title: ATAD3A-KI5

description:
Library name: ATAD3A-KI5
A24

value: Vehicle


title: ATAD3A-KI4

status: Public on Jun 20 2026

type: SRA

city: Shanghai

first: Jie

last: Lin

state: Shanghai

address: 180 Fenglin Road Street, Xuhui District

country: China

institute: Zhongshan Hospital, Fudan University

description:
Library name: ATAD3A-KI4
A21

library_source: transcriptomic

data_processing:
Raw reads were filtered to remove adaptor-contaminated and low-quality reads using Trim Galore, and read quality was assessed using FastQC.
Clean reads were aligned to the Mus musculus reference genome using HISAT2.
Gene expression levels were quantified and raw gene counts were generated for downstream analysis.
Differential expression analysis was performed using DESeq2.
Functional enrichment analysis was performed using clusterProfiler.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text file containing raw read counts for all genes in all samples.

molecule: total RNA

organism: Mus musculus

source_name: aorta

growth_protocol: Male mice were housed individually in ventilated cages under specific pathogen-free conditions at 24°C and 60% relative humidity with a 12 h light/dark cycle and free access to food and water.

extract_protocol:
Total RNA was extracted from mouse aortic tissues using TRIzol reagent according to the manufacturer’s instructions. RNA quantity was measured by Qubit 2.0 Fluorometer, and RNA integrity was assessed by agarose gel electrophoresis and Qsep/Bioanalyzer.
For eukaryotic samples, mRNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse-transcribed to first-strand cDNA using random hexamer primers. Second-strand cDNA was synthesized, followed by end repair, A-tailing, adaptor ligation, size selection, and PCR amplification. Qualified libraries were sequenced on an Illumina platform.

treatment_protocol: Mice were randomly assigned to experimental groups prior to aortic aneurysm and dissection (AAD) induction. For the BAPN-induced model, 3-week-old male mice received β-aminopropionitrile (BAPN, Sigma-Aldrich, A3134) in drinking water at 0.5% (w/v) for 28 consecutive days. Control mice received regular drinking water under the same conditions.

tag: tissue

value: aorta

tag: genotype

tag: treatment


title: ATAD3A-KI1

description:
Library name: ATAD3A-KI1
A11


title: ATAD3A-KI2

description:
Library name: ATAD3A-KI2
A12


title: ATAD3A-KI3

description:
Library name: ATAD3A-KI3
A19


title: BAPN5

description:
Library name: WT-BAPN5
B14

value: WT

value: BAPN


title: BAPN6

description:
Library name: WT-BAPN6
B15


title: BAPN4

description:
Library name: WT-BAPN4
B13


title: BAPN7

description:
Library name: WT-BAPN7
B16


title: BAPN2

description:
Library name: WT-BAPN2
B11


title: BAPN3

description:
Library name: WT-BAPN3
B12


title: BAPN1

description:
Library name: WT-BAPN1
B10


title: WT6

description:
Library name: WT6
W6


title: WT5

description:
Library name: WT5
W5


title: WT4

description:
Library name: WT4
W4


title: C4-2B MDVR cells, MR_SIGRIK5_2

city: Sacramento

first: Huan

last: Qu

address: 4645 2nd Ave, Research III Bldg

country: USA

institute: University of California-Davis

description: Library name: MR_SIGRIK5_2

data_processing:
The libraries were sequenced on an Illumina platform to generate 150-bp paired-end reads. Raw sequencing reads were filtered to remove adapt-er-contaminated reads, reads containing >10% ambiguous nucleotides (N), and low-quality reads in which >50% of bases had a Phred quality score <5. Clean reads were aligned to the human reference genome (hg38) using HISAT2. Gene expres-sion levels were quantified based on mapped reads and normalized as fragments per kilobase of transcript per million mapped reads (FPKM). Transcript assembly and abundance estimation were performed using StringTie.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file containing raw read counts for each gene across all samples, where rows represent Ensembl gene IDs and columns represent individual samples.

organism: Homo sapiens

source_name: Prostate

growth_protocol: C4-2B MDVR cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 20μM Enzalutamide, and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the cells using RNeasy mini plus kit (Qiagen) following the manufacturer's protocol. RNA quality and concentration were assessed using a NanoDrop spectrophotometer. Only samples with an RNA Integrity Number (RIN) > 8.0 were used for library construction.
Sequencing libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit and subjected to end repair, A-tailing, adapter ligation, PCR amplification, and purification.

treatment_protocol: Cells were seeded in 6-well plates and transfected with control siRNA (siRNA-NC) or two independent siRNAs targeting GRIK5 (siGRIK5#1 and siGRIK5#2) using Lipofectamine 2000 transfection reagent according to the manufacturer's instructions.

value: Prostate

tag: cell line

value: C4-2B MDVR

tag: cell type

value: Prostate cancer cells

value: GRIK5 knockdown


title: C4-2B MDVR cells, MR_SIGRIK5_1

description: Library name: MR_SIGRIK5_1


title: C4-2B MDVR cells, MR_SICON

description: Library name: MR_SICON


title: WT3

description:
Library name: WT3
W3


title: WT2

description:
Library name: WT2
W2


title: WT1

description:
Library name: WT1
W1


title: T47D treated with THZ1 repeat 1

city: Taipei

first: Yi-Ru

last: Tseng

address: No. 201, Sec. 2, Sh ipai Rd.

country: Taiwan

institute: Taipei Veterans General Hospita

description: Library name: TTHZ1_1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using CLC Genomics Workbench (v 25.0.3) (parameters- default)
Read count extraction  were performed using CLC Genomics Workbench (v 25.0.3)
Normalization were performed using CLC Genomics Workbench (v 25.0.3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: MCF-7 and T-47D were treated with DMEM/F12 and RPMI 1640 medium, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen™) and 1–bromo–3–chloropropane (BCP) (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries
RNA-seq

treatment_protocol: shRNA knockdown of CDK7, overexpress CDK6 in breast cancer cells or treat CDK7 inhibitor

value: breast


title: T47D treated with PIK75 repeat 2

description: Library name: TPIK75_2


title: 4T1-LP-184 03

city: Houston

first: Shiaw-Yih

state: TX

address: Z10.2030, 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description: Library name: Sample12

data_processing:
Raw reads were quality-checked and adaptor-trimmed using fastp. Clean reads were aligned to the Mus musculus (mm10) reference genome using STAR (v2.7). Gene-level counts were quantified with featureCounts (Subread v2.0). Downstream differential expression analysis was performed in R using edgeR, and P values were adjusted by the Benjamini–Hochberg method to control the false discovery rate (FDR). Single-cell cDNA libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ v4 chemistry and sequenced on an Illumina NovaSeq X instrument. Raw base-call files were processed with Cell Ranger (v7.0, 10x Genomics) using the mm10 reference genome to generate gene–barcode count matrices. Downstream analyses including quality control, normalization, clustering, and visualization were performed in Seurat (v5.1.0, R). Low-quality cells (<200 detected genes or >20% mitochondrial transcripts) and putative doublets were excluded prior to analysis.
Assembly: Reads were aligned to the Mus musculus (mm10) or Homo sapiens (hg38) reference genome using STAR (v2.7).
Supplementary files format and content: logCPM expression and edgeR differential expression tables (logFC, FDR, P value) for bulk RNA-seq, and 10x Genomics Cell Ranger filtered gene–barcode matrices for single-cell RNA-seq.
Supplementary files format and content: csv files include logCPM and DEGs with logFC and FDR

molecule: polyA RNA

extract_protocol:
RNA was extracted by following Qiagen RNA easy plus instructions
Bulk RNA seq library was constructed at Novogene; scRNASeq library was contructed by 10x GEM X Single cell 3' Gem kit v4 at single core at MD Anderson cancer center

value: TNBC


title: T47D treated with THZ1 repeat 2

description: Library name: TTHZ1_2


title: 4T1-LP-184 02

description: Library name: Sample11


title: 4T1-LP-184 01

description: Library name: Sample10


title: T47D treated with PIK75 repeat 1

description: Library name: TPIK75_1


title: 4T1-DMSO 03

description: Library name: Sample9

value: 4T1-DMSO 03


title: T47D treated with DMSO repeat 1

description: Library name: TDMSO_1

value: DMSO


title: T47D treated with DMSO repeat 2

description: Library name: TDMSO_2


title: 4T1-DMSO 02

description: Library name: Sample8

value: 4T1-DMSO 02


title: T47D with CDK6 overexpression treated with PIK75 repeat 2

description:
Library name: TOE_P2
raw file no longer available

source_name: T-47D with CDK6 overexpression

value: T-47D with CDK6 overexpression


title: 4T1-DMSO01

description: Library name: Sample7


title: ARID1-GFP-C_arid1_VN_IP_Rep2

first: Lei

last: Li

address: Xinjiangwancheng

institute: Fudan University

description: Library name: pollen_ARID1-GFP-C_arid1_VN_IP_Rep2

library_source: genomic

data_processing:
Following a FastQC (version 0.12.0) quality control, adapter trimming was performed using TrimGalore (version 0.4.1).
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 (version 2.1.0), and subsequently PCR duplicates were removed using sambamba (version 0.6.6).
Deeptools (version 3.1.2) was used to examine correlations between the ChIP samples and generate Genome browser tracks.
Peaks were called with MACS3 using an FDR cutoff of 0.05.
Assembly: TAIR10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: mature pollen VN

extract_protocol:
Approximately 50 µL of mature pollen was resuspended in ice-cold pollen nuclei buffer (1.3 mM H₃BO₃, 3.6 mM CaCl₂·2H₂O, 0.74 mM KH₂PO₄, 438 mM sucrose, 7 mM MOPS, 0.83 mM MgSO₄·7H₂O, pH 6.0) and transferred to a 2 mL tube containing 2 mm BashingBead™ beads. The mixture was homogenized by vortexing at 49 Hz for 3 min. Debris was removed by filtering the suspension through a 10 µm nylon mesh. The filtrate was then centrifuged to pellet the material, which was subsequently resuspended in 1 mL of fresh pollen nuclei buffer. Nuclei were stained with a 10,000× dilution of SYBR Green I and subjected to fluorescence-activated cell sorting (FACS). The collected vegetative nuclei were used for subsequent CUT&Tag library construction.
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD904) following the manufacturer’s instructions. The libraries were sequenced with an Illumina NovaSeq 6000 to generate pair-end 150 bp reads. Samples were prepared from three or two independent biological replicates.

value: mature pollen VN


title: T47D with CDK6 overexpression treated with PIK75 repeat 1

description:
Library name: TOE_P1
raw file no longer available


title: ARID1-GFP-C_arid1_VN_IP_Rep1

description: Library name: pollen_ARID1-GFP-C_arid1_VN_IP_Rep1


title: CHOL_SEMA

city: shenzhen

first: Yibo

last: Hou

state: State...

address: Guangdong province

institute: TsingHua university

description:
Library name: Sample 4
10x Genomics

data_processing:
Raw sequencing reads were processed using DNBC4Tools (BGI) for barcode processing, read filtering, transcript alignment, UMI counting, and cell calling to generate the gene expression matrix for each sample.
Gene expression matrices from all samples were imported into R (v4.4.1) and integrated using Seurat (v5.3.1). Low-quality cells were removed according to the following criteria: detected genes <200 or >12,500, UMI counts <500, log10(GenesPerUMI) <0.8, mitochondrial RNA percentage >20%, or ribosomal RNA percentage >30%.
Data were normalized using the LogNormalize method with a scale factor of 10,000. The top 2,000 highly variable genes were identified using the VST method, followed by scaling and principal component analysis.
Cell clustering was performed using the FindNeighbors and FindClusters functions with the top 40 principal components at a clustering resolution of 1.5. UMAP was used for dimensionality reduction and visualization.
Cell type annotation, differential gene expression analysis, functional enrichment analysis, and pseudotime trajectory inference were subsequently performed using canonical marker genes and standard downstream bioinformatics workflows.
Assembly: Evidence-based annotation of the human genome (GRCh38), version 47 (Ensembl release 113), was used as the reference genome for read alignment and transcript quantification.
Supplementary files format and content: The processed data are provided as standard output files from the Cell Ranger count pipeline (10x Genomics). For each sample, the dataset includes three files: (1) barcodes.tsv.gz, containing the cellular barcodes; (2) features.tsv.gz (or genes.tsv.gz), containing the Ensembl IDs and gene symbols; and (3) matrix.mtx.gz, representing the sparse matrix of raw digital gene expression (DGE) counts. Using the official BGI software DNBC4Tools with parameter settings, we performed filtering, alignment, quantification, and cell identification/recovery of raw data. After transcriptomic normalization processing, gene expression matrix files for each cell were obtained.

source_name: Organoid

growth_protocol: Human iPSC-derived forebrain organoids were generated and maintained in vitro according to an established forebrain differentiation protocol. All organoids were cultured under identical conditions until collection at day 30.

extract_protocol:
Day-30 organoids were collected and pooled for each biological replicate. Samples were washed three times with ice-cold PBS and dissociated into single-cell suspensions by incubation with 0.5 mg/mL digestive enzyme I for 30 min at 37°C. Cell suspensions were filtered through a 70 μm cell strainer, centrifuged at 500 g for 5 min, and resuspended in PBS containing 0.01% BSA.
Single-cell capture, barcoding, reverse transcription, and cDNA library construction were performed using the MGI DNBelab C-TaiM4 single-cell transcriptome platform according to the manufacturer's instructions. cDNA libraries were purified, amplified, ligated with sequencing adapters, quality-checked using an Agilent 2100 Bioanalyzer, and sequenced on the BGI DNBSEQ-T7 platform in paired-end 100 bp mode.

treatment_protocol: Four experimental conditions were included: untreated control organoids (CTR), cholesterol-treated organoids (CHOL; 10 μg/mL cholesterol from day 14 to day 30), semaglutide-treated organoids (SEMA; 100 nM semaglutide from day 14 to day 30), and cholesterol plus semaglutide co-treated organoids (CHOL+SEMA; 10 μg/mL cholesterol plus 100 nM semaglutide from day 14 to day 30).

value: Organoid

value: DXR

value: hiPSC

value: Cholesterol + Semaglutide

tag: batch


title: T47D with CDK6 overexpression treated with DMSO repeat 2

description:
Library name: TOE_D2
raw file no longer available


title: ARID1-GFP-C_arid1_VN_H3_2_Rep2

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3_2_Rep2


title: ARID1-GFP-C_arid1_VN_H3_2_Rep1

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3_2_Rep1


title: SEMA

description:
Library name: Sample 3
10x Genomics

value: WT

value: Semaglutide


title: T47D with CDK6 overexpression treated with DMSO repeat 1

description:
Library name: TOE_D1
raw file no longer available


title: ARID1-GFP_arid1_VN_IP_Rep1

description: Library name: pollen_ARID1-GFP_arid1_VN_IP_Rep1


title: ARID1-GFP_arid1_VN_IP_Rep2

description: Library name: pollen_ARID1-GFP_arid1_VN_IP_Rep2


title: ARID1-GFP_arid1_VN_H3_2_Rep2

description: Library name: pollen_ARID1-GFP_arid1_VN_H3_2_Rep2


title: MCF7 with CDK6 overexpression treated with PIK75 repeat 2

description:
Library name: MOE_P2
raw file no longer available

source_name: MCF-7 with CDK6 overexpression

value: MCF-7 with CDK6 overexpression


title: CHOL

description:
Library name: Sample 2
10x Genomics

value: Cholesterol


title: ARID1-GFP_arid1_VN_H3_2_Rep1

description: Library name: pollen_ARID1-GFP_arid1_VN_H3_2_Rep1


title: CTR

description:
Library name: Sample 1
10x Genomics

value: Control


title: ARID1-GFP-C_arid1_VN_H3K9me2_Rep3

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3K9me2_Rep3


title: chicklung_1222_dbit

city: Princeton

first: Pengfei

last: Zhang

state: NJ

address: 303 Hoyt Laboratory, William Street

department: ODBI

institute: Princeton University

description: Library name: sample3

data_processing:
Read 1 sequences were reformatted to extract unique molecular identifiers (UMIs), Barcode A sequences, and Barcode B sequences from the spatial transcriptomic reads.Read2 sequences were aligned to the chicken reference genome assembly GRCg7b and demultiplexed using the ST pipeline v1.8.1. Spatial gene-expression matrices were generated after filtering out pixels located outside tissue regions.
Assembly: GRCg7b
Supplementary files format and content: Processed files are provided in tab-delimited text and matrix formats compatible with downstream spatial transcriptomic analysis tools.
Library strategy: Spatial Transcriptomics

organism: Gallus gallus

source_name: Embryonic lung

growth_protocol: Fertilized White Leghorn chicken eggs (Gallus gallus) were incubated under standard humidified conditions at 37.5–38°C until embryonic day 5 (E5). Embryonic lungs were isolated from E5 chicken embryos in chilled phosphate-buffered saline (PBS) supplemented with 10-U/mL penicillin and 10-µg/mL streptomycin prior to downstream processing.

extract_protocol:
Dissected E5 chicken lungs were sequentially incubated in 20% sucrose, 30% sucrose, and 1:1 OCT:30% sucrose solution supplemented with diethyl pyrocarbonate (DEPC) before embedding in OCT compound. Embedded tissues were cryosectioned at approximately 7-µm thickness and mounted onto poly-L-lysine-coated glass slides. Prior to spatial transcriptomic processing, sections were fixed using an ice-cold methanol/DSP fixation solution containing DEPC, followed by PBS-based washing and tissue permeabilization. Spatially barcoded cDNA was generated through in-tissue reverse transcription and ligation using microfluidic deterministic barcoding. Tissue lysates were collected after Proteinase K digestion, and cDNA was purified using silica-column purification and streptavidin magnetic bead enrichment prior to second-strand synthesis and PCR amplification.
Sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit with custom P5 primers and sequenced on an Illumina NovaSeq SP 300-cycle flow cell with paired-end sequencing configuration of 80 bp for Read 1 and 250 bp for Read 3.

value: Embryonic lung


title: ARID1-GFP-C_arid1_VN_H3K9me2_Rep2

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3K9me2_Rep2


title: ARID1-GFP-C_arid1_VN_H3K9me2_Rep1

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3K9me2_Rep1


title: ARID1-GFP-C_arid1_VN_H3_Rep3

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3_Rep3


title: MCF7 with CDK6 overexpression treated with DMSO repeat 2

description:
Library name: MOE_D2
raw file no longer available

value: breast


title: MCF7 with CDK6 overexpression treated with DMSO repeat 1

description:
Library name: MOE_D1
raw file no longer available


title: ARID1-GFP-C_arid1_VN_H3_Rep1

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3_Rep1


title: chicklung_1018_dbit

description: Library name: sample2


title: ARID1-GFP-C_arid1_VN_H3_Rep2

description: Library name: pollen_ARID1-GFP-C_arid1_VN_H3_Rep2


title: chicklung_1009_dbit

description: Library name: sample1


title: ARID1-GFP_arid1_VN_H3K9me2_Rep3

description: Library name: pollen_ARID1-GFP_arid1_VN_H3K9me2_Rep3


title: MCF7 with CDK6 overexpression treated with PIK75 repeat 1

description:
Library name: MOE_P1
raw file no longer available


title: HCT116 H4R3me2a ChIP-seq

city: Nanjing

first: Mu

last: Xu

address: No.32, Gongqingtuan Road,

department: Nanjing First Hospital

institute: Nanjing Medical University

description:
Library name: hct116_h4r3me2a
H4R3me2a ChIP-seq from HCT116 cells in the ChIP-seq experiment.

data_processing:
Raw ChIP-seq reads were aligned to GRCh38 with Bowtie2.
Peaks were called for H4R3me2a ChIP relative to matched input DNA using MACS2 with q < 0.05.
CPM-normalized bigWig signal tracks were generated from uniquely mapped deduplicated alignments, and metagene profiles were generated with deepTools.
Assembly: GRCh38
Supplementary files format and content: bigWig files contain CPM-normalized ChIP-seq signal tracks for H4R3me2a ChIP and matched input DNA control.
Supplementary files format and content: narrowPeak and gzip-compressed tab-delimited files contain MACS2 H4R3me2a peaks and peak summary statistics.

source_name: colon

growth_protocol: HCT116 cells were cultured under standard mammalian cell culture conditions before ChIP-seq sample preparation.

extract_protocol:
CRC cells (~10^7 per sample) were cross-linked with 1% formaldehyde for 10 min, quenched with glycine and lysed. Chromatin was sheared to 200-500 bp by sonication. Immunoprecipitation was performed overnight at 4 C with H4R3me2a antibody or input DNA control, captured with Protein A/G magnetic beads. After washing, cross-link reversal and DNA purification, DNA was used for library preparation.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit and sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000.

treatment_protocol: No drug treatment was applied to these ChIP-seq samples.

value: colon

value: colorectal carcinoma cell line

tag: antibody

value: H4R3me2a antibody

tag: immunoprecipitation

value: H4R3me2a immunoprecipitated chromatin

tag: chip antibody_target


title: ARID1-GFP_arid1_VN_H3K9me2_Rep1

description: Library name: pollen_ARID1-GFP_arid1_VN_H3K9me2_Rep1


title: HCT116 ChIP-seq input control

description:
Library name: hct116_input
Input DNA control from HCT116 cells in the ChIP-seq experiment.

value: Input DNA

value: input DNA control

value: input


title: EU1 adult day 12, SULF, rep 6

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

description:
Library name: EU1_12_SULF_r6
SFN_mutants.featureCounts.txt

data_processing:
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in single-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 108)
Supplementary files format and content: Tab-delimited tables of raw gene counts for every gene and sample, for (1) two-group comparisons in wild type at each age, (2) additional wild type control series, and (3) skn-1 and daf-16 mutants at two ages.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans N2, PX991 (daf-16(fx107)), and EU1 (skn-1(zu67)) strains were maintained at 20°C and 80% RH on 60 mm nematode growth medium (NGM) plates seeded with E. coli OP50-1.

extract_protocol:
Worms were picked into 0.2 mL tubes containing 45 µL lysis buffer, 4 µL RNA-secure, 5 µL proteinase K and flash frozen with liquid nitrogen.
Libraries were prepared using the KAPA mRNA HyperPrep kit (KK8580 from Kapa Biosystems) as per manufacture protocol except that the total volume was adjusted to 1/4 per reaction.

treatment_protocol: Sulforaphane (Santa Cruz Biotech, sc-207495D) was mixed with DMSO (dimethyl sulfoxide) to create a stock solution. Stock solutions (DMSO for the controls) were then diluted with water to create working solutions and distributed onto 35 mm NGM plates containing 51 µM FUdR and previously seeded with OP50-1. Plates were treated with compound solutions such that the final volume was assumed equal to the volume of agar and the final concentration of DMSO was 0.25%. Worms were synchronized and added to treatment plates beginning on day 1 of adulthood. Biological replicates were aged and collected in tandem, with the exception of EU1, where biological replicates 4, 5, and 6 were temporally independent. Approximately 50 worms total were collected per age, intervention, and replicate.

value: whole worm

tag: strain

tag: age

value: adult day 12

value: sulforaphane


title: ARID1-GFP_arid1_VN_H3K9me2_Rep2

description: Library name: pollen_ARID1-GFP_arid1_VN_H3K9me2_Rep2

value: mature pollen VN


title: ARID1-GFP_arid1_VN_H3_Rep3

description: Library name: pollen_ARID1-GFP_arid1_VN_H3_Rep3


title: ARID1-GFP_arid1_VN_H3_Rep2

description: Library name: pollen_ARID1-GFP_arid1_VN_H3_Rep2


title: EU1 adult day 12, DMSO, rep 6

description:
Library name: EU1_12_DMSO_r6
SFN_mutants.featureCounts.txt

value: DMSO control


title: arid1_VN_H3K9me2_Rep3

description: Library name: pollen_arid1_VN_H3K9me2_Rep3


title: EU1 adult day 12, SULF, rep 5

description:
Library name: EU1_12_SULF_r5
SFN_mutants.featureCounts.txt


title: arid1_VN_H3K9me2_Rep2

description: Library name: pollen_arid1_VN_H3K9me2_Rep2


title: OCI-AML3 cells, shCLN7-4

city: Hefei

first: Miaomiao

last: Wu

address: 96 Jinzhai Road, Hefei, China

institute: The First Affiliated Hospital of USTC

description: Library name: OCIshCLN7_4

data_processing:
Raw reads were processed using fastp software with default parameters to remove adaptor contamination, low-quality bases, and undetermined bases.
The clean reads were mapped to the Homo sapiens GRCh38 reference genome using HISAT2 software.
Mapped reads were assembled using StringTie, and all transcriptomes from all samples were merged using gffcompare to reconstruct a comprehensive transcriptome.
StringTie was used to estimate transcript expression levels and calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing normalized gene expression values calculated as FPKM for all samples.

source_name: bone marrow

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. RNA quantity and purity were evaluated using NanoDrop ND-1000, and RNA integrity was assessed by Agilent Bioanalyzer 2100 ensuring RIN > 7.0
Poly(A) RNA was purified from  total RNA using Dynabeads Oligo (dT) and fragmented. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase, followed by U-labeled second-strand synthesis using dUTP to generate strand-specific libraries. After A-tailing, adapter ligation, and AMPureXP bead size selection, the UDG-treated products were PCR amplified. The final libraries (average insert size 300±50 bp) were sequenced via 2x150 bp paired-end sequencing on an Illumina NovaSeq 6000 platform.

value: bone marrow

value: myeloid leukemia cell

value: CLN7  knockdown


title: EU1 adult day 12, DMSO, rep 5

description:
Library name: EU1_12_DMSO_r5
SFN_mutants.featureCounts.txt


title: arid1_VN_H3K9me2_Rep1

description: Library name: pollen_arid1_VN_H3K9me2_Rep1


title: EU1 adult day 4, SULF, rep 6

description:
Library name: EU1_4_SULF_r6
SFN_mutants.featureCounts.txt

value: adult day 4


title: arid1_VN_H3_Rep3

description: Library name: pollen_arid1_VN_H3_Rep3


title: arid1_VN_H3_Rep2

description: Library name: pollen_arid1_VN_H3_Rep2


title: arid1_VN_H3_Rep1

description: Library name: pollen_arid1_VN_H3_Rep1


title: Col-0_VN_H3K9me2_Rep3

description: Library name: pollen_Col-0_VN_H3K9me2_Rep3


title: OCI-AML3 cells, shCLN7-3

description: Library name: OCIshCLN7_3


title: OCI-AML3 cells, shCLN7-2

description: Library name: OCIshCLN7_2

value: CLN7 knockdown


title: Col-0_VN_H3K9me2_Rep2

description: Library name: pollen_Col-0_VN_H3K9me2_Rep2


title: OCI-AML3 cells, shCLN7-1

description: Library name: OCIshCLN7_1


title: EU1 adult day 4, SULF, rep 5

description:
Library name: EU1_4_SULF_r5
SFN_mutants.featureCounts.txt


title: Col-0_VN_H3K9me2_Rep1

description: Library name: pollen_Col-0_VN_H3K9me2_Rep1


title: EU1 adult day 4, DMSO, rep 5

description:
Library name: EU1_4_DMSO_r5
SFN_mutants.featureCounts.txt


title: Col-0_VN_H3_Rep2

description: Library name: pollen_Col-0_VN_H3_Rep2


title: OCI-AML3 cells, scramble-4

description: Library name: OCIscramble_4

value: WT

value: scrambled shRNA


title: EU1 adult day 12, SULF, rep 4

description:
Library name: EU1_12_SULF_r4
SFN_mutants.featureCounts.txt


title: 4T1 Anti-PD1+LP-184-8

description: Library name: Sample16-8

library_source: transcriptomic single cell

source_name: tumor

value: tumor

value: TNBC

value: 4T1 Anti-PD1+LP-184


title: OCI-AML3 cells, scramble-3

description: Library name: OCIscramble_3


title: 4T1 Anti-PD1+LP-184-7

description: Library name: Sample16-7


title: EU1 adult day 12, DMSO, rep 4

description:
Library name: EU1_12_DMSO_r4
SFN_mutants.featureCounts.txt


title: OCI-AML3 cells, scramble-2

description: Library name: OCIscramble_2


title: 4T1 Anti-PD1+LP-184-5

description: Library name: Sample16-5


title: 4T1 Anti-PD1+LP-184-6

description: Library name: Sample16-6


title: EU1 adult day 12, SULF, rep 3

description:
Library name: EU1_12_SULF_r3
SFN_mutants.featureCounts.txt


title: 4T1 Anti-PD1+LP-184-4

description: Library name: Sample16-4


title: 4T1 Anti-PD1+LP-184-3

description: Library name: Sample16-3


title: EU1 adult day 12, DMSO, rep 3

description:
Library name: EU1_12_DMSO_r3
SFN_mutants.featureCounts.txt


title: 4T1 Anti-PD1+LP-184-2

description: Library name: Sample16-2


title: OCI-AML3 cells, scramble-1

description: Library name: OCIscramble_1


title: K562 cells, shCLN7-3

description: Library name: k562shCLN7_3


title: 4T1 Anti-PD1+LP-184-1

description: Library name: Sample16-1


title: EU1 adult day 12, SULF, rep 2

description:
Library name: EU1_12_SULF_r2
SFN_mutants.featureCounts.txt


title: ARID1-GFP_arid1_VN_H3_Rep1

description: Library name: pollen_ARID1-GFP_arid1_VN_H3_Rep1


title: OVCAR3-OE

city: Qingdao

first: Sun

last: Danting

state: Shandong

address: 1677 Wutai Mountain Road, Huangdao District, Qingdao, Shandong Province

department: Department of Gynecology

institute: The Affiliated Hospital of Qingdao University

description: Library name: Sample2

data_processing:
After the library passes quality control, it is sequenced using the Illumina Novaseq 6000 sequencing platform with a PE150 configuration. PE150 (Pair-end 150 bp) refers to a high-throughput paired-end sequencing strategy in which 150 bp are sequenced from each end.
Assembly: GRCh38
Supplementary files format and content: CSV file including FPKM for each sample
Supplementary files format and content: FPKM.csv

source_name: ovary

extract_protocol:
Use the TransZol Up Plus RNA Kit (Quanzhi Jin) to isolate and purify RNA from the total sample according to the manufacturer’s protocol. Then, use the Pono-650 (Porabio) to perform quality control on the total RNA for both quantity and purity. Next, the integrity of the RNA was assessed using the Qsep100 (BiOptic, Taiwan). Concentration > 20 ng/μL, RIN value > 7.0, and total RNA > 1 μg were confirmed to meet the requirements for downstream experiments.
PolyA-tagged mRNA was specifically captured using oligo(dT) magnetic beads (Cat. No. N403, Vazyme) through two rounds of purification. The captured mRNA was fragmented under high-temperature conditions using magnesium ions (all reagents are from the same kit, Cat. No. NR605, Vazyme). cDNA was synthesized from the fragmented RNA using reverse transcriptase. Double-stranded DNA was then synthesized, with dUTP incorporated into the double helix to generate blunt-ended DNA. A single A base was added to each end to enable ligation with a T-terminated adapter, followed by size-based fractionation and purification using magnetic beads. Subsequently, PCR was performed as follows: pre-denaturation at 98°C for 45 seconds, denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds, for a total of 12 cycles, followed by a final extension at 72°C for 1 minute, resulting in a library with fragment sizes ranging from 370 to 470 bp.

value: ovary

value: ovarian carcinoma cell line

value: overexpressing IGF2BP3


title: 4T1 Anti-PD1+Vehicle-8

description: Library name: Sample15-8

value: 4T1 Anti-PD1+Vehicle


title: OVCAR3-NC

description: Library name: Sample1

value: control


title: K562 cells, shCLN7-2

description: Library name: k562shCLN7_2


title: EU1 adult day 12, DMSO, rep 2

description:
Library name: EU1_12_DMSO_r2
SFN_mutants.featureCounts.txt

value: whole worm

value: adult day 12


title: 4T1 Anti-PD1+Vehicle-7

description: Library name: Sample15-7


title: 4T1 Anti-PD1+Vehicle-6

description: Library name: Sample15-6


title: EU1 adult day 12, SULF, rep 1

description:
Library name: EU1_12_SULF_r1
SFN_mutants.featureCounts.txt

value: sulforaphane


title: K562 cells, shCLN7-1

description: Library name: k562shCLN7_1

value: bone marrow

value: myeloid leukemia cell


title: 4T1 Anti-PD1+Vehicle-5

description: Library name: Sample15-5


title: 4T1 Anti-PD1+Vehicle-4

description: Library name: Sample15-4


title: K562 cells, scramble-3

description: Library name: k562scramble_3


title: 4T1 Anti-PD1+Vehicle-3

description: Library name: Sample15-3


title: EU1 adult day 12, DMSO, rep 1

description:
Library name: EU1_12_DMSO_r1
SFN_mutants.featureCounts.txt

value: DMSO control


title: 4T1 Anti-PD1+Vehicle-2

description: Library name: Sample15-2


title: K562 cells, scramble-2

description: Library name: k562scramble_2


title: EU1 adult day 4, SULF, rep 4

description:
Library name: EU1_4_SULF_r4
SFN_mutants.featureCounts.txt

value: adult day 4


title: 4T1 Anti-PD1+Vehicle-1

description: Library name: Sample15-1


title: 4T1 IgG+LP-184-7

description: Library name: Sample14-7


title: K562 cells, scramble-1

description: Library name: k562scramble_1

value: WT


title: 4T1 IgG+LP-184-5

description: Library name: Sample14-5


title: CD34+ HSPCs-RNA_CD34/LNPDP-2_3

city: Tianjin

first: Rao

last: Shuquan

address: No. 288, Nanjing Road, Heping District,

department: State Key Laboratory of Experimental Hematology

institute: National Clinical Research Center for Blood Diseases Institute of Hematology & Blood Diseases Hospital,

description: Library name: Sample 21

data_processing:
Raw reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b) with --quantMode GeneCounts. Differential expression analysis was carried out using the DESeq2 package (v1.48.1).
Assembly: Homo sapiens: GRCh38 (GENCODE release 47)
Supplementary files format and content: Normalized gene-level expression counts with rows representing genes and columns representing samples.

source_name: Cord blood

extract_protocol:
RNA was harvested the Rneasy mini plus kit (Qiagen). 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit   following manufacturer's protocols

value: Cord blood

value: CD34+ HSPCs

value: CD34+ hematopoietic stem and progenitor cells

value: wild type

value: CD34/LNPDP at 0.5 μg/mL for 24h


title: 4T1 IgG+LP-184-6

description: Library name: Sample14-6

value: tumor

value: TNBC


title: 4T1 IgG+LP-184-4

description: Library name: Sample14-4


title: EU1 adult day 4, DMSO, rep 4

description:
Library name: EU1_4_DMSO_r4
SFN_mutants.featureCounts.txt


title: EU1 adult day 4, SULF, rep 3

description:
Library name: EU1_4_SULF_r3
SFN_mutants.featureCounts.txt


title: Col-0_VN_H3_Rep3

description: Library name: pollen_Col-0_VN_H3_Rep3

value: mature pollen VN


title: 4T1 IgG+LP-184-2

description: Library name: Sample14-2


title: 4T1 IgG+LP-184-3

description: Library name: Sample14-3


title: EU1 adult day 4, DMSO, rep 3

description:
Library name: EU1_4_DMSO_r3
SFN_mutants.featureCounts.txt


title: 4T1 IgG+LP-184-1

description: Library name: Sample14-1


title: CD34+ HSPCs-RNA_CD34/LNPDP-2_1

description: Library name: Sample 19


title: 4T1 IgG+Vehicle-8

description: Library name: Sample13-8

value: 4T1 IgG+Vehicle


title: EU1 adult day 4, SULF, rep 2

description:
Library name: EU1_4_SULF_r2
SFN_mutants.featureCounts.txt

value: whole worm


title: 4T1 IgG+Vehicle-7

description: Library name: Sample13-7


title: CD34+ HSPCs-RNA_CD34/LNPDP-2_2

description: Library name: Sample 20


title: Col-0_VN_H3_Rep1

description: Library name: pollen_Col-0_VN_H3_Rep1


title: CD34+ HSPCs-RNA_IgG/LNPDP-2_3

description: Library name: Sample 18

value: IgG/LNPDP at 2 μg/mL for 24h


title: 4T1 IgG+Vehicle-9

description: Library name: Sample13-9


title: EU1 adult day 4, DMSO, rep 2

description:
Library name: EU1_4_DMSO_r2
SFN_mutants.featureCounts.txt


title: 4T1 IgG+Vehicle-6

description: Library name: Sample13-6


title: CD34+ HSPCs-RNA_IgG/LNPDP-2_2

description: Library name: Sample 17


title: EU1 adult day 4, DMSO, rep 1

description:
Library name: EU1_4_DMSO_r1
SFN_mutants.featureCounts.txt


title: CD34+ HSPCs-RNA_IgG/LNPDP-2_1

description: Library name: Sample 16


title: 4T1 IgG+Vehicle-2

description: Library name: Sample13-2


title: 4T1 IgG+Vehicle-3

description: Library name: Sample13-3


title: PX991 adult day 12, SULF, rep 4

description:
Library name: PX991_12_SULF_r4
SFN_mutants.featureCounts.txt

value: adult day 12

value: sulforaphane


title: CD34+ HSPCs-RNA_LNPDP-2_3

description: Library name: Sample 15

value: LNPDP at 2 μg/mL for 24h


title: 4T1 IgG+Vehicle-1

description: Library name: Sample13-1


title: RNA, Paused, Smad2_KO2, rep 4

city: Toronto

first: Giacomo

last: Furlan

state: ONTARIO

address: 25 Orde St

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: Library name: Sample 24

data_processing:
Read quality was assessed using FastQC. Single-end reads were trimmed using Trim Galore, and only high-quality reads passing these steps were retained for downstream analysis.
Reads were aligned to the Mus musculus (mm10) reference genome using HISAT2.
Raw counts per gene were obtained using the featureCounts function from Rsubread (v2.20.0) with parameters -t exon -g gene_id
Raw counts were imported into R and normalized using DESeq2. Differential gene expression was considered significant with an adjusted p-value (Padj) < 0.05 and an absolute log₂ fold change > 1
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for all genes in all samples

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in standard serum/LIF medium consisting of DMEM GlutaMAX supplemented with sodium pyruvate, 15% fetal bovine serum, 0.1 mM non-essential amino acids, 50 U mL-1 penicillin–streptomycin, 0.1 mM 2-mercaptoethanol, and 1,000 U mL-1 ESGRO LIF.

extract_protocol:
50,000 live cells were collected and RNA was extracted using the RNeasy Micro Kit with on-column DNase I digestion (QIAGEN). RNA integrity number was assesed by Fragment Analyser. 150ng of RNA per sample were used for library preparation.
Library preparation was done using the NEBNext Ultra II Directional Library Prep Kit for Illumina with the mRNA Magnetic Isolation Module from 1µg RNA, per manufacturer’s instructions (NEB).

treatment_protocol: To induce in vitro pausing, 200nM of the mTOR inhibitor INK128 was added to the culture medium for 12 hours.

value: embryonic stem cells

value: KO


title: CD34+ HSPCs-RNA_LNPDP-2_2

description: Library name: Sample 14


title: RNA, Paused, Smad2_KO2, rep 3

description: Library name: Sample 23


title: PX991 adult day 12, SULF, rep 3

description:
Library name: PX991_12_SULF_r3
SFN_mutants.featureCounts.txt


title: RNA, Paused, Smad2_KO2, rep 2

description: Library name: Sample 22


title: CD34+ HSPCs-RNA_LNPDP-2_1

description: Library name: Sample 13


title: RNA, Paused, Smad2_KO2, rep 1

description: Library name: Sample 21


title: PX991 adult day 12, DMSO, rep 3

description:
Library name: PX991_12_DMSO_r3
SFN_mutants.featureCounts.txt

value: DMSO control


title: RNA, Paused, Smad2_KO1, rep 4

description: Library name: Sample 20


title: CD34+ HSPCs-RNA_Mock-2_3

description: Library name: Sample 12

value: Cord blood

value: Mock


title: PX991 adult day 12, SULF, rep 2

description:
Library name: PX991_12_SULF_r2
SFN_mutants.featureCounts.txt


title: RNA, Paused, Smad2_KO1, rep 3

description: Library name: Sample 19


title: RNA, Paused, Smad2_KO1, rep 2

description: Library name: Sample 18


title: CD34+ HSPCs-RNA_Mock-2_2

description: Library name: Sample 11

value: CD34+ HSPCs

value: CD34+ hematopoietic stem and progenitor cells


title: RNA, Paused, Smad2_KO1, rep 1

description: Library name: Sample 17


title: PX991 adult day 12, DMSO, rep 2

description:
Library name: PX991_12_DMSO_r2
SFN_mutants.featureCounts.txt


title: 4T1 IgG+Vehicle-4

description: Library name: Sample13-4


title: PX991 adult day 12, DMSO, rep 4

description:
Library name: PX991_12_DMSO_r4
SFN_mutants.featureCounts.txt


title: RNA, Paused, WT, rep 4

description: Library name: Sample 16

value: WT


title: 4T1 IgG+Vehicle-5

description: Library name: Sample13-5

value: tumor


title: CD34+ HSPCs-RNA_Mock-2_1

description: Library name: Sample 10

value: wild type


title: RNA, Paused, WT, rep 3

description: Library name: Sample 15


title: CD34+ HSPCs-RNA_CD34/LNPDP-1_3

description: Library name: Sample 9

value: CD34/LNPDP at 4 μg/mL for 24h


title: CLO_High, rep4

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

description: Library name: CLO_H_4

data_processing:
Trimmed sequence reads are mapped to reference genome Ss11.1 using TopHat with
Aligned reads were sorted by genomic coordinate using samtools
Differential gene expression analysis was conducted using Cuffdiff v2.2.1
Assembly: Ss11.1
Supplementary files format and content: text file includes fpkm values for each sample

organism: Sus scrofa

source_name: Clofoctol-treated xenograft tumor

extract_protocol:
RNA was harvested using Rnaeasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using the KAPA RNA Hyperprep Kit with RiboErase following the manufacturer's instructions

value: Clofoctol-treated xenograft tumor

value: primary cells

value: wt

value: high dose clo


title: PX991 adult day 12, SULF, rep 1

description:
Library name: PX991_12_SULF_r1
SFN_mutants.featureCounts.txt

value: whole worm

value: adult day 12

value: sulforaphane


title: RNA, Paused, WT, rep 2

description: Library name: Sample 14

value: embryonic stem cells


title: PX991 adult day 12, DMSO, rep 1

description:
Library name: PX991_12_DMSO_r1
SFN_mutants.featureCounts.txt

value: DMSO control


title: CLO_High, rep3

description: Library name: CLO_H_3


title: CD34+ HSPCs-RNA_CD34/LNPDP-1_2

description: Library name: Sample 8

value: Cord blood


title: RNA, Paused, WT, rep 1

description: Library name: Sample 13


title: PX991 adult day 4, SULF, rep 4

description:
Library name: PX991_4_SULF_r4
SFN_mutants.featureCounts.txt

value: adult day 4


title: CD34+ HSPCs-RNA_CD34/LNPDP-1_1

description: Library name: Sample 7

value: CD34+ HSPCs


title: RNA, Ctrl, Smad2_KO2, rep 4

description: Library name: Sample 12

value: KO


title: CLO_High, rep2

description: Library name: CLO_H_2


title: CD34+ HSPCs-RNA_IgG/LNPDP-1_3

description: Library name: Sample 6

value: CD34+ hematopoietic stem and progenitor cells

value: IgG/LNPDP at 4 μg/mL for 24h


title: PX991 adult day 4, SULF, rep 3

description:
Library name: PX991_4_SULF_r3
SFN_mutants.featureCounts.txt


title: CLO_High, rep1

description: Library name: CLO_H_1


title: PX991 adult day 4, DMSO, rep 4

description:
Library name: PX991_4_DMSO_r4
SFN_mutants.featureCounts.txt


title: RNA, Ctrl, Smad2_KO2, rep 3

description: Library name: Sample 11


title: CLO_Low, rep4

description: Library name: CLO_L_4

value: low dose clo


title: CD34+ HSPCs-RNA_IgG/LNPDP-1_2

description: Library name: Sample 5

value: wild type


title: RNA, Ctrl, Smad2_KO2, rep 2

description: Library name: Sample 10


title: PX991 adult day 4, DMSO, rep 3

description:
Library name: PX991_4_DMSO_r3
SFN_mutants.featureCounts.txt


title: CLO_Low, rep3

description: Library name: CLO_L_3

value: Clofoctol-treated xenograft tumor


title: CD34+ HSPCs-RNA_IgG/LNPDP-1_1

description: Library name: Sample 4


title: RNA, Ctrl, Smad2_KO2, rep 1

description: Library name: Sample 9


title: PX991 adult day 4, SULF, rep 2

description:
Library name: PX991_4_SULF_r2
SFN_mutants.featureCounts.txt


title: CLO_Low, rep2

description: Library name: CLO_L_2

value: primary cells


title: RNA, Ctrl, Smad2_KO1, rep 4

description: Library name: Sample 8


title: PX991 adult day 4, DMSO, rep 2

description:
Library name: PX991_4_DMSO_r2
SFN_mutants.featureCounts.txt


title: CLO_Low, rep1

description: Library name: CLO_L_1

value: wt


title: CD34+ HSPCs-RNA_Mock-1_3

description: Library name: Sample 3

value: Mock


title: CD34+ HSPCs-RNA_Mock-1_2

description: Library name: Sample 2


title: RNA, Ctrl, Smad2_KO1, rep 3

description: Library name: Sample 7


title: PX991 adult day 4, SULF, rep 1

description:
Library name: PX991_4_SULF_r1
SFN_mutants.featureCounts.txt

value: whole worm


title: CLO_Control, rep4

description: Library name: CLO_CTR_4

value: control


title: PX991 adult day 4, DMSO, rep 1

description:
Library name: PX991_4_DMSO_r1
SFN_mutants.featureCounts.txt


title: CD34+ HSPCs-RNA_Mock-1_1

description: Library name: Sample 1


title: RNA, Ctrl, Smad2_KO1, rep 2

description: Library name: Sample 6


title: CAL51-TREX1 KO-2 02

description: Library name: Sample6

value: TNBC

value: CAL51-TREX1 KO-2 02


title: CLO_Control, rep3

description: Library name: CLO_CTR_3


title: RNA, Ctrl, Smad2_KO1, rep 1

description: Library name: Sample 5

value: embryonic stem cells


title: CLO_Control, rep2

description: Library name: CLO_CTR_2


title: N2 adult day 16, DMSO, rep 4, trial 3

description:
Library name: N2_16_DMSO_r4_tr3
N2_additional_controls.featureCounts.txt

value: adult day 16

value: WT

value: DMSO control


title: CAL51-TREX1 KO-2 01

description: Library name: Sample5

value: CAL51-TREX1 KO-2 01


title: RNA, Ctrl, WT, rep 4

description: Library name: Sample 4


title: N2 adult day 16, DMSO, rep 4, trial 2

description:
Library name: N2_16_DMSO_r4_tr2
N2_additional_controls.featureCounts.txt


title: CLO_Control, rep1

description: Library name: CLO_CTR_1


title: W6, Rep3, bACE

status: Public on Jun 21 2026

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

data_processing:
Raw reads were trimmed for base quality and adaptor sequences using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and reads below a length of 20 bases were discarded.
The trimmed reads were aligned to the reference genomes using Bismark (v0.22.3) with the following parameters -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2.
To account for A3A failure due to double-stranded DNA, reads with three or more consecutive non-converted cytosines in the CpH context were removed using the filter_non_conversion script included in the Bismark package.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing the chromosome, start position, end position, methylation percentage, count methylated, count unmethylated

source_name: Cortex

extract_protocol:
To isolate gDNA, brain was thawed and digested in lysis buffer (50mM Tris, pH8.0, 100mM EDTA, 0.5% SDS) with proteinase K (Sigma-Aldrich) overnight at 55°C. Genomic DNA was isolated using Phenol:Chloroform:Isoamyl Alcohol (Fisher BP17501-400) and ethanol precipitation. DNA samples resuspended in TE were stored at 4°C.
Purified mouse gDNA (200 ng) with 1 ng each of phiX, mCpG pUC19 (Zymo), and 5hmC T4 spike-in controls were sheared to approximately 350 bp using a Covaris instrument. Sheared gDNA was taken through end prep and adaptor ligation using the NEBNext Ultra II DNA Library Prep Kit (NEB). Custom-made pyrrolo-cytosine adaptors (IDT) were substituted for kit-supplied adaptors. Adapted samples were bisulfite treated using the Premium Bisulfite Kit (Diagenode) and eluted in nuclease-free water. Post bisulfite clean-up, each sample was split into two 10 µL aliquots. One aliquot was further purified with a 1.2x left-side SPRI purification (Beckman). The SPRI-purified aliquot was denatured and APOBEC3A-treated (NEB, E1725L). After A3A deamination, the sample was purified via SPRI beads (1.2x, left-sided). Quantitative PCR was used to determine the number of cycles for the indexing PCR. Indexing PCR was performed using the unique dual index primer pairs from NEBNext Multiplex Oligos for Enzymatic-Methyl Seq (NEB). After the indexing PCR, samples were purified with two 0.8x left-sided SPRI purifications. Libraries were quantified with a Qubit HS kit (Invitrogen,Q32851) and assessed for quality with an Agilent Bioanalyzer. The resulting libraries were then pooled and sequenced on an Illumina MiSeq using 150-bp read length on a nano or micro sequencing kit (Illumina).
BS-Seq, bACE-Seq

value: Cortex

value: Bisulfute + A3A (bACE-Seq)

tag: time

value: Week 6


title: Con_3

city: Shijiazhuang

first: Lingdan

last: Zhao

address: No. 361 Zhongshan East Road, Chang'an District

department: Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education

institute: Hebei Medical University

description: Library name: Con_3

data_processing:
Raw reads were trimmed for adapters and low-quality bases using Trimmomatic. Clean reads were aligned to GRCr8 with Bowtie2. Duplicate reads were removed using Picard. Peak calling was performed using MACS2 with a q-value threshold of 0.05. Peaks were annotated to nearest genes using ChIPseeker.
Assembly: GRCr8
Supplementary files format and content: bigWig, narrow Peak(except for iInput sample)

organism: Rattus norvegicus

source_name: VSMCs

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at RT, quenched with glycine, and lysed in SDS buffer. Chromatin was sheared by sonication to 200–500 bp fragments. After centrifugation, supernatants were incubated with target-specific antibody and protein A/G beads overnight at 4°C. Beads were washed sequentially with low-salt, high-salt, and LiCl buffers, then eluted with SDS buffer. Crosslinks were reversed at 65°C overnight, and DNA was purified by phenol-chloroform extraction.
ChIP-enriched DNA was end-repaired, A-tailed, and ligated to sequencing adapters. Adapter-ligated fragments were amplified by PCR (12–15 cycles) with barcoded primers. PCR products were size-selected (200–400 bp) using AMPure XP beads. Library quality was assessed by Qubit for concentration and Bioanalyzer for fragment size distribution.

value: VSMCs

value: VSMCs were treated with H2O for 24 h


title: N2 adult day 16, DMSO, rep 3, trial 3

description:
Library name: N2_16_DMSO_r3_tr3
N2_additional_controls.featureCounts.txt


title: RNA, Ctrl, WT, rep 3

description: Library name: Sample 3


title: CAL51-TREX1 KO-1 02

description: Library name: Sample4

value: CAL51-TREX1 KO-1 02


title: Control_030

description: Library name: NBO_030

source_name: primary cells

value: primary cells

value: wt


title: CAL51-TREX1 KO-1 01

description: Library name: Sample3

value: CAL51-TREX1 KO-1 01


title: N2 adult day 16, DMSO, rep 3, trial 2

description:
Library name: N2_16_DMSO_r3_tr2
N2_additional_controls.featureCounts.txt

value: whole worm


title: Control_026

description: Library name: NBO_026

value: control


title: CAL51-Ctrl 02

description: Library name: Sample2

value: TNBC

value: CAL51-Ctrl 02


title: RNA, Ctrl, WT, rep 1

description: Library name: Sample 1

value: embryonic stem cells


title: N2 adult day 16, DMSO, rep 2, trial 3

description:
Library name: N2_16_DMSO_r2_tr3
N2_additional_controls.featureCounts.txt

value: adult day 16

value: WT


title: RNA, Ctrl, WT, rep 2

description: Library name: Sample 2


title: EU1 adult day 4, DMSO, rep 6

description:
Library name: EU1_4_DMSO_r6
SFN_mutants.featureCounts.txt

value: adult day 4

value: DMSO control


title: Control_022

description: Library name: NBO_022


title: CAL51-Ctrl 01

description: Library name: Sample1

value: CAL51-Ctrl 01


title: N2 adult day 16, DMSO, rep 2, trial 2

description:
Library name: N2_16_DMSO_r2_tr2
N2_additional_controls.featureCounts.txt


title: ATAC, Paused, Smad2_KO2, rep 4

description:
Library name: Sample 24
Smad2_KO_2D

data_processing:
Read quality was assessed using FastQC. Paired-end reads were trimmed using Trim Galore, and only high-quality reads passing these steps were retained for downstream analysis.
Reads were aligned to the Mus musculus reference genome (mm10) using Bowtie2 (v2.4.1). Unaligned reads, mitochondrial reads, and PCR duplicates were removed at this stage.
Peak calling was performed with MACS3 (v3.0.3), using --nomodel and --nolambda parameters. Peaks overlapping with mouse ENCODE blacklist regions were excluded.
Differential accessibility analysis was performed in R using the DiffBind package (v3.16.0). Regions were considered significantly differentially accessible with a false discovery rate (FDR) < 0.05 and an absolute log₂ fold change > 1.
Genomic regions were annotated to nearby genes using GREAT (McLean et al., 2010), with the following settings: proximal = ±5 kb from transcription start site (TSS); distal = up to 1000 kb.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for all peaks in all samples

extract_protocol:
50,000 live cells were collected and resuspended in cold resuspension buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Following lysis, nuclei were washed in RSB containing 0.1% NP-40 and subjected to tagmentation using the transposition mixture: 25 μL of 2× TD buffer, 2.5 μL of Tn5 transposase (100 nM final concentration), 16.5 μL of 1× PBS, 0.5 μL of 1% digitonin, 0.5 μL of 10% Tween-20, and 5 μL of nuclease-free water. After transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit.
Library amplification was carried out as per protocol (Corces et al., 2017). Amplified libraries were purified using AMPure XP beads with a double-sided size selection to remove both primer dimers and large fragments (>1000 bp). Final libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit, pooled at equimolar concentrations, and sequenced on a NovaSeq X platform with a 10B flow cell, generating 150 bp paired-end reads.

value: KO

value: Paused


title: High, BMI 30, Age 55

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description: Library name: H13

data_processing:
cellranger 8.0.1 mkfastq
cellranger 8.0.1 count using refdata-cellranger-GRCh38-3.0.0
Assembly: hg38
Supplementary files format and content: Zipped output from cellranger count including matrix.tsv.gz, barcodes.tsv.gz and features.tsv.gz files

molecule: nuclear RNA

source_name: endometrial adenocarcinoma

growth_protocol: Biobanked Flash Frozen Tissues

extract_protocol:
The Chromium Nuclei Isolation Kit (10x Genomics, PN-1000493) was used to isolate single nuclei. Tissue samples were thawed and dissociation tubes (PN-2000564) pre-chilled on dry ice. Samples were dissociated on wet ice using lysis buffer and pestle agitation until samples reached homogenization. Dissociated tissues were centrifuged in nuclei isolation columns (PN-2000562) for initial removal of cell debris. To remove remaining cell debris, pelleted nuclei were washed by resuspending nuclei pellet once in Debris Removal Buffer and three times in Wash and Resuspension Buffer respectively, with centrifugation between washes. Nuclei were resuspended in Wash and Resuspension buffer on ice for further analysis. RNA-seq was performed by the Wayne State University Genome Sciences Core.
After sequencing, the snRNA-seq library was demultiplexed using CellRanger mkfastq. Then, the CellRanger count was used to align the reference genome and tabulate counts by gene region.

treatment_protocol: Patients had either normal body mass indexI or obese body mass index

value: endometrial adenocarcinoma

tag: bmi


title: Cortical neurons, shOpa1, shAtf4, Day 11, Rep4

status: Public on Jun 22 2026

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

institute: University of Ottawa

description: SP flowcell PE50

data_processing:
fastq files were verified with multiQC.
Sequencing adaptors were trimmed and duplicates were removed.
ATAC peaks were called using MACS2.
Bigwig files were generated using bamCoverage for data visualization.
Assembly: mm10
Supplementary files format and content: Consensus peaks from all ATAC-seq samples, in BED format on the mm10 genome assembly. Peaks called with MACS2 and consensus peaks called with rmspc

source_name: brain

growth_protocol: Primary cortical neurons were prepared from embryonic cortices at day E14.5-15 of CD1 mice and cultured in vitro for 11 days.

extract_protocol:
Cells were treated with DnaseI to eliminate DNA contamination. Tn5 transposomes were applied to lysed chromatin. Transposed chromatin was purified using Zymo DNA Clean & Concentrator-5 columns.
Transposed DNA libraries were prepared using NEBNext Ultra II Q5 Master Mix and Illumina-compatible unique 5′-i5 and 3′-i7 barcode sequences.

treatment_protocol:
Cells were seeded at a density of 1 million cells/ml. Neurons were cultured in neurobasal media containing 1X B27; 1X N2; 100 Units/mL Penicillin/Streptomycin, and 0.6 mM L-glutamine. Cells were treated with the mitotic inhibitor cytosine arabinoside at 2uM.
A 50 % Media change is performed every 3-4 days and a full media change 3 days following Ara-C treatment. Lentiviral transduction was performed at day 6 and cells were harvested for RNA extraction on day 11.

value: brain

value: primary cell

value: cortical neurons

value: neuron differentiation


title: Control_020

description: Library name: NBO_020

value: primary cells

value: wt


title: ATAC, Paused, Smad2_KO2, rep 3

description:
Library name: Sample 23
Smad2_KO_2C


title: High, BMI 31.4, Age 61

description: Library name: H12


title: N2 adult day 16, DMSO, rep 1, trial 3

description:
Library name: N2_16_DMSO_r1_tr3
N2_additional_controls.featureCounts.txt

value: whole worm


title: ATAC, Paused, Smad2_KO2, rep 2

description:
Library name: Sample 22
Smad2_KO_2B


title: Control_009

description: Library name: NBO_009

value: control


title: N2 adult day 16, DMSO, rep 1, trial 2

description:
Library name: N2_16_DMSO_r1_tr2
N2_additional_controls.featureCounts.txt


title: Control_007

description: Library name: NBO_007


title: High, BMI 35.8, Age 59

description: Library name: H10


title: ATAC, Paused, Smad2_KO2, rep 1

description:
Library name: Sample 21
Smad2_KO_2A

value: embryonic stem cells


title: Case_013

description: Library name: NBO_013

value: Lentivirs


title: N2 adult day 12, DMSO, rep 4, trial 3

description:
Library name: N2_12_DMSO_r4_tr3
N2_additional_controls.featureCounts.txt

value: adult day 12

value: WT


title: High, BMI 37, Age 72

description: Library name: H5


title: ATAC, Paused, Smad2_KO1, rep 4

description:
Library name: Sample 20
Smad2_KO_1D


title: Case_006

description: Library name: NBO_006


title: N2 adult day 12, DMSO, rep 4, trial 2

description:
Library name: N2_12_DMSO_r4_tr2
N2_additional_controls.featureCounts.txt

value: DMSO control


title: High, BMI 35.4, Age 84

description: Library name: H4


title: N2 adult day 12, DMSO, rep 3, trial 3

description:
Library name: N2_12_DMSO_r3_tr3
N2_additional_controls.featureCounts.txt


title: Case_004

description: Library name: NBO_004


title: High, BMI 31.7, Age 78

description: Library name: H3


title: ATAC, Paused, Smad2_KO1, rep 3

description:
Library name: Sample 19
Smad2_KO_1C


title: N2 adult day 12, DMSO, rep 3, trial 2

description:
Library name: N2_12_DMSO_r3_tr2
N2_additional_controls.featureCounts.txt


title: Cho_1

description: Library name: Cho_1

value: VSMCs

value: VSMCs were treated with cholesterol (30 μg/ml) for 24 h


title: W6, Rep1, bACE

value: Cortex

value: Bisulfute + A3A (bACE-Seq)

value: Week 6


title: Case_003

description: Library name: NBO_003


title: ATAC, Paused, Smad2_KO1, rep 2

description:
Library name: Sample 18
Smad2_KO_1B

value: KO

value: Paused


title: High, BMI 33.4, Age 68

description: Library name: H1

value: endometrial adenocarcinoma


title: ATAC, Paused, Smad2_KO1, rep 1

description:
Library name: Sample 17
Smad2_KO_1A


title: Case_002

description: Library name: NBO_002

value: primary cells


title: High, BMI 47.1, Age 49

description: Library name: H0


title: N2 adult day 12, DMSO, rep 2, trial 3

description:
Library name: N2_12_DMSO_r2_tr3
N2_additional_controls.featureCounts.txt


title: ATAC, Paused, WT, rep 4

description:
Library name: Sample 16
WT_D


title: Cortical neurons, shOpa1, shAtf4, Day 11, Rep3

description: SP flowcell PE50

value: brain

value: primary cell

value: cortical neurons

value: neuron differentiation


title: N2 adult day 12, DMSO, rep 2, trial 2

description:
Library name: N2_12_DMSO_r2_tr2
N2_additional_controls.featureCounts.txt

value: whole worm


title: Low, BMI 24.6, Age 58

description: Library name: L13


title: N2 adult day 12, DMSO, rep 1, trial 3

description:
Library name: N2_12_DMSO_r1_tr3
N2_additional_controls.featureCounts.txt

value: adult day 12


title: W6, Rep1, BS

value: Bisulfute (BS-Seq)


title: WT mouse cornea_3

city: Bengbu

first: Jing

address: Donghai road 2600

institute: Bengbu Medical University

description:
Library name: Sample 6
The corneal tissue of WT mouse.

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

source_name: Cornea

growth_protocol: Male SPF Muc13-/- and WT mice (6 weeks old) were maintained on a 12-h light/dark cycle. Corneas were collected post-mortem and subjected to transcriptomic profiling via RNA-seq.

extract_protocol:
Total RNA of cells or tissues were isolated with RNA extraction reagent (Servicebio, Cat#: G3013). cDNA was synthesized from 1 μg of total RNA with SweScript RT II First Strand cDNA Synthesis Kit (Servicebio, Cat#: G3333.). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitollowing manufacturer's protocols.

value: Cornea

value: WT


title: WT mouse cornea_2

description:
Library name: Sample 5
The corneal tissue of WT mouse.


title: Low, BMI 23.3, Age 63

description: Library name: L10


title: N2 adult day 12, DMSO, rep 1, trial 2

description:
Library name: N2_12_DMSO_r1_tr2
N2_additional_controls.featureCounts.txt

value: DMSO control


title: Low, BMI 24.5, Age 65

description: Library name: L12


title: ATAC, Paused, WT, rep 2

description:
Library name: Sample 14
WT_B

value: embryonic stem cells


title: ATAC, Paused, WT, rep 1

description:
Library name: Sample 13
WT_A


title: WT mouse cornea_1

description:
Library name: Sample 4
The corneal tissue of WT mouse.


title: ATAC, Ctrl, Smad2_KO2, rep 4

description:
Library name: Sample 12
Smad2_KO_2D

value: Ctrl


title: N2 adult day 8, DMSO, rep 4, trial 3

description:
Library name: N2_8_DMSO_r4_tr3
N2_additional_controls.featureCounts.txt

value: adult day 8


title: Muc13 KO mouse cornea_3

description:
Library name: Sample 3
The corneal tissue of Muc13 KO mouse.

value: Muc13 knock out


title: N2 adult day 8, DMSO, rep 4, trial 2

description:
Library name: N2_8_DMSO_r4_tr2
N2_additional_controls.featureCounts.txt


title: Low, BMI 19.6, Age 84

description: Library name: L4


title: ATAC, Ctrl, Smad2_KO2, rep 3

description:
Library name: Sample 11
Smad2_KO_2C

value: KO


title: Low, BMI 19, Age 82

description: Library name: L3

value: endometrial adenocarcinoma


title: N2 adult day 8, DMSO, rep 3, trial 2

description:
Library name: N2_8_DMSO_r3_tr2
N2_additional_controls.featureCounts.txt


title: ATAC, Ctrl, Smad2_KO2, rep 2

description:
Library name: Sample 10
Smad2_KO_2B


title: Low, BMI 18.8, Age 65

description: Library name: L1


title: U87MG cells, S/G(+)_3

city: Busan

first: Jong-Ho

last: Lee

address: 37 Nakdong-daero 550 Beon-gil

country: South Korea

institute: Dong-A University

data_processing:
ExDEGA  GraphicPlus_v2.1
Bowtie2
Supplementary files format and content: Read Count.xlsx

growth_protocol: U87MG epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: U87MG epithelial cells were cultured with serine/glycine-containing complete media or equivalent media lacking serine/glycine for 24h.

value: glioblastoma cell line

tag: cell state

value: Naïve

value: with serine and glycine DMEM

value: Day 1


title: N2 adult day 8, DMSO, rep 2, trial 3

description:
Library name: N2_8_DMSO_r2_tr3
N2_additional_controls.featureCounts.txt


title: ATAC, Ctrl, Smad2_KO1, rep 4

description:
Library name: Sample 8
Smad2_KO_1D


title: L02 cells，LY6D-OE，FFAs750μM，rep2

city: Chongqing

first: Xiaohe

last: Luo

state: Chongqing

address: No. 165, Xincheng Road, Wanzhou District, Chongqing

department: Central lab

institute: Chongqing University Three Gorges Hospital

description:
Library name: Sample 5
Column name in ExpressionProfile.txt: L6_2

data_processing:
RNA-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample,  please see the ExpressionProfile.txt for details.

growth_protocol: L02 hepatocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Retains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina Truseq RNA Sample Prep Kit (Cat#FC-111-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using stantard Illumina protocols.

treatment_protocol: Cells were fed with DMEM supplemented with 10% FBS and 750uM FFAs for 24 hours.

value: human embryonic hepatocytes

value: LY6D overexpression


title: U87MG cells, S/G(+)_1


title: L02 cells，LY6D-OE，FFAs750μM，rep1

description:
Library name: Sample 4
Column name in ExpressionProfile.txt: L6_1


title: N2 adult day 8, DMSO, rep 1, trial 2

description:
Library name: N2_8_DMSO_r1_tr2
N2_additional_controls.featureCounts.txt

value: whole worm


title: ATAC, Ctrl, Smad2_KO1, rep 2

description:
Library name: Sample 6
Smad2_KO_1B


title: U87MG cells, S/G(-)_3

value: without serine and glycine DMEM


title: L02 cells，LY6D-OE，FFAs750μM，rep3

description:
Library name: Sample 6
Column name in ExpressionProfile.txt: L6_3


title: N2 adult day 4, DMSO, rep 4, trial 2

description:
Library name: N2_4_DMSO_r4_tr2
N2_additional_controls.featureCounts.txt

value: adult day 4


title: L02 cells，Control，FFAs750μM，rep1

description:
Library name: Sample 1
Column name in ExpressionProfile.txt: Control_1

value: WT


title: ATAC, Ctrl, WT, rep 3

description:
Library name: Sample 3
WT_C


title: N2 adult day 4, DMSO, rep 3, trial 3

description:
Library name: N2_4_DMSO_r3_tr3
N2_additional_controls.featureCounts.txt

value: DMSO control


title: sorted cortical microglia, from WT control mice, rep3 (mouse 1102)

city: New Yiork

first: Carlos

last: Diaz-Salazar

state: NY

address: Jerome L Greene Science Center, 3227 Broadway, L8 Quad A

department: Zuckerman Institute

institute: Columbia University

description:
Library name: WT_102.bam
Column name in "WT_vs_cKO.counts.csv" : 1102

data_processing:
Reads were aligned to the GRCm39 mouse genome using BaseSpace DRAGEN RNA app (Illumina). Differential gene expression analysis was performed with pyDESeq2 81,82. Genes with less than 10 read counts in total were filtered out. ERT2 expression from the Tmem119creERT2 locus was mapped to the Esr1 gene and was thus filtered out
Assembly: GRCm39
Supplementary files format and content: csv file contains raw count matrix for all seven samples. Column header is each mouse ID.

source_name: mouse cortex

growth_protocol: srgap2-deficient microglia were generated by crossing the inducible, microglia-specific Tmem119creErt2 mouse line with the srgap2f/f line (MG-Srgap2F/F mice), and inducing sgrap2 deletion by tamoxifen gavage at P8. WT mice (srgap2f/f mice) also received tamoxifen gavage.

extract_protocol:
Fresh cortices from ice-cold PBS-perfused anesthetized P30 mice were quickly homogenized made into a single-cell suspension by passing it through a 100 mm filter. Immune cells were isolated by centrifuging a brain homogenate on a 40% Percoll gradient at 2000 rpm for 5 min at 4ºC. Myelin and fat debris were removed, cells washed with PBS, and incubated (2% FBS in PBS) with the following antibodies for 30 min at 4ºC: CD11b-APC (1:200,Tonbo), CD45-APCCy7 (1:200 Tonbo), Cx3Cr1-PECy7 (1:200 Biolegend). After washing twice, microglia (~100,000 cells / cortex) were sorted directly into TRIzol (Thermo Fisher Scientific) as CD11b+, CD45low, CX3CR1+ cells on a Sony MA900 (SONY) sorter with a 100 mm microfluidic chip. TRIzol containing the cell lysates was mixed with chloroform at a 5/1 ratio, shaken and spun at 12,000 g for 15 min at 4ºC. Clear supernatant was transferred to a fresh tube and washed with 70% ethanol. RNA cleanup was performed on a RNeasy Mini (Qiagen) according to manufacturer instructions. RNA quantity and quality was assessed with a 2100 Bioanalyzer (Agilent).
cDNA Libraries were prepared from samples with >8.5 RIN using the NEBNext Ultra II RNA Library Prep quit, the NEBNext Poly(A) mRNA Magnetic Isolation beads, and the NEBNex Multiplex Oligos for Illumina (all New England Biolabs), all according to manufacturer’s instructions.

treatment_protocol: mice received two doses (75 ug/g BW) of tamoxifen at P8 and P10

value: mouse cortex

value: microglia

value: WT (Srgap2f/f)

value: Tamoxifen at P8


title: Case_001

description: Library name: NBO_001

value: primary cells

value: wt

value: Lentivirs


title: RNA-Seq siLMO2_3

city: Beijing

first: Yushu

last: Zou

address: 38 Xueyuan Rd

institute: Peking University

data_processing:
Chip-seq raw reads were mapped to the human genome hg19 using bowtie(1.1.2) with defult parameters. Chip peaks were called using danpos(2.2.2) with de significance cut off p-value <= 1e-10. BigWig files were generated using WigToBigWig tools.
RNA-seq raw reads were mapped to the human genome hg19 using Tophat(v.2.1.1) with default parameters. SAM/BAM file formats were transformed by samtools (0.1.19-44428cd). Expression value (number of raw reads) for each gene was determined by the software HTSeq version v.0.11.3 under the parameters --stranded=no and --mode= intersection-nonempty.  Normalized (the TMM method) expression values were determined by edgeR version 3.40.2 ran with an R version 4.2.2.
Assembly: hg19
Supplementary files format and content: For Chip-seq data, BigWig files were generated.
Supplementary files format and content: For RNA-Seq data, BigWig files and tab-delimited text files contian raw count values for each gene of each sample.

source_name: umbilical vein

extract_protocol:
ChIP-Seq: DNA and protein were cross-linked by 1% formaldehyde. Chromatin was isolated and sonicated into 100-300 bp fragments. Then the DNA-protein complex was precipitated with control IgG or antibodies against LMO2 overnight at 4°C followed by protein A/G conjugated magnetic beads for 1 hr. Cross-links were reversed to extract DNA. RNA-Seq: HUVECs cells (3.3×106) transfected with LMO2 or negative control siRNA for 72 hr were harvested. RNA was extracted using the FastPure cell/tissue total RNA isolation kit V2 (Vazyme, cat. RC112-01).
ChIP-Seq: 10 ng enriched DNA and input DNA were sent to Novogene for library preparation using the KAPA HTP library preparation kit and sequenced in Illumina NovaSeq 6000 to obtain 20 million read pairs per sample. RNA-Seq: RNA samples were submitted to Annoroad Gene Technology Corporation (Beijing) for library construction and sequencing. Briefly, following the RNA quality check, ribosomal RNA was removed using Epicentre Ribo-ZeroTM Gold  Kits. Then sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s manual.

value: umbilical vein

value: HUVEC

value: Human endothelial cell

value: LMO2 siRNA


title: ATAC, Paused, WT, rep 3

description:
Library name: Sample 15
WT_C

value: embryonic stem cells

value: Paused


title: N2 adult day 4, DMSO, rep 3, trial 2

description:
Library name: N2_4_DMSO_r3_tr2
N2_additional_controls.featureCounts.txt

value: whole worm


title: ATAC, Ctrl, WT, rep 2

description:
Library name: Sample 2
WT_B

value: Ctrl


title: N2 adult day 8, DMSO, rep 3, trial 3

description:
Library name: N2_8_DMSO_r3_tr3
N2_additional_controls.featureCounts.txt

value: adult day 8

value: WT


title: sorted cortical microglia, from WT control mice, rep2 (mouse 1101)

description:
Library name: WT_101.bam
Column name in "WT_vs_cKO.counts.csv" : 1101

value: mouse cortex


title: ATAC, Ctrl, WT, rep 1

description:
Library name: Sample 1
WT_A


title: RNA-Seq siLMO2_2


title: ATAC, Ctrl, Smad2_KO2, rep 1

description:
Library name: Sample 9
Smad2_KO_2A

value: KO


title: N2 adult day 8, DMSO, rep 2, trial 2

description:
Library name: N2_8_DMSO_r2_tr2
N2_additional_controls.featureCounts.txt

value: DMSO control


title: N2 adult day 4, DMSO, rep 2, trial 3

description:
Library name: N2_4_DMSO_r2_tr3
N2_additional_controls.featureCounts.txt

value: adult day 4


title: sorted cortical microglia, from WT control mice, rep1 (mouse 1058)

description:
Library name: WT_058.bam
Column name in "WT_vs_cKO.counts.csv" : 1058

value: microglia

value: WT (Srgap2f/f)

value: Tamoxifen at P8


title: RNA-Seq siLMO2_1

value: umbilical vein


title: N2 adult day 4, DMSO, rep 2, trial 2

description:
Library name: N2_4_DMSO_r2_tr2
N2_additional_controls.featureCounts.txt


title: RNA-Seq control_3

value: HUVEC

value: Negative control siRNA


title: L02 cells，Control，FFAs750μM，rep3

description:
Library name: Sample 3
Column name in ExpressionProfile.txt: Control_3

value: human embryonic hepatocytes


title: N2 adult day 4, DMSO, rep 4, trial 3

description:
Library name: N2_4_DMSO_r4_tr3
N2_additional_controls.featureCounts.txt


title: N2 adult day 4, DMSO, rep 1, trial 3

description:
Library name: N2_4_DMSO_r1_tr3
N2_additional_controls.featureCounts.txt


title: RNA-Seq control_2

value: Human endothelial cell


title: sorted cortical microglia, from MG-srgap2f/f mice, rep3 (mouse 1105)

description:
Library name: cKO_105.bam
Column name in "WT_vs_cKO.counts.csv" : 1105


title: Paused, rep 2

description:
Library name: Sample 6
Ink_B

treatment_protocol: To induce in vitro pausing, 200nM of the mTOR inhibitor INK128 was added to the culture medium for 24 hours.

value: embryonic stem cells

value: pausing conditions (200 nM INK128)


title: N2 adult day 4, DMSO, rep 1, trial 2

description:
Library name: N2_4_DMSO_r1_tr2
N2_additional_controls.featureCounts.txt

value: whole worm


title: sorted cortical microglia, from MG-srgap2f/f mice, rep2 (mouse 1062)

description:
Library name: ckO_062.bam
Column name in "WT_vs_cKO.counts.csv" : 1062


title: N2 adult day 2, DMSO, rep 4, trial 3

description:
Library name: N2_2_DMSO_r4_tr3
N2_additional_controls.featureCounts.txt

value: adult day 2


title: Paused, rep 1

description:
Library name: Sample 5
Ink_A

value: WT


title: sorted cortical microglia, from MG-srgap2f/f mice, rep1 (mouse 1060)

description:
Library name: cKO_060.bam
Column name in "WT_vs_cKO.counts.csv" : 1060

value: mouse cortex


title: N2 adult day 2, DMSO, rep 4, trial 2

description:
Library name: N2_2_DMSO_r4_tr2
N2_additional_controls.featureCounts.txt


title: ChIP-Seq LMO2

value: LMO2 antibody


title: Ctrl, rep 3

description:
Library name: Sample 3
Ctrl_C

value: control condition


title: N2 adult day 2, DMSO, rep 3, trial 3

description:
Library name: N2_2_DMSO_r3_tr3
N2_additional_controls.featureCounts.txt

value: DMSO control


title: Paraburkholderia busanensis P39 exposed to Colletotrichum scovillei fungal biomass, biological replicate 3

first: Young-Su

last: Seo

address: Geumjeong-Gu

department: Microbiology

institute: Pusan National University

description:
Library name: P39_CS_3
P39 exposed to C. scovillei KC05 fungal biomass; biological replicate 3

data_processing:
Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1468790 and the sample-specific SRR accessions listed in this metadata file.
Reads were aligned to the Paraburkholderia busanensis P39 reference genome represented by GenBank accessions CP058248 and CP058249.
Gene-level raw count data contained 6,805 genes across six samples.
Genes with a zero count in at least one of the six samples were excluded before statistical testing, leaving 5,256 genes for downstream analysis.
Read count data were normalized using Relative Log Expression normalization in DESeq2. Regularized log transformation and log2(count+1) values were used for visualization and quality assessment.
Differential expression between P39_CS and P39 was tested using DESeq2 nbinomWaldTest. Significant genes were identified using |fold change| >= 2 and raw p-value < 0.05.
Hierarchical clustering was performed using Euclidean distance and complete linkage.
Assembly: Paraburkholderia busanensis P39 genome, GenBank accessions CP058248 and CP058249.
Supplementary files format and content: P39_RNAseq_raw_counts_matrix.txt is a tab-delimited matrix containing gene identifiers, annotation columns, and raw read counts for all six samples. Sample columns are named P39_1, P39_2, P39_3, P39_CS_1, P39_CS_2, and P39_CS_3.
Supplementary files format and content: P39_RNAseq_FPKM_matrix.txt is a tab-delimited matrix containing gene identifiers, annotation columns, and FPKM values for all six samples.
Supplementary files format and content: P39_RNAseq_RLE_normalized_counts_matrix.txt is a tab-delimited matrix containing gene identifiers, gene symbols, and RLE-normalized count values for all six samples.
Supplementary files format and content: Gene features are traceable by locus/gene identifiers and chromosome coordinates in the processed matrices, with reference genome accessions CP058248 and CP058249.

organism: Paraburkholderia busanensis

source_name: bacterial cells

growth_protocol: Paraburkholderia busanensis P39 was cultured under laboratory conditions for RNA-seq analysis. Samples consisted of P39 grown alone and P39 exposed to Colletotrichum scovillei KC05 fungal biomass, with three biological replicates per condition.

extract_protocol:
Total RNA was isolated from each bacterial sample and quality-checked before library preparation for transcriptome sequencing by Macrogen.
Paired-end RNA-seq libraries were constructed and sequenced by Macrogen on an Illumina HiSeq 4000 platform.

treatment_protocol: For the P39_CS condition, Paraburkholderia busanensis P39 was exposed to fungal biomass of Colletotrichum scovillei KC05 before RNA extraction. The P39 control condition was grown without fungal biomass exposure.

value: bacterial cells

value: wild type

value: exposure to Colletotrichum scovillei KC05 fungal biomass


city: Taipei

first: Yi-Ru

last: Tseng

address: No. 201, Sec. 2, Sh ipai Rd.

institute: Taipei Veterans General Hospita

description:
Library name: MCF7_2h_Ser5
MCF7 treated with PIK75 for 2 hr ChIP CTD-Ser5

data_processing:
ChIP-seq reads were trimmed using CLC Genomics Workbench 25.0.1 (Trim Reads 3.0) with quality trimming (quality limit = 0.01), ambiguous base trimming (maximum ambiguities = 2), and automatic adapter trimming using the TruSeq Trim Adapter List.
Reads were mapped to Homo sapiens (GRCh38.p14) with Map Reads to Reference 2.0, duplicate reads were removed using Remove Duplicate Mapped Reads 0.3, and peak calling was performed using Transcription Chip-Seq 2.0 and Histone Chip-Seq 0.14 with the parameters described above.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: MCF-7 and T-47D were treated with DMEM/F12 and RPMI 1640 medium,   supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Cell were fixed with 1% paraformaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico sonication device
ChIP-seq

value: breast

tag: chip antibody

value: CTD Ser-5 (Merck Millipore, 04-1572)


title: Ctrl, rep 2

description:
Library name: Sample 2
Ctrl_B


title: Grp10, mCherry quartile sort, lower quartile

city: Cleveland

first: Kenneth

last: Matreyek

state: Ohio

address: 2103 Cornell Rd, Room 5104

department: Pathology

institute: Case Western Reserve University

description: Library name: Grp10, eeBxb1, mCherry bin 1

data_processing:
DNA was sequenced using a NextSeq 550 Mid output (130 million reads) 150 cycle kit (Illumina) at the Case Western Reserve University Genomics Core Facility
Reads were converted to fastq format and demultiplexed by the Case Western Reserve University Genomics Core Facility.  Paired-end reads were combined using PEAR (PMC3933873) using default statistical settings.
Each paired end read was tested for exact matches from the expected library and included as a read for the appropriate library member if applicable.  Read count relative to total number of reads in the sample was used to calculate read frequency for each expected library member.
Read frequencies for quartiles from the same fluorophore sort and the same group were used to calculate a weighted average Sort-Seq score for each fluorophore for expected library member.  Scores were averaged across groups to provide a final Sort-Seq score for each expected library member.  The Sort-Seq scores were used for further analysis in the manuscript.
Assembly: Synthetic Sequences
Supplementary files format and content: "processed_data_counts_frequencies.csv" is a comma separated values data table containing read counts and read frequencies for all observed DNA sequences (library_sequence, column 1).  Each row represents a DNA sequence of interest, and each column represents either a read count ("_counted") or a read frequency ("_freq") for each sample ("IXXXX", corresponding with IXXXX from file names as described in SAMPLES section).

organism: synthetic construct

growth_protocol: DMEM with 10% FBS, 1 % Penicillin / Streptomycin, and 2 ug/mL doxycycline.

extract_protocol:
Genomic DNA was extracted using a Dneasy Blood and Tissue Kit (Qiagen, 69506) and DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265)
Extracted genomic DNA was used as a template to produce a 1564 nucleotide amplicon spanning the genomic integration junction.  Samples were run with gel electrophoresis, the appropriate band was extracted using a Bio-Rad Freeze 'N Squeeze DNA Gel Extraction Spin Column (Bio-Rad, 7326165) and cleaned using a Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4004).  The resulting DNA was used as the template for to produce a 299 nudleotide amplicon surrounding the DNA sequence of interest using distinct indices for each quartile to be run on the same Illumina NextSeq 550 kit run.  Samples were again run with gel electrophoresis, extracted, and cleaned.  DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265).  DNA amplicons were pooled to a final concentration of 10-20ng/uL in 21uL of nuclease free water using 15-20ng of DNA from each quartile prior to running the Illumina NextSeq 550 kit.

value: Cultured Cells

value: Recombination into


title: MCF7 treated with DMSO ChIP CTD-Ser5

description:
Library name: MCF7_DMSO_Ser5
MCF7 treated with DMSO ChIP CTD-Ser5

value: DMSO


title: Paraburkholderia busanensis P39 exposed to Colletotrichum scovillei fungal biomass, biological replicate 2

description:
Library name: P39_CS_2
P39 exposed to C. scovillei KC05 fungal biomass; biological replicate 2


title: Muscle, Individual 7, Summer (N2)

city: Santiago

first: Rorigo

last: Maldonado

address: Avenida Pedro de Valdivia 1509

country: Chile

institute: Universidad Finis Terrae

description: Library name: sm_7_N2

library_source: other

data_processing:
Processed data files were generated from raw small RNA sequencing reads following standard quality control and preprocessing steps. Raw FASTQ files provided at the lane level were concatenated per sample, and only read 1 (R1) files were retained, as small RNA inserts are fully contained within R1 reads.
Assembly: https://doi.org/10.6084/m9.figshare.28726535.v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include raw counts for each Sample

molecule: other

organism: Orestias ascotanensis

source_name: Muscle

growth_protocol: Specimens were collected from the Ascotan Salt Pan (21°29'46.5"S 68°15'26.3"W) at an elevation of 3,740 meters above sea level in July 2019 (n=7) and January 2020 (n=7) using a fishing net. Euthanasia was performed by administering an overdose of tricaine methanesulphonate (MS-222, 500 mg L−1; Sigma-Aldrich). Tissue samples from gills, skin, and muscle were harvested on-site. Each tissue sample was individually preserved in RNAlater (Invitrogen) immediately after dissection to stabilize and protect RNA. The samples were transported on ice to the laboratory and subsequently stored at -80°C until RNA extraction.

extract_protocol:
For small RNA sequencing, total RNA samples were enriched for short RNA species by size selection using denaturing polyacrylamide gel electrophoresis on Novex™ TBE–Urea gels (Invitrogen) run in TBE Running Buffer (LC6675). Gel fragments corresponding to the expected size range of small RNAs, including mature microRNAs, were excised and purified.
Small RNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina, 15016911) according to the manufacturer’s instructions. Libraries were sequenced by Quick Biology (Pasadena, CA, USA) on an Illumina NextSeq 500 platform using paired-end 75 bp reads. Although paired-end sequencing was performed, only read 1 (R1), which fully covers the mature small RNA insert, was used for downstream analyses.

value: Muscle

value: summer


title: Gills, Individual 7, Summer (N2)

description: Library name: sg_7_N2

source_name: Gills

value: Gills


title: MCF7 treated with PIK75 for 24 hr ChIP PolII

description:
Library name: MCF7_24h_PolII
MCF7 treated with PIK75 for 24 hr ChIP PolⅡ

value: Pol II (Cell Signaling Technology, #2629)


title: Control_H3K27ac_replicate2

city: New York

first: Norihiro

last: Goto

address: 413 East 69th Street

institute: Weill Cornell Medicine

description:
Library name: Control_H3K27ac_2
Control_H3K27ac

data_processing:
Paired-end sequencing reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were sorted and merged using Samtools.
Peaks were called using SEACR
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: H3K27ac_peak_counts.txt.gz is a tab delimited text of counts for filtered peaks
Library strategy: CUT&Run

source_name: Colon cancer organoids

extract_protocol:
Organoids were dissociated using TrypLE Express for 10 min at 37 °C, filtered through a 40 μm cell strainer, and 500,000 cells were collected, centrifuged, and washed twice with PBS. H3K27ac CUT&RUN libraries were prepared using the CUTANA CUT&RUN kit (EpiCypher, 14-1048) according to the manufacturer’s instructions.
CUT&RUN libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. Paired-end sequencing was performed on an Illumina NextSeq 2000.

value: Colon cancer organoids

tag: recipient mice

value: AKP


title: Paraburkholderia busanensis P39 exposed to Colletotrichum scovillei fungal biomass, biological replicate 1

description:
Library name: P39_CS_1
P39 exposed to C. scovillei KC05 fungal biomass; biological replicate 1


title: N2 adult day 2, DMSO, rep 2, trial 2

city: Eugene

first: Patrick

last: Phillips

address: 5289 University of Oregon

institute: University of Oregon

description:
Library name: N2_2_DMSO_r2_tr2
N2_additional_controls.featureCounts.txt

data_processing:
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in single-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 108)
Supplementary files format and content: Tab-delimited tables of raw gene counts for every gene and sample, for (1) two-group comparisons in wild type at each age, (2) additional wild type control series, and (3) skn-1 and daf-16 mutants at two ages.

source_name: whole worm

extract_protocol:
Worms were picked into 0.2 mL tubes containing 45 µL lysis buffer, 4 µL RNA-secure, 5 µL proteinase K and flash frozen with liquid nitrogen.
Libraries were prepared using the KAPA mRNA HyperPrep kit (KK8580 from Kapa Biosystems) as per manufacture protocol except that the total volume was adjusted to 1/4 per reaction.

value: whole worm

value: adult day 2

value: WT


title: Gills, Individual 6, Summer (N2)

description: Library name: sg_6_N2


title: MCF7 treated with PIK75 for 2 hr ChIP PolII

description:
Library name: MCF7_2h_PolII
MCF7 treated with PIK75 for 2 hr ChIP PolⅡ


title: Paraburkholderia busanensis P39 grown alone, biological replicate 3

description:
Library name: P39_3
P39 grown alone; biological replicate 3

value: bacterial cells


title: Pool 1-12

city: Cambridge

first: John

last: Xu

address: biomedical campus

country: United Kingdom

institute: Cambridge

description: Library name: UPX_003

data_processing:
The cleaned reads were aligned to the mouse/ rat reference genome using the star aligner (v2.7.10a) within a Singularity container, against Rattus_norvegicus.Rnor_6.0.102.gtf  and Mus_musculus.GRCm39.104. star was run with default parameters and the --quantMode TranscriptomeSAM option enabled, which produces transcriptome-aligned reads for downstream quantification. Gene- and transcript-level expression was quantified using rsem (v1.3.3). rsem was executed in paired-end mode with the star transcriptome-aligned reads as input, generating both raw read counts and normalized expression values (transcripts per million, TPM). Quality control reports from all steps (fastqc, trimmomatic (RRID:SCR_011848), star, and rsem) were aggregated using MultiQC to provide a comprehensive overview of data quality. Finally, downstream analyses—including differential expression testing, pathway enrichment analysis, unsupervised clustering, and data visualization—were performed using the OmicsPlayground platform (v2.8.19) with an FDR = 0.05. Gene expression values were normalized to counts per million and log-transformed for comparison across samples. Heatmaps were generated using Heatmapper (). MCL clustering (inflation parameter = 1.5) and DBSCAN clustering (epsilon = 15) were generated using string V.12.0 (www.string-db.org) (RRID:SCR_005223).
Transcript abundance quantification and normalization were performed across all experimental groups and presented in Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Assembly: Rattus_norvegicus.Rnor_6.0.102.gtf
Supplementary files format and content: raw_counts

source_name: Rat microglia nuclei

growth_protocol: Primary rat microglia were maintained in microglial culture media under standard humidified conditions at 37 °C with 5% CO₂, with in defined microglia culture medium consisting of DMEM/F12 supplemented with N2, 1 mM sodium pyruvate, 50 µg ml⁻¹ insulin, 3 mg ml⁻¹ N-acetylcysteine, 1.5 µg ml⁻¹ cholesterol, macrophage colony-stimulating factor (mCSF; 20 ng ml⁻¹ for rat, 100 ng ml⁻¹ for human) and transforming growth factor-β (TGFβ; 2 ng ml⁻¹ for rat, 5 ng ml⁻¹ for human), with optional penicillin–streptomycin. Feeding experiments were performed the day after seeding.

extract_protocol:
Nuclear RNA was isolated from primary rat microglial subcellular fractions following feeding conditions using Trizol and phenol-chloroform extraction. mRNA was subsequently purified using the PureLink RNA Mini Kit (Thermo Fisher Scientific, 12183018) with on-column DNase treatment. RNA samples underwent post-DNase digestion to minimize genomic DNA contamination prior to library preparation. RNA integrity and concentration were assessed using the RNA ScreenTape system (reagent: Agilent, #5067-5577, RNA ScreenTape: Agilent, 5067-5576, TapeStation: 4200 TapeStation System, Agilent) and NanoDrop spectrophotometry. Only high-quality RNA (RNA integrity number (RIN) > 7) was used for downstream applications.
RNA libraries were prepared from purified nuclear RNA using ERCC RNA Spike-In Mix controls using QIAseq® UPXome Low Input Kit (334705) and sequenced on the Illumina NovaSeq platform (SP flow cell configuration) using paired-end 150 bp sequencing read configuration.  UPX-002 ACCAGACTTG-CGATGAGCAC No Depletion pool UPX-003 ACTGGCGAAC-GATAAGTCGA Pool 1 1-12 UPX-004 GCGTTAGGCA-TCACGCCTTG Pool 2 13-24 UPX-005 TTATCGGCCT-AGGAACACAA Pool 3 25-35

treatment_protocol: Primary rat microglia were exposed to purified myelin debris, Pellet 1 fractions (brain tissue devoid of myelin), or control media conditions prior to nuclear RNA isolation. Experimental groups included: (1) myelin-fed rat microglia nuclei RNA (MN), (2) control rat microglia nuclei RNA (CN), (3) myelin-fed rat microglia cytoplasm RNA (MC), (4) control rat microglia cytoplasm RNA (CC), (5) input myelin RNA (MO/ MO+; ribosomal depletion and no depletion runs), and (6) Pellet 1-fed rat microglia nuclei RNA (PN), (7) Pellet 1-fed rat microglia cytoplasm RNA (PC) and (8) Pellet 1 RNA (P1).

value: Rat microglia nuclei

value: Myelin-fed


title: N2 adult day 2, DMSO, rep 1, trial 3

description:
Library name: N2_2_DMSO_r1_tr3
N2_additional_controls.featureCounts.txt

value: DMSO control


title: MCF7 treated with DMSO ChIP PolII

description:
Library name: MCF7_DMSO_PolII
MCF7 treated with DMSO ChIP PolⅡ

value: breast


title: Paraburkholderia busanensis P39 grown alone, biological replicate 2

description:
Library name: P39_2
P39 grown alone; biological replicate 2

value: wild type


title: Pool 13-24

description: Library name: UPX_004


title: T47D treated with PIK75 for 24 hr ChIP PolII

description:
Library name: T47D_24h_PolII
T47D treated with PIK75 for 24 hr ChIP PolⅡ

value: Pol II (Santa Cruz Biotechnology, sc-899)


title: Pool 25-35

description: Library name: UPX_005