-20230914-062_S158


title: IL-13_P06_E08

description: Library name: LigandScreen-P06-20230914-061_S157


title: IL-1β_P06_D08

description: Library name: LigandScreen-P06-20230914-060_S156


title: PACAP-27_P06_B10

description: Library name: LigandScreen-P06-20230914-074_S170


title: IFN-λ1_P06_C08

description: Library name: LigandScreen-P06-20230914-059_S155


title: N-expressing THP-1 macrophage-like cells, polyI:C transfected, 4hours, BioRep 1

city: Los Angeles

first: Pablo

middle: Aldair

last: Alvarez

state: CA

address: 615 Charles E Young Dr S

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

description:
Library name: Sample 15
Sequenced with BGI
M_N_pIC_tf_4h

data_processing:
The RNA-seq data were first processed to remove adapter sequences and low-quality reads using Trimmomatic, followed by the pseudoalignment to the human genome GCHr38 using Salmon (v1.10.2). The read counts of genes were generated by Tximeta, and the differential expression tests between the groups of interest were analyzed by edgeR under the GLM framework. The similarities of the samples were explored by generating multi-dimensional scaling (MDS) plots through edgeR, and the visualization of MDS plot was further polished through ggplot2. For gene ontology (GO) and pathway analysis, the selected differentially expressed genes (DEGs) were submitted to DAVID database or Enrichr to search for over-represented GO and pathway terms. For transcription factor prediction, the selected DEGs were submitted to the Erichr to search most relevant regulatory transcription factors in  TRRUST database. The volcano plots of gene expressions in N-expressing macrophages, the histograms of Delta variant fold changes of N DEGs, the bar charts of the GO analysis results and the lollipop plots of transcription factor predictions were all visualized by corresponding functions in ggplot2.  The Venn diagrams were generated through ggVennDiagram, and the giant heatmap of overlapped DEGs in all treatment conditions were plotted through pheatmap.
Assembly: GCHr38
Supplementary files format and content: Counts table: THP1_counts_4h.txt

growth_protocol: The THP-1 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI 1640, Gibco) supplemented with 10% FBS, 1X penicillin/streptomycin (P/S, Fisher Scientific), 1X non-essential amino acids (NEAA, Gibco), and 0.05 mM β-mercaptoethanol (Sigma-Aldrich). To differentiate THP-1 cells into macrophages, the cells were subjected to a 24-hour (h) stimulation with 50 ng/mL phorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich) in RPMI 1640 supplemented with 10% human AB serum (Sigma-Aldrich), 1X NEAA, 1X P/S, which is followed by a 24 h rest in human-serum containing RPMI 1640.

extract_protocol:
The parental and N-expressing THP-1 cells were seeded in biological duplicates at the density of 5 x 105 cells/well. After differentiation, doxycycline treatment and PRRs stimulation, the cells were lysed in TRizol reagent (invitrogen), followed by total RNA extraction with Direct-zol™ (Zymo). The purified RNAs were submitted to BGI for transcriptome sequencing.
Library construction was performed by BGI.

treatment_protocol: For PRR stimulation, the macrophages derived from stable THP-1 cell lines or parental THP-1 cells were treated with 2 mg/ml doxycycline in RPMI 1640 supplemented with 10% human AB serum, 1X NEAA, 1X P/S for 48 hours to induce N expression or serve as controls. The doxycycline-treated macrophages were then stimulated with 1 mg/ml CL097, an imidazoquinoline compound, to stimulate the TLR7/8 receptor, or 10 mg/ml poly (I:C) to stimulate the TLR3 receptor in RPMI 1640 supplemented with 5% human AB serum and 2 mg/ml doxycycline. For RLR stimulation, the final concentration of 2 mg/ml poly (I:C) was transfected into doxycycline-treated macrophages through lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. Four hours after PRR stimulation, the cells were harvested for downstream processing.

value: Monocyte-derived macrophages

value: SARS-CoV-2 Wuhan-Hu-1 N expressing

value: poly I:C transfection


title: IFN-γ_P06_B08

description: Library name: LigandScreen-P06-20230914-058_S154


title: N-expressing THP-1 macrophage-like cells, polyI:C treated, 4hours, BioRep 2

description:
Library name: Sample 14
Sequenced with BGI
M_N_pIC_4h

value: polyI:C treated in media


title: IGF-1_P06_A08

description: Library name: LigandScreen-P06-20230914-057_S153


title: N-expressing THP-1 macrophage-like cells, CL097 treated, 4hours, BioRep 2

description:
Library name: Sample 12
Sequenced with BGI
M_N_CL097_4h

value: CL097 treated in media


title: N-expressing THP-1 macrophage-like cells, polyI:C treated, 4hours, BioRep 1

description:
Library name: Sample 13
Sequenced with BGI
M_N_pIC_4h


title: IFN-β_P06_G07

description: Library name: LigandScreen-P06-20230914-055_S151


title: N-expressing THP-1 macrophage-like cells, CL097 treated, 4hours, BioRep 1

description:
Library name: Sample 11
Sequenced with BGI
M_N_CL097_4h


title: Histamine_P06_F07

description: Library name: LigandScreen-P06-20230914-054_S150


title: N-expressing THP-1 macrophage-like cells, No Treatment, 4hours, BioRep 2

description:
Library name: Sample 10
Sequenced with BGI
M_N_NT_4h

value: No treatment


title: HGF_P06_E07

description: Library name: LigandScreen-P06-20230914-053_S149


title: N-expressing THP-1 macrophage-like cells, No Treatment, 4hours, BioRep 1

description:
Library name: Sample 9
Sequenced with BGI
M_N_NT_4h


title: Parental THP-1 macrophage-like cells, polyI:C transfected, 4hours, BioRep 2

description:
Library name: Sample 8
Sequenced with BGI
M_pIC_tf_4h

value: Parental


title: Parental THP-1 macrophage-like cells, polyI:C treated, 4hours, BioRep 2

description:
Library name: Sample 6
Sequenced with BGI
M_pIC_4h


title: Parental THP-1 macrophage-like cells, polyI:C treated, 4hours, BioRep 1

description:
Library name: Sample 5
Sequenced with BGI
M_pIC_4h


title: Parental THP-1 macrophage-like cells, CL097 treated, 4hours, BioRep 2

description:
Library name: Sample 4
Sequenced with BGI
M_CL097_4h


title: Parental THP-1 macrophage-like cells, CL097 treated, 4hours, BioRep 1

description:
Library name: Sample 3
Sequenced with BGI
M_CL097_4h


title: CTRL-DMSO_P06_D06

description: Library name: LigandScreen-P06-20230914-044_S140


title: CTRL-Ethanol_P06_E06

description: Library name: LigandScreen-P06-20230914-045_S141


title: Galectin-3_P06_A07

description: Library name: LigandScreen-P06-20230914-049_S145


title: FGF-1_P06_G06

description: Library name: LigandScreen-P06-20230914-047_S143


title: CTRL-Ethanol_P06_F06

description: Library name: LigandScreen-P06-20230914-046_S142


title: GDNF_P06_C07

description: Library name: LigandScreen-P06-20230914-051_S147


title: GIP_P06_B07

description: Library name: LigandScreen-P06-20230914-050_S146


title: Parental THP-1 macrophage-like cells, No Treatment, 4hours, BioRep 2

description:
Library name: Sample 2
Sequenced with BGI
M_NT_4h


title: CTRL-DMSO_P06_C06

description: Library name: LigandScreen-P06-20230914-043_S139


title: Parental THP-1 macrophage-like cells, No Treatment, 4hours, BioRep 1

description:
Library name: Sample 1
Sequenced with BGI
M_NT_4h


title: CTRL-WM_P06_B06

description: Library name: LigandScreen-P06-20230914-042_S138


title: mBCC3 tumour RNAseq

city: London

first: Jun

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

description: RNA from the LCM sample

data_processing:
Output FASTQ files were aligned to the reference genome using TopHat2. The number of reads uniquely aligned (mapping quality score q>10) to the exonic region of each gene were counted using HTSeq, based on the Ensembl annotation (Release 75).
Only genes that achieved at least one count per million (CPM) mapped reads in at least three samples were included. After applying scale normalization, read counts were converted to log2 (CPM) using the voom function.
Analyses of differential gene expression between tumour and stroma samples were performed using the limma R package, with the model of paired tumour-stroma comparison accounting for the baseline differences among patients.
Gene Set Enrichment Analysis (GSEA) was performed for mBCC and nodBCC tumour-stroma comparisons using the GSEA tool to identify the dysregulated canonical pathways from the Molecular Signatures Database (MSigDB-C2 v5.0)
Genome_build: hg19 / GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw reads count for each sample generated from Htseq

source_name: mBCC tumour RNA

extract_protocol:
Extraction of high quality RNA (RIN>7 on Agilent RNA pico-chip) was required for RNA sequencing.  Due to the small sample sizes and meticulous LCM, low concentrations of RNA were obtained for some samples.
To allow for an impartial comparison, a low input library preparation protocol (SMARTer® Universal low input RNA kit from Clontech®) capable of a range between 200 pg to 10ng was employed for all samples regardless of total yield. Amplification of the low input samples only would have introduced bias when comparing against the standard library preparation. Despite the low input range, sample concentrations were greater than 100ng. Synthesised and adapter ligated copy DNA (cDNA) was then sequenced using 100 bp paired-ended reads on an Illumina® HiSeq2000 averaging 13 million paired end reads per sample by OGT.

value: tumour

tag: disease subtype

value: morphoeic basal cell carcinoma (BCC)


title: EGF_P06_G05

description: Library name: LigandScreen-P06-20230914-039_S135


title: CTRL-WM_P06_A06

description: Library name: LigandScreen-P06-20230914-041_S137


title: mBCC2 tumour RNAseq

description: RNA from the LCM sample


title: mBCC3 stromal RNAseq

description: RNA from the LCM sample

source_name: mBCC stromal RNA

value: stroma


title: ET-1_P06_D05

description: Library name: LigandScreen-P06-20230914-036_S132


title: mBCC1 stromal RNAseq

description: RNA from the LCM sample


title: Dopamine_P06_C05

description: Library name: LigandScreen-P06-20230914-035_S131


title: nodBCC11 tumour RNAseq

description: RNA from the LCM sample

source_name: nodBCC tumour RNA

value: nodular basal cell carcinoma (BCC)


title: CNTF_P06_F04

description: Library name: LigandScreen-P06-20230914-030_S126


title: nodBCC11 stromal RNAseq

description: RNA from the LCM sample

source_name: nodBCC stromal RNA


title: CNP_P06_G04

description: Library name: LigandScreen-P06-20230914-031_S127


title: mBCC2 stromal RNAseq

description: RNA from the LCM sample


title: nodBCC4 tumour RNAseq

description: RNA from the LCM sample


title: Chemerin_P06_E04

description: Library name: LigandScreen-P06-20230914-029_S125


title: nodBCC4 stromal RNAseq

description: RNA from the LCM sample


title: BDNF_P06_D04

description: Library name: LigandScreen-P06-20230914-028_S124


title: Insulin_P06_H07

description: Library name: LigandScreen-P06-20230914-056_S152


title: nodBCC3 tumour RNAseq

description: RNA from the LCM sample


title: BMP-4_P06_C04

description: Library name: LigandScreen-P06-20230914-027_S123


title: nodBCC3 stromal RNAseq

description: RNA from the LCM sample


title: BNP_P06_G03

description: Library name: LigandScreen-P06-20230914-023_S119


title: JIN3

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Library name: Sample 52
RiboMeth-seq

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Assembly: rDNA reference sequence from Krogh et al, NAR 2016 (find reference in the paper)
Supplementary files format and content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

source_name: Patient-derived cell line

extract_protocol:
Tissue and tumor samples were homogenized prior to RNA extraction, otherwise was whole cell RNA extracted using Trizol according to the manufacturer.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: Patient-derived cell line


title: NGF-β_P06_F03

description: Library name: LigandScreen-P06-20230914-022_S118


title: β-CGRP_P06_E03

description: Library name: LigandScreen-P06-20230914-021_S117


title: OPM2

description:
Library name: Sample 50
RiboMeth-seq


title: Parental THP-1 macrophage-like cells, polyI:C transfected, 4hours, BioRep 1

description:
Library name: Sample 7
Sequenced with BGI
M_pIC_tf_4h


title: AA_P06_C03

description: Library name: LigandScreen-P06-20230914-019_S115


title: MOLP2

description:
Library name: Sample 48
RiboMeth-seq


title: SK-MM2

description:
Library name: Sample 47
RiboMeth-seq


title: ApoE_P06_B03

description: Library name: LigandScreen-P06-20230914-018_S114


title: ANP_P06_A03

description: Library name: LigandScreen-P06-20230914-017_S113


title: ATP_P06_D03

description: Library name: LigandScreen-P06-20230914-020_S116


title: LP1

description:
Library name: Sample 49
RiboMeth-seq


title: Gene expression profiles of kidney of 5 adenine-diet mice at 12 wks of age with and without HMPA supplementaion exp1

type: RNA

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

description: Sample 1

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

organism: Mus musculus

source_name: CKD

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: Mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNAs of kidney were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: 7 weeks old male CD-1 mice were given AIN-93G with 2 g adenine/kg diet (0.2% w/w). Hydroxy-3-methoxyphenyl) propionic acid (HMPA) was added to adenine diet (2% w/w). The mice were randomly divided into an adenine group receiving the adenine diet and an HMPA group receiving the HMPA-mixed adenine diet for 1 week.

tag: strain

value: adenine-induced chronic kidney disease (CKD) model

source_name: CKD with HMPA

value: HMPA supplementaion


title: H929

description:
Library name: Sample 46
RiboMeth-seq


title: AngII_P06_G02

description: Library name: LigandScreen-P06-20230914-015_S111


title: U266

description:
Library name: Sample 45
RiboMeth-seq


title: EJM

description:
Library name: Sample 44
RiboMeth-seq


title: Adrenaline_P06_D02

description: Library name: LigandScreen-P06-20230914-012_S108


title: MOLP8

description:
Library name: Sample 43
RiboMeth-seq


title: ANGPT-1_P06_F02

description: Library name: LigandScreen-P06-20230914-014_S110


title: ID139_C

description:
Library name: Sample 39
RiboMeth-seq

source_name: Bone marrow

value: Bone marrow

value: Tumor

value: adult

value: normal


title: ADM_P06_E02

description: Library name: LigandScreen-P06-20230914-013_S109


title: Adipo_P06_C02

description: Library name: LigandScreen-P06-20230914-011_S107


title: ET-3_P06_F05

description: Library name: LigandScreen-P06-20230914-038_S134


title: ET-2_P06_E05

description: Library name: LigandScreen-P06-20230914-037_S133


title: mBCC1 tumour RNAseq

description: RNA from the LCM sample


title: Adenosine_P06_B02

description: Library name: LigandScreen-P06-20230914-010_S106


title: ID139_B

description:
Library name: Sample 38
RiboMeth-seq


title: Non-recombination control skin 2

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Dr

department: Dermatology

institute: Stanford University

description:
FFPE spatial transcriptomics sequencing
0088755__Region_5

hyb_protocol: Samples were subsequently fixed, permeabilized (CG000581, Rev A, 10x Genomics), and decoded using the Xenium decoding reagents (1000487, 1000461, 10x Genomics) on a Xenium Analyzer instrument (10x Genomics). Domain Assignment: Xenium data was imported into the Xenium Explorer software (10x Genomics). Domains were annotated as described previously

data_processing: For deconvolution, NiCo 1.1.0 was implemented as recommended by filtering and normalizing the reference dataset and Xenium ST datasets, finding commonly shared genes, performing SCTransform from Scanpy (Alternative 1), and Leiden clustering the Xenium data at a resolution of 0.7. Then find_anchor_cells_between_ref_and_query and nico_based_annotation were run to find anchors between the reference and Xenium ST datasets with a spatial dispersion cutoff of 0.15

label: Xenium probe set

source_name: Skin

label_protocol: Xenium probe set

growth_protocol: Not applicable

extract_protocol: tissue preparation protocol: Samples were fixed in 10% NPF for 24 hours, transferred to 70% ethanol until embedded in paraffin and sectioned on a microtome

treatment_protocol: Mice were treated with tamoxifen for 5 days (or 3 days for wounding experiments) and harvested 3 days post recombination

value: Skin

tag: tissue preservation method

value: FFPE

value: Tamoxifen

value: Nedd8+/+ Sumo2-/-


title: 7a,25-OHC_P06_G01

description: Library name: LigandScreen-P06-20230914-007_S103


title: ID139_A

description:
Library name: Sample 37
RiboMeth-seq


title: ID135_C

description:
Library name: Sample 36
RiboMeth-seq


title: CTRL-Ethanol_P06_E01

description: Library name: LigandScreen-P06-20230914-005_S101


title: Activin A_P06_A02

description: Library name: LigandScreen-P06-20230914-009_S105


title: CTRL-Ethanol_P06_F01

description: Library name: LigandScreen-P06-20230914-006_S102


title: Nedd8 knockout wound 2

description:
FFPE spatial transcriptomics sequencing
0088755__Region_4

scan_protocol: Samples were subsequently fixed, permeabilized (CG000581, Rev A, 10x Genomics), and decoded using the Xenium decoding reagents (1000487, 1000461, 10x Genomics) on a Xenium Analyzer instrument (10x Genomics). Domain Assignment: Xenium data was imported into the Xenium Explorer software (10x Genomics). Domains were annotated as described previously

value: Nedd8-/- Nrf2 +/+ K14 Cre


title: Nedd8 Nrf2 knockout 1

description:
FFPE spatial transcriptomics sequencing
0088755__Region_3

value: Nedd8-/- Nrf2-/- K14 Cre


title: CTRL-DMSO_P06_C01

description: Library name: LigandScreen-P06-20230914-003_S99


title: CTRL-DMSO_P06_D01

description: Library name: LigandScreen-P06-20230914-004_S100


title: ID135_B

description:
Library name: Sample 35
RiboMeth-seq


title: Nedd8 Nrf2 knockout 2

description:
FFPE spatial transcriptomics sequencing
0088755__Region_2


title: ID135_A

description:
Library name: Sample 34
RiboMeth-seq


title: Nrf2 knockout non recombination control

description:
FFPE spatial transcriptomics sequencing
0088755__Region_1


title: CTRL-WM_P06_B01

description: Library name: LigandScreen-P06-20230914-002_S98


title: ID115_C

description:
Library name: Sample 33
RiboMeth-seq


title: VEGF-A165_P05_F12

description: Library name: LigandScreen-P05-20230911-094_S94


title: CTRL-WM_P06_A01

description: Library name: LigandScreen-P06-20230914-001_S97


title: VEGF-A121_P05_E12

description: Library name: LigandScreen-P05-20230911-093_S93


title: Nedd8 knockout wound 1

description:
FFPE spatial transcriptomics sequencing
0088753__Region_5

value: Nedd8 -/- K14 Cre


title: VEGF-C_P05_G12

description: Library name: LigandScreen-P05-20230911-095_S95


title: ID115_B

description:
Library name: Sample 32
RiboMeth-seq


title: TNF-a_P05_B12

description: Library name: LigandScreen-P05-20230911-090_S90


title: TRAIL_P05_C12

description: Library name: LigandScreen-P05-20230911-091_S91


title: Non-recombination control wound

description:
FFPE spatial transcriptomics sequencing
0088753__Region_4

value: Nedd8 -/-


title: RPM1

description:
Library name: Sample 51
RiboMeth-seq


title: ID115_A

description:
Library name: Sample 31
RiboMeth-seq


title: Thrombin_P05_A12

description: Library name: LigandScreen-P05-20230911-089_S89


title: Sumo knockout 1

description:
FFPE spatial transcriptomics sequencing
0088753__Region_3

value: Sumo2 -/- K14 Cre


title: SHH_P05_G11

description: Library name: LigandScreen-P05-20230911-087_S87


title: Sumo knockout 2

description:
FFPE spatial transcriptomics sequencing
0088753__Region_2


title: ID112_B

description:
Library name: Sample 29
RiboMeth-seq


title: RSPO-1_P05_F11

description: Library name: LigandScreen-P05-20230911-086_S86


title: ID112_C

description:
Library name: Sample 30
RiboMeth-seq


title: Apelin_P05_E11

description: Library name: LigandScreen-P05-20230911-085_S85


title: PGE2_P05_B11

description: Library name: LigandScreen-P05-20230911-082_S82


title: Pleiotrophin_P05_A11

description: Library name: LigandScreen-P05-20230911-081_S81


title: PLG_P05_H10

description: Library name: LigandScreen-P05-20230911-080_S80


title: Non-recombination control skin 1

description:
FFPE spatial transcriptomics sequencing
0088753__Region_1

value: Sumo2 -/- Nedd8+/+


title: ID112_A

description:
Library name: Sample 28
RiboMeth-seq


title: Mk2i_3.fq.gz

city: Wuerzburg

first: Thomas

last: Guest

address: Am Hubland

institute: University of Wuerzburg

description: Library name: mk2i-treatment-r3

data_processing:
Generated reads were quality-checked using FastQC (v0.11.8) and adapters were trimmed using BBDUK (v1.16).
Bbmap was used to map reads. Deeptools was used to generate coverage plots.
Assembly: B. thetaiotaomicron VPI-5482 reference genome (NC_004663.1) and plasmid (NC_004703.1)
Supplementary files format and content: Genome coverage as .wig / .bw files

organism: Bacteroides thetaiotaomicron

growth_protocol: Grown in minimal medium (MM), supplemented with 0.5% glucose.

extract_protocol:
Total RNA was purified from bacterial pellets using the miRNeasy Mini kit (Qiagen) according to the protocol #3 described in (Popella, Jung, Popova, Durica-Mitic, et al., 2021). Briefly, cells were resuspended in 0.5 mg/mL lysozyme (Roth) in TE buffer (pH 8.0) and incubated for 5 min. Afterwards, RLT buffer supplemented with β-mercaptoethanol, and ethanol were added according to the manufacturer’s instructions. After sample loading, column wash-steps were performed according to the manual. RNA concentration was measured with a NanoDrop spectrophotometer.
Libraries were prepared with the NEBNext Multiplex Small RNA Library Prep kit for Illumina according to the manufacturer’s instructions.

value: 1.2 mM Mk2i


title: PEDF_P05_G10

description: Library name: LigandScreen-P05-20230911-079_S79


title: ID125_B

description:
Library name: Sample 27
RiboMeth-seq


title: PDGF-BB_P05_F10

description: Library name: LigandScreen-P05-20230911-078_S78


title: Mk2i_2.fq.gz

description: Library name: mk2i-treatment-r2


title: ID125_A

description:
Library name: Sample 26
RiboMeth-seq


title: PDGF-AA_P05_E10

description: Library name: LigandScreen-P05-20230911-077_S77


title: PAR1_P05_C10

description: Library name: LigandScreen-P05-20230911-075_S75


title: PTH_P05_D10

description: Library name: LigandScreen-P05-20230911-076_S76


title: Mk2i_1.fq.gz

description: Library name: mk2i-treatment-r1


title: ID111_B

description:
Library name: Sample 25
RiboMeth-seq


title: H2O_3.fq.gz

description: Library name: mock-control-r3


title: PACAP-27_P05_B10

description: Library name: LigandScreen-P05-20230911-074_S74


title: OXT_P05_A10

description: Library name: LigandScreen-P05-20230911-073_S73


title: ID111_A

description:
Library name: Sample 24
RiboMeth-seq


title: Noradrenaline_P05_H09

description: Library name: LigandScreen-P05-20230911-072_S72


title: H2O_2.fq.gz

description: Library name: mock-control-r2


title: NPY_P05_G09

description: Library name: LigandScreen-P05-20230911-071_S71


title: ID205_B

description:
Library name: Sample 23
RiboMeth-seq


title: NRG-1_P05_F09

description: Library name: LigandScreen-P05-20230911-070_S70


title: H2O_1.fq.gz

description: Library name: mock-control-r1


title: LTB4_P05_C09

description: Library name: LigandScreen-P05-20230911-067_S67


title: LPA_P05_D09

description: Library name: LigandScreen-P05-20230911-068_S68


title: LIF_P05_B09

description: Library name: LigandScreen-P05-20230911-066_S66


title: ID148_B

description:
Library name: Sample 21
RiboMeth-seq


title: ID205_A

description:
Library name: Sample 22
RiboMeth-seq


title: Het_M_137

city: Worcester

first: Ana Rita

last: Batista

state: MA

address: 366 Plantation St, N8-1099

department: Genetic and Cellular Medicine

institute: UMass Chan Medical School

description: Library name: HZ_M_137

data_processing:
The nf-core/rnaseq pipeline (v3.14.0) from the nf-core collection of NextFlow workflows was used for data QC and preprocessing, for mapping reads with the STAR aligner (2.7.9a) and for computing estimated read counts per gene per sample with Salmon (1.10.1).
Assembly: GRCm39/mm39 reference genome with GENCODE M34/Ensembl 111 annotations.
Supplementary files format and content: Tab-delimited text file with bias-adjusted estimated read counts per gene per sample from tximport.
Supplementary files format and content: Tab-delimited text file with bias-adjusted estimated read counts per gene per sample from tximport.
Supplementary files format and content: Tab-delimited text file with estimated read counts per gene per sample from tximport.
Supplementary files format and content: Tab-delimited text file with estimated TPM per gene per sample from tximport.

source_name: liver

extract_protocol:
Total RNA was isolated using TriZol Reagent (Invitrogen) according to the manufacturer instructions.
Libraries were prepared with ribosomal-RNA depletion (TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit; Illumina).

value: liver

value: Het

tag: Sex

value: male


title: AdrD11512_skinV; SJS33_spatial

description:
Library name: A11512Visium
Visium for FFPE v2

data_processing:
FASTQ files were processed with Cell Ranger (10x Genomics) and Space Ranger (10x Genomics). Downstream analyses were performed using Seurat. For scRNA-seq quality control, cells with >20% mitochondrial gene content, fewer than 200 detected genes, or a number of detected genes greater than the upper quartile plus 1.5 × interquartile range (UQ + 1.5 × IQR) were excluded. For spatial analysis, spots located outside the tissue were removed.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98); GRCh38-2020-A
Supplementary files format and content: For scRNA-seq, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz were provided. For the TCR library, filtered_contig_annotations.csv.gz was also provided.
Supplementary files format and content: For Visium, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, as well as spatial information generated by Space Ranger, were provided.
Library strategy: Spatial Transcriptomics

source_name: skin

value: skin

value: SJS/TEN


title: Leptin_P05_A09

description: Library name: LigandScreen-P05-20230911-065_S65


title: KO_M_136

description: Library name: KO_M_136

value: KO


title: IL-6_P05_H08

description: Library name: LigandScreen-P05-20230911-064_S64


title: ID148_A

description:
Library name: Sample 20
RiboMeth-seq

value: Bone marrow

value: Tumor

value: adult

value: normal


title: IL-4_P05_G08

description: Library name: LigandScreen-P05-20230911-063_S63


title: Het_F_126

description: Library name: HZ_F_126

value: female


title: IL-17A_P05_F08

description: Library name: LigandScreen-P05-20230911-062_S62


title: IL-13_P05_E08

description: Library name: LigandScreen-P05-20230911-061_S61


title: Het_M_125

description: Library name: HZ_M_125


title: IL-1β_P05_D08

description: Library name: LigandScreen-P05-20230911-060_S60


title: IFN-λ1_P05_C08

description: Library name: LigandScreen-P05-20230911-059_S59


title: ID147_B

description:
Library name: Sample 19
RiboMeth-seq


title: ID146_B

description:
Library name: Sample 17
RiboMeth-seq


title: ID147_A

description:
Library name: Sample 18
RiboMeth-seq


title: KO_F_123

description: Library name: KO_F_123


title: IGF-1_P05_A08

description: Library name: LigandScreen-P05-20230911-057_S57


title: ID146_A

description:
Library name: Sample 16
RiboMeth-seq


title: IFN-γ_P05_B08

description: Library name: LigandScreen-P05-20230911-058_S58


title: Insulin_P05_H07

description: Library name: LigandScreen-P05-20230911-056_S56


title: KO_M_122

description: Library name: KO_M_122


title: N-expressing THP-1 macrophage-like cells, polyI:C transfected, 4hours, BioRep 2

description:
Library name: Sample 16
Sequenced with BGI
M_N_pIC_tf_4h

value: Monocyte-derived macrophages

value: SARS-CoV-2 Wuhan-Hu-1 N expressing

value: poly I:C transfection


title: Gene expression profiles of kidney of 5 adenine-diet mice at 12 wks of age with and without HMPA supplementaion exp2

description: Sample 2

value: adenine-induced chronic kidney disease (CKD) model

value: HMPA supplementaion


title: IFN-β_P05_G07

description: Library name: LigandScreen-P05-20230911-055_S55


title: Het_M_119

description: Library name: HZ_M_119


title: Histamine_P05_F07

description: Library name: LigandScreen-P05-20230911-054_S54


title: HGF_P05_E07

description: Library name: LigandScreen-P05-20230911-053_S53


title: KO_M_118

description: Library name: KO_M_118


title: GH_P05_D07

description: Library name: LigandScreen-P05-20230911-052_S52


title: GIP_P05_B07

description: Library name: LigandScreen-P05-20230911-050_S50


title: GDNF_P05_C07

description: Library name: LigandScreen-P05-20230911-051_S51


title: ID144_B

description:
Library name: Sample 13
RiboMeth-seq


title: Het_F_115

description: Library name: HZ_F_115


title: KO_F_112

description: Library name: KO_F_112


title: Galectin-3_P05_A07

description: Library name: LigandScreen-P05-20230911-049_S49


title: ID145_B

description:
Library name: Sample 15
RiboMeth-seq


title: ID144_A

description:
Library name: Sample 12
RiboMeth-seq


title: FGF-2_P05_H06

description: Library name: LigandScreen-P05-20230911-048_S48


title: ID145_A

description:
Library name: Sample 14
RiboMeth-seq


title: Het_F_111

description: Library name: HZ_F_111


title: FGF-1_P05_G06

description: Library name: LigandScreen-P05-20230911-047_S47


title: CTRL-Ethanol_P05_F06

description: Library name: LigandScreen-P05-20230911-046_S46


title: ID140_B

description:
Library name: Sample 11
RiboMeth-seq


title: CTRL-Ethanol_P05_E06

description: Library name: LigandScreen-P05-20230911-045_S45


title: KO_F_108

description: Library name: KO_F_108


title: CTRL-DMSO_P05_D06

description: Library name: LigandScreen-P05-20230911-044_S44


title: CTRL-DMSO_P05_C06

description: Library name: LigandScreen-P05-20230911-043_S43


title: ID140_A

description:
Library name: Sample 10
RiboMeth-seq


title: Cortical NPCs, CHD1-R616Q, DHT, Anti-CHD1 CUT&RUN, Replicate 2

city: Reykjavik

first: Kimberley

middle: J

last: Anderson

address: Sturlugata 8

country: Iceland

institute: University of Iceland

description: Library name: Chd1-R616Q_DHT_CHD1_CUT_RUN_Rep2

library_source: genomic

data_processing:
CUT&RUN: Reads were mapped to the mouse mm10 genome using Bowtie, then aligned reads were converted to bam files using Samtools. Peaks were called with MACS3111 using the settings --max-gap 300 --keep-dup all, and an FDR q-value threshold of 0.01, using a matching IgG control sample.
Assembly: mm10
Supplementary files format and content: bam, bigWig, narrowPeak
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Embryonic cortex

growth_protocol: NPCs were cultured in neurobasal growth medium containing 1X B27 supplement (Thermo Fisher Scientific, 17504044), 1X Penicillin/Streptomycin (Thermo Fisher Scientific, 15140122), 1X Glutamax (Thermo Fisher Scientific, 35050038), 20 ng/mL FGF-2 (Peprotech, 100-18B), 20 ng/mL EFG (Peprotech, AF-100-15), and 2 μg/mL Heparin (MP Biomedicals, 210193125). NPCs were either sub-cultured or media was replaced every 2 days.

extract_protocol:
CUT&RUN was performed according to Epicypher CUTANA protocol (v.1.7) on 300.000 cells per sample. We permeabilized the cells with 0.01% digitonin (Sigma, D141). For normalization we spiked in E. Coli DNA (Epicypher, 23618-1401) at the final concentration of 0.2 ng per sample.
CUT&RUN: The library preparation was performed with the TrueSeq-Chip Sample preparation Kit (Illumina, IP-202-9001). Libraries were sequenced using on NovaSeq 6000 S4 with a minimum depth of 12 million paired end reads per sample.

treatment_protocol: NPCs were treated with 10nM DHT or DMSO vehicle control for 6h prior to harvesting for CUT&RUN.

value: Embryonic cortex

value: E18.5 cortical NPC

value: Neuronal progenitors

value: DHT

tag: cut&run antibody

value: CHD1 (D8C2) Rabbit mAb (Cell Signaling Technology, #4351)


title: CTRL-WM_P05_A06

description: Library name: LigandScreen-P05-20230911-041_S41


title: ID136_A

description:
Library name: Sample 8
RiboMeth-seq


title: EGF_P05_G05

description: Library name: LigandScreen-P05-20230911-039_S39


title: CTRL-WM_P05_B06

description: Library name: LigandScreen-P05-20230911-042_S42


title: Cortical NPCs, CHD1-R616Q, DHT, Rabbit IgG control CUT&RUN, Replicate 2

description: Library name: Chd1-R616Q_DHT_IgG_Rep2

value: Rabbit IgG Antibody, CUTANA™ CUT&RUN Negative Control (Epicypher, #23613-0042)


title: FPP_P05_H05

description: Library name: LigandScreen-P05-20230911-040_S40


title: ET-3_P05_F05

description: Library name: LigandScreen-P05-20230911-038_S38


title: Cortical NPCs, CHD1-R616Q, DHT, Anti-CHD1 CUT&RUN, Replicate 1

description: Library name: Chd1-R616Q_DHT_CHD1_CUT_RUN_Rep1


title: ID128_B

description:
Library name: Sample 7
RiboMeth-seq


title: ET-2_P05_E05

description: Library name: LigandScreen-P05-20230911-037_S37


title: Cortical NPCs, CHD1-R616Q, DHT, Rabbit IgG control CUT&RUN, Replicate 1

description: Library name: Chd1-R616Q_DHT_IgG_Rep1


title: ET-1_P05_D05

description: Library name: LigandScreen-P05-20230911-036_S36


title: ID128_A

description:
Library name: Sample 6
RiboMeth-seq


title: Dopamine_P05_C05

description: Library name: LigandScreen-P05-20230911-035_S35


title: ID136_B

description:
Library name: Sample 9
RiboMeth-seq


title: CNP_P05_G04

description: Library name: LigandScreen-P05-20230911-031_S31


title: CNTF_P05_F04

description: Library name: LigandScreen-P05-20230911-030_S30


title: Chemerin_P05_E04

description: Library name: LigandScreen-P05-20230911-029_S29


title: BMP-4_P05_C04

description: Library name: LigandScreen-P05-20230911-027_S27


title: BDNF_P05_D04

description: Library name: LigandScreen-P05-20230911-028_S28


title: Cortical NPCs, CHD1-R616Q, DMSO, Anti-CHD1 CUT&RUN, Replicate 1

description: Library name: Chd1-R616Q_DMSO_CHD1_CUT_RUN_Rep1

value: DMSO control


title: Cortical NPCs, CHD1-R616Q, DMSO, Rabbit IgG control CUT&RUN, Replicate 2

description: Library name: Chd1-R616Q_DMSO_IgG_Rep2


title: ID121_B

description:
Library name: Sample 5
RiboMeth-seq

value: Bone marrow


title: mpkCCD cells, Nfat5-KO 3, clone N3, 600 mosmol/kg

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

description: Library name: N3_3_600

data_processing:
Clean reads were obtained by removing the adapter and poly-N sequences, as well as low-quality reads, from the raw data using in-house scripts from Novogene.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
HTSeq was used to count the number of reads mapped to each gene, including both known and novel genes. The FPKM of each gene was then calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample group

source_name: mpkCCD

growth_protocol: The mpkCCD cells were cultivated in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham medium (D8437, Sigma Aldrich, St. Louis, Missouri, USA) supplemented with 10% FBS and 1% penicillin/streptavidin at 37 °C and 5% CO2.

extract_protocol:
Total RNA from mpkCCD cells was isolated using the Gen Elute Mammalian Total RNA prep kit (RTN350 389 19 390 1KT, Sigma Aldrich). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following manufacturer’s recommendations,

treatment_protocol:
The medium osmolality was adjusted to 600 mosmol/kg by the addition of 100  mM NaCl (71376, Sigma Aldrich) and 100 mM urea (U5378, Sigma Aldrich) to the  corresponding medium. Cells were exposed to isotonic (300 mosmol/kg) and hypertonic  medium (600 mosmol/kg) for 5 days.
We used two CRISPR/Cas9 mediated Nfat5 deleted mpkCCD (N1 and N3) clones generated before and mpkCCD cells that were transduced with a scramble (Scr) non targeting gRNA.

value: mpkCCD

value: cortical collecting duct

value: Nfat5 knockout

value: 600 mosmol/kg


title: Cortical NPCs, CHD1-R616Q, DMSO, Anti-CHD1 CUT&RUN, Replicate 2

description: Library name: Chd1-R616Q_DMSO_CHD1_CUT_RUN_Rep2


title: CXCL12_P05_H04

description: Library name: LigandScreen-P05-20230911-032_S32


title: BMP-2_P05_A04

description: Library name: LigandScreen-P05-20230911-025_S25


title: ID121_A

description:
Library name: Sample 4
RiboMeth-seq

value: Tumor

value: adult

value: normal


title: mpkCCD cells, Nfat5-KO 2, clone N3, 300 mosmol/kg

description: Library name: N3_2_300

value: 300 mosmol/kg


title: Cortical NPCs, CHD1-R616Q, DMSO, Anti-CHD1 CUT&RUN, Replicate 3

description: Library name: Chd1-R616Q_DMSO_CHD1_CUT_RUN_Rep3


title: BNP_P05_G03

description: Library name: LigandScreen-P05-20230911-023_S23


title: Cortical NPCs, CHD1-R616Q, DMSO, Rabbit IgG control CUT&RUN, Replicate 1

description: Library name: Chd1-R616Q_DMSO_IgG_Rep1


title: BMP-10_P05_H03

description: Library name: LigandScreen-P05-20230911-024_S24


title: ATP_P05_D03

description: Library name: LigandScreen-P05-20230911-020_S20


title: NGF-β_P05_F03

description: Library name: LigandScreen-P05-20230911-022_S22


title: Cortical NPCs, WT, DMSO, Anti-CHD1 CUT&RUN, Replicate 3

description: Library name: WT_DMSO_CHD1_CUT_RUN_Rep3

value: WT


title: AA_P05_C03

description: Library name: LigandScreen-P05-20230911-019_S19


title: mpkCCD cells, Nfat5-KO 1, clone N3, 300 mosmol/kg

description: Library name: N3_1_300


title: Cortical NPCs, WT, DMSO, Anti-CHD1 CUT&RUN, Replicate 2

description: Library name: WT_DMSO_CHD1_CUT_RUN_Rep2

value: Embryonic cortex


title: mpkCCD cells, Nfat5-KO 2, clone N3, 600 mosmol/kg

description: Library name: N3_2_600


title: mpkCCD cells, Nfat5-KO 3, clone N1, 600 mosmol/kg

description: Library name: N1_3_600


title: ApoE_P05_B03

description: Library name: LigandScreen-P05-20230911-018_S18


title: ANP_P05_A03

description: Library name: LigandScreen-P05-20230911-017_S17


title: mpkCCD cells, Nfat5-KO 3, clone N1, 300 mosmol/kg

description: Library name: N1_3_300


title: ANGPT-1_P05_F02

description: Library name: LigandScreen-P05-20230911-014_S14


title: AngII_P05_G02

description: Library name: LigandScreen-P05-20230911-015_S15


title: Cortical NPCs, WT, Rabbit IgG control CUT&RUN, Replicate 3

description: Library name: WT_IgG_Rep3

value: E18.5 cortical NPC


title: Cortical NPCs, WT, DMSO, Anti-CHD1 CUT&RUN, Replicate 1

description: Library name: WT_DMSO_CHD1_CUT_RUN_Rep1

value: Neuronal progenitors


title: mpkCCD cells, Nfat5-KO 1, clone N1, 600 mosmol/kg

description: Library name: N1_1_600


title: ADM_P05_E02

description: Library name: LigandScreen-P05-20230911-013_S13


title: Adrenaline_P05_D02

description: Library name: LigandScreen-P05-20230911-012_S12


title: mpkCCD cells, Nfat5-KO 1, clone N1, 300 mosmol/kg

description: Library name: N1_1_300


title: ACh_P05_H01

description: Library name: LigandScreen-P05-20230911-008_S8


title: mpkCCD cells, scramble4, 600 mosmol/kg

description: Library name: SCR4_600


title: 7a,25-OHC_P05_G01

description: Library name: LigandScreen-P05-20230911-007_S7


title: Cortical NPCs, WT, Rabbit IgG control CUT&RUN, Replicate 1

description: Library name: WT_IgG_Rep1


title: Cortical NPCs, WT, Rabbit IgG control CUT&RUN, Replicate 2

description: Library name: WT_IgG_Rep2


title: BV2, 6-Shogaol 30 µM + LPS, Rep2

city: seoul

first: taehyun

last: kim

address: 26-6, Kyungheedae-ro, Dongdaemun-gu

department: regulatory science

country: South Korea

institute: kyunghee univ.

description: Library name: 6S-30-rep2

data_processing:
Raw paired-end reads were adapter-trimmed using Trimmomatic v0.39 with the TruSeq3-PE-2 adapter file. Post-trimming read quality was assessed using FastQC v0.12.1.
Trimmed reads were aligned to the mouse reference genome, GRCm38 primary assembly, using STAR v2.7.11b with GENCODE release M25 FASTA and GTF annotation files. STAR alignment yielded coordinate-sorted genomic BAM files and transcriptome BAM files.
Gene- and isoform-level expression levels were quantified using RSEM v1.3.3.
Transcript-level abundance estimates from RSEM were imported into R v4.4.2 using tximport v1.32.0 and summarized to gene-level counts based on transcript-to-gene mappings derived from GENCODE vM25. Normalized count matrices were generated using DESeq2 v1.44.0.
Assembly: GRCm38 primary assembly (mm10)
Supplementary files format and content: Tab-delimited text files include expected counts, TPM, and FPKM values for each sample.
Supplementary files format and content: A comma-separated values (CSV) file containing gene-level normalized counts generated from raw read counts using DESeq2 v1.44.0.

source_name: BV2 cell

growth_protocol: BV2 murine microglial cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin-streptomycin at 37 ℃ with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent, and RNA integrity was evaluated prior to library preparation.
cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced in paired-end mode on an Illumina NovaSeq X platform. RNA extraction, library construction, and sequencing were conducted by Macrogen Inc. (Seoul, South Korea).

treatment_protocol: Cells were seeded in 12-well plates at a density of 3 x 10^5 cells per well. 24 hours after seeding, the medium was replaced with FBS-free DMEM, and cells were equilibrated for at least 4 hours prior to treatment with 6-Gingerol or 6-Shogaol. For LPS stimulation, cells were treated with LPS at a final concentration of 100 ng/mL 1 hour after compound treatment.

value: BV2 cell

value: microglia

value: 6-Shogaol 30 µM + LPS


title: Adenosine_P05_B02

description: Library name: LigandScreen-P05-20230911-010_S10


title: Adipo_P05_C02

description: Library name: LigandScreen-P05-20230911-011_S11


title: CTRL-Ethanol_P05_F01

description: Library name: LigandScreen-P05-20230911-006_S6


title: mpkCCD cells, scramble3, 300 mosmol/kg

description: Library name: SCR3_300


title: CTRL-Ethanol_P05_E01

description: Library name: LigandScreen-P05-20230911-005_S5


title: BV2, 6-Shogaol 30 µM + LPS, Rep1

description: Library name: 6S-30-rep1


title: CTRL-DMSO_P05_C01

description: Library name: LigandScreen-P05-20230911-003_S3


title: mpkCCD cells, scramble2, 300 mosmol/kg

description: Library name: SCR2_300


title: CTRL-WM_P05_B01

description: Library name: LigandScreen-P05-20230911-002_S2


title: CTRL-WM_P05_A01

description: Library name: LigandScreen-P05-20230911-001_S1


title: BV2, 6-Shogaol 10 µM + LPS, Rep2

description: Library name: 6S-10-rep2

value: 6-Shogaol 10 µM + LPS


title: mpkCCD cells, scramble1, 600 mosmol/kg

description: Library name: SCR1_600


title: VEGF-C_P04_G12

description: Library name: LigandScreen-P04-20230908-095_S287


title: BV2, 6-Shogaol 10 µM + LPS, Rep1

description: Library name: 6S-10-rep1


title: k49-3

city: Tianjin

first: qinyi

last: yu

address: 94 Weijin Road, Nankai District

country: China

institute: Nankai University, Tianjin, China

description: Library name: Sample 9

data_processing:
DESeq2 was used to analyze differentiated genes
clusterProfiler (4.8.1) was used for GO enrichment
http://www.broadinstitute.org/gsea/index.jsp was used for GSEA analysis
Assembly: mm10
Supplementary files format and content: HISAT2

growth_protocol: 4T1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% PS

extract_protocol:
RNA was extracted using TRIZOL
The library was constructed as described before (Parkhomchuk et al., 2009)

value: mouse mammary carcinoma

value: WDR82 knockout


title: TRAIL_P04_C12

description: Library name: LigandScreen-P04-20230908-091_S283


title: TGF-β1_P04_D12

description: Library name: LigandScreen-P04-20230908-092_S284


title: k49-2

description: Library name: Sample 8


title: VEGF-A165_P04_F12

description: Library name: LigandScreen-P04-20230908-094_S286


title: BV2, 6-Gingerol 30 µM + LPS, Rep2

description: Library name: 6G-30-rep2

value: 6-Gingerol 30 µM + LPS


title: VEGF-A121_P04_E12

description: Library name: LigandScreen-P04-20230908-093_S285


title: BV2, 6-Gingerol 30 µM + LPS, Rep1

description: Library name: 6G-30-rep1


title: Thrombin_P04_A12

description: Library name: LigandScreen-P04-20230908-089_S281


title: TNF-a_P04_B12

description: Library name: LigandScreen-P04-20230908-090_S282


title: BV2, 6-Gingerol 10 µM + LPS, Rep2

description: Library name: 6G-10-rep2

value: 6-Gingerol 10 µM + LPS


title: SHH_P04_G11

description: Library name: LigandScreen-P04-20230908-087_S279


title: k49-1

description: Library name: Sample 7


title: k28-3

description: Library name: Sample 6


title: RSPO-1_P04_F11

description: Library name: LigandScreen-P04-20230908-086_S278


title: BV2, 6-Gingerol 10 µM + LPS, Rep1

description: Library name: 6G-10-rep1


title: k28-2

description: Library name: Sample 5


title: PGE2_P04_B11

description: Library name: LigandScreen-P04-20230908-082_S274


title: Apelin_P04_E11

description: Library name: LigandScreen-P04-20230908-085_S277


title: BV2, LPS, Rep2

description: Library name: LPS-rep2

value: LPS


title: PLG_P04_H10

description: Library name: LigandScreen-P04-20230908-080_S272


title: PEDF_P04_G10

description: Library name: LigandScreen-P04-20230908-079_S271


title: k28-1

description: Library name: Sample 4


title: Pleiotrophin_P04_A11

description: Library name: LigandScreen-P04-20230908-081_S273


title: PDGF-BB_P04_F10

description: Library name: LigandScreen-P04-20230908-078_S270


title: BV2, LPS, Rep1

description: Library name: LPS-rep1


title: p2-3

description: Library name: Sample 3


title: BV2, untreated, Rep2

description: Library name: Con-rep2

value: untreated


title: PDGF-AA_P04_E10

description: Library name: LigandScreen-P04-20230908-077_S269


title: PTH_P04_D10

description: Library name: LigandScreen-P04-20230908-076_S268


title: p2-2

description: Library name: Sample 2


title: BV2, untreated, Rep1

description: Library name: Con-rep1


title: PAR1_P04_C10

description: Library name: LigandScreen-P04-20230908-075_S267


title: p2-1

description: Library name: Sample 1


title: PACAP-27_P04_B10

description: Library name: LigandScreen-P04-20230908-074_S266


title: B18LN

city: 广东省

first: LI

last: ShuJun

address: 广州市番禺区新造镇新造路1号

department: 附属第五医院

institute: 广州医科大学

data_processing:
The sequencing data is subjected to filtration using SOAPnuke (V2.1.0). This involves purging reads that contain adapter sequences, reads with more than 20% low-quality bases, and reads with more than 5% unknown bases.
Ultimately obtaining clean data and storing them in FASTQ format. The subsequent analysis and data mining were performed
Assembly: GCF_0000014053.9_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lymph node metastatic tissue

extract_protocol:
Extract tissue total RNA using miRNeasy Tissue/Cells Advanced Micro Kit (Qiagen). The concentration and RNA integrity were then determined by using Equalbit RNA BR Assay Kit (vazyme) and Qubit Fluorometer (Invitrogen). The samples that meet quality control requirements can be used for library preparation.
Sequencing libraries were generated using MGIEasy RNA Library preparation kit (MGI) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Eventually, circularized DNA were sequenced with MGISEQ-2000 system.

value: lymph node metastatic tissue


title: OXT_P04_A10

description: Library name: LigandScreen-P04-20230908-073_S265


title: B17LN

address: 广州市番禺区新造镇新造路1号


title: MR_LA_3

city: Tainan

first: Wei-Ting

last: Chang

state: Tainan

address: 901 ZhongHua Rd. YongKang Dist

institute: Chi-Mei Medical Center

description: Library name: Sample 6

data_processing:
Total RNA was extracted using TRIzol reagent. RNA integrity was assessed using an Agilent Bioanalyzer. Libraries were prepared using poly(A) selection and sequenced on an Illumina platform to generate 150 bp paired-end reads.
Assembly: Raw FASTQ files were processed as follows:  Adapter trimming and quality filtering were performed using fastp.  Quality control metrics were assessed using FastQC and MultiQC.  Clean reads were aligned to the mouse reference genome (GRCm39) using HISAT2 (v2.1.0). SAM files were converted to BAM format using SAMtools. Gene-level read counts were quantified using featureCounts (subread v2.0.1). Differential gene expression analysis was performed using DESeq2. Genes with |log2 fold change| > 1 and adjusted p-value < 0.05 were considered significantly differentially expressed. Functional enrichment analyses were performed using clusterProfiler for Gene Ontology (GO) and KEGG pathway analysis. Reference genome: GRCm39 (Mus musculus)
Supplementary files format and content: csv

source_name: Heart (left atrium; LA)

extract_protocol:
The purified RNA was used to prepare sequencing libraries with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocol. Briefly, mRNA was purified from 1 μg of total RNA using oligo (dT)-coupled magnetic beads and then fragmented at an elevated temperature.
The qualified libraries were sequenced on an Illumina NovaSeq platform, generating 150 bp paired-end reads at Genomics, BioSci & Tech Co. in New Taipei City, Taiwan.

value: Heart (left atrium; LA)

value: MR puncture


title: Noradrenaline_P04_H09

description: Library name: LigandScreen-P04-20230908-072_S264

data_processing:
Sequence reads were aligned using STAR (version 2.7.9a)
Counts matrix was generated using RSEM (version 1.3.1)
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: RSEM_Counts_Cardiopedia-Ligand.xlsx file includes raw counts for each sample


title: NRG-1_P04_F09

description: Library name: LigandScreen-P04-20230908-070_S262


title: B16LN

address: 广州市番禺区新造镇新造路1号


title: MDK_P04_E09

description: Library name: LigandScreen-P04-20230908-069_S261


title: MR_LA_1

description: Library name: Sample 4


title: LPA_P04_D09

description: Library name: LigandScreen-P04-20230908-068_S260


title: NPY_P04_G09

description: Library name: LigandScreen-P04-20230908-071_S263


title: B15LN

address: 广州市番禺区新造镇新造路1号


title: LTB4_P04_C09

description: Library name: LigandScreen-P04-20230908-067_S259


title: MR_LA_2

description: Library name: Sample 5


title: Sham_LA_3

description: Library name: Sample 3

value: Sham


title: LIF_P04_B09

description: Library name: LigandScreen-P04-20230908-066_S258


title: B14LN

address: 广州市番禺区新造镇新造路1号


title: Leptin_P04_A09

description: Library name: LigandScreen-P04-20230908-065_S257


title: IL-4_P04_G08

description: Library name: LigandScreen-P04-20230908-063_S255


title: IL-6_P04_H08

description: Library name: LigandScreen-P04-20230908-064_S256


title: IL-17A_P04_F08

description: Library name: LigandScreen-P04-20230908-062_S254


title: Sham_LA_1

description: Library name: Sample 1


title: B13LN

address: 广州市番禺区新造镇新造路1号


title: IL-13_P04_E08

description: Library name: LigandScreen-P04-20230908-061_S253


title: Y8_4

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Library name: Y8_4

data_processing:
Adapters from reads were removed using TrimGalore with default parameters.
Reads were aligned to the mm10 version of musmusculus using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package using the Entrez gene annotation
Assembly: GRCm38.102
Supplementary files format and content: Count matrix in excel format

source_name: epidermis

extract_protocol:
RNA was extracted from epidermal cell pellets frozen in Trizol using the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Kit (RS-122-2201/2202, Illumina) according to the manufacturer's protocol, using 150 to 300 ng of total RNA; ribosomal RNA depletion, RNA was then fragmented for 4.5 min at 94ºC. The remaining steps were followed according to the manufacturer’s instructions. Final libraries were analysed on an Agilent Technologies 2100 Bioanalyzer system using the Agilent DNA 1000 chip to estimate the quantity and validate the size distribution; libraries were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (07960204001, Roche) before amplification with Illumina’s cBot.

treatment_protocol: Epidermal cells suspensions were obtained from the skin of adult (18-25 weeks old) and aged (80-90 weeks old) that were sacrificed at different times of the day (ZT0, 4, 8, 12, 16, 20).

value: epidermis

tag: age

value: Y

tag: time

tag: replicate


title: B12LN

address: 广州市番禺区新造镇新造路1号


title: Sham_LA_2

description: Library name: Sample 2


title: B10LN

address: 广州市番禺区新造镇新造路1号


title: IFN-γ_P04_B08

city: Brisbane

first: James

institute: QIMR Berghofer Medical Research Institute

description: Library name: LigandScreen-P04-20230908-058_S250

extract_protocol:
Total RNA was isolated using the NuceloMag RNA kit (Macherey-Nagel) on the EpMotion 5075t
RNA libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit (polyA RNA selection) on the EpMotion 5075t


title: IGF-1_P04_A08

description: Library name: LigandScreen-P04-20230908-057_S249


title: B9LN

address: 广州市番禺区新造镇新造路1号


title: Y8_3

description: Library name: Y8_3


title: Histamine_P04_F07

description: Library name: LigandScreen-P04-20230908-054_S246


title: IFN-λ1_P04_C08

description: Library name: LigandScreen-P04-20230908-059_S251


title: Y8_2

description: Library name: Y8_2


title: HGF_P04_E07

description: Library name: LigandScreen-P04-20230908-053_S245


title: B8LN

address: 广州市番禺区新造镇新造路1号


title: B7LN

address: 广州市番禺区新造镇新造路1号


title: Y8_1

description: Library name: Y8_1


title: GDNF_P04_C07

description: Library name: LigandScreen-P04-20230908-051_S243


title: GH_P04_D07

description: Library name: LigandScreen-P04-20230908-052_S244


title: Y4_4

description: Library name: Y4_4


title: Galectin-3_P04_A07

description: Library name: LigandScreen-P04-20230908-049_S241


title: B6LN

address: 广州市番禺区新造镇新造路1号


title: FGF-2_P04_H06

description: Library name: LigandScreen-P04-20230908-048_S240


title: Y4_3

description: Library name: Y4_3


title: FGF-1_P04_G06

description: Library name: LigandScreen-P04-20230908-047_S239


title: B5LN

address: 广州市番禺区新造镇新造路1号


title: CTRL-Ethanol_P04_E06

description: Library name: LigandScreen-P04-20230908-045_S237


title: Y4_2

description: Library name: Y4_2


title: CTRL-Ethanol_P04_F06

description: Library name: LigandScreen-P04-20230908-046_S238


title: B4LN

address: 广州市番禺区新造镇新造路1号


title: GIP_P04_B07

description: Library name: LigandScreen-P04-20230908-050_S242


title: CTRL-DMSO_P04_C06

description: Library name: LigandScreen-P04-20230908-043_S235


title: Y4_1

description: Library name: Y4_1


title: Y20_4

description: Library name: Y20_4


title: CTRL-WM_P04_A06

description: Library name: LigandScreen-P04-20230908-041_S233


title: B3LN

address: 广州市番禺区新造镇新造路1号


title: B2LN

address: 广州市番禺区新造镇新造路1号


title: CTRL-WM_P04_B06

description: Library name: LigandScreen-P04-20230908-042_S234


title: FPP_P04_H05

description: Library name: LigandScreen-P04-20230908-040_S232


title: EGF_P04_G05

description: Library name: LigandScreen-P04-20230908-039_S231


title: Y20_3

description: Library name: Y20_3


title: B1LN

address: 广州市番禺区新造镇新造路1号


title: ET-3_P04_F05

description: Library name: LigandScreen-P04-20230908-038_S230


title: ET-1_P04_D05

description: Library name: LigandScreen-P04-20230908-036_S228


title: Y20_2

description: Library name: Y20_2


title: ET-2_P04_E05

description: Library name: LigandScreen-P04-20230908-037_S229


title: Y20_1

description: Library name: Y20_1


title: Dopamine_P04_C05

description: Library name: LigandScreen-P04-20230908-035_S227


title: CXCL12_P04_H04

description: Library name: LigandScreen-P04-20230908-032_S224


title: B17T

address: 广州市番禺区新造镇新造路1号

source_name: tumor tissues

value: tumor tissues


title: CNP_P04_G04

description: Library name: LigandScreen-P04-20230908-031_S223


title: CNTF_P04_F04

description: Library name: LigandScreen-P04-20230908-030_S222


title: B16T

address: 广州市番禺区新造镇新造路1号


title: Y16_3

description: Library name: Y16_3


title: Y16_2

description: Library name: Y16_2


title: BDNF_P04_D04

description: Library name: LigandScreen-P04-20230908-028_S220


title: BMP-4_P04_C04

description: Library name: LigandScreen-P04-20230908-027_S219


title: B14T

address: 广州市番禺区新造镇新造路1号


title: BNP_P04_G03

description: Library name: LigandScreen-P04-20230908-023_S215


title: Y16_1

description: Library name: Y16_1


title: NGF-β_P04_F03

description: Library name: LigandScreen-P04-20230908-022_S214


title: B13T

address: 广州市番禺区新造镇新造路1号


title: β-CGRP_P04_E03

description: Library name: LigandScreen-P04-20230908-021_S213


title: Y12_4

description: Library name: Y12_4


title: Y12_3

description: Library name: Y12_3


title: ApoE_P04_B03

description: Library name: LigandScreen-P04-20230908-018_S210


title: B10T

address: 广州市番禺区新造镇新造路1号


title: ANP_P04_A03

description: Library name: LigandScreen-P04-20230908-017_S209


title: Y12_2

description: Library name: Y12_2


title: ANGPT-1_P04_F02

description: Library name: LigandScreen-P04-20230908-014_S206


title: B8T

address: 广州市番禺区新造镇新造路1号


title: Y0_4

description: Library name: Y0_4


title: Adenosine_P04_B02

description: Library name: LigandScreen-P04-20230908-010_S202


title: Extracted Mouse reads from AAP16 PDX Model treated with Vehicle control (Replicate 3)

city: HOUSTON

first: John Paul

last: Shen

state: TX

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: Library name: AAP16_VC3_Mouse

data_processing:
Xenome (version 1.0.1-r) was used to segregate mouse and human reads from raw RNAseq files of PDX models. Mouse reference genome (GRCm39) and gene annotation file (Gencode.vM26) were used for mapping and annotating mouse reads. Extracted human reads for each PDX sample were stored in FASTQ files and input to the downstream STAR (version 2.7.2b) RNASeq alignment tool. Raw FASTQ files were mapped to the human reference genome (hg38) and mouse reference genome (GRCm39) separately using STAR (version 2.7.2b) RNASeq alignment tool. Biobambam (version 0.0.191) was used to mark duplicates and index raw files before alignment.
HTSeq (version 0.11.0) was utilized to extract raw read counts from STAR-aligned RNAseq BAM files of PDX models.
Assembly: hg38, GRCm39
Supplementary files format and content: tab-delimited csv file include raw counts of human and mouse reads for each sample

source_name: Appendiceal Adenocarcinoma

growth_protocol: Female NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice, 5–7 weeks of age, were purchased from The Jackson Laboratory (Bar Harbor, ME, USA), and used for tumor implantation. The animals were maintained under specific pathogen-free conditions. Housing and all procedures involving animals were performed according to protocols approved by the Institutional Animal Care and Use Committee of MD Anderson Cancer Center and conducted in accordance with U.S. Common Rule. AA tumors from The Jackson Laboratory for TM00351 (KRASG12D) and the University of Texas MD Anderson Cancer Center for AAPDX-16 (KRASG12V) were implanted into NSG mice in the peritoneal cavity. The well-being of the mice was carefully monitored, and mice were sacrificed when signs of disease, mainly abdominal distension together with a rough coat and reduced mobility, were seen. The tumor was harvested, cut into ~ 25–30 mm3 fragments, six of which were placed in the peritoneal cavity, both upper and lower abdominal quadrants, and both flank sides, of NSG mice.

extract_protocol:
Bulk RNA sequencing was performed on tumor tissue harvested from the AAPDX-01 (KRASG12D) and AAPDX-16 (KRASG12V) IP-PDX models following four weeks of treatment with MRTX1133, RMC-6236, or vehicle control, respectively. RNA was extracted using RNAqueous™ Total RNA Isolation Kit (Catalog number: AM1912). RNA concentraction ≥ 20 ng/µl for each sample was used for library construction.
Before library construction, quality control for each RNA samples was performed to guarantee the reliability of the data. RNA degradation and potential contamination were tested by Agarose Gel Electrophoresis. Agilent 2100 was used to check the RNA integrity and quantitation. After the QC procedures, mRNA from each smaple was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: MRTX1133 (synthesized in in TRACTION, the University of Texas MD Anderson Cancer Center) were freshly dissolved in 10% Captisol in 50 mM citrate buffer pH 5.0. PDX mice were intraperitoneally (IP) injected with MRTX1133 (15 mg/kg), twice a day. RMC-6236 (Selleck Chemicals, Houston, TX, USA) were dissolved in DMSO, PEG300, and Tween80, then added with ddH2O to adjust volume to 0.5 mL per mouse (final concentration of 5%DMSO/40%PEG300/5%Tween/50%ddH2O). PDX mice were IP injected with RMTRACTION, the University of Texas MD Anderson Cancer Center) was freshly dissolved in 10% Captisol in 50 mM citrate buffer,C-6236 (20 mg/kg, an equal mole of MRTX1133) daily. As a control, mice were IP injected with the same amount of vehicle at the same schedule.

value: Appendiceal Adenocarcinoma

value: Vehicle Control


title: Y0_3

description: Library name: Y0_3


title: Adipo_P04_C02

last: Hudson

address: 300 Herston Rd, Herston QLD 4006

description: Library name: LigandScreen-P04-20230908-011_S203


title: Activin A_P04_A02

description: Library name: LigandScreen-P04-20230908-009_S201


title: B6T

address: 广州市番禺区新造镇新造路1号


title: Extracted Mouse reads from AAP16 PDX Model treated with Vehicle control (Replicate 2)

description: Library name: AAP16_VC2_Mouse


title: Y0_2

description: Library name: Y0_2


title: B5T

address: 广州市番禺区新造镇新造路1号


title: Extracted Mouse reads from AAP16 PDX Model treated with Vehicle control (Replicate 1)

description: Library name: AAP16_VC1_Mouse


title: Y0_1

description: Library name: Y0_1


title: Extracted Mouse reads from AAP16 PDX Model treated with RMC-6236 (Replicate 2)

description: Library name: AAP16_RMC2_Mouse


title: O8_4

description: Library name: O8_4

value: O


title: CTRL-Ethanol_P04_E01

description: Library name: LigandScreen-P04-20230908-005_S197


title: B3T

address: 广州市番禺区新造镇新造路1号


title: Extracted Mouse reads from AAP16 PDX Model treated with RMC-6236 (Replicate 1)

description: Library name: AAP16_RMC1_Mouse


title: O8_3

description: Library name: O8_3


title: B2T

address: 广州市番禺区新造镇新造路1号


title: CTRL-DMSO_P04_D01

description: Library name: LigandScreen-P04-20230908-004_S196


title: Extracted Mouse reads from AAP01 PDX Model treated with Vehicle control (Replicate 3)

description: Library name: AAP01_VC3_Mouse


title: CTRL-Ethanol_P04_F01

description: Library name: LigandScreen-P04-20230908-006_S198


title: Casp3⁻/⁻ P815 cells CTL_treated, rep3

status: Public on Jun 26 2026

city: Lørenskog

first: Shixiong

last: Wang

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

description: Library name: Sample6

library_source: other

data_processing:
Screening data were analyzed using MAGeCK-VISPR  to identify significantly enriched or depleted sgRNAs/genes. In brief, sgRNA counting was first performed with mageck count function on Fastq files with option --trim-5 22,23,24,25,26,28,29,30 to trim the 5 prime stagger sequences.
CD8 T cells treated and control treatments were compared with mageck test function, and the normalization was performed by using control sgRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with gene ranking summary
Library strategy: CRISPR Screen

molecule: other

extract_protocol:
Genomic DNA was extracted from 2 × 10⁷ cells per replicate using the NucleoSpin™ Blood L Midi kit (Macherey-Nagel; #740954.20).
sgRNA sequences were amplified and prepared for next-generation sequencing (NGS) using a two-step PCR strategy. In the first PCR (30–45 cycles), sgRNA-containing regions were amplified from genomic DNA using eight staggered forward primers (PCR1_Fwd_1–8) together with a vector-specific reverse primer, using Q5® High-Fidelity DNA Polymerase (New England Biolabs; M0491S). PCR products were pooled and purified using the NucleoSpin™ Gel and PCR Clean-up Midi kit (Macherey-Nagel; #740986.20). In the second PCR (8 cycles), Illumina P5 and P7 adapters and sample-specific indices were added. Final libraries were purified using SpeedBeads (GE65152105050250, Cytiva), quantified using a Qubit fluorometer (Thermo Fisher Scientific), and quality-checked using TapeStation system with D1000 ScreenTape (5067-5582, Agilent). Libraries were pooled equimolarly and sequenced on a NovaSeq X platform (Illumina), targeting a depth of 20–30 million reads per sample.

treatment_protocol: 7.5 × 10⁷ Casp3⁻/⁻ P815 cells were transduced with the Brie lentiviral library at a multiplicity of infection (MOI) of 0.3 to ensure single integration events per cell. 48 hours post-transduction, cells were selected with puromycin (0.6 µg/mL). After 48 h of selection, surviving cells were pooled, cultured in puromycin-free medium, and subjected to cytotoxic T lymphocyte (CTL) selection. For CTL selection, 8 × 10⁶ target cells were co-cultured with activated human CD8⁺ T cells at equal effector-to-target ratios in the presence of 5 µg/mL anti-CD3 antibody. After 24 h of co-culture, cells were collected and treated with puromycin to eliminate residual CD8⁺ T cells. Surviving P815 cells were expanded, and CTL selection was repeated three times. Following selection, surviving cells were expanded, and genomic DNA was extracted from 2 × 10⁷ cells per replicate.

tag: cell type

value: Mastocytoma

value: CTL


title: 319 STING 3

city: Lausanne

first: Andrea

last: Ablasser

address: Rte Cantonale

institute: EPFL

description: Library name: 319 STING 3

data_processing:
The analysis of the RNA-seq was performed in the Galaxy server (https://usegalaxy.eu/). Briefly, RNA was mapped to human genome assembly GRCh38 using STAR aligner (Version 2.7.11b) and the counts were generated with featureCounts (Version 2.1.1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containg raw counts for each sample

extract_protocol:
RNA was isolated with RNeasy micro kit (Qiagen, 74004)
Samples were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760L) with ribodepletion starting from 750 ng of RNAs.

value: Human monocytic leukemia cells (monocyte-like)

value: THP-1 STING1-knockout

value: D319K/D310K STING overexpression


title: B1T

address: 广州市番禺区新造镇新造路1号