title: clf-28,R1,Input

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

country: France

institute: University Grenoble Alpes

description: Library name: clf-28_R1_Input

data_processing:
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): reads were aligned using bwa 0.6.2-r126; For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): reads were aligned using bwa 0.7.17-r1188
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): files were converted into bam formate using samtools 0.1.19+; For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): files were converted into bam formate using samtools 1.16.1
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): duplicated reads were removed using Picard-tools 1.93 (not for R3 due to saturation); For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): duplicated reads were removed using Picard-tools 2.26.10
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): bed files were generated using bedtools v2.17.0-97-ge80528b; For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): ChIP and input samples with more than 30% higher read numbers than the replicates average were down-sampled to fall within the average (this concerned the input ult1 and IP WT for Rep.1) using samtools. Bam files were converted into BEDPE format using bedtools (Quinlan and Hall, 2010) (v2.30.0). Paired reads were merged into one fragment using awk (4.1.4). Sub-nucleosomal fragments (<146 bases), large undigested fragments (>500bp), reads mapping to regions prone for artificial signals (Klasfeld et al., 2022), a region surrounding the centromere of chromosome 4 (low signal in input of clf-28, putative inversion caused by T-DNA) and all reads mapping to the plastid or mitochondria genome were removed at this step. To avoid normalisation problems due to differences in fragment size, all fragments were set to a length of 146 bases around the fragment center and reads of both replicates were merged for further analysis.
H3K27me3 and H3K4me3 positive islands were determined using SICER V1.1 with window size 200 bp, gap size 400 bp and effective genome size of 90 % , a FDR-cutt-off of 0.0001 was employed
Assembly: tair10
Supplementary files format and content: bed files containing regions of significant enrichment of the H3K4me3 or H3K27me3 histone mark over input
Supplementary files format and content: bw files containing normalised (CPM) counts in bigwig format

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown in long day (LD) conditions of 16 h light (18 degrees) and 8 h darkness (16 degrees) on Murashige and Skoog medium (Sigma-Aldrich, Lyon, France) supplemented with 0.3% sucrose in growth cabinets (Percival, Percival Scientific Incorporated, provided by CLF Plant Climatics, Emersacker, Germany) for 8 days.

extract_protocol:
For single read samples ( Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3):Formaldehyde cross-linking and extraction of nuclei was performed as described in Carles and Fletcher (2009) with the following modifications: infiltration time was prolongated (6 min), filtration of the extract after grinding was performed through 75 µm and 50 µm nylon meshes and sonication was done for 13x 30 sec on, 1 min off, position H. Immunoprecipitation reactions were set up as described in Carles and Fletcher (2009) except that 15 µg of chromatin was used and the chromatin was incubated with the antibody alone for 5 hours prior to addition of Protein A Agarose beads without salmon sperm DNA (Millipore). Washing of the ChIP reaction was performed using binding/wash buffer as described in Carles and Fletcher (2009) but for four times 10 min at 4°C and once 10 min at room temperature (RT).  Elution and reverse cross-linking was performed as described in Kaufmann et al. (2010) except that the elution was done by vortex mixing for 1 min at RT and input samples (1/3 of the chromatin used for one ChIP sample) were brought to the same volume by adding elution buffer and Tris pH9 in the same ratio as to the ChIP samples. Reverse cross-linked samples were purified using the MinElute Reaction Cleanup Kit (Quiagen) and DNA was eluted in 30 µl Elution buffer. Three technical replicates of ChIP were performed on the same nuclear extract and pooled on one MinElute column.   For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): chromatin preparation and immuno-precipitation was performed as described in (Zhu et al., New Phytol, 2024)
For single read samples ( Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): ChIP-seq library preparation was performed using the Truseq ChIP sample preparation kit (Illumina, ref. IP-202-1012) according to the manufacturer's instructions except that PCR amplification was performed prior to size selection. Briefly, sonicated chromatin was repaired prior to 3' ends adenylation. Illumina's indexed adapters were ligated to the adenylated double-stranded DNA fragments. A 18-cycles PCR was performed on the ligated DNA using Illumina's PCR primers. The libraries were then size-selected between 300 and 700 bp on a 2% agarose gel. Each library was validated using high sensitivity chip (Agilent, ref. 5067-4626) on an Agilent Bioanalyzer and quantified using the Kapa library quantification kit (Clinisciences, ref. KK4824). Equimolar amounts of 4 libraries were pooled, diluted to 10 nM, denatured, and diluted again to 7 pM. 100 µl of the diluted pool were hybridized on one lane of an Illumina's Flow Cell. Clustering and 50 cycles sequencing were performed according to Illumina's instructions on a Hiseq2000. Libraries were multiplexed by three (H3K4me3 samples) or four and sequenced on a HiSeq2000 (Illumina) sequencer, yielding 50 bp single-end reads.  For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): Library preparation was performed as described in (Zhu et al., New Phytol, 2024) with 100-300bp insert size at BGI, China.

value: seedlings


title: Extracted Mouse reads from AAP01 PDX Model treated with Vehicle control (Replicate 2)

status: Public on Jun 25 2026

type: SRA

city: HOUSTON

first: John Paul

last: Shen

state: TX

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: Library name: AAP01_VC2_Mouse

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Appendiceal Adenocarcinoma

tag: genotype

tag: treatment

value: Vehicle Control

tag: batch


title: B18N

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

country: China

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

organism: Homo sapiens

source_name: normal 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: normal tissue


title: CTRL-WM_P04_B01

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-P04-20230908-002_S194

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: Extracted Mouse reads from AAP01 PDX Model treated with Vehicle control (Replicate 1)

description: Library name: AAP01_VC1_Mouse


title: O8_1

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: O8_1

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: O

tag: time

tag: replicate


title: O4_4

description: Library name: O4_4


title: VEGF-C_P03_G12

description: Library name: LigandScreen-P03-20230901-095_S191


title: B17N

address: 广州市番禺区新造镇新造路1号


title: ult1-3,R2,Col-0,K27

description: Library name: ult1-3_R2_Col-0_K27

library_source: genomic

molecule: genomic DNA


title: ult1-3clf-28,R1,K27

description: Library name: ult1-3clf-28_R1_K27

value: ult1-3 clf-28


title: Extracted Mouse reads from AAP01 PDX Model treated with MRTX1133 (Replicate 3)

description: Library name: AAP01_MRTX3_Mouse


title: B18T

address: 广州市番禺区新造镇新造路1号

source_name: tumor tissues

value: tumor tissues


title: O4_3

description: Library name: O4_3


title: VEGF-A165_P03_F12

description: Library name: LigandScreen-P03-20230901-094_S190


title: Y16_4

description: Library name: Y16_4

value: Y


title: B16N

address: 广州市番禺区新造镇新造路1号


title: Extracted Mouse reads from AAP01 PDX Model treated with MRTX1133 (Replicate 2)

description: Library name: AAP01_MRTX2_Mouse


title: O4_2

description: Library name: O4_2


title: Chemerin_P04_E04

description: Library name: LigandScreen-P04-20230908-029_S221


title: B15T

address: 广州市番禺区新造镇新造路1号


title: BMP-2_P04_A04

description: Library name: LigandScreen-P04-20230908-025_S217


title: B15N

address: 广州市番禺区新造镇新造路1号


title: O8_2

description: Library name: O8_2


title: Extracted Mouse reads from AAP01 PDX Model treated with MRTX1133 (Replicate 1)

description: Library name: AAP01_MRTX1_Mouse


title: TGF-β1_P03_D12

description: Library name: LigandScreen-P03-20230901-092_S188


title: O4_1

description: Library name: O4_1


title: B14N

address: 广州市番禺区新造镇新造路1号


title: CD8+ T cell transduced with Runx3-TurboID construct replicate 2

status: Public on Jun 26 2026

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Library name: TID_REP2
See corresponding column

data_processing:
Reads were processed using nf-core/rnaseq v3.14.0. Briefly, raw read quality was assessed with FastQC v0.12.1, and adapter sequences and low-quality bases were trimmed using Trim Galore! v0.6.7. Trimmed reads were aligned to the GRCm38 reference genome with STAR, and the resulting transcriptome-level alignments were quantified with Salmon v1.10.1. Genome alignments were coordinate-sorted and indexed with SAMtools v1.17, duplicate reads were marked with Picard v3.0.0, and normalized genome coverage tracks were generated with BEDTools v2.30.0. Post-alignment quality control included read distribution, gene-body coverage, and strand-specificity metrics (RSeQC, Qualimap, and inference via Salmon), duplication assessment (dupRadar), library-complexity estimation (Preseq), and gene-biotype quantification with featureCounts (Subread v2.0.1). Sample-to-sample similarity was evaluated by principal component analysis and hierarchical clustering of regularized log-transformed counts using DESeq2 v1.40.2. Differential gene expression analysis was performed in R using DESeq2 v1.40.2. Gene-level counts from the star_salmon quantification were filtered to retain genes with a mean raw count ≥ 5 across all samples, and a model of the form “~ group” was fit to test pairwise contrasts between each RUNX3 fusion construct (FT, LOV, APEX, ULTRA, MINI, TID) and the empty-vector (EV) and wild-type RUNX3 (WT) controls using the Wald test. Genes with a Benjamini–Hochberg-adjusted p-value ≤ 0.05 and |log₂ fold-change| ≥ 1 were considered differentially expressed.
Assembly: GRCm38 (mouse)
Supplementary files format and content: Tab-separated values (TSV) file containing gene-level raw counts from Salmon/STAR quantification. Rows represent genes (n = 45,706), with columns for Ensembl gene ID, gene name, and raw read counts for 2 biological replicates across 7 conditions (APEX, EV, FT, LOV, MINI, TID, ULTRA, WT)

source_name: primary cell

growth_protocol: CD8+ T cells were isolated from splenocytes and cultured ex vivo with anti-CD3/CD28 stimulation and transduced with RUNX3 retroviral constructs as described in the CD8+ T cell transduction protocol.

extract_protocol:
T cells were collected and centrifuged at 750 × g for 5 minutes. Cells were lysed with DNA/RNA Shield (Zymo Research, #1100-50) at a density of 1 × 10⁶ cells per 50 µL. Lysed samples were submitted to Plasmidsaurus for library construction and sequencing.
Library construction and RNA-seq sequencing (10 million reads/sample) were performed by Plasmidsaurus. In brief, they converted mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation and library indexing and amplification.

treatment_protocol: Sixteen hours post-activation, cells were spinfected with retroviral supernatant to express different Runx3-tagged constructs: FT(FlAsH-tag), LOV*, APEX2, ultraID, miniTurbo, TurboID, WT, and Empty vector control.

value: primary cell

tag: cell type

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3-TurboID construct


title: VEGF-A121_P03_E12

description: Library name: LigandScreen-P03-20230901-093_S189


title: CTRL-DMSO_P04_C01

description: Library name: LigandScreen-P04-20230908-003_S195


title: ATP_P04_D03

description: Library name: LigandScreen-P04-20230908-020_S212


title: O20_4

description: Library name: O20_4


title: M2 PEMA 3

city: Ann Arbor

first: Hannah

last: Viola

state: Michigan

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

description:
Library name: 8589-KG-8
colname in processed data: M2 NP 3

data_processing:
BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).  Martin,M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMB net.journal, 17, 10–12.
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010)  Andrews,S. (2010) FastQC: A quality control tool for high throughput sequence data.
Fastq Screen v0.15.3 was used to screen for various types of contamination (Wingett and Andrews, 2018).  Wingett,S.W. and Andrews,S. (2018) Fastq screen: A tool for multi-genome mapping and quality control [version 1; referees: 3 approved, 1 approved with reservations]. F1000Research, 7, 1–13
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.  Dobin,A. et al. (2013) STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15–21. Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics.
Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016)  Ewels,P. et al. (2016) MultiQC: Summarize analysis results for multiple tools and samples in a single report
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: gene_expected_count.annot.txt
Supplementary files format and content: raw counts matrix

molecule: polyA RNA

source_name: Bone-marrow derived macrophage

growth_protocol: Bone marrow (BM) was harvested from tibias and fibulas of female BALB/c mice 6-12 weeks of age. BM was pushed out of cutoff long bones using an 23G needle, then lysed, filtered (70 µm), counted, and plates on non-tissue culture treated 10 cm dish at 2 million cells in 10 mL macrophage differentiation media (LCM: RPMI 1640 supplemented with 10 v/v% FBS, 1x P/S, and 4 mM L-glutamine; MPM: 80 v/v% LCM  supplemented with 20 v/v% L929 fibroblast conditioned media) and were cultured for 8 days.

extract_protocol:
RNA was extracted using the Direct-Zol™ RNA MiniPrep Plus with Zymo-Spin™ IIICG Columns (Zymo Research Corporation R2070) according to manufacturer instructions. RNA quality and concentration were quantified by the University of Michigan Advanced Genomics Core (AGC) via RNA gel (Agilent TapeStation).
AGC conducted library prep with poly-A enrichment and next-generation sequencing (Illumina NovaSeq) according to manufacturer instructions. A TruSeq-based kit was used during library preparation. The adapter sequences for this kit are  R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT  The product name of the library preparation kit is NEB.  This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000, Control Software Version: 1.8.1, RTA Version: v3.4.4).

treatment_protocol: Macrophages were polarized for 24 hours on day 8 to M2 with stimulation by 10 ng/mL each of IL-4 and IL-13 (ThermoFisher Scientific). On day 9, M2 macrophages were treated with 200 ug/mL NPs for 24 hours followed by rinsing to remove residual NPs.

value: Bone-marrow derived macrophage

value: WT

tag: strain

value: Balb/c

tag: Sex

value: female

value: PEMA

value: 24 hours


title: B12T

address: 广州市番禺区新造镇新造路1号


title: TRAIL_P03_C12

description: Library name: LigandScreen-P03-20230901-091_S187


title: AA_P04_C03

description: Library name: LigandScreen-P04-20230908-019_S211


title: M2 PEMA 2

description:
Library name: 8589-KG-12
colname in processed data: M2 NP 2


title: B13N

address: 广州市番禺区新造镇新造路1号


title: O20_3

description: Library name: O20_3


title: B9T

address: 广州市番禺区新造镇新造路1号


title: ADM_P04_E02

description: Library name: LigandScreen-P04-20230908-013_S205


title: TNF-a_P03_B12

description: Library name: LigandScreen-P03-20230901-090_S186


title: B12N

address: 广州市番禺区新造镇新造路1号


title: M2 PEMA 1

description:
Library name: 8589-KG-7
colname in processed data: M2 NP 1


title: O20_2

description: Library name: O20_2


title: Thrombin_P03_A12

description: Library name: LigandScreen-P03-20230901-089_S185


title: M2 PBS 3

description:
Library name: 8589-KG-5
colname in processed data: M2 PBS 3

value: PBS


title: B10N

address: 广州市番禺区新造镇新造路1号

value: normal tissue


title: M2 PBS 2

description:
Library name: 8589-KG-13
colname in processed data: M2 PBS 2


title: O16_4

description: Library name: O16_4

value: epidermis


title: B8N

address: 广州市番禺区新造镇新造路1号


title: O16_3

description: Library name: O16_3

value: O


title: M2 PBS 1

description:
Library name: 8589-KG-4
colname in processed data: M2 PBS 1


title: Day 21 bleo vehicle-treated mouse 4

description:
Library name: 12757-HV-12
Column name in gene_expected_count.annot.txt: X12757.HV.12

data_processing:
BCL Convert Conversion Software v4.3.6 (Illumina) was used to generate de-multiplexed fastq files.
The reads were trimmed using Cutadapt v4.8 (Martin, 2011).  Martin,M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMB net.journal, 17, 10–12.
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010)  Andrews,S. (2010) FastQC: A quality control tool for high throughput sequence data.
Fastq Screen v0.15.3 was used to screen for various types of contamination (Wingett and Andrews, 2018).  Wingett,S.W. and Andrews,S. (2018) Fastq screen: A tool for multi-genome mapping and quality control [version 1; referees: 3 approved, 1 approved with reservations]. F1000Research, 7, 1–13
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.  Dobin,A. et al. (2013) STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15–21. Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics.
Multiqc v1.20 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016)  Ewels,P. et al. (2016) MultiQC: Summarize analysis results for multiple tools and samples in a single report
Assembly: GRCm38
Supplementary files format and content: tab-delimited counts with genes on rows and samples on columns. First four columns contain Ensembl database terms "gene_id", "entrezgene_id", "external_gene_name", and "description", followed by counts columns for all samples.
Supplementary files format and content: gene_expected_count.annot.txt: raw counts
Supplementary files format and content: gene_FPKM_annot.txt: FPKM (Fragments Per Kilobase Million) normalized counts
Supplementary files format and content: gene_TPM_annot.txt: TPM (Transcripts Per Kilobase Million) normalized counts

source_name: Lung

extract_protocol:
Whole lung lobes were excised from large airway and trachea, and all 5 lobes were homogenized at 15000 rpm for 1-3 minutes in 1 mL TRIzol® reagent (Zymo Research) to achieve a pipetteable solution. This solution was spun to remove solids and 150 μL supernatant was diluted with 650 μL TRIzol®. Then, RNA was extracted using the Direct-Zol™ RNA MiniPrep Plus with Zymo-Spin™ IIICG Columns (Zymo Research Corporation R2070) according to manufacturer instructions.
A TruSeq-based kit was used during library preparation. The adapter sequences for this kit are
R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
The product name of the library preparation kit is NEB.
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000, Control Software Version: 1.8.1, RTA Version: v3.4.4).

treatment_protocol: We fabricated polymeric NPs comprised of a poly(lactide-co-glycolide) (PLG) core coated with the surfactant poly(ethylene-alt-maleic anhydride) (PEMA) using oil-in-water emulsion followed by solvent evaporation. NPs had a mean diameter of  609.22 ± 15.30 nm, polydispersity index (PDI) of 0.322 ± 0.099, and surface charge of -45.61 ± 5.48 mV across 5 independent batches. Pulmonary fibrosis was induced using the oropharyngeal bleomycin mouse model (0.0125 U/mouse ~ 0.5 U/kg). NPs were delivered intravenously via retro-orbital injection at 2 mg/dose in phosphate-buffered saline (Vehicle) beginning on day 14 post-bleomycin and daily until Day 18 for 5 total doses (2 mg/dose). Bulk RNA-sequencing was conducted on whole lung homogenates from 3 conditions: Day 14 (pre-treatment, n=4), Day 21 NP (n=4), and Day 21 Vehicle (n=4) (mean 44 ± 7.7 million reads/sample).

value: Lung

value: male

value: 10 weeks

value: Day 21

value: intravenous saline


title: B7N

address: 广州市番禺区新造镇新造路1号


title: PGE2_P03_B11

description: Library name: LigandScreen-P03-20230901-082_S178


title: Day 21 bleo vehicle-treated mouse 3

description:
Library name: 12757-HV-11
Column name in gene_expected_count.annot.txt: X12757.HV.11


title: O16_1

description: Library name: O16_1


title: B6N

address: 广州市番禺区新造镇新造路1号


title: B9N

address: 广州市番禺区新造镇新造路1号


title: Day 21 bleo vehicle-treated mouse 2

description:
Library name: 12757-HV-10
Column name in gene_expected_count.annot.txt: X12757.HV.10


title: B5N

address: 广州市番禺区新造镇新造路1号


title: O12_4

description: Library name: O12_4


title: PLG_P03_H10

description: Library name: LigandScreen-P03-20230901-080_S176


title: B4N

address: 广州市番禺区新造镇新造路1号


title: Day 21 bleo vehicle-treated mouse 1

description:
Library name: 12757-HV-9
Column name in gene_expected_count.annot.txt: X12757.HV.9


title: O12_3

description: Library name: O12_3


title: Day 21 bleo NP-treated mouse 4

description:
Library name: 12757-HV-8
Column name in gene_expected_count.annot.txt: X12757.HV.8

value: intravenous NPs


title: PDGF-BB_P03_F10

description: Library name: LigandScreen-P03-20230901-078_S174


title: B3N

address: 广州市番禺区新造镇新造路1号


title: O12_2

description: Library name: O12_2


title: B2N

address: 广州市番禺区新造镇新造路1号


title: Day 21 bleo NP-treated mouse 3

description:
Library name: 12757-HV-7
Column name in gene_expected_count.annot.txt: X12757.HV.7


title: PDGF-AA_P03_E10

description: Library name: LigandScreen-P03-20230901-077_S173


title: O0_4

description: Library name: O0_4


title: PTH_P03_D10

description: Library name: LigandScreen-P03-20230901-076_S172


title: ref6-3,R2,Input

data_processing:
Base-calling performed with Casava 1.8.2
reads were aligned using bwa 0.6.2-r126
files were converted into bam formate using samtools 0.1.19+
duplicated reads were removed using Picard-tools 1.93 (not for R3 due to saturation)
bed files were generated using bedtools v2.17.0-97-ge80528b
H3K27me3 and H3K4me3 positive islands were determined using SICER V1.1 with window size 200 bp, gap size 400 bp and effective genome size of 90 % , a FDR-cutt-off of 0.0001 was employed
Assembly: tair10
Supplementary files format and content: bed files containing regions of significant enrichment of the H3K4me3 or H3K27me3 histone mark over input
Supplementary files format and content: bw files containing normalised (CPM) counts in bigwig format

extract_protocol:
Formaldehyde cross-linking and extraction of nuclei was performed as described in Carles and Fletcher (2009) with the following modifications: infiltration time was prolongated (6 min), filtration of the extract after grinding was performed through 75 µm and 50 µm nylon meshes and sonication was done for 13x 30 sec on, 1 min off, position H. Immunoprecipitation reactions were set up as described in Carles and Fletcher (2009) except that 15 µg of chromatin was used and the chromatin was incubated with the antibody alone for 5 hours prior to addition of Protein A Agarose beads without salmon sperm DNA (Millipore). Washing of the ChIP reaction was performed using binding/wash buffer as described in Carles and Fletcher (2009) but for four times 10 min at 4°C and once 10 min at room temperature (RT).  Elution and reverse cross-linking was performed as described in Kaufmann et al. (2010) except that the elution was done by vortex mixing for 1 min at RT and input samples (1/3 of the chromatin used for one ChIP sample) were brought to the same volume by adding elution buffer and Tris pH9 in the same ratio as to the ChIP samples. Reverse cross-linked samples were purified using the MinElute Reaction Cleanup Kit (Quiagen) and DNA was eluted in 30 µl Elution buffer. Three technical replicates of ChIP were performed on the same nuclear extract and pooled on one MinElute column.
ChIP-seq library preparation was performed using the Truseq ChIP sample preparation kit (Illumina, ref. IP-202-1012) according to the manufacturer's instructions except that PCR amplification was performed prior to size selection. Briefly, sonicated chromatin was repaired prior to 3' ends adenylation. Illumina's indexed adapters were ligated to the adenylated double-stranded DNA fragments. A 18-cycles PCR was performed on the ligated DNA using Illumina's PCR primers. The libraries were then size-selected between 300 and 700 bp on a 2% agarose gel. Each library was validated using high sensitivity chip (Agilent, ref. 5067-4626) on an Agilent Bioanalyzer and quantified using the Kapa library quantification kit (Clinisciences, ref. KK4824). Equimolar amounts of 4 libraries were pooled, diluted to 10 nM, denatured, and diluted again to 7 pM. 100 µl of the diluted pool were hybridized on one lane of an Illumina's Flow Cell. Clustering and 50 cycles sequencing were performed according to Illumina's instructions on a Hiseq2000. Libraries were multiplexed by three (H3K4me3 samples) or four and sequenced on a HiSeq2000 (Illumina) sequencer, yielding 50 bp single-end reads.

value: seedlings


title: O0_3

description: Library name: O0_3


title: Day 21 bleo NP-treated mouse 1

description:
Library name: 12757-HV-5
Column name in gene_expected_count.annot.txt: X12757.HV.5


title: PAR1_P03_C10

description: Library name: LigandScreen-P03-20230901-075_S171


title: ref6-3,R1,Input


title: O0_2

description: Library name: O0_2


title: PACAP-27_P03_B10

description: Library name: LigandScreen-P03-20230901-074_S170


title: WT,Col-0,R2,Input


title: Day 14 bleo mouse 3

description:
Library name: 12757-HV-3
Column name in gene_expected_count.annot.txt: X12757.HV.3

value: Day 14


title: WT,Col-0,R1,Input


title: OXT_P03_A10

description: Library name: LigandScreen-P03-20230901-073_S169


title: Day 14 bleo mouse 2

description:
Library name: 12757-HV-2
Column name in gene_expected_count.annot.txt: X12757.HV.2

value: WT


title: O0_1

description: Library name: O0_1


title: CGHNC9, si-LUCAT1

city: Taoyuan City

first: Ann-Joy

last: Cheng

address: 259 Wen-Hua 1st Road

country: Taiwan

institute: Chang Gung University

description:
Library name: Sample 4
Column name in RSEM_TPM_All_sample.txt: C9_si_LUCAT1

data_processing:
Raw sequencing reads were assessed for quality using FastQC. High-quality reads were aligned to the human reference genome (GRCh38.p13) using the GDC mRNA analysis pipeline with GENCODE v43 annotation. Gene-level expression quantification was performed using RSEM (v1.3.3). Expression values were calculated as transcripts per million (TPM).
Assembly: GRCh38.p13 (GENCODE v43)
Supplementary files format and content: Processed data files contain gene-level expression quantification results generated by RSEM (v1.3.3). Expression values are reported as TPM for each annotated gene (Ensembl gene ID and gene symbol) based on GENCODE v43. Files are provided in tab-delimited text (.txt) format for each sample.

source_name: Oral squamous cell carcinoma

growth_protocol: OECM1 human head and neck cancer cells were cultured in RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic solution. CGHNC9 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Thermo Fisher Scientific) supplemented with 10% FBS and 1% antibiotic-antimycotic solution. Cells were incubated at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from cultured HNC cells using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Strand-specific mRNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the manufacturer’s instructions. Poly(A)+ RNA was enriched prior to library construction. Library quality and fragment size distribution were verified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 platform to generate 150-bp paired-end reads.

treatment_protocol: Cells were transfected with small interfering RNA (siRNA) targeting LUCAT1 or with a non-targeting control siRNA using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. Transfected cells were incubated at 37°C for 24 hours prior to RNA extraction. Knockdown efficiency was validated by RT-qPCR before downstream RNA sequencing analysis.

value: Oral squamous cell carcinoma

value: Epithelial cell


title: Noradrenaline_P03_H09

description: Library name: LigandScreen-P03-20230901-072_S168


title: 35S::ULT1,R3,Input


title: CGHNC9, si-NC

description:
Library name: Sample 3
Column name in RSEM_TPM_All_sample.txt: C9_NC

value: si-NC


title: Day 14 bleo mouse 1

description:
Library name: 12757-HV-1
Column name in gene_expected_count.annot.txt: X12757.HV.1


title: 35S::ULT1,R1,Input


title: OECM1, si-LUCAT1

description:
Library name: Sample 2
Column name in RSEM_TPM_All_sample.txt: OEC_si_LUCAT1


title: NRG-1_P03_F09

description: Library name: LigandScreen-P03-20230901-070_S166


title: ult1-2,R2,Input


title: OECM1, si-NC

description:
Library name: Sample 1
Column name in RSEM_TPM_All_sample.txt: OEC_NC


title: Mouse medial prefrontal cortex tissue from LPS and sedanolide co-treated group replicate 4

city: hangzhou

first: fangla

last: luo

address: zhejiang university zijingang campus

institute: zhejiang university

description: Library name: LPS_SDN4

data_processing:
Raw sequencing reads were filtered using fastp. Clean reads were aligned to the mouse reference genome using HISAT2. Transcript assembly and quantification were performed using StringTie and RSEM. Differentially expressed genes were identified using DESeq2 and DEGseq.
Assembly: Mus musculus GRCm39release-109
Supplementary files format and content: Processed data files contain gene-level expression values quantified by RSEM and reported as TPM (transcripts per million). Differential expression analysis results generated using DESeq2/DEGseq are provided as tab-delimited text files.

source_name: medial prefrontal cortex

extract_protocol:
Total RNA was extracted from mouse medial prefrontal cortex tissues using TRIzol reagent according to the manufacturer's instructions. RNA quality was assessed using NanoDrop ND-2000 and Agilent 5300 Bioanalyzer.
RNA libraries were prepared using Illumina Stranded mRNA Prep, Ligation kit. Poly(A)-containing mRNA was enriched using oligo(dT) beads.

value: medial prefrontal cortex

value: brain tissue

value: Sedanolide administration (20 mg/kg, i.g.) starting 3 days before LPS injection and continuing for 8 days; LPS (1 mg/kg, i.p.) injection for 5 consecutive days


title: MDK_P03_E09

description: Library name: LigandScreen-P03-20230901-069_S165


title: ult1-2,R1,Input


title: Mouse medial prefrontal cortex tissue from LPS and sedanolide co-treated group replicate 3

description: Library name: LPS_SDN3


title: moDCs_LPS_CTLA4Ig_2

city: Heraklion

first: Prodromos

last: Sidiripoulos

address: Andrea Kalokerinou 13

department: Medical School

country: Greece

institute: University of Crete

description: Library name: 2B

data_processing:
Raw FASTQ files were quality checked using FastQC and summarized with MultiQC.
Reads were aligned to the Homo sapiens reference genome (hg38) using HISAT2 v2.1.0 with default parameters.
Alignment files were sorted with SAMtools v1.9.
Reads were assigned to genomic features using featureCounts v1.5.0-p1 with GENCODE v34 primary assembly annotation.
Assembly: hg38, GENCODE v34 primary assembly annotation
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for all samples

source_name: monocyte-derived dendritic cell

growth_protocol: Magnetically isolated CD14+ monocytes were cultured in RPMI 1640 supplemented with 10% heat-inactivated FBS, 100 IU/mL penicillin and 100 μg/mL streptomycin, 0.01 M Hepes and 50 μM 2-mercaptoethanol in the presence of 100 ng/ml IL4 and 100 ng/ml GM-CSF for 6 days at 1× 10^6 cells/ml. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.  On day 3, culture medium was refreshed and supplemented with 50 ng/ml IL4 and GM-CSF.

extract_protocol:
Total RNA from treated DCs was isolated using the PureLink RNA mini kit (catalog no. 12183018A, Invitrogen) according to the manufacturer’s instructions. RNA quantity was assessed by NanoDrop spectrophotometry, and RNA integrity was evaluated using the Agilent Bioanalyzer RNA Nano Kit. 1ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer's instructions.100-bp single-end reads were generated per sample on an Illumina NovaSeq 6000 instrument.

treatment_protocol: On day 6, cells were stimulated with LPS (100 ng/ml) in the presence of either CTLA4-Ig (50 μg/ml) or control IgG (50 μg/ml) for 18 hours.

value: monocyte-derived dendritic cell

value: LPS + CTLA4-Ig

value: 18 hours


title: siTGS1_BioRep2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description:
Library name: 230814b
siTGS1_2

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT); HG19 human genome reference; T2T.CHM13v2.0 human telomere-to-telomere human reference.
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

source_name: BJ1 Fibroblast Cell line

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent). Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction.

value: BJ1 Fibroblast Cell line

value: BJ1 human cell-line transfected with siRNA against TGS1

tag: growth

value: Growth in EMEM with 10% FBS at 37°C with 5% CO2


title: LPA_P03_D09

description: Library name: LigandScreen-P03-20230901-068_S164


title: Mouse medial prefrontal cortex tissue from LPS and sedanolide co-treated group replicate 2

description: Library name: LPS_SDN2


title: siCntrl_BioRep2

description:
Library name: 230814a
siCntrl_2

value: BJ1 human cell-line transfected with control siRNA


title: ult1-3,R3,Input


title: LTB4_P03_C09

description: Library name: LigandScreen-P03-20230901-067_S163


title: ult1-3,R1,Input


title: Mouse medial prefrontal cortex tissue from LPS and sedanolide co-treated group replicate 1

description: Library name: LPS_SDN1


title: siTGS1_BioRep1

description:
Library name: 250710b
siTGS1_1


title: LIF_P03_B09

description: Library name: LigandScreen-P03-20230901-066_S162


title: Mouse medial prefrontal cortex tissue from sedanolide-treated group replicate 5

description: Library name: SDN_5

value: Sedanolide administration (20 mg/kg, i.g.) for 8 consecutive days; saline intraperitoneal injection for 5 days


title: Leptin_P03_A09

description: Library name: LigandScreen-P03-20230901-065_S161


title: WT,Ler,R1,Input

value: seedlings

value: Ler


title: Mouse medial prefrontal cortex tissue from sedanolide-treated group replicate 4

description: Library name: SDN_4

value: WT


title: M3_ishZMAT3_DOX_S11

city: Paris

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

description: Library name: M3_ishZMAT3_DOX_S11

data_processing:
Sequencing reads were pseudo aligned to the GRCh38v96 version of the human genome and gene counts quantified using Kallisto
Normalized counts were exported using R package Sleuth
Assembly: GRCh38v96
Supplementary files format and content: Comma-separated values including normalized counts for all samples.

source_name: skin

extract_protocol:
Total RNA was extracted using QIAGEN RNAeasy plus mini kit following manufacturer's instructions
Strand-specific libraries were prepared using custom protocol derived from Illumina TruSeq Stranded Kit to generate First stranded RNAseq libraries

value: skin

value: fibrobast

value: untreated


title: AdrD1150_PBMC, AdrD5833_2_PBMC, AdrD8172_PBMC; STP1, STP2, STP3 [TCR]

city: Taoyuan

first: Chuang-Wei

last: Wang

address: No. 5, Fusing St

institute: cgmh

description:
Library name: A1150TCR
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.

source_name: 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.

value: PBMC

tag: disease

value: SJS/TEN


title: IL-6_P03_H08

description: Library name: LigandScreen-P03-20230901-064_S160


title: ref6-3,R2,K4

tag: antibody


title: Mouse medial prefrontal cortex tissue from sedanolide-treated group replicate 3

description: Library name: SDN_3

value: medial prefrontal cortex

value: brain tissue


title: M3_ishZMAT3_DOX_MMC_S12

description: Library name: M3_ishZMAT3_DOX_MMC_S12

value: MMC


title: ref6-3,R1,K4


title: IL-4_P03_G08

description: Library name: LigandScreen-P03-20230901-063_S159


title: Mouse medial prefrontal cortex tissue from sedanolide-treated group replicate 2

description: Library name: SDN_2


title: M3_ishRen_DOX_S5

description: Library name: M3_ishRen_DOX_S5

value: ishRen


title: IL-17A_P03_F08

description: Library name: LigandScreen-P03-20230901-062_S158


title: WT,Col-0,R2,K4


title: M3_ishRen_DOX_MMC_S6

description: Library name: M3_ishRen_DOX_MMC_S6


title: WT,Col-0,R1,K4


title: Mouse medial prefrontal cortex tissue from LPS-treated group replicate 5

description: Library name: LPS_5

value: Saline gavage starting 3 days before LPS injection and continuing for 8 days; LPS (1 mg/kg, i.p.) injection for 5 consecutive days


title: M2_ishZMAT3_DOX_S9

description: Library name: M2_ishZMAT3_DOX_S9


title: IL-1β_P03_D08

description: Library name: LigandScreen-P03-20230901-060_S156


title: 35S::ULT1,R3,K4


title: Mouse medial prefrontal cortex tissue from LPS-treated group replicate 4

description: Library name: LPS_4


title: M2_ishZMAT3_DOX_MMC_S10

description: Library name: M2_ishZMAT3_DOX_MMC_S10


title: WT,Ler,R3,Input


title: siCntrl_BioRep1

description:
Library name: 250710a
siCntrl_1

value: BJ1 Fibroblast Cell line


title: Fenoldopam_P07_A08

description: Library name: LigandScreen-P07-20230914-057_S249


title: 35S::ULT1,R1,K4


title: Ozanimod_P07_A09

description: Library name: LigandScreen-P07-20230914-065_S257


title: MRS2365_P07_F08

description: Library name: LigandScreen-P07-20230914-062_S254


title: M2_ishRen_DOX_S3

description: Library name: M2_ishRen_DOX_S3


title: IFN-γ_P03_B08

description: Library name: LigandScreen-P03-20230901-058_S154


title: O20_1

description: Library name: O20_1

value: epidermis

value: O


title: ult1-2,R2,K4


title: SHH_P03_G11

description: Library name: LigandScreen-P03-20230901-087_S183


title: RSPO-1_P03_F11

description: Library name: LigandScreen-P03-20230901-086_S182


title: M2_ishRen_DOX_MMC_S4

description: Library name: M2_ishRen_DOX_MMC_S4


title: IGF-1_P03_A08

description: Library name: LigandScreen-P03-20230901-057_S153


title: Mouse medial prefrontal cortex tissue from LPS-treated group replicate 2

description: Library name: LPS_2


title: ult1-2,R1,K4


title: Apelin_P03_E11

description: Library name: LigandScreen-P03-20230901-085_S181


title: Mouse medial prefrontal cortex tissue from LPS-treated group replicate 1

description: Library name: LPS_1


title: M1_ishZMAT3_DOX_S7

description: Library name: M1_ishZMAT3_DOX_S7


title: Pleiotrophin_P03_A11

description: Library name: LigandScreen-P03-20230901-081_S177


title: O16_2

description: Library name: O16_2


title: IFN-λ1_P03_C08

description: Library name: LigandScreen-P03-20230901-059_S155


title: ult1-3,R3,K4


title: Insulin_P03_H07

description: Library name: LigandScreen-P03-20230901-056_S152


title: Mouse medial prefrontal cortex tissue from control group replicate 5

description: Library name: CTRL_5

value: No treatment; saline gavage for 8 days and saline intraperitoneal injection for 5 days


title: M1_ishZMAT3_DOX_MMC_S8

description: Library name: M1_ishZMAT3_DOX_MMC_S8


title: ult1-3,R1,K4

value: seedlings


title: Mouse medial prefrontal cortex tissue from control group replicate 4

description: Library name: CTRL_4


title: M1_ishRen_DOX_S1

description: Library name: M1_ishRen_DOX_S1


title: Histamine_P03_F07

description: Library name: LigandScreen-P03-20230901-054_S150


title: Mouse medial prefrontal cortex tissue from sedanolide-treated group replicate 1

description: Library name: SDN_1

value: Sedanolide administration (20 mg/kg, i.g.) for 8 consecutive days; saline intraperitoneal injection for 5 days


title: Fenoldopam_P07_C07

description: Library name: LigandScreen-P07-20230914-051_S243


title: IL-13_P03_E08

description: Library name: LigandScreen-P03-20230901-061_S157


title: PEDF_P03_G10

description: Library name: LigandScreen-P03-20230901-079_S175


title: Mouse medial prefrontal cortex tissue from control group replicate 2

description: Library name: CTRL_2

value: WT


title: Mouse medial prefrontal cortex tissue from LPS-treated group replicate 3

description: Library name: LPS_3


title: HGF_P03_E07

description: Library name: LigandScreen-P03-20230901-053_S149


title: M1_ishRen_DOX_MMC_S2

description: Library name: M1_ishRen_DOX_MMC_S2

value: skin


title: WT,Ler,R2,K4

value: Ler


title: WT,Ler,R1,K4


title: O12_1

description: Library name: O12_1


title: Mouse medial prefrontal cortex tissue from control group replicate 1

description: Library name: CTRL_1


title: DK23067-iPSC-neutrophil-WT-UT-2

city: Yushima, Bunkyo-ku

first: FUMIKO

last: OZAKI

state: Tokyo

country: Japan

institute: Tokyo medical and dental university

data_processing:
The mRNA profiles were compiled using Cufflinks (ver 2.2.1) software program and expressed as Reads per million mapped reads (PKM).
Assembly: hg38
Supplementary files format and content: xlsx files include RPM value for each sample

source_name: iPSCs derived cells

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen). In DK21052, 1 ng of total RNA was used to construct the sequencing library. For DK2220 and DK22223, 25 ng of total RNA was used, and for DK23067, 0.75 ng of total RNA was used.
Using the QuantSeq 3'mRNA-Seq Library Prep Kit, libraries for the NextSeq next-generation sequencer were prepared following the manual's protocol.

value: iPSCs derived cells

value: neutrophils

value: untreated


title: GH_P03_D07

description: Library name: LigandScreen-P03-20230901-052_S148


title: B1N

address: 广州市番禺区新造镇新造路1号

value: normal tissue


title: ref6-3,R2,K27


title: Mouse corneal tissue Cationorm3

city: tianjin

first: Zhihui

last: Zhang

address: No. 251 Fukang Road, Xiqing District, Tianjin

institute: tianjin medical university eye hospital

description: Library name: Cationorm3

data_processing:
Raw sequencing reads were quality-checked, and adaptor sequences and low-quality reads were removed. Clean reads were aligned to the mouse reference genome. Gene expression quantification was performed, and differential expression analysis was conducted using DESeq2 with an adjusted P value < 0.05 as significance threshold.
Assembly: Mus musculus genome assembly GRCm39 (mm39)
Supplementary files format and content: Processed data include gene-level read counts matrix and differentially expressed gene (DEG) tables generated from RNA-seq analysis.

source_name: cornea

growth_protocol: Male C57BL/6J mice (6–8 weeks old) were maintained under specific pathogen-free conditions with a 12-hour light/dark cycle and free access to food and water.

extract_protocol:
Total RNA was extracted from mouse corneal tissues using TRIzol reagent according to the manufacturer’s instructions. RNA purity and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared using standard Illumina TruSeq protocols following mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: Contact lens-related dry eye (CLDE) was induced by topical application of 0.1% benzalkonium chloride (5 μL/eye, twice daily) combined with daily contact lens wear (6 h/day). After model establishment, mice were treated with normal saline, hyaluronic acid, or Cationorm® (5 μL/eye, twice daily) for 14 days.

value: cornea

tag: condition

value: CLDE

value: in vivo tissue

value: wild-type

value: single batch


title: DK23067-iPSC-neutrophil-WT-UT-1


title: GDNF_P03_C07

description: Library name: LigandScreen-P03-20230901-051_S147


title: ref6-3,R1,K27


title: DK23067-iPSC-neutrophil-E250Q-UT-2


title: WT,Col-0,R2,K27


title: Galectin-3_P03_A07

description: Library name: LigandScreen-P03-20230901-049_S145


title: DK23067-iPSC-neutrophil-E250K-UT-2


title: FGF-2_P03_H06

description: Library name: LigandScreen-P03-20230901-048_S144


title: Mouse corneal tissue Control3

description: Library name: Control3


title: WT,Col-0,R1,K27


title: 35S::ULT1,R3,K27


title: Mouse corneal tissue Control2

description: Library name: Control2


title: DK23067-iPSC-neutrophil-E250K-UT-1


title: 35S::ULT1,R1,K27


title: DK22223-iPSC-neutrophil-WT-UT-2

description: all.rpm_DK22223-iPSC-neutrophil_WT_E250K_S100KO.xlsx


title: Mouse corneal tissue Control1

description: Library name: Control1


title: FGF-1_P03_G06

description: Library name: LigandScreen-P03-20230901-047_S143


title: CTRL-Ethanol_P03_F06

description: Library name: LigandScreen-P03-20230901-046_S142


title: IFN-β_P03_G07

description: Library name: LigandScreen-P03-20230901-055_S151


title: ult1-2,R3,K27


title: MFS 2Y 4 [193_209]

city: New Haven

first: Jay

last: Humphrey

state: CT

address: 55 Prospect St

department: Department of Biomedical Engineering

institute: Yale University

description:
Library name: Sample 8
Raw counts in processed data file

data_processing:
Sequenced reads were imported into CLC Genomics Workbench V23 (Qiagen).
Following quality control, reads were trimmed and aligned/mapped to a Mus musculus reference genome.
Reads were then automatically processed using trimmed mean of M values (TMM) normalization, log counts per million (CPM) transformation, and Z-Score normalization to generate principal component analysis (PCA) and heat map plots (Euclidean distance and complete linkage for clustering).
Assembly: GRCm39
Supplementary files format and content: csv files include raw counts for each sample

source_name: Aorta

extract_protocol:
RNA was isolated using an RNeasyMini Kit (Qiagen) according to manufacturer's specifications.
Whole-transcriptome sequencing was performed by The Yale Center for Genome Analysis using a NovaSeq 6000 System (Illumina, Inc.).

value: Aorta

value: 2 Years


title: CTRL-Ethanol_P03_E06

description: Library name: LigandScreen-P03-20230901-045_S141


title: ult1-2,R1,K27

source_name: seedlings


title: MFS 2Y 3 [192_314]

description:
Library name: Sample 7
Raw counts in processed data file


title: MFS 2Y 2 [172_326]

description:
Library name: Sample 6
Raw counts in processed data file


title: DK22223-iPSC-neutrophil-WT-S100KO-UT-1

value: PSTPIP1-E250K, S100A8-KO


title: CTRL-DMSO_P03_C06

description: Library name: LigandScreen-P03-20230901-043_S139


title: DK22223-iPSC-neutrophil-WT-S100KO-LPS-2

value: LPS


title: WT,Ler,R3,K27

value: seedlings


title: MFS 12Wk 4 [12wk_M-4]

description:
Library name: Sample 4
Raw counts in processed data file

value: 12 Weeks


title: DK22223-iPSC-neutrophil-WT-S100KO-LPS-1


title: CTRL-WM_P03_A06

description: Library name: LigandScreen-P03-20230901-041_S137


title: WT,Ler,R1,K27


title: hypoTO3

city: New haven

first: Woo Sub

last: Yang

address: 10 Amistad St, Room 214j

description:
Library name: RNA-seq sample6
truseq stranded mrna library

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in)
Assembly: GRCh38
Supplementary files format and content: For RNA-seq, csv file including TPM. For scRNA-seq, matrix, features and barcode files.

source_name: Brain organoid

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 20,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P v4 (GEM-X)  protocol (10X Genomics)

value: Brain organoid

value: BMP4 (20ng/ml)


title: MFS 12Wk 3 [12wk_M-3]

description:
Library name: Sample 3
Raw counts in processed data file


title: DK22223-iPSC-neutrophil-WT-LPS-2

value: iPSCs derived cells


title: MFS 12Wk 2 [12wk_M-2]

description:
Library name: Sample 2
Raw counts in processed data file


title: DK22223-iPSC-neutrophil-WT-LPS-1

value: neutrophils


title: EGF_P03_G05

description: Library name: LigandScreen-P03-20230901-039_S135


title: hypoTO2

description:
Library name: RNA-seq sample5
truseq stranded mrna library


title: DK22223-iPSC-neutrophil-E250K-UT-2

value: untreated


title: ET-3_P03_F05

description: Library name: LigandScreen-P03-20230901-038_S134


title: hypoTO1

description:
Library name: RNA-seq sample4
truseq stranded mrna library


title: DK22223-iPSC-neutrophil-E250K-UT-1

description: all.rpm_DK22223-iPSC-neutrophil_WT_E250K_S100KO.xlsx


title: ET-2_P03_E05

description: Library name: LigandScreen-P03-20230901-037_S133


title: hypo3

description:
Library name: RNA-seq sample3
truseq stranded mrna library


title: DK22223-iPSC-neutrophil-WT-S100KO-UT-2


title: DK22223-iPSC-neutrophil-E250K-S100KO-UT-2


title: hypo2

description:
Library name: RNA-seq sample2
truseq stranded mrna library


title: Dopamine_P03_C05

description: Library name: LigandScreen-P03-20230901-035_S131


title: hypo1

description:
Library name: RNA-seq sample1
truseq stranded mrna library


title: DK22223-iPSC-neutrophil-E250K-S100KO-UT-1


title: Nanocapsule_Anti-PD1_3

city: Los Angeles

first: Jeffrey

last: Harding

state: CA

address: 405 Hilgard Avenue

institute: University of California Los Angeles

description: Library name: Sample_N_3

data_processing:
Deseq2 pipeline
Assembly: GRCm38
Supplementary files format and content: Tab deliominated file of raw counts for each sample

growth_protocol: 4T1 cells were injected to the right flank of female BALB/c mice (4-6 weeks old)

extract_protocol:
Lung tissues were collected, and RNA was then extracted with the QIAamp RNA blood mini kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The mice were treated with PBS, anti-PD1, or nanocapsules of anti-PD1 (150 µg/mouse) at day 7 and day 14 after tumor engraftment. On day 21, lung tissues were collected for RNA sequencing.

value: Lung


title: DK22223-iPSC-neutrophil-E250K-S100KO-LPS-2


title: DKK-1_P03_A05

description: Library name: LigandScreen-P03-20230901-033_S129

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


title: YO1058_Cortisol-3

description:
Library name: RNA-seq sample30
truseq stranded mrna library

tag: disease state

value: Angelman syndrome

value: 10uM Cortisol


title: CXCL12_P03_H04

description: Library name: LigandScreen-P03-20230901-032_S128


title: YO1058_Cortisol-2

description:
Library name: RNA-seq sample29
truseq stranded mrna library


title: Nanocapsule_Anti-PD1_1

description: Library name: Sample_N_1


title: DK22223-iPSC-neutrophil-E250K-LPS-2


title: CNP_P03_G04

description: Library name: LigandScreen-P03-20230901-031_S127


title: YO1058_Cortisol-1

description:
Library name: RNA-seq sample28
truseq stranded mrna library


title: Anti-PD1_3

description: Library name: Sample_A_3


title: CNTF_P03_F04

description: Library name: LigandScreen-P03-20230901-030_S126


title: DK22223-iPSC-neutrophil-E250K-LPS-1


title: YO1058-3

description:
Library name: RNA-seq sample27
truseq stranded mrna library


title: DK22200-MOsMPs-WT-UT-2

description: all.rpm_DK22200-MOsMPs-WT_E250K_E250Q_S100A8KO.xlsx

value: monocytes/macrophages


title: Chemerin_P03_E04

description: Library name: LigandScreen-P03-20230901-029_S125


title: DK22223-iPSC-neutrophil-E250K-S100KO-LPS-1


title: Anti-PD1_1

description: Library name: Sample_A_1


title: DK22200-MOsMPs-WT-UT-1


title: BDNF_P03_D04

description: Library name: LigandScreen-P03-20230901-028_S124


title: YO1058-1

description:
Library name: RNA-seq sample25
truseq stranded mrna library


title: Hypoxia+rSRGN 3

first: lifeng

last: feng

state: State...

address: china

institute: nankai university

description:
Library name: Samples9
S3

data_processing:
Reads containing adapter sequences, low-quality reads, and unknown bases (N) were filtered out to obtain clean reads.Clean reads were mapped to the Mus musculus reference genome (mm10) using HISAT2 software.Gene expression levels were quantified using FeatureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file including raw read counts for each sample.

source_name: Primary NMVMs

growth_protocol: Primary neonatal mouse ventricular myocytes (NMVMs) were isolated from 1 day old C57BL/6J mice and cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
Poly(A)-enriched mRNA was used for library construction. Sequencing was performed on an Illumina NovaSeq 6000 platform.

treatment_protocol: For the Hypoxia and Hypoxia+rSRGN groups, cells were washed and switched to glucose-free, serum-free DMEM. Hypoxia was induced by incubating cells in a sealed chamber using an AnaeroPack-MIC (Mitsubishi A-07) system for 6 hours. Recombinant SRGN (rSRGN) was added to the medium in the designated group during the hypoxic period. The Control group was maintained in normoxic conditions with complete medium.

value: Primary NMVMs

value: primary neonatal mouse ventricular myocytes

value: WT

value: Hypoxia+rSRGN


title: DK22200-MOsMPs-WT-LPS-2


title: Mouse corneal tissue Cationorm2

description: Library name: Cationorm2

value: cornea

value: CLDE

value: in vivo tissue

value: wild-type

value: single batch


title: Anti-PD1_2

description: Library name: Sample_A_2


title: DK23067-iPSC-neutrophil-E250Q-UT-1


title: Mouse corneal tissue Cationorm1

description: Library name: Cationorm1


title: GIP_P03_B07

description: Library name: LigandScreen-P03-20230901-050_S146


title: BMP-4_P03_C04

description: Library name: LigandScreen-P03-20230901-027_S123


title: SD6010_Cortisol-3

description:
Library name: RNA-seq sample24
truseq stranded mrna library

value: Brain organoid


title: Hypoxia+rSRGN 2

description:
Library name: Samples8
S2


title: BMP-2_P03_A04

description: Library name: LigandScreen-P03-20230901-025_S121


title: CTRL-DMSO_P03_D06

description: Library name: LigandScreen-P03-20230901-044_S140


title: ult1-3,R3,K27

city: Grenoble

first: Christel

last: Carles

address: 17 rue des Martyrs, bât. C2

institute: University Grenoble Alpes

value: seedlings


title: DK22200-MOsMPs-WT-LPS-1

value: iPSCs derived cells

value: LPS


title: YO1058-2

description:
Library name: RNA-seq sample26
truseq stranded mrna library


title: SD6010_Cortisol-2

description:
Library name: RNA-seq sample23
truseq stranded mrna library


title: Hypoxia+rSRGN 1

description:
Library name: Samples7
S1


title: DK22223-iPSC-neutrophil-WT-UT-1

description: all.rpm_DK22223-iPSC-neutrophil_WT_E250K_S100KO.xlsx

value: neutrophils

value: untreated


title: DK22200-MOsMPs-E250Q-UT-2


title: CTRL-WM_P03_B06

last: Hudson

description: Library name: LigandScreen-P03-20230901-042_S138


title: MFS 2Y 1 [166_257]

description:
Library name: Sample 5
Raw counts in processed data file

value: Aorta

value: 2 Years


title: ult1-3,R1,K27


title: BMP-10_P03_H03

description: Library name: LigandScreen-P03-20230901-024_S120


title: SD6010_Cortisol-1

description:
Library name: RNA-seq sample22
truseq stranded mrna library

value: Angelman syndrome

value: 10uM Cortisol


title: Hypoxia3

description:
Library name: Samples6
I3

value: Primary NMVMs

value: primary neonatal mouse ventricular myocytes

value: WT

value: Hypoxia


title: BNP_P03_G03

description: Library name: LigandScreen-P03-20230901-023_S119


title: SD6010-3

description:
Library name: RNA-seq sample21
truseq stranded mrna library


title: DK22200-MOsMPs-E250Q-LPS-2

description: all.rpm_DK22200-MOsMPs-WT_E250K_E250Q_S100A8KO.xlsx

value: monocytes/macrophages


title: Hypoxia2

description:
Library name: Samples5
I2


title: DK22200-MOsMPs-E250Q-UT-1


title: NGF-β_P03_F03

description: Library name: LigandScreen-P03-20230901-022_S118


title: FPP_P03_H05

description: Library name: LigandScreen-P03-20230901-040_S136


title: Hypoxia1

description:
Library name: Samples4
I1


title: SD6010-2

description:
Library name: RNA-seq sample20
truseq stranded mrna library


title: DK22200-MOsMPs-E250Q-LPS-1


title: SD6010-1

description:
Library name: RNA-seq sample19
truseq stranded mrna library


title: β-CGRP_P03_E03

description: Library name: LigandScreen-P03-20230901-021_S117


title: Con3

description:
Library name: Samples3
CON3

value: Control


title: MFS 12Wk 1 [12wk_M-1]

description:
Library name: Sample 1
Raw counts in processed data file

value: 12 Weeks


title: ATP_P03_D03

description: Library name: LigandScreen-P03-20230901-020_S116


title: DK22200-MOsMPs-E250K-UT-2


title: Con2

description:
Library name: Samples2
CON2


title: AA_P03_C03

description: Library name: LigandScreen-P03-20230901-019_S115


title: SH2_Cortisol-3

description:
Library name: RNA-seq sample18
truseq stranded mrna library

value: Brain organoid

value: Healty control


title: DK22200-MOsMPs-E250K-S100KO-UT-2

value: iPSCs derived cells

value: PSTPIP1-E250K, S100A8-KO


title: DK22200-MOsMPs-E250K-UT-1


title: SH2_Cortisol-1

description:
Library name: RNA-seq sample16
truseq stranded mrna library


title: ANP_P03_A03

description: Library name: LigandScreen-P03-20230901-017_S113


title: Cachectic BAT, LLC injected 4

city: Rome

first: Andrea

last: Ninni

address: Via della ricerca scientifica 1

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

description:
Library name: CAC 4
Column name in countMatrix.txt:  CAC_4

data_processing:
The RNAseq data were quality-checked using FastQC v0.11.9 and subsequently aligned to the gen code mouse reference genome (mm10) using Hisat2 v2.2.1 3 with default parameters.
The number of reads for all RefSeq genes were counted using feature Counts v2.0.34 using the multi-mapping option.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: Brown Adipose Tissue

growth_protocol: Mice were maintained at 21.0 ± 0.5°C under a 12 h/12 h light/dark cycle (lights on at 6:00 a.m., lights off at 6:00 p.m.). Food and water were provided ad libitum. Experiments were carried out according to institutional procedures.

extract_protocol:
Total RNAs from Brown Adipose Tissue were extracted using Direct-zolTM RNA MiniPrep (ZYMO RESEARCH) according to the manufacturer’s instructions. Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from 50 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl), which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 75 cycle strategy (Illumina Inc.).

treatment_protocol: For the cancer cachexia model, 8–10-week-old male or female C57BL/6J mice from The Jackson Laboratory (strain no. 000664) were subcutaneously injected in the right flank with 3 × 10⁶ LLC cells suspended in 100 μL sterile PBS. Control mice were injected with PBS alone (CTR).

value: Brown Adipose Tissue

value: LLC injection


title: Control_3

description: Library name: Sample_C_3

value: Lung


title: SH2-3

description:
Library name: RNA-seq sample15
truseq stranded mrna library


title: DK22200-MOsMPs-E250K-S100KO-LPS-2

value: LPS


title: Cachectic BAT, LLC injected 3

description:
Library name: CAC 3
Column name in countMatrix.txt:  CAC_3


title: ANGPT-1_P03_F02

city: Brisbane

first: James

address: 300 Herston Rd, Herston QLD 4006

institute: QIMR Berghofer Medical Research Institute

description: Library name: LigandScreen-P03-20230901-014_S110


title: SH2_Cortisol-2

description:
Library name: RNA-seq sample17
truseq stranded mrna library


title: SH2-2

description:
Library name: RNA-seq sample14
truseq stranded mrna library


title: DK22200-MOsMPs-E250K-S100KO-LPS-1

description: all.rpm_DK22200-MOsMPs-WT_E250K_E250Q_S100A8KO.xlsx


title: Cachectic BAT, LLC injected 2

description:
Library name: CAC 2
Column name in countMatrix.txt:  CAC_2


title: ADM_P03_E02

description: Library name: LigandScreen-P03-20230901-013_S109


title: Con1

description:
Library name: Samples1
CON1


title: SH2-1

description:
Library name: RNA-seq sample13
truseq stranded mrna library


title: Cachectic BAT, LLC injected 1

description:
Library name: CAC 1
Column name in countMatrix.txt:  CAC_1


title: Adrenaline_P03_D02

description: Library name: LigandScreen-P03-20230901-012_S108


title: KOLF_Cortisol-3

description:
Library name: RNA-seq sample12
truseq stranded mrna library


title: DK22200-MOsMPs-E250K-LPS-2


title: Control BAT, PBS 4

description:
Library name: Ctrl 4
Column name in countMatrix.txt:  CTRL_4

value: CTRL


title: DK22200-MOsMPs-E250K-LPS-1


title: Control BAT, PBS 3

description:
Library name: Ctrl 3
Column name in countMatrix.txt:  CTRL_3


title: 7a,25-OHC_P03_G01

description: Library name: LigandScreen-P03-20230901-007_S103


title: Control BAT, PBS 2

description:
Library name: Ctrl 2
Column name in countMatrix.txt:  CTRL_2


title: KOLF_Cortisol-1

description:
Library name: RNA-seq sample10
truseq stranded mrna library

value: 10uM Cortisol


title: DK21052-PAMI-Pt-iPSC-neutrophils

description: all.rpm_DK21052-HC-iPSCs_Neutro_MOsMPs.xlsx

value: neutrophils

value: untreated


title: KOLF_Cortisol-2

description:
Library name: RNA-seq sample11
truseq stranded mrna library


title: DK21052-PAMI-Pt-iPSC-MOsMPs


title: CTRL-Ethanol_P03_F01

description: Library name: LigandScreen-P03-20230901-006_S102


title: Control BAT, PBS 1

description:
Library name: Ctrl 1
Column name in countMatrix.txt:  CTRL_1

value: WT


title: CTRL-Ethanol_P03_E01

description: Library name: LigandScreen-P03-20230901-005_S101


title: KOLF-3

description:
Library name: RNA-seq sample9
truseq stranded mrna library


title: KOLF-2

description:
Library name: RNA-seq sample8
truseq stranded mrna library


title: DK21052-HC-2-iPSCs

source_name: iPSCs

value: iPSCs


title: WT_Inp_rep2

city: Greater Noida

first: Sanjeev

last: Galande

state: Uttar Pradesh

address: Center of Excellence in Epigenetics  Department of Life Sciences  School of Natural Sciences  Shiv Nadar Institute of Eminence  NH91, Tehsil Dadri

country: India

institute: Shiv Nadar University

description: Library name: Sample 18

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v 1.24, then mapped to mm10 genome using bowtie2 using default setting in paired-end more. Only paired end reads were kept in the bam processed files using the command samtools view -F 0x04 -f 0x02. Bigwig files were generated using bamCoverage using RPGC normalization. Bam files were used for peak calling using MACS2 using default settings,with –nomodel parameter. Bigwig files were used to plot IGV graphs. Delimited narrowpeak files from MACS2 output were used for differential analysis in R v4.12.
Assembly: mm10
Supplementary files format and content: Tab-delimited narrowpeak files
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

source_name: Thymus

extract_protocol:
DP thymocytes from WT and Satb1 KO mice were used for CUT&RUN using the benchtop protocol. One million cells were sorted and washed in ice-cold phosphate-buffered saline (PBS). Nuclei were isolated by hypotonic lysis in 1 ml NE1 (20 mM HEPES-KOH pH 7.9; 10 mM KCl; 1 mM MgCl 2 ; 0.1% Triton X-100; 20% Glycerol) for 5 min on ice followed by centrifugation as above. Nuclei were briefly washed in 1.5 ml Buffer 1 (20 mM HEPES pH 7.5; 150 mM NaCl; 2 mM EDTA; 0.5 mM Spermidine; 0.1% BSA) and were incubated with pre-washed Concanavalin A magnetic beads on RT for 5 min. Nuclei-bound beads were washed in 1.5 ml Buffer 2 (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 0.1% BSA). Nuclei were resuspended in 500 μl Buffer 2 and 10 μl SMC1A antibody (Abcam) or CTCF (Cell Signaling Technologies) was added and incubated at 4°C for 2 hr. Nuclei were washed 3 x in 1 ml Buffer 2 to remove unbound antibody. Nuclei were resuspended in 300 μl Buffer 2 and 5 μl pAG-MNase (EpiCypher) added and incubated at 4°C for 1 hr. Nuclei were washed 3 x in 0.5 ml Buffer 2 to remove unbound pA-MN. Tubes were placed in a metal block in ice-water and quickly mixed with 100 mM CaCl2 to a final concentration of 2 mM. The reaction was quenched by the addition of EDTA and EGTA to a final concentration of 10 mM and 20 mM respectively. Cleaved fragments were liberated into the supernatant by incubating the nuclei at 4°C for 1 h, and nuclei were pelleted by centrifugation as above. DNA fragments were extracted from the supernatant and used for the construction of sequencing libraries.
he NEB-Next UltraII library prep kit (NEB) was utilized to prepare a library with an equivalent quantity of DNA (~5 ng) as input. Quantitative PCR (qPCR) analysis was used to estimate the number of cycles required for the amplification of adapter- ligated libraries. Using the HiPrep PCR clean up system (MagBio Genomics, USA), final libraries were purified. Prior to pooling libraries at an equimolar ratio, the library concentration was ascertained using Qubit, and the average fragment size was measured using the dsDNA HS test on the Bioanalyzer 2100 (Agilent). The HiseqX platform was utilized to acquire sequencing reads (150 bp PE).

value: Thymus

value: Primary

value: DP

value: Tamoxifen


title: DK21052-HC-2-iPSC-neutrophils+G6


title: KOLF-1

description:
Library name: RNA-seq sample7
truseq stranded mrna library

value: Brain organoid

value: Healty control


title: WT_Inp_rep1

description: Library name: Sample 17


title: CTRL-DMSO_P03_D01

description: Library name: LigandScreen-P03-20230901-004_S100


title: CTRL-DMSO_P03_C01

description: Library name: LigandScreen-P03-20230901-003_S99


title: vKO_Inp_rep2

description: Library name: Sample 16

value: Satb1 KO


title: CTRL-WM_P03_B01

description: Library name: LigandScreen-P03-20230901-002_S98


title: DK21052-HC-1-iPSCs


title: DK21052-HC-2-iPSC-neutrophils

value: iPSCs derived cells


title: vKO_Inp_rep1

description: Library name: Sample 15


title: WT_Smc1a_rep2

description:
Library name: Sample 14
bigwig file, peakfile (delimited text) attached


title: HES3-3

description:
Library name: RNA-seq sample3
truseq stranded mrna library


title: VEGF-A165_P01_F12

description: Library name: LigandScreen-P01-20230825-094_S94


title: WT_Smc1a_rep1

description:
Library name: Sample 13
bigwig file, peakfile (delimited text) attached


title: DK21052-HC-1-iPSC-neutrophils+G6


title: DK21052-HC-1-iPSC-neutrophils


title: VEGF-A121_P01_E12

description: Library name: LigandScreen-P01-20230825-093_S93


title: HES3-2

description:
Library name: RNA-seq sample2
truseq stranded mrna library


title: WT_DP_K27ac_rep2

description:
Library name: Sample 12
bigwig file attached


title: DK21052-HC-1-iPSC-MOsMPs

description: all.rpm_DK21052-HC-iPSCs_Neutro_MOsMPs.xlsx

value: monocytes/macrophages


title: WT_DP_K27ac_rep1

description:
Library name: Sample 11
bigwig file attached


title: HES3-1

description:
Library name: RNA-seq sample1
truseq stranded mrna library


title: TRAIL_P01_C12

description: Library name: LigandScreen-P01-20230825-091_S91


title: MCF7, Myricetin, CM11, 6h, G04

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description: Library name: CM11_T8_D3_G04

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: Breast; Mammary gland

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma

value: test


title: WT_DP_IgG

description:
Library name: Sample 10
bigwig file attached


title: MCF7, Myricetin, CM11, 6h, F07

description: Library name: CM11_T8_D3_F07


title: WT_DP_Ctcf_rep2

description:
Library name: Sample 9
bigwig file, peakfile (delimited text) attached


title: DK21052-HC-1-E250K-iPSC-neutrophils

value: neutrophils


title: Thrombin_P01_A12

description: Library name: LigandScreen-P01-20230825-089_S89


title: MCF7, Myricetin, CM11, 6h, E10

description: Library name: CM11_T8_D3_E10


title: WT_DP_Ctcf_rep1

description:
Library name: Sample 8
bigwig file, peakfile (delimited text) attached


title: DK21052-HC-1-E250K-iPSC-MOsMPs

value: untreated


title: SHH_P01_G11

description: Library name: LigandScreen-P01-20230825-087_S87


title: MCF7, Myricetin, CM11, 6h, A02

description: Library name: CM11_T8_D3_A02


title: vKO_Smc1a_rep2

description:
Library name: Sample 7
bigwig file, peakfile (delimited text) attached


title: TNF-a_P01_B12

description: Library name: LigandScreen-P01-20230825-090_S90


title: CHIP068, Input, FRDA + shNIPBL, rep1

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description: H3K9me2_PT_shNIPBL_1_AK81_M100.inpLg2_1kb.woTNR.e100.S10Kb.bw

data_processing:
Basecalls were performed using bcl2fastq v2.20.
ChIP-seq reads were deduplicated and trimmed using fastp v0.23.2. Low complexity reads were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.1. Only uniquely mapping reads with a MAPQ >20 were retained using sambamba 1.0.0.
To create ChIP-seq coverage plots of LB1 and H3K9me2, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, normalized (to counts per million, cpm) and log2 normalized against their corresponding inputs. The resulting bigwig files were generated using deeptools v3.1.3. Bigwigs for RAD21 were generated using macs2 version 2.2.6 representing a fold enrichment over their corresponding inputs. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
RAD21 peaks were called using MACS v2.2.6 with the significance cut-off q-value <=0.01. Broad domains for LB1 or H3K9me2 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed and narrowPeak files with domain calls per condition as described above.

source_name: FRDA fibroblast

growth_protocol: Human skin non-treatment control (NTC) fibroblasts and fibroblasts from a Freidrich's Ataxia patient (FRDA) fibroblast cells were cultured in DMEM (Gibco #11965084) supplemented with 10% fetal bovine serum (Cytiva SH30910.03), 1% penicillin/streptomycin (Invitrogen #15140122), and 1% non-essential amino acids (Invitrogen # 11140050) at 37C with 20% O2 and 5% CO2. RAD21-mAID-HCT116 cells were cultured in McCoys (Invitrogen #16600082) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin at 37C with 20% O2 and 5% CO2.

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms
Libraries were quantified and pooled for sequencing; input libraries were always run with associated ChIP samples. If possible, replicate samples were run together on the same sequencing run.

treatment_protocol: Human fibroblasts were grown in complete media (DMEM, 10% FBS, 1% penicillin/streptomycin) and plated at 40% confluency. The next day, dCas9-KRAB-FXN guide or dCas9-KRAB-Scramble guide was introduced into NTC fibroblasts for 2d followed by 2d selection in blasticidin. RAD21-mAID-HCT116 cells were propagated in standard medium (McCoy’s with 10% FBS and 1% penicillin/streptomycin) and plated in 10cm dishes at 40% density and grown overnight. The following morning, a time course was started for three conditions (DMSO control, triptolide-only, and auxin + triptolide). At time 0, DMSO control and triptolide-only cells were incubated in fresh media alone; auxin + triptolide cells were incubated in fresh media + 1μM auxin (5-Ph-IAA, Tocris Bioscience). After 1 hour, 200nM final triptolide (Selleckchem) was added to triptolide-only and auxin + triptolide cells. 12 hours post-triptolide, all cells were harvested for ChIP (see “ChIP and library preparation for sequencing”). DMSO was used as a vehicle control.

value: FRDA fibroblast

tag: chip antibody

value: Input

value: FRDA + shNIPBL


title: MCF7, Myricetin, CM11, 6h, H01

description: Library name: CM11_T8_D2_H01

tag: tissue


title: HES3_Cortisol-2

description:
Library name: RNA-seq sample5
truseq stranded mrna library

value: 10uM Cortisol


title: RSPO-1_P01_F11

description: Library name: LigandScreen-P01-20230825-086_S86


title: vKO_Smc1a_rep1

description:
Library name: Sample 6
bigwig file, peakfile (delimited text) attached

value: Thymus

value: Primary

value: DP

tag: genotype


title: CHIP067, H3K9me2, FRDA + shNIPBL, rep1

value: H3K9me2 (Active Motif, #39239)

tag: treatment


title: Apelin_P01_E11

description: Library name: LigandScreen-P01-20230825-085_S85


title: PGE2_P01_B11

description: Library name: LigandScreen-P01-20230825-082_S82


title: vKO_DP_K27ac_rep2

description:
Library name: Sample 5
bigwig file attached

value: Satb1 KO

value: Tamoxifen

tag: batch


title: CHIP065, Input, CRISPRi + shNIPBL, rep1

description: H3K9me2_iFXN_shNipbl_2_AK118_M105.inpLg2_1kb.woTNR.e100.S10Kb.bw

source_name: WT fibroblast

tag: cell line

value: WT fibroblast

value: Human fibroblast

value: CRISPRi + shNIPBL


title: MCF7, Myricetin, CM11, 6h, E07

description: Library name: CM11_T8_D2_E07

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma


title: CHIP064, H3K9me2, CRISPRi + shNIPBL, rep1


title: MCF7, Myricetin, CM11, 6h, D10

description: Library name: CM11_T8_D2_D10

value: test


title: CHIP063, Input, CRISPRi , rep1_part2

description: H3K9me2_iFXN_3_AK59_AK60.inpLg2_1kb.woTNR.e100.S10Kb.bw

value: CRISPRi


title: PLG_P01_H10

description: Library name: LigandScreen-P01-20230825-080_S80


title: MCF7, Myricetin, CM11, 6h, G01

description: Library name: CM11_T8_D1_G01


title: vKO_DP_Ctcf_rep2

description:
Library name: Sample 2
bigwig file, peakfile (delimited text) attached


title: CHIP061, H3K9me2, CRISPRi , rep1_part2


title: PEDF_P01_G10

description: Library name: LigandScreen-P01-20230825-079_S79


title: vKO_DP_Ctcf_rep1

description:
Library name: Sample 1
bigwig file, peakfile (delimited text) attached


title: MCF7, Myricetin, CM11, 6h, E04

description: Library name: CM11_T8_D1_E04


title: CHIP059, Input, NTC, rep1

description: H3K9me2_WT_1_AK2_AK3.inpLg2_1kb.woTNR.e100.S10Kb.bw

value: Input

value: NTC


title: MCF7, Myricetin, CM11, 6h, F04

description: Library name: CM11_T8_D2_F04


title: PDGF-BB_P01_F10

description: Library name: LigandScreen-P01-20230825-078_S78


title: vKO_DP_K27ac_rep1

description:
Library name: Sample 4
bigwig file attached


title: MCF7, Myricetin, CM11, 6h, D07

description: Library name: CM11_T8_D1_D07


title: DK22200-MOsMPs-E250K-S100KO-UT-1

description: all.rpm_DK22200-MOsMPs-WT_E250K_E250Q_S100A8KO.xlsx

value: iPSCs derived cells

value: monocytes/macrophages

value: PSTPIP1-E250K, S100A8-KO

value: untreated


title: AngII_P03_G02

description: Library name: LigandScreen-P03-20230901-015_S111


title: vWT_rep3_CD4

description:
Library name: Sample12
column name in cd4_wt_vko_counts.txt: WT3 DP

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10. HISATv2.0.1 was used to map the paired reads Count matrix were generated using feature counts of the SubRead package v1.0.1. DE was performed using Deseq2 in R v4.1.5
Assembly: mm10
Supplementary files format and content: Tab-delimited txt files including raw counts of each sample

extract_protocol:
RNA was extracted from 1-3 million sorted cells using TRIzol (Thermo F isher Scientific) for bulk RNA-seq. The Agilent 2100 Bioanalyzer was used to quantify and qualify the total RNA. Following this, 1 μg of total RNA was utilized to prepare the library.
The poly(A) mRNA magnetic isolation module was used to carry out the poly(A) mRNA isolation. First strand synthesis mix (NEB) was used to create first- strand cDNA, while second strand synthesis enzyme mix (NEB) was used to create second-strand cDNA. Three steps were taken with the isolated double-stranded cDNA: adapter ligation, 3'-dA tailing, and end repair. The number of PCR cycles was determined by qPCR. Ligated DNA was amplified using six to ten cycles with Illumina P5/P7 primers. PCR products were purified using magnetic beads and quantified using a Qubit 4.0 Fluorometer (Thermo Fisher Scientific). The resulting libraries were pooled and sequenced using 2×150 bp paired-end chemistry.

value: Thymus

value: Primary

value: WT


title: CHIP058, H3K9me2, NTC, rep1

value: WT fibroblast

value: H3K9me2 (Active Motif, #39239)


title: Pleiotrophin_P01_A11

description: Library name: LigandScreen-P01-20230825-081_S81


title: PDGF-AA_P01_E10

description: Library name: LigandScreen-P01-20230825-077_S77


title: vKO_DP_IgG

description:
Library name: Sample 3
bigwig file attached

value: DP

value: Satb1 KO

value: Tamoxifen


title: MCF7, Myricetin, CM11, 6h, B10

description: Library name: CM11_T8_D1_B10

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma


title: vWT_rep2_CD4

description:
Library name: Sample11
column name in cd4_wt_vko_counts.txt: WT2 DP


title: CHIP022, Input, CRISPRi , rep2

description:
RAD21_iFXN_FE.100bp.bw
RAD21_iFXN_peaks.narrowPeak

value: Human fibroblast

value: Input

value: CRISPRi


title: PTH_P01_D10

description: Library name: LigandScreen-P01-20230825-076_S76


title: MCF7, DMSO, CM11, 6h, G08

description: Library name: CM11_DMSO_G08

value: vehicle


title: vWT_rep1_CD4

description:
Library name: Sample10
column name in cd4_wt_vko_counts.txt: WT1 DP


title: Adipo_P03_C02

description: Library name: LigandScreen-P03-20230901-011_S107


title: PAR1_P01_C10

description: Library name: LigandScreen-P01-20230825-075_S75


title: MCF7, DMSO, CM11, 6h, F05

description: Library name: CM11_DMSO_F05


title: CHIP021, Input, CRISPRi , rep1


title: CHIP020, RAD21, CRISPRi , rep2

value: RAD21 (Abcam, #ab992)


title: vKO_rep3_CD4

description:
Library name: Sample9
column name in cd4_wt_vko_counts.txt: cKO3 DP


title: PACAP-27_P01_B10

description: Library name: LigandScreen-P01-20230825-074_S74


title: vKO_rep2_CD4

description:
Library name: Sample8
column name in cd4_wt_vko_counts.txt: cKO2 DP


title: MCF7, DMSO, CM11, 6h, D02

description: Library name: CM11_DMSO_D02


title: CHIP019, RAD21, CRISPRi , rep1


title: Noradrenaline_P01_H09

description: Library name: LigandScreen-P01-20230825-072_S72


title: MCF7, DMSO, CM11, 6h, C10

description: Library name: CM11_DMSO_C10


title: vKO_rep1_CD4

description:
Library name: Sample7
column name in cd4_wt_vko_counts.txt: cKO1 DP


title: CHIP016, Input, FRDA, rep2

description:
LB1_PT.inpLg2_1kb.woTNR.e100.S10Kb.bw
LB1_PT.inpLg2_15kb.woTNR.e100.S75Kb.znormChr_15_woBlklst_domains.bed

value: FRDA fibroblast

value: FRDA


title: MCF7, DMSO, CM11, 6h, B12

description: Library name: CM11_DMSO_B12


title: HES3_Cortisol-3

description:
Library name: RNA-seq sample6
truseq stranded mrna library

value: Brain organoid

value: 10uM Cortisol