title: VCAP_DXL_DMSO_SRC2

status: Public on Jul 14 2026

first: Arul

last: Chinnaiyan

address: 1500 East Medical Center Dr

department: MCTP

description: Library name: VCAP_DXL_DMSO_SRC2

data_processing:
ChIP-seq reads were trimmed using Trimmomatic (v0.39, settings TruSeq3-PE-2.fa:2:30:10, minlen 50). Alignment was then performed separately to both the human genome (hg38) and the drosophila genome (dm6) using BWA (v0.7.17 “bwa mem”, options -5S -T0, version 0.7.17-r1198-dirty). Low-quality and duplicate reads were filtered with SAMtools and Picard, respectively. Normalization ratios were calculated based on the lowest amount of uniquely aligned reads per ChIP target to each genome as reccomended in ActiveMotifs protocols. Reads were then downsampled per the normalization ratios. P300 Samples did not have this normalization step. Then peak calling was performed with MACS2 using narrow or broad settings depending on the target, and blacklisted genomic regions were removed using BEDTools with the ENCODE exclusion list. MACS was run with a bam vcap IgG control. Processed data were converted to BigWig format using UCSC wigToBigWig for visualization. Read density heatmaps and average enrichment profiles were generated using deepTools. For histone marks, signals were plotted within ±2.5 kb of the reference point, and for other transcriptome factors within ±1 kb. The parameters --skipZeros, --averageType mean, and --plotType se were applied. ENCODE blacklist regions (ENCFF356LFX) were excluded from analysis.
Assembly: hg38
Supplementary files format and content: .bed: peak locations from macs bed calling with blacklist removed; .bw: signal files

growth_protocol: VCaP cells were maintained in DMEM GlutaMAX supplemented with 10% FBS (Thermo Fisher Scientific).

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed as previously described18. In brief, cells were crosslinked in 1% formaldehyde, quenched with glycine, and lysed for chromatin extraction. Chromatin was sheared to 200–600 bp fragments using a Bioruptor (Diagenode) and subjected to immunoprecipitation with antibodies against transcription factors (AR, FOXA1, p300, ERG, and BRD4) or histone marks (H3K27ac, H2BK20ac, and RNA Pol II) using the iDeal ChIP-seq Kit (Diagenode). Drosophila spike-in chromatin (Active Motif, 53083) and spike-in antibody (Active Motif, 61686) were added during the overnight incubation. After reverse crosslinking and DNA purification, sequencing libraries were prepared and sequenced on an Illumina HiSeq 2500 platform. For PR, SRC2 and CBP ChIP-seq, we performed the double-cross-linking. Briefly, 10 million cells were cross-linked with 250 μl of 200 mM DSP (Thermo Fisher Scientific, 22585) for 30 min at room temperature. PBS was then added to a final volume of 9 ml, followed by 40 μl of 0.5 M EDTA. Formaldehyde (250 μl, 37%) was added, and the cells were incubated for an additional 10 min at room temperature. Cross-linking was quenched by adding 1 ml of 1.25 M glycine and 200 μl of 10% Tween-20, followed by incubation for 5 min. Samples were then processed according to the ChIP–seq protocol described previously.
ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 1 and 3 hours

value: cell line

value: VCaP

value: prostate cancer


title: VCAP_DXL_100nM_JZY3032_3h_SRC2

type: SRA

city: Ann Arbor

state: MI

country: USA

institute: University of Michigan

description: Library name: VCAP_DXL_100nM_JZY3032_3h_SRC2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: VCAP_DXL_100nM JZY3032_3h_PR

description: Library name: VCAP_DXL_100nM JZY3032_3h_PR


title: VCAP_DXL_100nM JZY3032_3h_CBP

description: Library name: VCAP_DXL_100nM JZY3032_3h_CBP


title: VCAP_DXL_DMSO_CBP

description: Library name: VCAP_DXL_DMSO_CBP

value: DMSO


title: H41CNE2-3

city: Haikou

first: Liu

last: Jie

address: hainan university

country: China

institute: Hai Nan University

description: Library name: H41CNE2-3_raw

library_source: transcriptomic

data_processing:
Raw sequencing data were quality-controlled and aligned to the human reference genome (GRCh38) using HISAT2 software.
Gene expression levels were quantified using featureCounts.
Differential expression analysis was performed using the DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: Comma-separated and tab-delimited text files containing raw read counts and FPKM normalized expression values.

molecule: total RNA

source_name: Nasopharynx

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
Library construction was performed by BGI Genomics Co., Ltd. according to their standard procedures.

value: Nasopharynx

value: Epithelial cell

value: Treated with 5.62 uM H41 for 24 hours


title: H41CNE2-2

description: Library name: H41CNE2-2_raw


title: H41CNE2-1

description: Library name: H41CNE2-1_raw


title: ctrlCNE2-3

description: Library name: ctrlCNE2-3_raw


title: VCAP_DXL_DMSO_PR

description: Library name: VCAP_DXL_DMSO_PR


title: ctrlCNE2-2

description: Library name: ctrlCNE2-2_raw


title: ctrlCNE2-1

description: Library name: ctrlCNE2-1_raw


title: PDX

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description:
Library name: Sample20
PDX

data_processing:
Raw fastq files were processed using nf-core RNA-seq pipeline (v3.14) with default parameters
Transcript level quantification was conducted with Salmon, then counts were summarized to gene level.
Counts were normalized to TPM and organized into a gene x sample table.
Example nf-core run script and all scripts used for data analysis can be found on GitHub: https://github.com/pirl-unc/PRAME_in_NUT_Carcinoma
Assembly: hg38
Supplementary files format and content: tab delineated file containing gene x sample raw TPM normalized counts

molecule: polyA RNA

source_name: PDX

growth_protocol: Cell lines were maintained in DMEM with 10% FBS and 1% penicillin/streptomycin in a humidified atmosphere at 5% CO2,  37C

extract_protocol:
RNA was isolated using RNEasy columns (Qiagen)
Library preparation used Illumina’s Stranded mRNA Prep Ligation kit, starting with 125 ng of RNA

treatment_protocol: Control scrambled siRNAs tranfected with lipofectamine RNA imax per manufacturers protocols

value: PDX

value: scrambled siRNA


title: JCM1,REP2

description:
Library name: Sample18
JCM1_rep2


title: 14169.REP4

description:
Library name: Sample16
14169_rep3


title: 14169,REP2

description:
Library name: Sample14
14169_rep1


title: 14169,REP3

description:
Library name: Sample15
14169_rep2


title: 14169,REP1

description:
Library name: Sample13
14169_rep0


title: 10-15,REP4

description:
Library name: Sample12
1015_rep3


title: 10-15,REP3

description:
Library name: Sample11
1015_rep2


title: 10-15,REP1

description:
Library name: Sample9
1015_rep0


title: 10-15,REP2

description:
Library name: Sample10
1015_rep1


title: TC-797,REP4

description:
Library name: Sample8
797_rep3


title: TC-797,REP3

description:
Library name: Sample7
797_rep2


title: TC-797,REP2

description:
Library name: Sample6
797_rep1


title: CTRL-P_1

status: Public on Jul 15 2026

city: 合肥

first: 曹硕

last: 曹

state: 安徽

address: 九龙路

institute: 安徽大学

description:
Library name: SAMPLE1
Nsd1_KO_CTRL_FRAS200000015-1a

data_processing:
RNA Sequencing and Differentially Expressed Genes Analysis.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: tsv file of raw counts

organism: Mus musculus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: stem cell


title: TC-797,REP1

description:
Library name: Sample5
797_rep0


title: PER403,REP4

description:
Library name: Sample4
PER403_rep3


title: HCC827 cells, Osimertinib-resistant, SMAD3 (CUT&Tag)

city: Guangzhou

first: aochu

last: liu

state: Guangdong

address: No. 1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

description: Library name: Sample15

data_processing:
Raw reads were first mapped to the hg19 reference genome using Bwa (version 0.7.17) with default parameters. High-quality mapped reads were then extracted and sorted using SAMtools (version 1.13) . PCR duplicates were removed with the Picard MarkDuplicates tool (version 1.136), and blacklist regions were filtered out using bedtools (version 2.30.0).
Peaks were identified with MACS2 using default options, and Bigwig files were generated using the deepTools bamCoverage function with standard settings.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: The HCC827AR (resistance) cell lines were cultured in RPMI-1640 media, containing 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Cut&Tag was performed according to the manufacturer's instructions (TD903, Vazyme ).
The TruePrep Index Kit V2 for IIIumina (TD202, Vazyme) was used to create a library.

treatment_protocol: Osimertinib resistant cell lines, defined as HCC827AR, are estabolised by stepwise incubate the parental cell line HCC827 with increasing doses of AZD9291,from 10 nM to 500 nM. To maintained the resistance, 500 nM AZD9291 routinely supplemented in the culture medium.

tag: genotype

value: WT

tag: chip antibody


title: PER403,REP3

description:
Library name: Sample3
PER403_rep2


title: 3D PMS iMac at day 9

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
For RNA-seq, reads were trimmed using TrimGalore software (version 0.4.4) with default settings. Subsequently, the adaptor-trimmed paired-end RNA-Seq reads were aligned to the hg38 whole genome employing hisat2 with the -p16 parameter. Read counts were determined by utilizing htseq-count (version 0.11.1) and specifying the following parameters: -r pos -a 10 -t exon -s no -i gene_id -m union. Normalization of raw data counts and identification of differentially expressed genes were carried out with the aid of DESeq2 software, adhering to specific criteria (|log2fc| ≥ 1 and false discovery rate [FDR] ≤ 0.05). For ATAC-seq, all paired-end raw reads underwent processing with TrimGalore (version 0.4.4) to eliminate adapters and low-quality sequences. The adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq data were then aligned to the hg38 genome using bowtie2 (version 2.3.5) 52, employing the following parameters: --t --q --N 1 --L 25. PCR duplicates and multiply mapped reads were subsequently removed by utilizing Picard tools MarkDuplicates (available at https://broadinstitute.github.io/picard/). Following this, replicate BAM files for each time point were consolidated, and reads aligning to blacklisted genomic regions were discarded prior to peak calling with MACS253 (version 2.2.6). The enriched transcription factor motifs were analyzed using Homer (version 4.10.4, findMotifsGenome). Additionally, signal tracks for each sample were created with the bamCoverage function from deeptools and normalized to Reads Per Kilobase Million (RPKM) for ease of visualization.
Assembly: GRCh38
Supplementary files format and content: For single-cell datasets, processed data are UMI matrix and cell barcodes produced by Cellranger pipeline.
Supplementary files format and content: bw

extract_protocol:
Total RNA were extracted by TRIZol.
RNA-seq library were prepared according to SMART-seq2 protocol. ATAC-seq library were prepared according to the omni-ATAC-seq protocol.  CHIP-seq library were prepared according an ultra-low-input native ChIP-seq protocol.Single-cell libraries were prepared according to 10X genomics' manual.

value: macrophage

tag: time point

value: day 9

tag: protocol


title: H5/DOTMA-55-d14

type: protein

city: Irvine

first: Li

last: Liang

state: CA

address: 847 Health Sciences

institute: University of California Irvine

hyb_protocol: The microarray slides were probed with mouse sera diluted 1:100 in protein array blocking buffer (GVS Life Sciences, Sanford, ME) overnight at 4°C and washed with TTBS buffer (20mM Tris-HCl, 150mM NaCl, 0.05% Tween 20 in double-distilled water (ddH2O) adjusted to pH 7.5 and filtered) three times for 5 min each. Mouse IgG  secondary antibody conjugated to AF647, was applied to each of the microarray pads and incubated for 2 h at room temperature, and pads were then washed with TTBS three times for 5 min each and dried.

scan_protocol: The slides were imaged using an ArrayCam imager (Grace Bio-Labs). The output RGB TIFF files generated by the imager were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.

molecule: protein

source_name: Plasma

tag: days post prime immunization


title: H5/DOTMA-54-d14


title: PER403,REP2

description:
Library name: Sample2
PER403_rep1


title: H5/DOTMA-51-d14


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with RRM1&RRM2 domain duplication rescue, rep3

city: Cambridge

first: Ryan

middle: Yue

last: Muller

state: Massachusetts

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

description: Library name: PABP1212_rescue_25d_rep3

data_processing:
Reads were mapped to hg38 using Spliced Transcripts Alignment to a Reference (STAR) with default soft clipping.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

growth_protocol: Cells were cultured in McCoy's 5A Medium supplemented with 10% FBS and incubated at 37 °C and 5% CO2. Cell lines were passaged by subcultivation (1:5 ratio) every 2–3 days at 70–90% confluency using 0.25% Trypsin-EDTA.

extract_protocol:
Total RNA was phenol chloroform extracted and 1μg RNA from each sample was used as an input for sequencing preparation.
Sequencing libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase according to manufacturer's protocols.

treatment_protocol: To induce PABPC1 and PABPC4 degradation and expression of PABPC variants, cells were treated with 1μg/mL doxycycline and 0.5 mM Indole-3-acetic acid (IAA)

value: colon cancer

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-with RRM1&RRM2 domain duplication

tag: time

value: 25 days


title: PER403,REP1

description:
Library name: Sample1
PER403_rep0


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with RRM1&RRM2 domain duplication rescue, rep2

description: Library name: PABP1212_rescue_25d_rep2

value: 1μg/mL doxycycline and 0.5 mM Indole-3-acetic acid (IAA)


title: H5/IVAX-1-Chol-45-d14


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with RRM1&RRM2 domain duplication rescue, rep1

description: Library name: PABP1212_rescue_25d_rep1


title: Patient 8-NSCLC, pre-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample8

source_name: NSCLC

value: NSCLC

value: pre-treatment

value: H3K27ac (Abcam, #ab4729)


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-RRM4 domain deletion rescue, rep3

description: Library name: RRM4-deletion_rescue_48h_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-RRM4 domain deletion

value: 48 hours


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-RRM4 domain deletion rescue, rep1

description: Library name: RRM4-deletion_rescue_48h_rep1


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-RRM4 domain deletion rescue, rep2

description: Library name: RRM4-deletion_rescue_48h_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC4L-RRM4 domain swap rescue, rep3

description: Library name: C4L-RRM4-swap_rescue_48h_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-with PABPC4L-RRM4 domain swap


title: Susceptible,Panicle,normal night temperature,inoculated B.glumae,rep 3

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Library name: S_NT_P3

data_processing:
RNA-Seq reads were first trimmed with Trim Galore version 0.6.4 (Krueger, 2019; Martin, 2011) which includes filtering reads shorter than 30 bp and low-quality ends from reads (Phred score: <20) and the option of removing reads with Ns. The quality of reads before and after trimming was confirmed using FastQC version 0.12.1 (Andrews, 2019)
The filtered reads were then aligned to the Oryza sativa Japonica genome (EnsemblPlants IRGSP-1.0; GCA_001433935.1) using STAR version 2.7.10b (Dobin et al., 2013) with default parameters and --sjdbOverhang of 149. The alignment files generated by STAR were then used to generate gene counts using Subread version 2.0.0 (featureCounts), with default parameters (Liao et al., 2014). A data matrix of gene counts for all samples was created using a custom Python script, which was used for further differential gene expression analysis
Differential gene expression analysis was performed separately for the resistant and susceptible accessions using DESeq2 version 1.38.3 (Love et al., 2014). A Wald test was employed to calculate p-values, and genes with a Benjamini-Hochberg adjusted p-value less than 0.05 and a log2 fold change greater than 1 were considered differentially expressed
Assembly: EnsemblPlants IRGSP-1.0; GCA_001433935.1
Supplementary files format and content: A tab-delimited data matrix of raw feature counts with features (genes) in rows and sample names in columns.

organism: Oryza sativa

source_name: panicle

growth_protocol: The selected accessions were grown until heading stage in the greenhouse.

extract_protocol:
Panicles were ground using 1600 MiniG® automated tissue homogenizer (Spex Sample Prep, Metuchen NJ), and total RNA was extracted using Trizol reagent (Life Technologies, Carlsbad, CA). RNA was precipitated with 5M Potassium Acetate pH 5.2, and 100% ice-cold ethanol and air-dried. RNA pellets were resuspended in 20 µl of RNAse-free water
RNA purity and integrity was evaluated using the ExperionTM Automated Electrophoresis system (BioRad, Hercules, CA).  RNA sequencing was performed by Novogene (Davis, CA) for 150 bp paired-end read sequencing on the Illumina PE250 platform

treatment_protocol: Emerging panicles were inoculated with B. glumae (Pathogen, P) or treated with water (Mock, M) and maintained at normal night temperature (22C) and high night temperature (28C) conditions for 3 days.

value: panicle

value: B.glumae inoculation


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC4L-RRM4 domain swap rescue, rep2

description: Library name: C4L-RRM4-swap_rescue_48h_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC5-RRM4 domain swap rescue, rep3

description: Library name: C5-RRM4-swap_rescue_48h_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-with PABPC5-RRM4 domain swap


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC5-RRM4 domain swap rescue, rep2

description: Library name: C5-RRM4-swap_rescue_48h_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC5-RRM4 domain swap rescue, rep1

description: Library name: C5-RRM4-swap_rescue_48h_rep1


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC4L-RRM4 domain swap rescue, rep1

description: Library name: C4L-RRM4-swap_rescue_48h_rep1


title: HCT116, PABPC1&PABPC4 depletion, PABPC1 rescue-48hour, rep3

description: Library name: PABPC1_rescue_48h_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1


title: HCT116, PABPC1&PABPC4 depletion, PABPC1 rescue-48hour, rep2

description: Library name: PABPC1_rescue_48h_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1 rescue-48hour, rep1

description: Library name: PABPC1_rescue_48h_rep1


title: H5/IVAX-1-Chol-41-d14


title: HCT116, PABPC1&PABPC4 depletion, no rescue, rep3

description: Library name: Null_rescue_48h_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of empty vector


title: HCT116, PABPC1&PABPC4 depletion, no rescue, rep2

description: Library name: Null_rescue_48h_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with S.c. PAB1-RRM4 domain swap rescue, rep3

description: Library name: S.c.PAB1-RRM4-swap_rescue_25d_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-with S.c. PAB1-RRM4 domain swap


title: HCT116, PABPC1&PABPC4 depletion, no rescue, rep1

description: Library name: Null_rescue_48h_rep1


title: A1: Asymptomatic COVID-19 sample 1 bulkRNAseq

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: WI

address: 8727 W Watertown Plank Road

institute: Versiti Blood Research Institute

data_processing:
Fastq data were aligned using STAR aligner and MAPR-Seq workflow v3.0
Genome_build: GRCh38.p13 Gencode v32 (based on Ensembl v98)
Supplementary_files_format_and_content: csv of unnormalized read counts per gene per sample

source_name: Blood Draw

extract_protocol:
PBMCs were isolated from blood draws using Lymphoprep reagent using manufacturer instructions. RNA was isolated using Qiagen Rneasy mini kit using manufacturer's instructions
RNA-seq libraries were prepared using Illumina's TruSeq stranded mRNA library protocol with dual indexing

value: PBMCs

tag: infection

tag: response

value: Asymptomatic


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with S.c. PAB1-RRM4 domain swap rescue, rep2

description: Library name: S.c.PAB1-RRM4-swap_rescue_25d_rep2

value: colon cancer


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with S.c. PAB1-RRM4 domain swap rescue, rep1

description: Library name: S.c.PAB1-RRM4-swap_rescue_25d_rep1

value: 25 days


title: JCM1,REP3

description:
Library name: Sample19
JCM1_rep3

value: scrambled siRNA


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC1L-RRM4 domain swap rescue, rep3

description: Library name: C1L-RRM4-swap_rescue_25d_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-with PABPC1L-RRM4 domain swap

value: 1μg/mL doxycycline and 0.5 mM Indole-3-acetic acid (IAA)


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC1L-RRM4 domain swap rescue, rep2

description: Library name: C1L-RRM4-swap_rescue_25d_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1-with PABPC1L-RRM4 domain swap rescue, rep1

description: Library name: C1L-RRM4-swap_rescue_25d_rep1


title: HCT116, PABPC1&PABPC4 depletion, PABPC4 rescue, rep3

description: Library name: PABPC4_rescue_25d_rep3

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC4


title: HCT116, PABPC1&PABPC4 depletion, PABPC4 rescue, rep2

description: Library name: PABPC4_rescue_25d_rep2


title: HCT116, PABPC1&PABPC4 depletion, PABPC4 rescue, rep1

description: Library name: PABPC4_rescue_25d_rep1


title: Resistant,Panicle,normal night temperature,inoculated B.glumae,rep 2

description: Library name: R_NT_P2


title: HCT116, PABPC1&PABPC4 depletion, PABPC1 rescue-25day, rep1

description: Library name: PABPC1_rescue_25d_rep1


title: HCT116, PABPC1&PABPC4 depletion, PABPC1 rescue-25day, rep3

description: Library name: PABPC1_rescue_25d_rep3


title: HCT116, no PABPC1&PABPC4 depletion, null rescue, rep3

description: Library name: Null_rescue_no_depletion_25d_rep3


title: HCT116, no PABPC1&PABPC4 depletion, null rescue, rep2

description: Library name: Null_rescue_no_depletion_25d_rep2


title: JCM1,REP1

description:
Library name: Sample17
JCM1_rep1


title: HCT116, PABPC1&PABPC4 depletion, PABPC1 rescue-25day, rep2

description: Library name: PABPC1_rescue_25d_rep2


title: HCT116, no PABPC1&PABPC4 depletion, null rescue, rep1

description: Library name: Null_rescue_no_depletion_25d_rep1


title: HOOK62_HB202

city: Wien

first: Sarah

last: Szaffich

address: Schenk-danzinger-gasse 6/4/17

country: Austria

institute: Hookipa Biotech GmbH

description:
Library name: S11485Nr27
10x Genomics

data_processing:
FASTQ files were processed with CellRanger v8.0.0 (10x Genomics) for demultiplexing and alignment to the hg38 reference genome including the sequences of the viral coding regions of HB-201 and HB-202.
Assembly: homo sapiens (hg38)
Assembly: open reading frames of HB-201 and HB-202 viral vectors
Supplementary files format and content: Tab-separated values file and matrix file

source_name: peripheral blood

extract_protocol:
Human peripheral blood mononuclear cells were thawed, seeded with a concentration of 1 million cells per well in a 24-well plate in complete medium (RPMI 1640 medium (Gibco) + 10% human serum (Sigma-Aldrich), 1% GlutaMax, 1% Sodium Pyruvate, 1% NEAA, 1% PenStrep, 0.01% b-Mercaptoethanol) and infected at a MOI of 1. The cells were incubated for 5-6 hours at 37°C before replacing the cell culture supernatant with fresh medium Infection was carried out for a total of 24 hours.  After 24 hours, the cells were harvested using 0.05% Trypsin-EDTA, transferred in FACS buffer (PBS, 2.5% FBS, 10mM EDTA), blocked (human Fc Block, BD Biosciences) and stained with PE anti-human HLA-DR Antibody (BioLegend). After 30 minutes at 4°C, the cells were washed once with FACS buffer and once with MACS buffer (MACS BSA stock solution 1:20 with autoMacs Rinsing Solution from Miltenyi) before adding 20 µL Anti-PE MicroBeads for enrichment of HLA-DR expressing cells by magnetic separation.
Sequencing libraries were prepared following the manufacturer’s protocol for single-cell RNA sequencing using the 10x Genomics Chromium GEM-X Single Cell 5’ Immune Profiling kit. Quality and quantity of single final libraries were determined using the Qubit (Thermo Fisher) and the Tapestation 4200 system (Agilent). Final quality control and sequencing were performed by CeGat GmbH (Tübingen, Germany). Samples were sequenced in one run with an Illumina NovaSeq 6000 system (S2 100-cycle cartridge) with calculated requirements of at least 30,000 reads per cell and 4,000 cells per sample. Data was delivered as raw, untrimmed FASTQ files.

value: peripheral blood

value: peripheral blood mononuclear cells

tag: batch


title: Ezh2 KO2

description:
Library name: SAMPLE8
Ezh2_KO_Ezh2_KO_FRAS202404799-1r

value: stem cell


title: HOOK62_MOCK

description:
Library name: S11485Nr25
10x Genomics


title: HOOK60_HB202

description:
Library name: S11485Nr24
10x Genomics


title: HOOK26_HB202

description:
Library name: S11485Nr21
10x Genomics


title: HOOK60_HB201

description:
Library name: S11485Nr23
10x Genomics


title: HOOK26_MOCK

description:
Library name: S11485Nr19
10x Genomics


title: 111-0001_C1D1_HB201

description:
Library name: S11485Nr17
10x Genomics


title: HOOK26_HB201

description:
Library name: S11485Nr20
10x Genomics


title: 111-0001_C1D1_MOCK

description:
Library name: S11485Nr16
10x Genomics


title: 109-0015_SCR_HB202

description:
Library name: S11485Nr15
10x Genomics


title: 109-0015_SCR_MOCK

description:
Library name: S11485Nr13
10x Genomics


title: 106-0005_SCR_HB201

description:
Library name: S11485Nr11
10x Genomics


title: 106-0005_SCR_MOCK

description:
Library name: S11485Nr10
10x Genomics


title: 115-0017_SCR_HB202

description:
Library name: S11485Nr9
10x Genomics


title: 109-0015_SCR_HB201

description:
Library name: S11485Nr14
10x Genomics


title: 115-0017_SCR_MOCK

description:
Library name: S11485Nr7
10x Genomics


title: 109-0003_C1D1_HB202

description:
Library name: S11485Nr6
10x Genomics


title: 109-0003_C1D1_HB201

description:
Library name: S11485Nr5
10x Genomics


title: 109-0003_C1D1_MOCK

description:
Library name: S11485Nr4
10x Genomics


title: 101-0006_SCR_HB202

description:
Library name: S11485Nr3
10x Genomics


title: 101-0006_SCR_HB201

description:
Library name: S11485Nr2
10x Genomics


title: 101-0006_SCR_MOCK

description:
Library name: S11485Nr1
10x Genomics


title: Day 9

first: Xiujie

last: Yang

address: 38 Xueyuan Road

institute: Peking University

description:
Library name: Sample3
CR-hBO255

data_processing:
Sequencing reads (FASTQ files) were aligned to the human reference genome (GRCh38) with GENCODE v32/Ensembl 98 annotations, and unique molecular identifier (UMI) count matrices were generated. Low-quality cells, defined as those with fewer than 200 detected genes or with >15% mitochondrial transcripts, were excluded, resulting in a final dataset of 31,669 single cells. Data preprocessing was performed using Scanpy (v1.8) 65. Counts were normalized by total expression per cell (scale factor = 10,000) and log-transformed using pp.log1p. Highly variable genes were identified using pp.highly_variable_genes. Dimensionality reduction was conducted by principal component analysis (tl.pca), followed by graph-based clustering using pp.neighbors. Uniform manifold approximation and projection (UMAP; tl.umap) was used for 2D and 3D visualization. Cluster-specific marker genes were identified using the Seurat FindAllMarkers function (Wilcoxon rank-sum test; P < 0.05 and log2 fold change > 0.5). Cell trajectory inference was performed using Slingshot (v2.0) based on UMAP embeddings, with the “Quiescent MSC” cluster defined as the root for pseudotime analysis. Cell plasticity was quantified using CytoTRACE (v1.0). Cell cycle phases (G1, S, and G2/M) were assigned using Seurat CellCycleScoring. All sequencing and bioinformatic analyses were performed by Genechem (Shanghai, China).
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz represents Sparse UMI count matrix
Supplementary files format and content: features.tsv.gz represents Gene feature annotation table
Supplementary files format and content: barcodes.tsv.gz represents Cell barcode list, each line represents one single cell

source_name: tumor

extract_protocol:
Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 1 mg/mL collagenase I (Gibco)，1 mg/mL collagenase II，60U/mL Hyaluronidase (Sigma), 10U/mL Liberase (Roche) and 0.02mg/mL DNase I (Roche) for 90 min at 37°C, with agitation . After digestion, samples were sieved through a 100µm and 40µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Gibco) to lyse red blood cells.  After washing with DPBS containing 0.5% BSA, the cell pellets were re-suspended in DPBS containing 0.5% BSA，stained and counted.
The Chromium instrument and the Single Cell 3’ Reagent kit V3.1 (Dual Index) was used to prepare individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol (10X Genomics). Briefly, sample partitioning and molecular barcoding were done on the Chromium Controller (10x Genomics), where we loaded cellular suspensions together with the Single-cell 3’ Gel Beads on a Single-cell 3’ chip, in which gel beads in emulsion (GEM) generation took place. RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell reagent kit V3.1 (10X Genomics). Sequencing was performed with Illumina (NovaSeq) according to the manufacturer’s instructions.

value: tumor

value: mesenchymal stem cell

value: MSCYAP-PSMA administration


title: Caco-2, Control prior run, rep 1

city: Los Angeles

first: Isabella

last: Lin

address: 615 Charles E Young Dr S

institute: University of California Los Angeles

description:
Library name: CACO2-old-1
CACO2_star_featureCounts_GeneTable_final.csv

data_processing:
Samples were demultiplexed after sequencing, and fastq sequencing files were processed using established pipelines in the Arboleda lab. Raw read quality, adaptor content, and duplication rates were assessed with FastQC v0.11.8.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e (3) with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 (4) from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene.
Differential expression analysis was completed using DESeq2 v1.24.0 (5).
Assembly: GRCh38
Supplementary files format and content: csv file with gene counts generated using featureCounts

source_name: Colorectal carcinoma

growth_protocol: Human embryonic kidney (HEK293T) and colorectal adenocarcinoma (Caco-2) were maintained in DMEM with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA extraction via RNeasy Plus Mini Kit (Qiagen, 74136)
All samples were then prepared with QIAseq FastSelect −rRNA HMR (Qiagen, 334386) and TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599)

treatment_protocol: Using Lipofectamine™ 3000, cells were transfected with 2.5ug of plasmid or mock. Transfected cells were incubated for 48 hours transfection.

value: Colorectal carcinoma

value: WT

value: Untransfected


title: Caco-2, Control, rep 3

description:
Library name: CACO2-neg-2022-3
CACO2_star_featureCounts_GeneTable_final.csv

value: Transfection (control)


title: Day 6

description:
Library name: Sample2
CR-hBO256


title: Caco-2, Control, rep 2

description:
Library name: CACO2-neg-2022-2
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, Control GFP, rep 3

description:
Library name: CACO2-GFP-2022-3
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, Control GFP, rep 2

description:
Library name: CACO2-GFP-2022-2
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, Control GFP, rep 1

description:
Library name: CACO2-GFP-2022-1
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, Control, rep 1

description:
Library name: CACO2-neg-2022-1
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, ASXL1 Transfection 1-479, rep 3

description:
Library name: CACO2-ASXL1-1-479-3
CACO2_star_featureCounts_GeneTable_final.csv

value: Transfection


title: Caco-2, ASXL1 Transfection 1-479, rep 2

description:
Library name: CACO2-ASXL1-1-479-2
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, ASXL1 Transfection 1-1304, rep 3

description:
Library name: CACO2-ASXL1-1-1304-3
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, ASXL1 Transfection 1-479, rep 1

description:
Library name: CACO2-ASXL1-1-479-1
CACO2_star_featureCounts_GeneTable_final.csv


title: Caco-2, ASXL1 Transfection 1-1304, rep 1

description:
Library name: CACO2-ASXL1-1-1304-1
CACO2_star_featureCounts_GeneTable_final.csv


title: IPF_11_RNA

city: Nashville

first: Ana

last: Serezani

state: TN

address: 1161 21st Ave. S, MCN B1320B

department: Medicine

institute: Vanderbilt Medical Center

description:
Library name: Sample 32_RNA
10xgenomics

data_processing:
CellRanger 6.0.0-6.1.1
Assembly: GRCh38-2020-A
Supplementary files format and content: h5
Supplementary files format and content: Raw Matrix files
Library strategy: CITE-seq

source_name: Lung

extract_protocol:
Tissue samples were obtained from fibrotic lungs [Idiopathic Pulmonary Fibrosis (IPF), Interstitial Pneumonia with Autoimmune Features (IPAF), and Connective Tissue Disease-associated Interstitial Lung Disease (CTD-ILD), Nonspecific Interstitial pneumonia (NSID)] removed at the time of lung transplant surgery or non-fibrotic control lungs (declined donors) obtained at the time of organ procurement at Vanderbilt University Medical Center. Lung tissue biopsies were washed in PBS, minced, and frozen in RPMI media containing 10% DMSO until analysis. Minced lungs were thawed at 37oC for 3 minutes and digested in an enzymatic cocktail [Collagenase XI and DNAse I, type IV (Sigma)] and using a gentleMACS Octo Dissociator (Miltenyi Inc.) at 37°C and filtered using 100-μm sterile filters (Fisher). Whole lung cell suspensions (up to 1 million cells) were incubated with an Fc receptor blocking reagent (TrueStain FcX, BioLegend, USA) for 15 minutes, followed by staining with a panel of flow cytometry antibodies [anti-CD45 (APC-Cy7), anti-CD3 (PE-Cy5), and fourteen oligo-conjugated TotalSeq-C human antibodies (BioLegend)] for 30 minutes. Cells were washed three times with PBS containing 1% BSA and stained with a viability dye (Zombie Aqua kit, BioLegend). Up to 25,000 viable CD45⁺CD3⁺ cells were sorted per sample using a BD FACS ARIA and submitted for sequencing on the 10x Genomics Chromium platform. Briefly, 10,000 cells were loaded onto a 10x Chromium single-cell encapsulation chip, and libraries were prepared according to the manufacturer’s instructions. Sequencing was performed on Illumina platforms at a depth of at least 80 million reads per library.
10x_Single Cell 5' PE

value: Lung

value: Not apply

value: CD3+ T cell

tag: library type

value: mRNA


title: IPF_10_RNA

description:
Library name: Sample 31_RNA
10xgenomics


title: IPF_10_ADT

description:
Library name: Sample 31_ADT
Antibody-derived oligonucleotide

library_source: other

value: ADT

tag: adt

value: TotalSeq_CD3 TotalSeq_CD8 TotalSeq_CD56 TotalSeq_CD4 TotalSeq_CD25 TotalSeq_CD45RO TotalSeq_PD1 TotalSeq_CD103 TotalSeq_CCR7 TotalSeq_CTLA4 TotalSeq_LAG3 TotalSeq_HLADR TotalSeq_CD57 TotalSeq_CD28 TotalSeq_KLRG1


title: IPF_1b_ADT

description:
Library name: Sample 30_ADT
Antibody-derived oligonucleotide


title: NSIP_ADT

description:
Library name: Sample 29_ADT
Antibody-derived oligonucleotide


title: CTD-ILD_5_RNA

description:
Library name: Sample 28_RNA
10xgenomics


title: CTD-ILD_3b_RNA

description:
Library name: Sample 24_RNA
10xgenomics


title: non-diseased control_9_RNA

description:
Library name: Sample 26_RNA
Antibody-derived oligonucleotide


title: CTD-ILD_4_RNA

description:
Library name: Sample 25_RNA
10xgenomics


title: CTD-ILD_1_ADT

description:
Library name: Sample 21_ADT
Antibody-derived oligonucleotide


title: CTD-ILD_1_RNA

description:
Library name: Sample 21_RNA
10xgenomics


title: IPAF_4_RNA

description:
Library name: Sample 20_RNA
10xgenomics


title: IPAF_3_ADT

description:
Library name: Sample 19_ADT
Antibody-derived oligonucleotide


title: NSIP_RNA

description:
Library name: Sample 29_RNA
10xgenomics


title: H-3,20 months

first: di

last: deng

address: No. 11, Beisanhuan East Road, Chaoyang District, Beijing

institute: Beijing University of Chinese Medicine

description:
Library name: Sample11
L-NH-14

data_processing:
Raw reads of fastq format were firstly processed using fastpi and the low quality reads were removed to obtain the clean reads.
Assembly: mm39
Supplementary files format and content: FPKMi of each gene was calculated and the read counts of each gene were obtained

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: hippocampus

value: H


title: non-diseased control_10_RNA

description:
Library name: Sample 27_RNA
10xgenomics


title: CTD-ILD_5_ADT

description:
Library name: Sample 28_ADT
Antibody-derived oligonucleotide


title: CTD-ILD_3a_RNA

description:
Library name: Sample 23_RNA
10xgenomics


title: H-2,20 months

description:
Library name: Sample10
L-NH-13


title: CTD-ILD_2a_RNA

description:
Library name: Sample 22_RNA
10xgenomics


title: H-1,20 months

description:
Library name: Sample9
L-NH-12


title: IPAF_4_ADT

description:
Library name: Sample 20_ADT
Antibody-derived oligonucleotide


title: IPAF_1_ADT

description:
Library name: Sample 17_ADT
Antibody-derived oligonucleotide


title: C-3,20 months

description:
Library name: Sample8
L-NH-9

value: C


title: C-2,20 months

description:
Library name: Sample7
L-NH-8


title: C-1,20 months

description:
Library name: Sample6
R-NH-10


title: CTD-ILD_2b_RNA

description:
Library name: Sample 16_RNA
10xgenomics


title: L-5,20 months

description:
Library name: Sample5
L-NH-3

value: L


title: IPF_7_ADT

description:
Library name: Sample 15_ADT
Antibody-derived oligonucleotide


title: L-4,20 months

description:
Library name: Sample4
L-NH-2


title: IPF_7_RNA

description:
Library name: Sample 15_RNA
10xgenomics


title: L-3,20 months

description:
Library name: Sample3
R-NH-5


title: IPF_6_ADT

description:
Library name: Sample 14_ADT
Antibody-derived oligonucleotide


title: L-2,20 months

description:
Library name: Sample2
R-NH-4


title: IPF_6_RNA

description:
Library name: Sample 14_RNA
10xgenomics


title: IPAF_3_RNA

description:
Library name: Sample 19_RNA
10xgenomics


title: L-1,20 months

description:
Library name: Sample1
R-NH-1


title: IPF_5_ADT

description:
Library name: Sample 13_ADT
Antibody-derived oligonucleotide


title: IPAF_2_RNA

description:
Library name: Sample 18_RNA
10xgenomics


title: GWCBD30LPS: GWI mice received CBD and with LPS 4

first: Kwang-Mook

last: Jung

address: 3105 Gillespie NRF

department: Anatomy&Neurobiology

institute: University of California, Irvine

description: Library name: GWCBD30LPS_4

data_processing:
Reads were aligned to GRCm38/mm10 to produce gene-level counts.
Assembly: mouse reference genome GRCm38/mm10
Supplementary files format and content: Gene readcount values csv file

source_name: Microglia (FACS-purified)

extract_protocol:
Total RNA was extracted using Trizol/Rneasy hybrid method, and samples with RNA integrity number ≥ 8.5 were used for RNA sequencing.
Poly(A)-enriched stranded libraries were prepared and sequenced on an Illumina platform with paired‑end 150‑bp reads (PE150) at Novogene (Bejing, People’s Republic of China).

value: Microglia (FACS-purified)

value: GW chemicals, CBD, LPS


title: HOOK62_HB201

description:
Library name: S11485Nr26
10x Genomics

value: peripheral blood

value: peripheral blood mononuclear cells


title: IPF_5_RNA

description:
Library name: Sample 13_RNA
10xgenomics


title: GWCBD30LPS: GWI mice received CBD and with LPS 3

description: Library name: GWCBD30LPS_3


title: HOOK60_MOCK

description:
Library name: S11485Nr22
10x Genomics


title: non-diseased control_8

description:
Library name: Sample 12_ADT
Antibody-derived oligonucleotide


title: 111-0001_C1D1_HB202

description:
Library name: S11485Nr18
10x Genomics


title: IPAF_1_RNA

description:
Library name: Sample 17_RNA
10xgenomics


title: GWCBD30LPS: GWI mice received CBD and with LPS 2

description: Library name: GWCBD30LPS_2


title: CTD-ILD_2b

description:
Library name: Sample 16_ADT
Antibody-derived oligonucleotide


title: 106-0005_SCR_HB202

description:
Library name: S11485Nr12
10x Genomics


title: 115-0017_SCR_HB201

description:
Library name: S11485Nr8
10x Genomics


title: GWCBD30LPS: GWI mice received CBD and with LPS 1

description: Library name: GWCBD30LPS_1


title: non-diseased control_7

description:
Library name: Sample 11_ADT
Antibody-derived oligonucleotide


title: non-diseased control_8_RNA

description:
Library name: Sample 12_RNA
10xgenomics


title: GWCBD30: GWI mice received CBD_3

description: Library name: GWCBD30_4

value: GW chemicals, CBD


title: non-diseased control_7_RNA

description:
Library name: Sample 11_RNA
10xgenomics


title: GWCBD30: GWI mice received CBD_1

description: Library name: GWCBD30_2


title: GWCBD30: GWI mice received CBD_2

description: Library name: GWCBD30_3


title: non-diseased control_6

description:
Library name: Sample 10_ADT
Antibody-derived oligonucleotide


title: non-diseased control_6_RNA

description:
Library name: Sample 10_RNA
10xgenomics


title: Day 0

description:
Library name: Sample1
CR-hBO254

value: tumor

value: mesenchymal stem cell

value: MSCYAP-PSMA administration


title: GWLPS: GWI model mice with LPS_3

description: Library name: GWLPS_4

value: GW chemicals, LPS


title: non-diseased control_5

description:
Library name: Sample 9_ADT
Antibody-derived oligonucleotide

value: Lung

value: Not apply

value: CD3+ T cell


title: GWLPS: GWI model mice with LPS_1

description: Library name: GWLPS_2


title: Caco-2, Control prior run, rep 2

description:
Library name: CACO2-old-2
CACO2_star_featureCounts_GeneTable_final.csv

value: Colorectal carcinoma

value: WT

value: Untransfected


title: non-diseased control_5_RNA

description:
Library name: Sample 9_RNA
10xgenomics

value: mRNA


title: GWLPS: GWI model mice with LPS_2

description: Library name: GWLPS_3


title: GW: GWI model mice_4

description: Library name: GW_4

value: GW chemicals


title: IPF_4_ADT

description:
Library name: Sample 8_ADT
Antibody-derived oligonucleotide

value: ADT

value: TotalSeq_CD3 TotalSeq_CD8 TotalSeq_CD56 TotalSeq_CD4 TotalSeq_CD25 TotalSeq_CD45RO TotalSeq_PD1 TotalSeq_CD103 TotalSeq_CCR7 TotalSeq_CTLA4 TotalSeq_LAG3 TotalSeq_HLADR TotalSeq_CD57 TotalSeq_CD28 TotalSeq_KLRG1


title: IPF_4_RNA

description:
Library name: Sample 8_RNA
10xgenomics


title: IPF_3_ADT

description:
Library name: Sample 7_ADT
Antibody-derived oligonucleotide


title: GW: GWI model mice_2

description: Library name: GW_2

value: Microglia (FACS-purified)


title: GW: GWI model mice_3

description: Library name: GW_3


title: Caco-2, ASXL1 Transfection 1-1304, rep 2

description:
Library name: CACO2-ASXL1-1-1304-2
CACO2_star_featureCounts_GeneTable_final.csv

value: Transfection


title: GW: GWI model mice_1

description: Library name: GW_1


title: IPF_3_RNA

description:
Library name: Sample 7_RNA
10xgenomics


title: IPF_2_ADT

description:
Library name: Sample 6_ADT
Antibody-derived oligonucleotide


title: VehLPS: Ctrl mice with LPS_4

description: Library name: VehLPS_4

value: Vehicle, LPS


title: IPF_1a_ADT

description:
Library name: Sample 5_ADT
Antibody-derived oligonucleotide


title: VehLPS: Ctrl mice with LPS_3

description: Library name: VehLPS_3


title: VehLPS: Ctrl mice with LPS_2

description: Library name: VehLPS_2


title: IPF_1b_RNA

description:
Library name: Sample 30_RNA
10xgenomics


title: IPF_2_RNA

description:
Library name: Sample 6_RNA
10xgenomics


title: IPF_1a_RNA

description:
Library name: Sample 5_RNA
10xgenomics


title: VehLPS: Ctrl mice with LPS_1

description: Library name: VehLPS_1


title: non-diseased control_4_ADT

description:
Library name: Sample 4_ADT
Antibody-derived oligonucleotide


title: Veh: Ctrl mice_4

description: Library name: Veh_4

value: Vehicle


title: non-diseased control_4_RNA

description:
Library name: Sample 4_RNA
10xgenomics


title: Veh: Ctrl mice_3

description: Library name: Veh_3


title: non-diseased control_3_ADT

description:
Library name: Sample 3_ADT
Antibody-derived oligonucleotide


title: non-diseased control_3_RNA

description:
Library name: Sample 3_RNA
10xgenomics


title: Veh: Ctrl mice_1

description: Library name: Veh_1


title: GWCBD30LPS: GWI mice received CBD and with LPS_4

description: Library name: GWCBD304LPS

source_name: Brain (whole)

value: Brain (whole)

value: GW chemicals, CBD, LPS


title: non-diseased control_1_ADT

description:
Library name: Sample 1_ADT
Antibody-derived oligonucleotide


title: GWCBD30LPS: GWI mice received CBD and with LPS_3

description: Library name: GWCBD303LPS


title: GWCBD30LPS: GWI mice received CBD and with LPS_1

description: Library name: GWCBD301LPS


title: HT-29 cells, TSZ

city: Suzhou

first: Haohao

last: Lu

state: Jiangsu

address: No. 100 Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample2

data_processing:
Sequencing data quality analysis was performed starting with a preliminary statistical assessment of the raw sequencing data. The raw reads were then processed and optimized using Cutadapt (version 1.9.1) to remove primer and adapter sequences, trim bases with quality scores below 20 at both ends, and discard reads where the proportion of ambiguous bases (N) exceeded 10%, followed by a statistical analysis of the resulting clean data. Subsequently, the paired-end Clean Reads (Read1 and Read2) were merged into full-length sequences based on their overlap region using Pandaseq (version 2.7), and the length distribution of the assembled sequences was statistically analyzed. Finally, target sequences were extracted by identifying regions flanked by specific 10-nucleotide sequences upstream and downstream, and their abundances were quantified.
Supplementary files format and content: tab-delimited text file includes raw counts for each sgRNA
Library strategy: CRISPR Screen

extract_protocol:
The CRISPR-Cas9 screen was performed using a sgRNA library from Addgene, targeting ubiquitination-related proteins (Cat#174592). Lentiviruses were produced in 293T cells by co-transfecting with the packaging plasmid pMD2.G, psPAX2, and the lentiviral plasmid containing the sgRNA library along with Cas9. HT-29 cells were then infected with these lentiviruses for 72 hours. Subsequently, the cells were treated with either DMSO or TNF (1 ng/ml), Smac mimetic (100 nM) and z-VAD (25 μM) for 24 hours, followed by a recovery period of an additional 24 hours, marking one round of positive screening. After four rounds of positive screening, both control and necroptosis-resistant cells were harvested to extract genomic DNA. All sgRNAs were amplified through high-fidelity PCR and analyzed using amplicon sequencing.
For amplicon sequencing library preparation, more than 20 ng of purified PCR product is subjected to end repair—including 5’-end phosphorylation and 3’-end dA-tailing—using the End Prep Enzyme Mix, followed by ligation of sequencing adapters to both ends. The product is then purified with magnetic beads and amplified using P5 and P7 primers. The resulting amplification product is again purified with magnetic beads to obtain the final library, which subsequently undergoes quality control. DNA libraries with different index tags are pooled and sequenced using the Illumina NovaSeq platform according to the manufacturer's protocol for PE150 paired-end sequencing.

value: human colorectal adenocarcinoma epithelial cells

value: wild type

value: TSZ


title: HT-29 cells, DMSO

description: Library name: Sample1

value: DMSO


title: GWCBD30: GWI mice recieved CBD_4

description: Library name: GWCBD304

value: GW chemicals, CBD


title: GWCBD30: GWI mice recieved CBD_3

description: Library name: GWCBD303


title: DNAseq TCP_X4_S38

city: Manchester

first: Carlos

last: Lopez Garcia

state: Greater Manchester

address: Paterson Building, Wilmslow Rd

department: TLCB

country: United Kingdom

institute: CRUK-MI

description: Library name: CLG8_38_TCP_X4_S38

data_processing:
Data were aligned to both GRCh38 and GRCm38 independently using STAR-aligner (RNA; version 2.5.1b) or B37 and mm10 with BWA (DNA; version 0.7.17).
Xenofilter (version 1.6) was used to split data from human and mouse aligned data.
RNA counts quantified using FeatureCounts (rsubread version 2.8.2)
Somatic mutations extracted from WES using Mutect2 (GATK version 4.40) -- comparing tumour to parental (PI) samples.
Assembly: GRCh38/B37
Supplementary files format and content: i) Gene counts for all samples used within comparisons [including those from PMID: 40185723].
Supplementary files format and content: ii) Sample annotations defining metadata and sequencing run origin.

extract_protocol:
PDX mice were generated as described within methods.
RNA-seq libraries perared using Quant-seq protocol (Lexogen); WES libraries were preares using Twits exome 2.0 protocol.

value: Lung

value: Bronchial epithelial cells

value: Xenograft

value: TC+P


title: GWCBD30: GWI mice recieved CBD_2

description: Library name: GWCBD302


title: DNAseq TCPK_X4_S37

description: Library name: CLG8_37_TCPK_X4_S37

value: TC+PK


title: GWCBD30: GWI mice recieved CBD_1

description: Library name: GWCBD301


title: DNAseq TCPK_X5_S36

description: Library name: CLG8_36_TCPK_X5_S36


title: GWVehLPS: GWI model mice with LPS_4

description: Library name: GWVeh4LPS

value: GW chemicals, LPS


title: DNAseq TCP_X3_S35

description: Library name: CLG8_35_TCP_X3_S35


title: GWVehLPS: GWI model mice with LPS_3

description: Library name: GWVeh3LPS


title: DNAseq TCP_X5_S34

description: Library name: CLG8_34_TCP_X5_S34


title: GWVehLPS: GWI model mice with LPS_2

description: Library name: GWVeh2LPS


title: DNAseq TCPK_X3_S33

description: Library name: CLG8_33_TCPK_X3_S33


title: GWVehLPS: GWI model mice with LPS_1

description: Library name: GWVeh1LPS


title: DNAseq TCK_PI_S32

description: Library name: CLG8_32_TCK_PI_S32

value: Pre-injection

value: TC+K


title: GWVeh: GWI model mice_4

description: Library name: GWVeh4

value: GW chemicals


title: DNAseq TCPKS_X5_S31

description: Library name: CLG8_31_TCPKS_X5_S31

value: TC+PKS


title: DNAseq TCPS_X3_S30

description: Library name: CLG8_30_TCPS_X3_S30

value: TC+PS


title: GWVeh: GWI model mice_2

description: Library name: GWVeh2

value: Brain (whole)


title: GWVeh: GWI model mice_1

description: Library name: GWVeh1


title: CtrlVehLPS: Ctrl mice with LPS_2

description: Library name: CtrlVeh2LPS

value: Vehicle, LPS


title: CtrlVehLPS: Ctrl mice with LPS_1

description: Library name: CtrlVeh1LPS


title: DNAseq TCPKS_PI_S25

description: Library name: CLG8_25_TCPKS_PI_S25


title: CtrlVeh: Ctrl mice_3

description: Library name: CtrlVeh3

value: Vehicle


title: DNAseq TCPKS_X4_S24

description: Library name: CLG8_24_TCPKS_X4_S24


title: CtrlVeh: Ctrl mice_2

description: Library name: CtrlVeh2


title: DNAseq TCP_X1_S23

description: Library name: CLG8_23_TCP_X1_S23


title: DNAseq TCPS_X2_S22

description: Library name: CLG8_22_TCPS_X2_S22


title: CtrlVeh: Ctrl mice_1

description: Library name: CtrlVeh1


title: MPI-2 uninfected cells at day 5 biol rep 4

city: Milano

first: Riccardo

last: Nodari

address: Via F. Sforza

country: Italy

institute: University of Milan

description: Library name: Sample16

data_processing:
Reads mapped to GRCm39 annotated reference genome using STAR
Reads count per gene generated directly using the "--quantMode GeneCounts" option in STAR
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Max Plank Institute (MPI-2) cells

growth_protocol: MPI cells (alveolar-like macrophages) were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated Fetal Bovine Serum, 1% Glutamine, 1% Penicillin and Streptomycin, 20 mM HEPES and 0,6 µg/mL of GM-CSF. Cell cultures were maintained in the incubator at 37°C with 5% CO2. Cells were split twice a week and plated at 2 x 105 cells/mL to avoid confluence. MPI from p8 to p50 were used.

extract_protocol:
Samples were prepared according to the Maxwell RSC simplyRNA Cells Kit (#AS1390) and loaded onto Maxwell® RSC Cartridges for automated RNA extraction, which was performed on Maxwell Instrument.
RNA libraries were constructed using 2μg poly-A RNA for each sample which were subjected to subsequent quality control, library construction and high-throughput sequencing at Eurofins Genomics.

value: Max Plank Institute (MPI-2) cells

value: alveolar-like macrophages

value: Wildtype

value: Uninfected

value: day 5


title: DNAseq TCP_PI_S21

description: Library name: CLG8_21_TCP_PI_S21

value: Lung

value: Bronchial epithelial cells


title: MPI-2 uninfected cells at day 5 biol rep 3

description: Library name: Sample15


title: DNAseq TCPK_PI_S20

description: Library name: CLG8_20_TCPK_PI_S20

value: TC+PK


title: MPI-2 uninfected cells at day 5 biol rep 2

description: Library name: Sample14


title: DNAseq TCK_X2_S19

description: Library name: CLG8_19_TCK_X2_S19

value: Xenograft


title: MPI-2 uninfected cells at day 5 biol rep 1

description: Library name: Sample13


title: DNAseq TC_PI_S18

description: Library name: CLG8_18_TC_PI_S18

value: Pre-injection

value: TC


title: MPI-2 uninfected cells at day 1 biol rep 4

description: Library name: Sample12

value: day 1


title: DNAseq TCKS_PI_S17

description: Library name: CLG8_17_TCKS_PI_S17

value: TC+KS


title: MPI-2 uninfected cells at day 1 biol rep 3

description: Library name: Sample11


title: DNAseq TCK_X6_S16

description: Library name: CLG8_16_TCK_X6_S16

value: TC+K


title: MPI-2 uninfected cells at day 1 biol rep 2

description: Library name: Sample10


title: MPI-2 uninfected cells at day 1 biol rep 1

description: Library name: Sample9


title: MPI-2 exposed to Mycobacterium abscessus cells at day 5 biol rep 4

description: Library name: Sample8

value: exposed to Mycobacterium abscessus


title: DNAseq TCPKS_X2_S14

description: Library name: CLG8_14_TCPKS_X2_S14

value: TC+PKS


title: DNAseq TCPK_X2_S13

description: Library name: CLG8_13_TCPK_X2_S13


title: MPI-2 exposed to Mycobacterium abscessus cells at day 5 biol rep 2

description: Library name: Sample6


title: DNAseq TCPKS_X6_S11

description: Library name: CLG8_11_TCPKS_X6_S11


title: DNAseq TCS_PI_S10

description: Library name: CLG8_10_TCS_PI_S10

value: TC+S


title: DNAseq TCP_X6_S12

description: Library name: CLG8_12_TCP_X6_S12

value: TC+P


title: MPI-2 exposed to Mycobacterium abscessus cells at day 5 biol rep 3

description: Library name: Sample7

value: Max Plank Institute (MPI-2) cells

value: alveolar-like macrophages


title: DNAseq TCPS_PI_S15

description: Library name: CLG8_15_TCPS_PI_S15

value: TC+PS


title: DNAseq TCPKS_X1_S9

description: Library name: CLG8_09_TCPKS_X1_S9


title: MPI-2 exposed to Mycobacterium abscessus cells at day 1 biol rep 4

description: Library name: Sample4

value: Wildtype


title: DNAseq TCP_X2_S8

description: Library name: CLG8_08_TCP_X2_S8

value: Lung


title: MPI-2 exposed to Mycobacterium abscessus cells at day 5 biol rep 1

description: Library name: Sample5

value: day 5


title: MPI-2 exposed to Mycobacterium abscessus cells at day 1 biol rep 3

description: Library name: Sample3


title: GWCBD30LPS: GWI mice received CBD and with LPS_2

description: Library name: GWCBD302LPS

value: Brain (whole)

value: GW chemicals, CBD, LPS


title: Veh: Ctrl mice_2

description: Library name: Veh_2

value: Microglia (FACS-purified)

value: Vehicle


title: non-diseased control_2_RNA

description:
Library name: Sample 2_RNA
10xgenomics

value: Not apply

value: CD3+ T cell

value: mRNA


title: non-diseased control_2_ADT

description:
Library name: Sample 2_ADT
Antibody-derived oligonucleotide

value: ADT

value: TotalSeq_CD3 TotalSeq_CD8 TotalSeq_CD56 TotalSeq_CD4 TotalSeq_CD25 TotalSeq_CD45RO TotalSeq_PD1 TotalSeq_CD103 TotalSeq_CCR7 TotalSeq_CTLA4 TotalSeq_LAG3 TotalSeq_HLADR TotalSeq_CD57 TotalSeq_CD28 TotalSeq_KLRG1


title: non-diseased control_1_RNA

description:
Library name: Sample 1_RNA
10xgenomics


title: DNAseq TCK_X3_S6

description: Library name: CLG8_06_TCK_X3_S6

value: Bronchial epithelial cells

value: Xenograft

value: TC+K


title: MPI-2 exposed to Mycobacterium abscessus cells at day 1 biol rep 2

description: Library name: Sample2

value: Max Plank Institute (MPI-2) cells

value: alveolar-like macrophages

value: exposed to Mycobacterium abscessus

value: day 1


title: DNAseq TCPKS_X3_S7

description: Library name: CLG8_07_TCPKS_X3_S7

value: Lung

value: TC+PKS


title: MPI-2 exposed to Mycobacterium abscessus cells at day 1 biol rep 1

description: Library name: Sample1

value: Wildtype


title: RAW264.7 IgG CUT&Tag, LPS + CCS1477

city: Shanghai

first: Panyu

last: Chen

address: 1111 Xianxia Road

department: Department of Gastroenterology, Shanghai Tongren Hospital

institute: Shanghai Jiao Tong University

description:
Library name: CCS_IgG
IgG negative control for CCS1477-pretreated and LPS-stimulated RAW264.7 macrophages.

data_processing:
Adapter sequences and low-quality reads were removed using Trimmomatic.
Clean reads were aligned to the Mus musculus reference genome (mm10_gencode) using BWA.
Genome-wide EP300-enriched regions were identified using MACS2 with the corresponding IgG sample as background control.
Signal tracks were generated in bigWig format for visualization in the Integrative Genomics Viewer (IGV).
Peak files were generated in narrowPeak format for downstream analysis.
Assembly: mm10_gencode
Supplementary files format and content: bigWig (.bw) files containing normalized genome-wide CUT&Tag signal tracks.
Supplementary files format and content: narrowPeak files containing EP300-enriched genomic regions identified by MACS2.
Library strategy: CUT&Tag

source_name: cell culture

growth_protocol: RAW264.7 macrophages were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified incubator with 5% CO₂. Only exponentially growing cells were used for experiments.

extract_protocol:
Cells were incubated with anti-EP300 antibody or normal rabbit IgG overnight at 4°C, followed by incubation with a secondary antibody and the pA-Tn5 transposome. After tagmentation, DNA fragments were purified for library preparation.
Purified DNA fragments generated by CUT&Tag were used for library preparation according to the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: RAW264.7 cells were pretreated with CCS1477 for 2 h, followed by stimulation with lipopolysaccharide (LPS) in the presence or absence of CCS1477 for 6 h. Untreated cells served as the negative control.

value: cell culture

value: macrophage

value: wild type

value: LPS + CCS1477


title: DNAseq TCK_X1_S4

description: Library name: CLG8_04_TCK_X1_S4


title: RAW264.7 EP300 CUT&Tag, LPS + CCS1477

description:
Library name: CCS_EP300
CUT&Tag profiling of EP300 binding after CCS1477 pretreatment followed by LPS stimulation.


title: RAW264.7 IgG CUT&Tag, LPS

description:
Library name: LPS_IgG
IgG negative control for LPS-treated RAW264.7 macrophages.

value: LPS


title: DNAseq TCPK_X1_S5

description: Library name: CLG8_05_TCPK_X1_S5

value: TC+PK


title: DNAseq TCPK_X6_S3

description: Library name: CLG8_03_TCPK_X6_S3


title: DNAseq Parental_S2

description: Library name: CLG8_02_Parental_S2

value: Parental

value: Wild type


title: RAW264.7 IgG CUT&Tag, Control

description:
Library name: NC_IgG
IgG negative control for untreated RAW264.7 macrophages.

value: vehicle control


title: RAW264.7 EP300 CUT&Tag, LPS

description:
Library name: LPS_EP300
CUT&Tag profiling of EP300 binding after LPS stimulation.


title: DNAseq TCK_X4_S1

description: Library name: CLG8_01_TCK_X4_S1

value: Bronchial epithelial cells

value: Xenograft

value: TC+K


title: RAW264.7 EP300 CUT&Tag, Control

description:
Library name: NC_EP300
CUT&Tag profiling of EP300 binding in untreated RAW264.7 macrophages.


title: RNAseq TCPK_9-3_S37

description: Library name: CLG7_37_TCPK_9-3_S37


title: RAW264.7 Input, LPS + CCS1477

description:
Library name: LPSCCS_Input
Input DNA from RAW264.7 macrophages pretreated with CCS1477 for 2 hours followed by LPS stimulation in the presence of CCS1477 for 6 hours. Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation, and one sequencing library was generated.

data_processing:
Raw sequencing reads were subjected to quality control and adapter trimming.
Clean reads were aligned to the mouse reference genome (mm10) using BWA.
Duplicate reads were removed before downstream analysis.
Peaks were identified using MACS2 with the corresponding input DNA as control.
Normalized signal tracks (bigWig) were generated for visualization in genome browsers.
Assembly: mm10
Supplementary files format and content: bigWig files containing normalized genome-wide signal tracks.
Supplementary files format and content: MACS2 narrowPeak files containing identified H3K27ac enrichment peaks.

growth_protocol: RAW264.7 macrophages were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified incubator with 5% CO2. Only exponentially growing cells were used for experiments.

extract_protocol:
Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation. Chromatin was cross-linked with 1% formaldehyde, lysed, fragmented by micrococcal nuclease digestion, immunoprecipitated with an anti-H3K27ac antibody or collected as input DNA, and purified according to the manufacturer's protocol.
ChIP-seq libraries were prepared from immunoprecipitated DNA and input DNA according to the manufacturer's protocol and sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

treatment_protocol: RAW264.7 macrophages were divided into three groups: untreated control (DMSO), LPS stimulation for 6 hours, and pretreatment with CCS1477 for 2 hours followed by LPS stimulation in the continued presence of CCS1477 for 6 hours.

value: CCS1477 pretreatment (2 h) followed by LPS + CCS1477 (6 h)


title: GWVeh: GWI model mice_3

description: Library name: GWVeh3

value: Brain (whole)

value: GW chemicals


title: RAW264.7 Input, LPS

description:
Library name: LPS_Input
Input DNA from RAW264.7 macrophages stimulated with LPS for 6 hours. Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation, and one sequencing library was generated.

value: LPS (6 h)


title: RNAseq TCPK_10-3B_S35

description: Library name: CLG7_35_TCPK_10-3B_S35

value: Lung


title: DNAseq TCPS_X1_S29

description: Library name: CLG8_29_TCPS_X1_S29

value: TC+PS


title: DNAseq TCK_X5_S28

description: Library name: CLG8_28_TCK_X5_S28


title: RNAseq TCPK_ALI_S36

description: Library name: CLG7_36_TCPK_ALI_S36

value: ALI


title: RNAseq TCPS_ALI_S34

description: Library name: CLG7_34_TCPS_ALI_S34


title: RAW264.7 Input, Control

description:
Library name: DMSO_Input
Input DNA from untreated RAW264.7 macrophages. Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation, and one sequencing library was generated.

value: cell culture

value: macrophage

value: wild type

value: DMSO


title: RAW264.7 H3K27ac ChIP, LPS + CCS1477

description:
Library name: LPSCCS_H3K27ac
H3K27ac ChIP-seq of RAW264.7 macrophages pretreated with CCS1477 for 2 hours followed by LPS stimulation in the presence of CCS1477 for 6 hours. Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation, and one sequencing library was generated.


title: RNAseq WT_ALI_S33

description: Library name: CLG7_33_WT_ALI_S33


title: DNAseq TCPS_X4_S26

description: Library name: CLG8_26_TCPS_X4_S26


title: RAW264.7 H3K27ac ChIP, LPS

description:
Library name: LPS_H3K27ac
H3K27ac ChIP-seq of RAW264.7 macrophages stimulated with LPS for 6 hours. Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation, and one sequencing library was generated.


title: DNAseq TCPS_X5_S27

description: Library name: CLG8_27_TCPS_X5_S27


title: CtrlVehLPS: Ctrl mice with LPS_3

description: Library name: CtrlVeh3LPS

value: Vehicle, LPS


title: RNAseq TCP_6-3_S32

description: Library name: CLG7_32_TCP_6-3_S32

value: TC+P


title: RAW264.7 H3K27ac ChIP, Control

description:
Library name: DMSO_H3K27ac
H3K27ac ChIP-seq of untreated RAW264.7 macrophages. Cells from three independent biological experiments were pooled prior to chromatin immunoprecipitation, and one sequencing library was generated.


title: RNAseq TCP_5-3_S31

description: Library name: CLG7_31_TCP_5-3_S31


title: RNAseq TCK_7-1_S30

description: Library name: CLG7_30_TCK_7-1_S30


title: Liver CD45+ immune cells, ACLF + CCS1477

description:
Library name: ACLF_CCS_scRNA
Liver CD45+ immune cells were isolated from CCS1477-treated ACLF mice. Cells from three biological replicate mice were individually labeled with BD Sample Tags, pooled for multiplexed library preparation, and demultiplexed using the BD Rhapsody Sequence Analysis Pipeline.

data_processing:
BD Rhapsody Sequence Analysis Pipeline v2.0.
The pipeline included read quality filtering, read annotation, molecular annotation, cell calling, and generation of gene-by-cell UMI count matrices.
Downstream quality control and analysis were performed using Seurat v4.3.0. Cells with low-quality transcriptomes or high mitochondrial gene content were removed. Data were normalized using NormalizeData, integrated using Harmony, and clustered based on principal component analysis.
Assembly: GRCm38 (mm10)
Supplementary files format and content: CSV files containing gene-by-cell UMI count matrices (RSEC_MolsPerCell) generated by the BD Rhapsody Sequence Analysis Pipeline v2.0. *processed data files format and content
Supplementary files format and content: CSV files containing Sample_Tag_Calls used for sample demultiplexing.

source_name: liver

extract_protocol:
Liver non-parenchymal cells were isolated by collagenase digestion and Percoll gradient centrifugation. CD45+ viable immune cells were purified by fluorescence-activated cell sorting (FACS). Purified cells were washed, filtered through a 30-μm cell strainer, resuspended in RPMI 1640 containing 2% fetal bovine serum, adjusted to 600–1200 cells/μl, and immediately processed for BD Rhapsody single-cell capture.
Single-cell suspensions were loaded onto the BD Rhapsody microwell cartridge for cell capture. cDNA libraries were generated using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification Kit according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150-bp reads.

treatment_protocol: Male C57BL/6J mice were intraperitoneally injected with CCl4 (0.2 ml/kg, twice weekly) for 8 weeks. Acute-on-chronic liver failure (ACLF) was induced by administration of a double dose of CCl4 (0.4 ml/kg), followed by intraperitoneal injection of Klebsiella pneumoniae. CCS1477 (10 mg/kg) was administered intraperitoneally 2 hours before bacterial challenge. Liver tissues were collected 36 hours after Klebsiella pneumoniae injection.

value: liver

value: CD45+ immune cells

value: ACLF induced by CCl4 and Klebsiella pneumoniae; CCS1477 treatment


title: RNAseq TCPK_10-2C_S29

description: Library name: CLG7_29_TCPK_10-2C_S29

value: Bronchial epithelial cells

value: Xenograft

value: TC+PK


title: Liver CD45+ immune cells, ACLF + Vehicle

description:
Library name: ACLF_VEH_scRNA
Liver CD45+ immune cells were isolated from vehicle-treated ACLF mice. Cells from three biological replicate mice were individually labeled with BD Sample Tags, pooled for multiplexed library preparation, and demultiplexed using the BD Rhapsody Sequence Analysis Pipeline.

value: ACLF induced by CCl4 and Klebsiella pneumoniae; vehicle treatment


title: RNAseq TCP_5-2_S27

description: Library name: CLG7_27_TCP_5-2_S27


title: RNAseq TCPS_15-1_S28

description: Library name: CLG7_28_TCPS_15-1_S28


title: Liver CD45+ immune cells, Fibrosis

description:
Library name: Fibrosis_scRNA
Liver CD45+ immune cells were isolated from mice treated with CCl4 for 8 weeks. Cells from three biological replicate mice were individually labeled with BD Sample Tags, pooled for multiplexed library preparation, and demultiplexed using the BD Rhapsody Sequence Analysis Pipeline.

value: Chronic CCl4 treatment


title: RNAseq TCP_6-2_S26

description: Library name: CLG7_26_TCP_6-2_S26

value: Lung


title: LL2 cells treated with 20 mM lactic acid for 24 h, biological replicate 2

city: chendu

first: lilan

last: he

address: yulin

institute: Sichuan University

description:
Library name: lactic_acid_2
Biological replicate 2; 150-bp paired-end sequencing.

data_processing:
Base calls were converted to FASTQ format using CASAVA. Raw reads were processed using Novogene in-house Perl scripts (version not specified) to remove reads containing adapters, reads containing poly-N, and low-quality reads; Q20, Q30, and GC content were calculated.
Clean paired-end reads were aligned to the Ensembl Mus musculus reference genome GRCm38.p6 (mm10; assembly accession GCA_000001635.8) using HISAT2 v2.0.5.
Gene-level raw read counts were generated using featureCounts v1.5.0-p3. Reads with mapping quality below 10, improperly paired reads, and multi-mapping reads were excluded from quantification.
FPKM values were calculated from gene length and mapped read counts. Transcript assembly/quantification was performed using StringTie v1.3.3b.
Differential expression analysis between the lactic-acid and PBS-control groups was performed using DESeq2 v1.16.1.
Assembly: GRCm38.p6 (mm10), Ensembl Mus musculus reference genome; assembly accession GCA_000001635.8
Supplementary files format and content: gene_count.txt is a tab-delimited plain-text file containing gene-level raw read counts for NS_1, NS_2, lactic_acid_1, and lactic_acid_2, together with gene annotation columns.
Supplementary files format and content: gene_fpkm.txt is a tab-delimited plain-text file containing gene-level FPKM values for NS_1, NS_2, lactic_acid_1, and lactic_acid_2, together with gene annotation columns.

growth_protocol: LL2 cells were maintained under standard cell-culture conditions prior to treatment.

extract_protocol:
Total RNA was extracted from LL2 cells using TRIzol reagent according to the manufacturer's instructions. RNA samples were submitted to a commercial sequencing service for quality assessment, library preparation, and sequencing.
A total of 1 µg total RNA per sample was used for library preparation. Poly(A)+ mRNA was purified using poly-T oligo-attached magnetic beads. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions. Purified mRNA was fragmented using divalent cations, reverse-transcribed to cDNA, end-repaired, A-tailed, adaptor-ligated, size-selected to approximately 250–300 bp, and PCR-amplified. Library quality was assessed using an Agilent Bioanalyzer 2100. Libraries were clustered using a TruSeq PE Cluster Kit v3-cBot-HS and sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads (PE150).

treatment_protocol: LL2 cells were treated with 20 mM lactic acid added directly to the culture medium for 24 h. Control cells received an equal volume of PBS for 24 h.


title: LL2 cells treated with PBS for 24 h, control biological replicate 1

description:
Library name: NS_1
Control biological replicate 1; 150-bp paired-end sequencing.

value: An equal volume of PBS was added to the culture medium for 24 h


title: LL2 cells treated with PBS for 24 h, control biological replicate 2

description:
Library name: NS_2
Control biological replicate 2; 150-bp paired-end sequencing.


title: RNAseq TCK_8-1_S25

description: Library name: CLG7_25_TCK_8-1_S25

value: TC+K


title: LL2 cells treated with 20 mM lactic acid for 24 h, biological replicate 1

description:
Library name: lactic_acid_1
Biological replicate 1; 150-bp paired-end sequencing.

value: 20 mM lactic acid added directly to the culture medium for 24 h


title: RNAseq TCPK_10-1C_S24

description: Library name: CLG7_24_TCPK_10-1C_S24


title: Pancreas Sox9CreER Nphp3FF

city: Brussels

first: Patrick

last: Jacquemin

address: 75, Avenue Hippocrate bte B1.75.03

country: Belgium

institute: de Duve Institute SSS/DDUV

description: Library name: MRB2F

data_processing:
Raw sequencing data were processed using standard 10x Genomics pipelines to generate filtered and raw count matrices. Ambient RNA contamination was corrected using SoupX. Downstream analyses were performed in Seurat and included quality control, SCTransform normalization, PCA, UMAP embedding, graph-based clustering, marker identification, and cell type annotation. Comparative analyses with published ductal and mesothelial reference datasets were performed using Harmony integration and Seurat anchor-based mapping approaches.
Assembly: GRCm38
Supplementary files format and content: Processed data files include filtered and ambient RNA-corrected gene expression count matrices generated from single-cell RNA-seq data. Files are provided in tab-delimited text and/or Matrix Market format and contain gene-by-cell UMI count matrices together with associated barcode and feature annotation files.

source_name: pancreatic tissue

extract_protocol:
Mouse pancreatic tissue was dissociated into single-cell suspensions using a modified FixNCut protocol. Briefly, tissue was fixed in DSP fixation buffer, quenched with Tris-HCl, and digested with Liberase TM at 37°C. Cell suspensions were filtered through 70 μm and 40 μm strainers, washed in PBS containing 1% BSA, and resuspended in PBS with RNase inhibitor. Cell concentration was determined using a LUNA automated cell counter.
Single-cell libraries were generated using the Chromium™ Next GEM Single Cell 3′ Kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Cells were partitioned into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller, followed by reverse transcription, cDNA amplification, and library preparation.

value: pancreatic tissue


title: RNAseq TCPS_16-2_S22

description: Library name: CLG7_22_TCPS_16-2_S22

value: TC+PS


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Upf3af/f;Bmp2f/f mice, H3K4me3 (ChIP) 2

city: Fuzhou

first: Chensheng

state: Fujian

address: 18 Wulongjiangzhong Avenue, Shangjie Town

department: College of Life Sciences

institute: Fujian Normal University

description:
Library name: IP_Bmp2cKO_Upf3acKO_2
IP2036_3_H3K4me3

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp).
Adapter sequences and low-quality reads were removed using Trimmomatic (v0.36).
Clean reads were aligned to the mouse reference genome GRCm39 using BWA (v0.7.15).
SAMtools (v1.3.1) was used to remove PCR duplicates. Peaks were called using MACS2 (v2.1.2) with default parameters (bandwidth 300 bp; model fold 5-50; P value 0.001).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: PN0 mandibular molar tooth germs

extract_protocol:
PN0 mandibular molar tooth germs were collected in ice-cold PBS, and each sequencing sample consisted of 10 tooth germs pooled as one biological replicate. Tissues were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with glycine (125 mM final concentration). Samples were lysed in buffer containing 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS, and protease inhibitor cocktail, and chromatin was sheared by sonication to an average fragment size of 200-500 bp.
ChIP-seq were performed by Wuhan IGENEBOOK Biotechnology Co.,Ltd (http://www.igenebook.com) .An aliquot of chromatin was reserved as DNA input, and immunoprecipitation was performed overnight at 4°C with rabbit anti-H3K4me3 (ABCam, ab8580; 10 μg antibody per reaction). Immune complexes were captured using protein beads and washed sequentially as described (low-salt, high-salt/LiCl, and TE washes). Bound chromatin was eluted in 100 mM NaHCO₃ with 1% SDS, treated with RNase A (final concentration 8 μg/mL) at 65°C, followed by proteinase K digestion (final concentration 345 μg/mL) at 45°C. ChIP DNA was purified and used to prepare sequencing libraries using the NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing (NOVA-5143-02, Bioo Scientific).

value: PN0 mandibular molar tooth germs


title: RNAseq TCPK_9-1_S23

description: Library name: CLG7_23_TCPK_9-1_S23


title: non-diseased control_9_ADT

description:
Library name: Sample 26_ADT
10xgenomics

value: Not apply

value: CD3+ T cell

value: mRNA


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Bmp2f/f mice, H3K4me3 (ChIP) 2

description:
Library name: IP_Bmp2cKO_2
IP2036_2_H3K4me3


title: RNAseq TCPKS_18-2_S21

description: Library name: CLG7_21_TCPKS_18-2_S21

value: TC+PKS


title: RNAseq TCP_6-1_S20

description: Library name: CLG7_20_TCP_6-1_S20

value: TC+P


title: PN0 mandibular molar tooth germs, wild-type mice, H3K4me3 (ChIP) 2

description:
Library name: IP_Ctrl_2
IP2036_1_H3K4me3

value: wild-type


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Upf3af/f;Bmp2f/f mice, H3K4me3 (Input) 2

description:
Library name: IN_Bmp2cKO_Upf3acKO_2
INPUT2036_3


title: RNAseq TCK_8-3_S19

description: Library name: CLG7_19_TCK_8-3_S19

value: Bronchial epithelial cells

value: Xenograft


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Bmp2f/f mice, H3K4me3 (Input) 2

description:
Library name: IN_Bmp2cKO_2
INPUT2036_2


title: RNAseq TCP_5-1_S18

description: Library name: CLG7_18_TCP_5-1_S18


title: PN0 mandibular molar tooth germs, wild-type mice, H3K4me3 (Input) 2

description:
Library name: IN_Ctrl_2
INPUT2036_1


title: Bone marrow-derived MSC, donor 6, Laboratory B (BM6)

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

description:
Library name: BM6
Out-of-thaw human BM-MSC, donor 6, Lab B.

data_processing:
Demultiplexing, cell-barcode and UMI extraction, adapter/quality trimming, alignment and UMI counting were performed with the Illumina BaseSpace SureCell RNA Single-Cell App v1.1.0 (ISAS analysis software 1.1.0.61+master).
Reads were aligned with STAR 2.5.2b to the human reference genome UCSC hg19; BAM processing with SAMtools 1.3. Only reads with mapping quality >=12 (except abundant features) were retained.
Per-cell genic UMI count matrices were generated, and a UMI knee-point filter was applied per sample to retain cell barcodes above the knee threshold (SureCell 'cells passing knee filter'), producing the *.passingKneeFilter.table.csv matrices.
In each processed count table, rows are individual cells and the first column 'CellId' is the 18-bp cell barcode; the remaining columns are gene symbols with per-cell UMI counts. A per-sample cell-barcode list (*.barcodes.txt, one barcode per line) is provided for each sample.
Downstream QC, clustering and differential expression used SC3 and Seurat (normalization to counts per 10,000; Wilcoxon rank-sum test).
Assembly: Homo sapiens, UCSC hg19
Supplementary files format and content: Two processed files per sample:
(1) *.counts.umiCounts.passingKneeFilter.table.csv - a comma-separated cell-by-gene genic UMI count matrix (rows = cells; first column 'CellId' = 18-bp cell barcode; remaining columns = gene symbols; values = UMI counts), output by the SureCell pipeline after knee filtering;
(2) *.barcodes.txt - the list of cell barcodes passing the knee filter for that sample (one per line; identical to the CellId column).

source_name: bone marrow

growth_protocol: Human BM-MSCs (six male donors; seven lots) were purchased cryopreserved from RoosterBio Inc. (Frederick, MD) and expanded per the RoosterBio protocol (BM-hMSC High Performance Media Kit: basal media SU-005 + Media Booster GTX SU-003); seeded at 3,500-4,000 cells/cm^2 in T-225 flasks, grown at 37C to >80% confluency, harvested, and cryopreserved in CryoStor CS-10. BM1 and BM2a were expanded in Laboratory A; BM2b, BM3, BM4, BM5, BM6 in Laboratory B. Cells profiled at population doubling level 12-15.

extract_protocol:
Single cells were co-encapsulated with barcoded beads and lysis/RT reagents in droplets on the Illumina-Bio-Rad ddSEQ Single-Cell Isolator; mRNA captured, reverse-transcribed and cell-barcoded within droplets.
Illumina Bio-Rad SureCell WTA 3' workflow: cell suspensions loaded on a ddSEQ cartridge with RT master mix, encapsulated/barcoded by the Single-Cell Isolator; droplets disrupted, cDNA pooled for second-strand synthesis; libraries generated by direct cDNA tagmentation (Nextera), 3' enrichment and sample indexing; QC on Agilent Bioanalyzer 2100; sequenced on Illumina NextSeq 500 (paired-end 75 bp, mid-output v2.5) at the Georgia Tech IBB Molecular Evolution Core.

treatment_protocol: Cells were characterized directly out of thaw: frozen vials (~1e6 cells) thawed ~2 min at 37C, transferred to RPMI, counted (NucleoCounter), centrifuged (200 g, 10 min), resuspended, re-counted and processed immediately for scRNA-seq.

value: bone marrow

value: mesenchymal stromal cell

value: out-of-thaw (thawed immediately before profiling)


title: Bone marrow-derived MSC, donor 5, Laboratory B (BM5)

description:
Library name: BM5
Out-of-thaw human BM-MSC, donor 5, Lab B.


title: Bone marrow-derived MSC, donor 4, Laboratory B (BM4)

description:
Library name: BM4
Out-of-thaw human BM-MSC, donor 4, Lab B.


title: Bone marrow-derived MSC, donor 3, Laboratory B (BM3)

description:
Library name: BM3
Out-of-thaw human BM-MSC, donor 3, Lab B.


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Upf3af/f;Bmp2f/f mice, H3K4me3 (ChIP) 1

description:
Library name: IP_Bmp2cKO_Upf3acKO_1
IP1999_3_H3K4me3


title: RNAseq TCS_ALI_S16

description: Library name: CLG7_16_TCS_ALI_S16

value: Lung

value: ALI

value: TC+S


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Bmp2f/f mice, H3K4me3 (ChIP) 1

description:
Library name: IP_Bmp2cKO_1
IP1999_2_H3K4me3


title: ΔcooS1_syngas_B2

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Bioengineering

country: Estonia

institute: University of Tartu

description: Library name: Sample 16

data_processing:
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum LAbrini (GenBank CP110420.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Assembly: CP110420.1
Supplementary files format and content: RPKM value tab-delimited text files

organism: Clostridium autoethanogenum

source_name: bacterial

growth_protocol: Clostridium autoethanogenum strains were grown on syngas or CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1 day-1

extract_protocol:
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research). Ribosomal RNA was removed with QIAseq® FastSelect™ Kit (335925; Qiagen).
Stranded mRNA libraries were prepared with QIAseq® Stranded RNA Lib Kit (180743; Qiagen). Constructed mRNA libraries were prepared for sequencing using the NextSeq 2000 P1 300 cycles sequencing kit (Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

value: bacterial

tag: sample group


title: ΔcooS1_syngas_B3

description: Library name: Sample 17


title: RNAseq TC_ALI_S17

description: Library name: CLG7_17_TC_ALI_S17

value: TC


title: RNAseq TCK_7-3_S15

description: Library name: CLG7_15_TCK_7-3_S15

value: TC+K


title: Bone marrow-derived MSC, donor 2, Laboratory B (BM2b)

description:
Library name: BM2b
Out-of-thaw human BM-MSC, donor 2, Lab B (same donor as BM2a).


title: PN0 mandibular molar tooth germs, wild-type mice, H3K4me3 (ChIP) 1

description:
Library name: IP_Ctrl_1
IP1999_1_H3K4me3

value: PN0 mandibular molar tooth germs


title: Bone marrow-derived MSC, donor 2, Laboratory A (BM2a)

description:
Library name: BM2a
Out-of-thaw human BM-MSC, donor 2, Lab A (same donor as BM2b). Larger technical-replicate profile (BM2a_2) reported.


title: RNAseq TCK_ALI_S14

description: Library name: CLG7_14_TCK_ALI_S14


title: ΔcooS1_syngas_B1

description: Library name: Sample 15


title: ΔcooS1_CO_B2

description: Library name: Sample 14


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Upf3af/f;Bmp2f/f mice, H3K4me3 (Input) 1

description:
Library name: IN_Bmp2cKO_Upf3acKO_1
INPUT1999_3


title: RNAseq TCPKS_ALI_S13

description: Library name: CLG7_13_TCPKS_ALI_S13


title: Bone marrow-derived MSC, donor 1, Laboratory A (BM1)

description:
Library name: BM1
Out-of-thaw human BM-MSC, donor 1, Lab A. Larger of two technical-replicate profiles (BM1_2) reported.


title: ΔcooS1_CO_B1

description: Library name: Sample 13


title: PN0 mandibular molar tooth germs, Wnt1-Cre;Bmp2f/f mice, H3K4me3 (Input) 1

description:
Library name: IN_Bmp2cKO_1
INPUT1999_2


title: RNAseq TCPS_15-2_S12

description: Library name: CLG7_12_TCPS_15-2_S12

value: TC+PS


title: PN0 mandibular molar tooth germs, wild-type mice, H3K4me3 (Input) 1

description:
Library name: IN_Ctrl_1
INPUT1999_1


title: LeuSNP_CO_B4

description: Library name: Sample 12


title: MCF10A_HP1AKD_HP1b, rep1

city: Oslo

first: Fabiana

last: Patalano

address: Blindernveien 31

country: Norway

institute: University of Oslo

description: Library name: TS9_S9

data_processing:
Raw reads were trimmed with Trimmomatic (45) and aligned using Bowtie2. Post-alignment, SAMtools was used to exclude low-quality, mitochondrial, and duplicate reads. Broad peaks were called using MACS3 with the BAMPE option.
Assembly: hg38
Supplementary files format and content: broadPeak

source_name: mammary gland

extract_protocol:
Approximately 1× 107 to 6 × 107 cells were cross-linked in fresh complete DMEM/F12 media supplemented with 1.2% formaldehyde at room temperature for 12 minutes.
Libraries were prepared using a ChIP-Seq Sample Prep Kit (Illumina) according to the manufacturer's protocol and sequenced on an Illumina NextSeq 500 instrument using 76 bp paired-end reads in high output mode.

value: mammary gland

value: Breast epithelial cells HP1A knock-down

value: HP1A knock-down


title: MCF10A_HP1AKD_HP1b, rep2

description: Library name: TS10_S10


title: LeuSNP_CO_B3

description: Library name: Sample 11


title: RNAseq TCPKS_18-3_S11

description: Library name: CLG7_11_TCPKS_18-3_S11

value: TC+PKS


title: Bv2OGD3

city: Wuhan

first: Yang

last: Zhihao

state: Hubei

address: Shizishan street

department: College of Life Sciences & Technology

institute: Huazhong Agricultural University

description:
Library name: Sample 6
glucose oxygen deprivation

data_processing:
Discard a paired reads if either one read contains adapter contamination;
Discard a paired reads if more than 10% of bases are uncertain in either one read;
Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample
Supplementary files format and content: txt file include FPKM values for each sample

growth_protocol: Bv2 cells, purchased from Procell (Wuhan, China), were cultured with DMEM medium (Procell Wuhan, China) supplemented with 1% Penicillin streptomycin (Biosharp BL505A Hefei, China) and 10% fetal bovine serum (BI, Beit Haemek, Israel).

extract_protocol:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

treatment_protocol: After infection for 72 h, Bv2 cells were treated 100% N2 for 30 min, followed by the OGD/R induction. Briefly, to achieve OGD, cells were maintained in D-glucose-free DMEM medium without fetal bovine serum and placed inside a chamber for 2 h with a gas mixture of 94% N2, 5% CO2 and 1% O2. For reperfusion (R), cells were further cultured with standard medium containing fetal bovine serum at 37 ℃ with 5% CO2 for 24 h.

value: Microglia

value: WT

value: glucose oxygen deprivation


title: MCF10A_WT_HP1b, rep2

description: Library name: TS8_S8

value: Breast epithelial cells


title: RNAseq TCP_ALI_S10

description: Library name: CLG7_10_TCP_ALI_S10

value: Bronchial epithelial cells

value: TC+P


title: Bv2OGD2

description:
Library name: Sample 5
glucose oxygen deprivation


title: LeuSNP_CO_B2

description: Library name: Sample 10


title: Bv2OGD1

description:
Library name: Sample 4
glucose oxygen deprivation


title: MCF10A_HP1B_KD_HP1a, rep2

description: Library name: TS1_S4

value: Breast epithelial cells HP1B knock-down

value: HP1B knock-down


title: RNAseq TCPKS_17-3_S9

description: Library name: CLG7_09_TCPKS_17-3_S9

value: Lung

value: Xenograft


title: MCF10A_WT_HP1b, rep1

description: Library name: TS7_S7


title: RNAseq TCPKS_17-02_S8

description: Library name: CLG7_08_TCPKS_17-02_S8


title: LeuSNP_CO_B1

description: Library name: Sample 9

value: bacterial


title: Bv2CON3

description:
Library name: Sample 3
control

value: control


title: MCF10A_HP1B_KD_HP1a, rep1

description: Library name: TS1_S3


title: RNAseq TCPKS_18-1_S7

description: Library name: CLG7_07_TCPKS_18-1_S7


title: LAbrini_syngas_B4

description: Library name: Sample 8


title: Bv2CON2

description:
Library name: Sample 2
control


title: LAbrini_syngas_B3

description: Library name: Sample 7


title: MCF10A_WT_HP1a, rep2

description: Library name: TS1_S2


title: RNAseq TCPKS_17-1_S6

description: Library name: CLG7_06_TCPKS_17-1_S6


title: LAbrini_syngas_B2

description: Library name: Sample 6


title: Bv2CON1

description:
Library name: Sample 1
control


title: MCF10A_WT_HP1a, rep1

description: Library name: TS1_S1


title: RNAseq TCPS_16-3_S5

description: Library name: CLG7_05_TCPS_16-3_S5

value: TC+PS


title: LAbrini_CO_B4

description: Library name: Sample 4


title: LAbrini_syngas_B1

description: Library name: Sample 5


title: RNAseq TCK_8-2_S4

description: Library name: CLG7_04_TCK_8-2_S4

value: TC+K


title: BEKO high density, replicate 2

city: Stockholm

first: Taras

last: Kreslavsky

address: Karolinska University Hospital L8:03, Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 4
Column name in BEKO_RNA_tpm.txt: TPM_4

data_processing:
Analysis was performed as described previously (Glaros et al, 2021).  The data sets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 2014). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Assembly: MM9
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: BEKO

extract_protocol:
RNA was isolated using ZYMO Quick-RNA Microprep Kit.
Eukaryotic Strand-Specific Transcriptome Library was constructed by Novogene.

value: BEKO

value: thymic lymphoma cells


title: LS8 cells, NaF, H3K27Ac (ChIP)

city: Davie

first: Maiko

last: Suzuki

state: Florida

address: 3300 S. University Drive

department: College of Dental Medicine

institute: Nova Southeastern University

description: Library name: AcH3K27_NaF_S2_R1.fastq

data_processing:
Sequencing was performed on the Nextseq500 (Illumina) using the High Output v2.5 kit, with a 75-cycle single-read protocol.
BCL files generated via the Nextseq500 were converted to FASTQ files for the downstream analysis. The FASTQ files had quality scores above 35 on a scale of 1 to 40, with 20 to 30 million reads obtained per sample.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Cell line

extract_protocol:
Cells were fixed with 1% formaldehyde for the crosslinking was stopped by adding glycine. Cells were subsequently lysed, and the isolated chromatin was sheared in the kit-provided lysis buffer via sonication (30 s ON, 30 s OFF, 30 cycles) using a Bioruptor®® Pico (Diagenode).
ChIP-seq librarieswere prepared using the TruSeq ChIP Library PreparationKit (Illumina, San Diego, CA, USA). The prepared library was examined via a bioanalyzer and Qubit (Thermo Fisher Scientific) to test library quality and quantity, respectively.

value: Cell line

value: Mouse ameloblast-like cells

value: NaF