title: T-47D DSG2 KO#1, xenograft, animal 4197

city: Brno

first: Ondřej

last: Vacek

email: vacek@ibp.cz, ooondra.vacek@gmail.com

address: Královopolská 135

department: Department of Cytokinetics

country: Czech Republic

institute: Institute of Biophysics of the Czech Academy of Science

description:
Library name: OV-4197-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO1_tumors_vs_WT.tsv

data_processing:
Raw reads were quality checked (FastQC, MultiQC, minion, swan), preprocessed (Trimmomatic, FastQC, MultiQC) and mapped (STAR, Samtools, MultiQC) to the reference genome with gene annotation (genome version: GRCh38-p10). Mapped reads were counted and summarized to genes with featureCounts, Salmon in alignment mode and only uniquely mapped and uniquely assigned reads were counted. The following checks were performed to estimate the overall sample quality: rRNA content estimate (fastq_screen), Read duplication rate (dupRadar, Picard tools), Sequenced (targeted) regions (RSeQC, Picard tools), 5’/3’ coverage bias (Picard tools), Expressed gene biotypes (featureCounts), and Library strandness (RSeQC).
Assembly: GRCh38-p10
Supplementary files format and content: tab delimited text fime contains following data: Ensembl_Id, baseMean, log2FoldChange, lfcSE, pvalue, padj, significant_DE, Feature_name, biotype, stat, normCounts, raw Counts
Supplementary files format and content: Processed data are organized in seven files according to comparisions: DSG2 KO cells (clone #1+#2) vs DSG2 WT cells, DSG2 KO#1 KO cells vs DSG2 WT cells, DSG2 KO#2 cells vs DSG2 WT cells, DSG2 KO xenografts (clone #1+#2) vs  WT xenografts, DSG2 KO#1 xenografts vs  WT xenografts, DSG2 KO#2 xenografts vs  WT xenografts, Trop-2 KO xenografts vs WT xenografts

source_name: xenograft, breast tumor

growth_protocol: In vitro T-47D cell line (ATCC) and derived clones were cultured in RPMI 1640 (Gibco, TFS) supplemented with 5 μg/ml insulin (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany).  Cell lines were cultured in sterile conditions and were supplemented with 10% fetal bovine serum (Gibco, TFS) and 1% Penicillin/Streptomycin (Biosera, Nuaille, France). In vivo -  1×10^6 cells from T-47D clones were injected (suspension in PBS) into the fourth mammary fat pad of immunodeficient 6- to 8-week-old female NOD.Cg-Rag1tm1Mom Il2rgtm1Wjl/SzJ mice. T-47D Trop-2 KO cells grew for 18 weeks, T-47D DSG2 KO experiment ran for 10 weeks. Two days before cell implantation, the animals were treated subcutaneously with β-Estradiol 17-Valerate (Sigma-Aldrich, Merck KGaA) at a concentration of 1 μg per animal in 50 μl of peanut oil. Supplementation was continued twice a week throughout the study.

extract_protocol:
RNA was isolated from either 1x106 cells or 5-15 mg of tissue using the RNeasy Mini Kit for RNA isolation (Qiagen, Hilden, Germany). 400 ng of total RNA was used as input for library preparation.
Library was prepared using QuantSeq 3′ mRNA-Seq FWD with UDI 12 nt Kit (v.2) (Lexogen, Vienna, Austria) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD. Library quantity and size distribution was checked using the QuantiFluor dsDNA System (Promega) and the High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies).

treatment_protocol: Cell lines in vitro were supplemented with with 5 μg/ml insulin, animals with growing tumors were supplemented with β-Estradiol 17-Valerate (Sigma-Aldrich, Merck KGaA) at a concentration of 1 μg per animal in 50 μl of peanut oil. All treatments were applied on all experimental groups to enhance the ability of cells to expand.

value: xenograft, breast tumor

value: breast cancer cell line

tag: genotype

value: DSG2 KO

tag: animal model

value: NRG female mouse; Mammary fat pad tumor


title: Aged Mlkl-/- HSC, ATAC-seq, rep2

status: Public on Feb 10 2026

type: SRA

city: Memphis

first: Masayuki

last: Yamashita

state: TN

address: 262 Danny Thomas Place

department: Division of Experimental Hematology, Department of Hematology

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: Aged_Mlkl-/-_Rep2

library_source: genomic

data_processing:
Sequencing reads were mapped to the mouse reference genome (mm10) with Bowtie2 (v2.5.3).
Peaks were called with MACS2 (v2.2.7.1) using the nomodel function and a q-value cutoff of 0.001.
All called peaks overlapping by at least one base pair were merged using bedtools (v2.31.0) merge to generate a comprehensive peak catalog.
Reads at each peak in the catalog were quantified with the bedtools map function.
Differentially accessible regions were detected using edgeR (v3.30.3).
Assembly: mm10
Supplementary files format and content: BED file containing peak summits for each sample.
Supplementary files format and content: BigWig file providing signal tracks for visualization across the genome.

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630). Nuclei were spun down and immediately subjected to the transposase reaction.
Nuclei were incubated in transposase reaction mix consisting of Tagment DNA buffer (Illumina) and Tagment DNA enzyme (Illumina). Transposed fragments were purified with MinElute PCR Purification Kit (QIAGEN). Libraries were amplified using NEBNext High Fidelity 2×PCR Master Mix (New England Biolabs) with index primers, size-selected between 240 and 360 base pairs by using BluePippin (Sage Science), and sequenced on a NextSeq500 (Illumina) with 70 bp single-read length.

tag: tissue

value: bone marrow

tag: strain

tag: cell type

value: hematopoietic stem cell

value: Mlkl-/-

tag: age

value: 18 months old


title: T-47D DSG2 KO#1, xenograft, animal 4113

description:
Library name: OV-4113-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO1_tumors_vs_WT.tsv

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: control 3

city: shanghai

first: ling

middle: ling

last: xu

address: tianlin street

country: China

institute: shanghai jiaotong university

description: Library name: Sample 3

data_processing:
Data quality control Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.New transcript prediction Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster.
Quantification of gene expression levels Use featureCounts v1.6.2 to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels.
Difference analysis DESeq2 v1.22.1 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Differential gene enrichment analysis The enrichment analysis is performed based on the hypergeometric test. For KEGG, the hypergeometric distribution test is performed with the unit of pathway; for GO, it is performed based on the GO term.GSEA Use gsea--3.0.jar for gene set enrichment analysis.
Assembly: mm10
Supplementary files format and content: gene fpkm files

source_name: heart

growth_protocol: The mouse MIRI model was established as previously reported45. Briefly, after mice were anesthetized by inhalation using 3% isoflurane (1 L/min), an incision (≈2 cm) was made with sterile scissors at the thoracic location of the mice where the heartbeat was most intense. A 4-0 purse-string suture was created, and the thorax above the heart was bluntly dissected through the fourth intercostal space using curved forceps. The chest was lightly pressed to squeeze out the heart from the chest cavity and position the heart in the sutured opening. At this time, it was ensured that there was as little air in the chest cavity as possible. A 6-0 surgical suture was used to tie a surgical slipknot on the left anterior descending coronary artery, with one end of the suture being exposed outside the chest. The heart was immediately placed back into the chest cavity, with the excess air expelled, and the epidermis was sutured closed. After 45 minutes, the slipknot for cardiac reperfusion was opened. Surgical wounds were sutured using sterile 5-0 sutures, and the mice were returned to the rearing cage for continued feeding.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) .RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Mice were divided into four groups: Sham group, MIRI group, MIRI+PB group, and MIRI+PB@PM group. Next, 0.5mg/kg PB or PB@PM (containing 0.5mg/kg PB) was administrated via the tail vein to the corresponding group at 1 hour and 24 hours after reperfusion, and the equal amount of 0.9% saline was applied to the Sham and MIRI groups.

value: heart

value: cardiomyocyte

tag: treatment

value: total RNA


title: Mouse H3K27acCUT&Tag WT, Rep2

city: Los Angeles

first: Jeong Hyun

last: Ji

state: CA

address: 615 Charles E Young Dr S, Rm 247

institute: University of California, Los Angeles

description: Library name: Mouse_H3K27acCUT_Tag_WT_Rep2

data_processing:
FastQC (v0.12.0), Trimmomatic (v0.39), and Bowtie2 (v2.5.4)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: NK cells

extract_protocol:
Nuclei were harvested using nuclear extraction buffer (20mM HEPES, 10mMKCl, 0.1% Triton X-100, 20% glycerol, protease inhibitor [Sigma 11836170001], 0.5mM spermidine)
CUT&Tag libraries were constructed as previously described in Cheng et al., 2023.

value: NK cells

value: WT


title: Aged WT HSC, ATAC-seq, rep2

description: Library name: Aged_WT_Rep2


title: T-47D DSG2 KO#2, xenograft, animal 4121

description:
Library name: OV-4121-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO2_tumors_vs_WT.tsv


title: Aged WT HSC, ATAC-seq, rep3

description: Library name: Aged_WT_Rep3


title: Young Mlkl-/- HSC, ATAC-seq, rep3

description: Library name: Young_Mlkl-/-_Rep3

value: 3 months old


title: Young Mlkl-/- HSC, ATAC-seq, rep2

description: Library name: Young_Mlkl-/-_Rep2


title: Aged WT HSC, ATAC-seq, rep1

description: Library name: Aged_WT_Rep1


title: Basal culture (Lane 1-4)

city: Thuwal

first: Xabier

last: Martinez de Morentin

address: Kaust

country: Saudi Arabia

institute: KAUST

description: Library name: rna_fastq_basal

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and UMI counting performed with 10x Genomics Cell Ranger 3.0.1 (scRNA-seq). Reads aligned to GRCh38 using STAR. Quality filtering: cells with <3,250 counts or <1,500 features removed; genes expressed in <3 cells removed; mitochondrial reads ≥10% removed. Doublets removed using DoubletFinder (7.5% estimated rate).
Assembly: Human genome reference GRCh38 (Ensembl).
Supplementary files format and content: scRNA-seq: counts matrices (.mtx), barcodes (.csv), gene/features (.csv). scATAC-seq: cistopic_obj (.pkl)

molecule: polyA RNA

source_name: Brain

growth_protocol: NPCs derived from XCL1 DCXpGFP were cultured on CellMatrix Basement Membrane Gel coated plates in NPC expansion medium (DMEM/F-12 supplemented with Growth Kit for Neural Progenitor Cell Expansion). Cells were incubated at 37°C with 5% CO₂, seeded at 0.30 ×10⁶ per well for expansion, and 8×10⁴ cells/cm² for differentiation.

extract_protocol:
Cells were harvested by Accutase detachment, washed with DPBS, and centrifuged at 13,000 rpm. Cell pellets were resuspended in 0.05% BSA in PBS. Dead cells were stained with TO-PRO-3 and viable cells were sorted using MoFlo Astrios EQs based on negative TOPRO-3 signal.
scRNA-seq: 10x Genomics NEXTGEM Single Cell 3’ v3.1 Kit; cells loaded at 500–1,000 cells/µL on Chromium Controller to generate GEMs. cDNA synthesized, PCR-amplified, fragmented, end-repaired, A-tailed, and ligated to Illumina adapters. Libraries indexed and quality-controlled with Qubit and TapeStation. Sequencing on NextSeq500 (Read1:28 cycles, Read2:55 cycles, i7 index: 8 cycles). scATAC-seq: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, following 10x Genomics protocol.

treatment_protocol: For control, differentiation medium was added from Day 1 to Day 20. For disease condition, Aβ 1-42 peptide (50 nM) was added concurrently with differentiation medium from Day 1, with medium changes every 2–3 days. Cells were harvested at Days 0, 7, 13, and 20.

value: Brain

value: XCL1 DCXpGFP


title: T-47D DSG2 KO#2, xenograft, animal 4133

description:
Library name: OV-4135-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO2_tumors_vs_WT.tsv


title: Mouse H3K27acCUT&Tag WT, Rep1

description: Library name: Mouse_H3K27acCUT_Tag_WT_Rep1


title: Young Mlkl-/- HSC, ATAC-seq, rep1

description: Library name: Young_Mlkl-/-_Rep1


title: Mouse H3K27acCUT&Tag Fli1 KO, Rep3

description: Library name: Mouse_H3K27acCUT_Tag_Fli1KO_Rep3

value: Fli1 KO


title: Young WT HSC, ATAC-seq, rep1

description: Library name: Young_WT_Rep1


title: Mouse H3K27acCUT&Tag Fli1 KO, Rep2

description: Library name: Mouse_H3K27acCUT_Tag_Fli1KO_Rep2


title: T-47D DSG2 KO#1, xenograft, animal 4111

description:
Library name: OV-4111-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO1_tumors_vs_WT.tsv

value: xenograft, breast tumor


title: T-47D DSG2 KO#2, xenograft, animal 4135

description:
Library name: OV-4133-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO2_tumors_vs_WT.tsv

value: breast cancer cell line


title: Aged Mlkl-/- HSC, ATAC-seq, rep1

description: Library name: Aged_Mlkl-/-_Rep1


title: T-47D DSG2 KO#2, xenograft, animal 4134

description:
Library name: OV-4134-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv
DESeq2-DSG2KO2_tumors_vs_WT.tsv

value: DSG2 KO


title: Mouse H3K27acCUT&Tag WT, Rep3

description: Library name: Mouse_H3K27acCUT_Tag_WT_Rep3


title: Young WT HSC, ATAC-seq, rep2

description: Library name: Young_WT_Rep2


title: E13.5 SRSF3 mutant

city: Oxford

first: Andia

middle: Nicole

last: Redpath

address: IDRM IMS-Tetsuya Nakamura Building, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

description:
FACS sorted Wt1CreERT2;Srsf3fl/fl ;tdTomato+ve cells
e13.rds

data_processing:
NextSeq500 sequencing
The data was aligned to the mm10 genome with the tdtomato gene added. STAR (v.2.3.3a) with Gencode (v.M16) annotations used to map the SMART-Seq2 data. CellRanger was used for cell calling and mapping the 10x Genomics data.
Seurat3 for normalisation and clustering
Assembly: mm10
Supplementary files format and content: e13.rds is a Seurat Object that contains E13 samples. Dimensionsional reduction pca = 50.
Supplementary files format and content: e13mutant_epi.rds is a Seurat Object that contains E13 mutant epi subcluster. Dimensionsional reduction pca = 50.
Supplementary files format and content: e15.rds is a Seurat Object that contains E15 samples. Dimensionsional reduction cca = 30.

source_name: epicardium/epicardium-derived cells

extract_protocol:
Hearts were dissociated using the Neonatal Heart Dissociation Kit from Miltenyi Biotech.
E13.5 scRNA-seq libraries were produced using the 10x Genomics Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3, E15.5 scRNA-seq libraries were produced using the SMART-Seq2 protocol.

tag: processing

value: 10X Genomics


title: E13.5 control

description: FACS sorted Wt1CreERT2;Srsf3+/+ ;tdTomato+ve cells


title: Mouse H3K27acCUT&Tag Fli1 KO, Rep1

description: Library name: Mouse_H3K27acCUT_Tag_Fli1KO_Rep1


title: T-47D Trop-2 KO, xenograft, animal 2807

description:
Library name: OV-2807-RNA
DESeq2-Trop2KO_tumors_vs_WT.tsv

value: TACSTD2 (Trop-2) KO

value: NRG female mouse; Mammary fat pad tumor


title: E15.5 SRSF3 mutant

description: FACS sorted Wt1CreERT2;Srsf3fl/fl ;tdTomato+ve cells


title: Mouse Fli1CUT&Tag WT, Rep3

description: Library name: Mouse_Fli1CUT_Tag_WT_Rep3


title: T-47D Trop-2 KO, xenograft, animal 2818

description:
Library name: OV-2818-RNA
DESeq2-Trop2KO_tumors_vs_WT.tsv


title: Aged Mlkl-/- HSC, RNA-seq, rep2

description: Library name: Aged_Mlkl-/-_Rep2

data_processing:
Data quality was verified using FastQC (v0.12.0).
Demultiplexing was performed with bcl2fastq (v2.20).
Sequencing reads were mapped to the mouse reference genome (mm10) with HISAT2 (v2.2.1) and quantified with StringTie (v2.2.3).
Normalization and pairwise differential expression analyses were performed using edgeR (v3.30.3).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN) following the manufacturer's instructions.
Double-stranded cDNA was generated using SMART-Seq HT Kit (Takara Bio) and fragmented using M220 Focused ultrasonicator (Covaris). Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit (New England Biolabs). Different index primers were used for multiplexing samples in one lane, and pooled libraries were sequenced on NextSeq2000 (Illumina) with single-read 70 base pairs.

value: bone marrow

value: hematopoietic stem cell

value: Mlkl-/-


title: Mouse Fli1CUT&Tag WT, Rep2

description: Library name: Mouse_Fli1CUT_Tag_WT_Rep2


title: T-47D Trop-2 KO, xenograft, animal 2817

description:
Library name: OV-2817-RNA
DESeq2-Trop2KO_tumors_vs_WT.tsv


title: Aged Mlkl-/- HSC, RNA-seq, rep1

description: Library name: Aged_Mlkl-/-_Rep1

value: 18 months old


title: T-47D WT, xenograft, animal 2810

description:
Library name: OV-2810-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv


title: Aged WT HSC, RNA-seq, rep4

description: Library name: Aged_WT_Rep4


title: Aged WT HSC, RNA-seq, rep1

description: Library name: Aged_WT_Rep1


title: Aged Mlkl-/- HSC, RNA-seq, rep3

description: Library name: Aged_Mlkl-/-_Rep3


title: Aged WT HSC, RNA-seq, rep2

description: Library name: Aged_WT_Rep2


title: T-47D Trop-2 KO, xenograft, animal 2815

description:
Library name: OV-2815-RNA
DESeq2-Trop2KO_tumors_vs_WT.tsv


title: Aged Mlkl-/- HSC, RNA-seq, rep4

description: Library name: Aged_Mlkl-/-_Rep4


title: Young Mlkl-/- HSC, RNA-seq, rep3

description: Library name: Young_Mlkl-/-_Rep3


title: Aged WT HSC, RNA-seq, rep3

description: Library name: Aged_WT_Rep3


title: T-47D WT, xenograft, animal 2812

description:
Library name: OV-2812-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv


title: Mouse Fli1CUT&Tag Fli1 KO, Rep3

description: Library name: Mouse_Fli1CUT_Tag_Fli1KO_Rep3


title: Mouse Fli1CUT&Tag Fli1 KO, Rep1

description: Library name: Mouse_Fli1CUT_Tag_Fli1KO_Rep1


title: Mouse ATACseq NTC, Rep3

description: Library name: Mouse_ATACseq_NTC_Rep3

data_processing:
FastQC (v0.12.0), Trimmomatic (v0.39), and Bowtie2 (v2.5.4)
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were harvested using ATAC Lysis Buffer (Zymo).
ATAC libraries were constructed using the Zymo-Seq ATAC Library kit following manufacturer's instructions.

value: NTC


title: Young Mlkl-/- HSC, RNA-seq, rep2

description: Library name: Young_Mlkl-/-_Rep2


title: T-47D DSG2 KO#2, cell line, rep3

description:
Library name: OV-13D-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv
DESeq2-DSG2KO2_cells_vs_DSG2WT.tsv

source_name: in vitro cell culture

value: in vitro cell culture


title: T-47D WT, xenograft, animal 2808

description:
Library name: OV-2808-RNA
DESeq2-DSG2KO_tumors_vs_WT.tsv

value: WT


title: Mouse ATACseq NTC, Rep2

description: Library name: Mouse_ATACseq_NTC_Rep2

value: NK cells


title: Young Mlkl-/- HSC, RNA-seq, rep1

description: Library name: Young_ Mlkl-/-_Rep1

value: 3 months old


title: Young WT HSC, ATAC-seq, rep3

description: Library name: Young_WT_Rep3


title: Mouse Fli1CUT&Tag Fli1 KO, Rep2

description: Library name: Mouse_Fli1CUT_Tag_Fli1KO_Rep2


title: Young WT HSC, RNA-seq, rep2

description: Library name: Young_WT_Rep2


title: Young WT HSC, RNA-seq, rep1

description: Library name: Young_WT_Rep1


title: Young WT HSC, RNA-seq, rep3

description: Library name: Young_WT_Rep3


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate9

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl9
2x100bp

data_processing:
see scEdU-seq (Nature Methods, 2024)
Assembly: hg38
Supplementary files format and content: count tables

source_name: bone

growth_protocol: U2OS cells were cultured in DMEM with Glutamax and 10% FCS plus PenStep (Gibco)

extract_protocol:
Proteinase K digestion
see scEdU-seq (Nature Methods, 2024)

value: bone

value: osteosarcoma cells

value: Wild-type

tag: batch


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate8

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl8
2x100bp


title: T-47D DSG2 KO#2, cell line, rep2

description:
Library name: OV-13C-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv
DESeq2-DSG2KO2_cells_vs_DSG2WT.tsv

value: breast cancer cell line


title: T-47D DSG2 KO#2, cell line, rep1

description:
Library name: OV-13B-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv
DESeq2-DSG2KO2_cells_vs_DSG2WT.tsv

value: DSG2 KO


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate6

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl6
2x100bp


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate5

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl5
2x100bp


title: T-47D DSG2 KO#1, cell line, rep3

description:
Library name: OV-12D-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv
DESeq2-DSG2KO1_cells_vs_DSG2WT.tsv


title: Mouse ATACseq Fli1 KO, Rep3

description: Library name: Mouse_ATACseq_Fli1KO_Rep3

value: Fli1 KO


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate3

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl3
2x100bp


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate4

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl4
2x100bp


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate2

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl2
2x100bp


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate9

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl9
2x100bp


title: Mouse ATACseq Fli1 KO, Rep1

description: Library name: Mouse_ATACseq_Fli1KO_Rep1


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate7

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl7
2x100bp


title: T-47D WT, cell line, rep2

description:
Library name: OV-11C-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv


title: Mouse RNAseq NTC, Rep2

description: Library name: Mouse_RNAseq_NTC_Rep2

data_processing:
FastQC (v0.12.0), Trimmomatic (v0.39), and STAR (v2.7.11)
Assembly: mm10
Supplementary files format and content: Comma-separated text file includes raw counts for each sample.

extract_protocol:
RNA was harvested using the Quick-RNA microprep kit (Zymo). 10ng of RNA was used for library preparation.
RNA libraries were constructed using the Illumina RNA Prep with Enrichment kit following manufacturer's instructions.


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate8

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl8
2x100bp


title: Mouse RNAseq Fli1 KO, Rep3

description: Library name: Mouse_RNAseq_Fli1KO_Rep3


title: T-47D WT, cell line, rep3

description:
Library name: OV-11D-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv


title: Mouse ATACseq NTC, Rep1

description: Library name: Mouse_ATACseq_NTC_Rep1


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate4

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl4
2x100bp


title: T-47D WT, cell line, rep1

description:
Library name: OV-11B-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv


title: Mouse ATACseq Fli1 KO, Rep2

description: Library name: Mouse_ATACseq_Fli1KO_Rep2


title: Mouse RNAseq NTC, Rep1

description: Library name: Mouse_RNAseq_NTC_Rep1


title: T-47D DSG2 KO#1 cell line, rep1

description:
Library name: OV-12A-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv
DESeq2-DSG2KO1_cells_vs_DSG2WT.tsv


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate5

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl5
2x100bp


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate3

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl3
2x100bp


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate6

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl6
2x100bp


title: Mouse RNAseq Fli1 KO, Rep2

description: Library name: Mouse_RNAseq_Fli1KO_Rep2


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate2

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl2
2x100bp


title: T-47D DSG2 KO#1, cell line, rep2

description:
Library name: OV-12C-RNA
DESeq2-DSG2KO_cells_vs_DSG2WT.tsv
DESeq2-DSG2KO1_cells_vs_DSG2WT.tsv


title: Mouse RNAseq Fli1 KO, Rep1

description: Library name: Mouse_RNAseq_Fli1KO_Rep1


title: CAC227_S3_L001

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

description:
Library name: CAC227_S3
10x Genomics

data_processing:
data were processed using cell ranger and analyzed using Seurat
Assembly: human hg38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Colon

growth_protocol: Epithelial organoids were isolated and propagated per our published protocols (Sarvestani et al, Oncotarget, 2018). Fibroblasts were isolated from corresponding tissues and maintained in culture on plastic in DMEM with 10% fetal bovine serum. All cellular constructs were tested for mycoplasma contamination, and treated if necessary. Short-tandem repeat was used to confirm the integrity of the cellular constructs prior to use in the co-culture assay.

extract_protocol:
To isolate nuclei from the in vivo co-cultures we utilized the protocols created by Habib et al. 21 Briefly, sorted dissociated xenograft cells were washed and suspended in ice cold nuclei EZ lysis buffer (Sigma, Cat#NUC-101) and homogenized using a glass dounce tissue grinder (20 times per passage for both a loose and tight pestle) and incubated on ice for 5 minutes following the addition of 2 mL of ice-cold nuclei EZ lysis buffer. The nuclei were centrifuged at 500g for 6 minutes at 4 Celsius, washed with nuclei EZ lysis buffer and filtered through a 40 µm strainer. The nuclei are then resuspended in 4 mL of nuclei suspension buffer (1x PBS, 0.01% BSA and 0.1% RNAse inhibitor) and filtered through a 20 µm strainer. Nuclei were counted and then processed according to 10x Genomics Single Cell 3’ v3 kits in preparation for sequencing.
library was constructed using the 10x Genomics Single Cell 3’ v3 kits.

treatment_protocol: Organoids in culture were washed in ice cold PBS and dissociated with 0.25% Trypsin-EDTA(Gibco). Cells were strained through a 70 uM strainer and subsequently through a 40 uM Flowmi pipette tip strainer to derive a single cell suspension. Cells were counted using a hemocytometer and with viability determined with trypan blue exclusion. Fibroblast were simultaneously washed and dissociated using 0.25% Trypsin-EDTA.  Organoids and fibroblast were mixed in a ratio of 7:1 fibroblast:organoids and resuspended in 100 ul of Matrigel prior to inoculation into the subcutaneous space of immunocompromised NOD-SCID IL2 γ receptor null mice (JAX 005557). Mice were weighed and tumors measured weekly with calipers for 12 weeks. At 12 weeks, mice were euthanized with a mixture of ketamine/xylazine and tumor xenografts were harvested. The five xenografts per condition were pooled, dissociated using a mixture of Hanks’ Buffered Salt Solution (HBSS) and Collagenase IA (Sigma, Cat#C9891-1G) in a shaking water bath at 37degrees Celsius for 30-45 minutes. The cells were then washed twice in HBSS supplemented with fetal bovine serum (FBS), filtered using a 70 uM followed by 40 uM strainer then enumerated.  Fluorescence Associated Cell Sorting (FACS) To remove any contaminating mouse cells, dissociated tumor cells underwent FACS sorting with negative selection for murine classical MHC Class I molecules utilizing H2-Kd and H2-Dd. Briefly, the dissociated cells were resuspended and blocked to prevent non-specific binding with Sandoglobin on ice for 20 minutes. The appropriate FACS controls were generated including autofluorescence, DAPI (Invitrogen Cat#D21490) and murine H-2Kd/H-2Dd (SouthernBiotech, Cat#1911-08). The dissociated cells were incubated with murine H-2Kd/H-2Dd antibody. The dissociated cells and murine H-2Kd/H-2Dd control were incubated with a secondary PE-Cy™5 Streptavidin antibody (BD-Pharmingen, Cat# 554062). The sample and controls were washed with HBSS supplemented with FBS then resuspended in appropriate volume of HBSS supplemented with 2% FBS. Finally, DAPI was added to all of the controls and sample with the exception of the autofluorescence control. The cells were sorted to retain DAPI-(living cells), human EPCAMhi and murine H-2Kd-/H-2Dd- (human cells).

value: Colon

value: Colitis-associated cancer epithelial organoids

value: wild-type


title: CAC227PF_S2_L001

description:
Library name: CAC227PF_S2
10x Genomics

value: Colitis-associated cancer epithelial organoids co-inoculated with matched colitis-associated cancer fibroblasts (ratio 1:7) in NSG mouse flanks

value: mutant

value: colitis-associated cancer fibroblasts


title: HHst.30, dorsal retina, replicate 3

city: Midlothian

first: Joe

last: Rainger

address: Roslin Institute, Easter Bush Campus

institute: Roslin Institute

description:
Library name: BCT2-11_S11
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st30_dorsal.bed

data_processing:
Adaptor sequences were detected and cut out using Trimgalore! and Cutadapt v1.16. Sequence quality pre- and post-trimming was evaluated using FastQC.
Read pairs were aligned to the Ensembl chicken reference genome (galGal6) to generate binary aligned map (BAM) files using Bowtie2 version 2.3.4.3 with the following parameters: --very-sensitive -X 1500 -k 10
Bowtie aligned BAM files of technical replicates were merged, sorted by query name and indexed using Samtools version 1.6
Peaks of each condition were called from the corresponding biological replicates using the Genrich pipeline version 0.6
bigwig files were converted from BAM file of each sample using the bamToBigWig function in Deeptools 3.5.0. The bigwig file results were normalised to 1x chicken genome size (GRCg6a).
Assembly: GRCg6a (galGal6)
Supplementary files format and content: bigwig files of individual sample, normalised to 1X effective chicken genome
Supplementary files format and content: bed file containing peak called at each biological condition. Peaks are jointly called from samples of the same biological condition.

organism: Gallus gallus

source_name: Dorsal retina

growth_protocol: Fertilised wildtype hy-line chicken eggs were incubated at 37oC.

extract_protocol:
Fissure and dorsal tissue were manually dissected from each embryonic eye and were separately collected into cold Ringer’s solution. Single cell dissociation of dissected tissues was conducted based on previously described methods (Williams et al., 2021). 50,000 isolated cells were counted using a haemacytometer and were resuspended in PBS.
Nuclei extraction, transposition reaction, library preparation were all conducted following the previously described ‘omni-ATACseq’ method (Corces et al., 2017). Libraries were cleaned using AMPure XP beads (Beckman Coulter, Cat no A63880). Library concentration was quantified using Qubit dsDNA High Sensitivity Assay Kits (Invitrogen, Q32851), while library quality was determined using 4200 Tapestation System (Agilent). 75bp paired-end sequencing of pooled libraries was then conducted using the Nextseq 2000 platform (Illumina), with at least 189 million reads generated per sample.

value: Dorsal retina

tag: Stage

value: Wildtype


title: DC2.4 cells, DNAse3

city: New Ypok

first: Mengying

last: Hu

state: New York

address: 413 E 69th St, New York, NY 10021

institute: Weill Cornell Medical College

description: Library name: Sample-12

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (version 2.0.11) (http://ccb.jhu.edu/software/tophat/index.shtml), and transcriptome reconstruction was performed by Cufflinks (version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in fragments per kilobase of exon model per million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: DC2.4 cells were cultured in RPMI supplemented with 10% FBS and 1× penicillin/streptomycin (P/S)

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen, 74134) following the manufacturer’s instructions.
TruSeq stranded mRNA library was prepared according to manufacturer's instructions

treatment_protocol: DC2.4 cells were seeded at a density of 1 × 105 cells mL-1 per well in 1mL of complete RPMI medium in a 12-well plate and treated with PBS, 15 µg mL-1 of mouse ATEVs or 30 µg mL-1 of mouse NTEVs (corresponding to 5 µg mL-1 of EV-DNA), or 15 µg mL-1 of Baseline-ZERO DNase-pretreated ATEVs after overnight incubation. The following day, DC2.4 in each group were harvested and reseeded at the same density in a 12-well plate. The procedure was repeated 3 times

value: dendritic cell line

value: WT

value: DNAse+ATEVs


title: DC2.4 cells, DNAse2

description: Library name: Sample-11


title: HHst.30, dorsal retina, replicate 2

description:
Library name: BCT2-9_S9
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st30_dorsal.bed


title: 786-O,RNAseq,control,rep2

city: Tianjin

first: Chen

last: Kexin

address: No.22, Qixiangtai Road, Hepin

institute: Tianjin Medical University

data_processing:
The raw sequencing reads were quantified by Salmon.
Differential expression analysis was performed using the DESeq2, identifying genes that exhibited significant changes in expression (P < 0.05 and |Log2 fold change| > 0.5) between the CRISPRi cells and control cells.
Pathway enrichment for KEGG was analyzed in KOBAS.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM value for each Sample

growth_protocol: 786-O(ATCC, CRL-1932) and769-P(ATCC, CRL-1933) human renal cell adenocarcinoma cell line  were all cultured in Roswell Park Memorial Institute (RPMI) 1640  supplemented with 10% fetal bovine serum. Cells were cultrued at 37℃ at 5% CO2.

extract_protocol:
total RNA was extracted from cells utilizing the TRIzol reagent.
total RNA were sent to the Novogene for constructing libraries and sequencing.

treatment_protocol: sgRNAs targeting the rs28684409, rs179785 and negative control sgRNA were synthesized and cloned into CROP-seq-opti vector following digestion with the BsmBI. The CROP-seq-opti vectors containing target sgRNAs were subsequently packaged into lentiviruses. The lentiviruses were transduced into CRISPRi 786-O cells, followed by puromycin selection (2 μg/ml).

value: Human clear cell renal cell carcinoma cell lines


title: HHst.34, dorsal retina, replicate 2

description:
Library name: BCT2-10_S10
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st34_dorsal.bed


title: HHst.30, dorsal retina, replicate 1

description:
Library name: BCT2-7_S7
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st30_dorsal.bed


title: HHst.34, dorsal retina, replicate 1

description:
Library name: BCT2-8_S8
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st34_dorsal.bed


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate1

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl1
2x100bp

value: bone

value: osteosarcoma cells


title: CAC227TF_S1_L001

description:
Library name: CAC227F_S1
10x Genomics

value: Colitis-associated cancer epithelial organoids co-inoculated with matched proximal fibroblasts (ratio 1:7) in NSG mouse flanks


title: HHst.34, optic fissure margin, replicate 3

description:
Library name: BCT2-6_S6
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st34_OFM.bed

source_name: Optic fissure margin

value: Optic fissure margin


title: HHst.30, optic fissure margin, replicate 3

description:
Library name: BCT2-5_S5
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st30_OFM.bed


title: DC2.4 cells, DNAse1

description: Library name: Sample-10


title: HHst.30, optic fissure margin, replicate 2

description:
Library name: BCT2-3_S3
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st30_OFM.bed


title: DC2.4 cells, NTEV3

description: Library name: Sample-9

value: NTEVs


title: HHst.34, dorsal retina, replicate 3

description:
Library name: BCT2-12_S12
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st34_dorsal.bed


title: DC2.4 cells, NTEV2

description: Library name: Sample-8


title: HHst.34, optic fissure margin, replicate 1

description:
Library name: BCT2-2_S2
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st34_OFM.bed


title: 786-O,RNAseq,785,rep1


title: DC2.4 cells, NTEV1

description: Library name: Sample-7


title: Mouse Fli1CUT&Tag WT, Rep1

description: Library name: Mouse_Fli1CUT_Tag_WT_Rep1

value: NK cells


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 2 plate1

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repB-pl1
2x100bp

value: Wild-type


title: HHst.30, optic fissure margin, replicate 1

description:
Library name: BCT2-1_S1
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st30_OFM.bed


title: Tcells, CD3E epigentic silencing, donor 2 rep 3

city: Dresden

first: Frank

last: Buchholz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

description: Library name: EpiE_d2_3

data_processing:
Aligned to the human genome GRCh38/hg38 using STAR v2.7.3a for paired-end reads.
Aligned reads fed through featureCounts v2.0.6 of the subread package to generate the count matrix.
Assembly: GRCh38
Supplementary files format and content: Count matrix with sample IDs for columns and gene names for rows.

source_name: primary cells

growth_protocol: T cells were activated with TransAct CD3/CD28 4 days before electroporation. After electroporation, T cells were recovered in TexMACS Medium supplemented with IL-2,7,15 for 3 days. Subsequently, T cells were rested in RPMI without cytokines for 24h before RNA isolation.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads following Novogene NGS RNA Library Prep Set protocol. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The non-directional library was complete following end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: T cells were electroporated with mRNA of mCherry (mock) Cas9 (TCR-KO) or epigenetic editor (CD3E-EpiE) and synthetic sgRNA (TCR-KO and CD3E-EpiE) and RNA was isolated 4 days after.

value: blood

value: T cells

value: TCR-

value: CD3E epigenetic silencing

value: donor 2


title: 786-O,RNAseq,rs28684409,rep2


title: 786-O,RNAseq,control,rep1


title: HHst.34, optic fissure margin, replicate 2

description:
Library name: BCT2-4_S4
Two technical replicates of raw files are included. Peaks are jointly called by samples of the same biological conditions. And thus are indicated by the same bed file containing Genrich peak calling result.
st34_OFM.bed

value: Wildtype


title: DC2.4 cells, ATEV3

description: Library name: Sample-6

value: dendritic cell line

value: ATEVs


title: 786-O,RNAseq,785,rep2


title: Tcells, CD3E epigentic silencing, donor 2 rep 1

description: Library name: EpiE_d2_1


title: Tcells, CD3E epigentic silencing, donor 2 rep 2

description: Library name: EpiE_d2_2


title: CRISPR screening, Caki-1,CRISPRa, Day21, replicate 2

data_processing:
The raw sequencing data from 10x Genomics was initial processed with cell ranger-7.1.0 and resulting data were further filtered using Seurat v4.0.372.
Cells with mitochondrial percentage exceeding 10% or having less than 200 gene UMI were removed and genes that were expressed in less than 0.525% of cells were filtered out.
Droplets were also identified and removed using scDblFinder73. Raw sequencing data of enriched sgRNA transcripts was also processed using cell ranger and reads that failed to align to the reference genome was extracted using Samtools74 to calculated the distribution of sgRNAs.
Assembly: hg38
Supplementary files format and content: raw sgRNA counts for each cell lines
Library strategy: CRISPR screen

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultrued at 37℃ at 5% CO2

extract_protocol:
The cells were further processed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10x Genomics) according to the manufacturer’s protocol.
To enrich for sgRNA transcripts, PCR was performed on 10 ng of cDNA from the 3’ single-cell RNA libraries using specific primers. The libraries were sequenced on Illumina (Novogene), using a configuration identical to that of standard 10x Genomics libraries.

treatment_protocol: RCC cell lines stably expressing dCas9-KRAB or dCas9-VP64 were transduced with pooled sgRNAs at low MOI of 0.5. Twenty-four hours after infection, cells were selected using puromycin (2 μg/ml) for 7 days. Cells were split into triplicates every 3 days, and maintained at 300X coverage throughout the screen. Cells were harvested in replicates on day 0, day 14 and day 21 after puromycin selection. sgRNA was amplified by PCR using specific primers, the amplified products were sent to the Beijing Genomics Institute (BGI) for library construction and sequencing.


title: 786-O,RNAseq,rs28684409,rep1


title: Tcells, TCR knockout, donor 2 rep 1

description: Library name: KO_d2_1

value: CRISPR/Cas9 TCR knockout


title: Tcells, untreated, donor 2 rep 3

description: Library name: WT_d2_3

value: TCR+

value: untreated


title: Tcells, TCR knockout, donor 2 rep 3

description: Library name: KO_d2_3


title: DC2.4 cells, ATEV2

description: Library name: Sample-5

value: WT


title: Tcells, untreated, donor 2 rep 1

description: Library name: WT_d2_1


title: CRISPR screening, Caki-1,CRISPRa, Day21, replicate 1

value: Human clear cell renal cell carcinoma cell lines


title: DC2.4 cells, ATEV1

description: Library name: Sample-4


title: DC2.4 cells, PBS3

description: Library name: Sample-3

value: PBS


title: Tcells, untreated, donor 2 rep 2

description: Library name: WT_d2_2


title: DC2.4 cells, PBS2

description: Library name: Sample-2


title: KSR_RPE 2

city: Chongqing

first: FAN

last: ZHANG

state: - Select -

address: Building 4, Room 211, 313 Jin Yue Road, Gao Xin District

institute: Jinfeng Laboratory

description: Library name: Sample 5

data_processing:
Raw data in fastq format were first subjected to quality control through in-house Perl scripts. Clean high-quality data were then mapped to the reference genome, the index of the reference genome was built via HISAT2 v2.0.5, and paired-end clean reads were aligned to the reference genome via HISAT2 v2.0.5. The quantification of the gene expression level featureCounts v1.5.0 - p3 was used to count the number of reads mapped to each gene. The FPKM value of each gene was calculated on the basis of the length of the gene and the number of reads mapped to that gene. Differential expression analysis was performed via the DESeq2 R package (1.20.0). The resulting P values were adjusted via Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: GRCh38
Supplementary files format and content: xls.file includes raw counts for each sample

source_name: iPSC-derived RPE

extract_protocol:
Total RNA was extracted from the iPRE maintained in KSR or B27 medium for 4 weeks via TRIzol™ Reagent (Invitrogen)
mRNA was purified from total RNA via poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized via random hexamer primers and M-MulV reverse transcriptase (RNase H-). Second-strand cDNA synthesis was subsequently performed via DNA polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of the DNA fragments, adaptors with hairpin loop structures were ligated to prepare for hybridization. To preferentially select cDNA fragments 370-420 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. Then, the PCR products were purified, and library quality was assessed on an Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System via the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform, and 150 bp paired-end reads were generated.

value: iPSC-derived RPE

value: RPE

value: wild type


title: CRISPR screening, Caki-1,CRISPRa, Day14, replicate 2


title: KSR_RPE 3

description: Library name: Sample 6


title: CRISPR screening, Caki-1,CRISPRa, Day14, replicate 1


title: KSR_RPE 1

description: Library name: Sample 4


title: CRISPR screening, Caki-1,CRISPRa, Day0, replicate 1


title: B27_RPE 3

description: Library name: Sample 3


title: Tcells, TCR knockout, donor 2 rep 2

description: Library name: KO_d2_2

value: blood


title: DC2.4 cells, PBS1

description: Library name: Sample-1


title: B27_RPE 1

description: Library name: Sample 1


title: DNAse2

description: Library name: Sample-8

source_name: pancreatic cancer cells

growth_protocol: KPCY cells were cultured in RPMI supplemented with 10% FBS and 1× penicillin/streptomycin (P/S)

treatment_protocol: KPCY cells were seeded at a density of 5 × 104 cells mL-1 per well in 1mL of complete DMEM medium in a 12-well plate and treated with PBS, 15 µg mL-1 of mouse ATEVs or 30 µg mL-1 of mouse NTEVs (corresponding to 5 µg mL-1 of EV-DNA), or 15 µg mL-1 of Baseline-ZERO DNase-pretreated ATEVs after overnight incubation. The following day, tumor cells in each group were harvested and reseeded at the same density in a 12-well plate. The procedure was repeated 8 times

value: pancreatic cancer cells

value: DNAse+ATEVs


title: NTEV2

description: Library name: Sample-6

value: NTEVs


title: B27_RPE 2

description: Library name: Sample 2


title: Wild-type U2OS cells or depleted for KANSL1 or KANSL3 treated replicate 1 plate7

description:
Library name: JvB-178-U2OS-KANSL1-3-15E-60WO-15E-F-repA-pl7
2x100bp

value: bone

value: osteosarcoma cells

value: Wild-type


title: DNAse1

description: Library name: Sample-7


title: NTEV1

description: Library name: Sample-5


title: CRISPR screening, Caki-1,CRISPRi, Day21, replicate 2


title: p300KO_Triptolite_20J_exp_tript_rep1

city: Miami

first: Carolina

middle: Paula

last: Banuelos

state: Florida

address: 1580 NW 10th Ave

department: Medicine

institute: University of Miami

description: Library name: p300KO_Triptolite_20J_exp_tript_rep1

data_processing:
For strand-bias analysis, paired-end ChIPseq fastq files were aligned to the human genome hg19 using BWA-MEM v 0.7.17-r1188. The aligned files were converted to BAM files and sorted using Samtools v1.9. Duplicates reads were removed with Picard v3.00. Reads from each DNA strand (plus and minus) and split using Samtools. bamCoverage v3.3.1 using RPKM option was used to generate normalized ChIP-seq peak profiles for each sample. The resulting BigWig output files were visualized in the UCSC Genome Browser (https://genome.ucsc.edu). The Strand Specificity Index (SSI) was calculated based on the numbers of forward and reverse mapped reads, using the formula presented in Supplemental Figure 4E. Positive and negative SSI values indicate bidirectional gene orientation. Genes with fewer than 1 RPM were excluded from the analysis. The results were visualized with plotProfile from deepTools v 3.5.3.
Assembly: hg19
Supplementary files format and content: Bigwig files with RPKM normalization with the reads of plus or minus DNA strand

source_name: HeLa

growth_protocol: DMEM (Gibco, #11965-092) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #10437-028), 1X GlutaMAX (Gibco, #35050-061), 1X MEM non-essential amino acids (Corning 25-025-Cl) and 1X Antibiotic Antimycotic solution (Corning, #30-004-Cl), 5% CO2, and 21% O2.

extract_protocol:
Cells were cross-linked with ChIP Cross-link Gold (Diagenode, #C01019027) following manufacturer instructions. After incubation at room temperature for 30 min, the cells were fixed with a 1% formaldehyde solution (Thermo Fisher Scientific, #28908) for 10 min at room temperature. To stop the fixation, 125 mM glycine was added and incubated for 5 min. The cells were then washed twice with PBS and harvested on ice using cell scrapers. The harvested cells were resuspended in ChIP lysis buffer supplemented with protease inhibitors (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.25% SDS) and sonicated on a Bioruptor Pico for 4 rounds of 10 cycles each at 4 °C with a short vortex between rounds to generate DNA fragments <500 bp. The sonicated cells were centrifuged, and the supernatants were transferred to new tubes and diluted with one volume of IP Dilution buffer (1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM Tris-HCl pH 8.0, proteases and phosphatases inhibitors). For the immunoprecipitation step, 1 mg of pre-cleared protein extracts were incubated with 10 g of antibodies, along with 1 g of Spike-in antibody (Active Motif, #61686) and 50 ng of Spike-in chromatin from Drosophila (Active Motif, #53083) overnight at 4 °C with gentle rotation. For the negative control, Normal Rabbit IgG (Cell Signaling, #2729S) was employed. The next day, 50 l of Protein A/G PLUS-Agarose beads (Santa Cruz, #sc-2003) were added to each IP reaction and incubated for 2 h at 4 °C with rotation. The beads were washed twice with IP Dilution buffer supplemented with 0.1% SDS (final), 3 times with ChIP wash buffer (IP Dilution buffer plus 0.5 M NaCl, 0.1% SDS, and 1% [w/v] Sodium Deoxycholate), and once with TE buffer (10mM Tris-HCl, 1mM EDTA) containing 50 mM NaCl. Elution of immunocomplexes from beads was performed with Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) and incubation at 65 °C for 15 min. Then, the supernatants were reverse crosslinked at 65 °C for 3 h, treated sequentially with RNAse A (Sigma-Aldrich, #R5503) at 37 °C for 2 h, and then treated with Proteinase K (New England Biolabs, #P8107S) at 55 °C for 2 h. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen, #28106).
Purified DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, #7370) following the manufacturer’s instructions.

value: HeLa

value: Human epithelial cell line derived from cervical cancer

tag: chip antibody

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: WT_IgG_exp_tript

description: Library name: WT_IgG_exp_tript

value: DMSO

value: Normal Rabbit IgG (Cell Signaling Technology, 2729)


title: p300KO_IgG_exp_tript

description: Library name: p300KO_IgG_exp_tript


title: p300KO_Triptolite_0J_exp_tript_rep1

description: Library name: p300KO_Triptolite_0J_exp_tript_rep1

value: Triptolite


title: CRISPR screening, Caki-1,CRISPRi, Day14, replicate 2

value: Human clear cell renal cell carcinoma cell lines


title: CRISPR screening, Caki-1,CRISPRa, Day0, replicate 2


title: p300KO_DMSO_20J_exp_tript_rep2

description: Library name: p300KO_DMSO_20J_exp_tript_rep2


title: ATEV1

description: Library name: Sample-3

value: WT

value: ATEVs


title: p300KO_DMSO_0J_exp_tript_rep1

description: Library name: p300KO_DMSO_0J_exp_tript_rep1


title: p300KO_Triptolite_0J_exp_tript_rep2

description: Library name: p300KO_Triptolite_0J_exp_tript_rep2


title: CRISPR screening, Caki-1,CRISPRi, Day21, replicate 1


title: p300KO_Triptolite_20J_exp_tript_rep2

description: Library name: p300KO_Triptolite_20J_exp_tript_rep2


title: p300KO_DMSO_0J_exp_tript_rep2

description: Library name: p300KO_DMSO_0J_exp_tript_rep2


title: PBS2

description: Library name: Sample-2

value: PBS


title: CRISPR screening, Caki-1,CRISPRi, Day14, replicate 1


title: ATEV2

description: Library name: Sample-4


title: p300KO_DMSO_20J_exp_tript_rep1

description: Library name: p300KO_DMSO_20J_exp_tript_rep1


title: WT_Triptolite_0J_exp_tript_rep2

description: Library name: WT_Triptolite_0J_exp_tript_rep2


title: CRISPR screening, Caki-1,CRISPRi, Day0, replicate 1


title: CRISPR screening, 786-O,CRISPRa, Day21, replicate 2


title: WT_Triptolite_0J_exp_tript_rep1

description: Library name: WT_Triptolite_0J_exp_tript_rep1


title: WT_DMSO_20J_exp_tript_rep2

description: Library name: WT_DMSO_20J_exp_tript_rep2


title: CRISPR screening, Caki-1,CRISPRi, Day0, replicate 2


title: WT_Triptolite_20J_exp_tript_rep1

description: Library name: WT_Triptolite_20J_exp_tript_rep1


title: WT_Triptolite_20J_exp_tript_rep2

description: Library name: WT_Triptolite_20J_exp_tript_rep2


title: WT_DMSO_20J_exp_tript_rep1

description: Library name: WT_DMSO_20J_exp_tript_rep1


title: Blood, FF030BASO_B2

city: Guangzhou

first: xie

last: xinyang

address: 58 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: sample5
10x Genomics

data_processing:
To obtain high-quality clean reads, raw sequencing reads were processed using Cutadapt (v1.9) (https://cutadapt.readthedocs.io/en/stable/) to remove low-quality sequences. Clean reads were then aligned to the mouse reference genome (v101) using the HISAT2 package (v2.2.1) (https://daehwankimlab.github.io/hisat2/). HISAT2 first removed low-quality reads based on the quality scores provided in the sequencing output and subsequently mapped the filtered reads to the reference genome with high accuracy. Gene expression quantification and differential expression analysis were performed using DESeq2 software. Genes with a p-value < 0.05 and an absolute fold change ≥ 2 were considered differentially expressed genes (DEGs). The identified DEGs were subjected to enrichment analysis of Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to explore their biological significance.
Assembly: v101
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: Blood

extract_protocol:
0.5–1 mL mouse peripheral blood was collected into EDTA coated tubes. Red blood cells were lysed using RBC lysis buffer (Sigma-Aldrich). All live, CD45+Lin-CD49b+FcεRIα/IgE+ basophils from WT mice were sort-purified on a FACSAria cell sorter (BD Biosciences). Isolated basophils (2 × 104 – 5 × 104 cells /mL) were then conducted for the transcriptome sequencing using the Smart-seq2 protocol.
A cDNA library constructed by technology from the pooled RNA was sequenced at the Illumina NovaseqTM 6000 sequence platform (LC Sciences, USA). The Illumina paired-end RNA-seq approach was employed, generating 2 × 150 bp paired-end reads, with a total yield of approximately 1 million reads per sample.

treatment_protocol: AD-like disease was induced by daily topical application of MC903 (2 nmol in 10 µL of 100% ethanol; Tocris Bioscience) to the bilateral ear skin of mice from day 0 to day 6. Control mice were treated with 100% ethanol (EtOH) following the same schedule.

value: Blood


title: WT_DMSO_0J_exp_tript_rep2

description: Library name: WT_DMSO_0J_exp_tript_rep2


title: Blood, FF030BASO_B3

description:
Library name: sample6
10x Genomics


title: CRISPR screening, 786-O,CRISPRa, Day21, replicate 1


title: PBS1

description: Library name: Sample-1

value: pancreatic cancer cells


title: Poly_Purif_p300KO_ActD_rep1

description:
Library name: Poly_Purif_p300KO_ActD_rep1
Polysome Enriched fractions-5EU Purification

library_source: other

data_processing:
RNA-seq FASTQ files were generated using BCL converter v4.2.7 (Illumina) for index identification. Sample quality was analyzed with FastQC v0.12.1. Reads were trimmed using Cutadapt v2.3 with the following parameters: -j 4 -m 18. Subsequently, reads were aligned to the hg19 and D. melanogaster genome using STAR 2.7.10a. Duplicate reads were removed using Picard v2.18.29. FeatureCounts v2.0.3 was employed to calculate gene counts against either the human genome hg19 or the spike-in D. melanogaster, using default parameters. Differential expressed genes (DEGs) were identified using DESeq2 v1.34.0 and R v4.1.1, setting a q-value threshold of less than 0.05 and log2FC of 1.5 or 1.0 for 5-EU RNAseq. The geometric mean of the D. melanogaster spike-in was used for sample normalization. For DRB-5EUseq, a sample without 5EU was used as negative control to filter the signal using bigwigCompare from deepTools v3.5.6
Assembly: hg19
Supplementary files format and content: Tables with the comparision values between control and treatment using DESEQ2 and spike-in normalization

molecule: other

extract_protocol:
Trizol
NEBNext Ultra II RNA Library Prep Kit (E7770), following the manufacturer’s instructions.

treatment_protocol: For Polysome-enriched RNA purification, 10x10^6 cells for each condition (Control or 20 J/m2 of UV irradiation, with DMSO or Actinomycin D 2 ug/ml ) were incubated with 1 mM of 5EU for 30 minutes, 1 h and 30 min after UV irradiation for 2h, and 2 h and 30 min for 3 h. Then, cells were incubated with 100 µg/ml cycloheximide (CHX) in growth media for 5 min at 37 °C and 5% CO2. Subsequently, cells were washed twice with 10 ml of ice-cold 1x PBS containing 100 µg/ml CHX. Cells were gently scraped, collected with 5 ml of 100 µg/ml PBS-CHX, and centrifuged at 300 xg for 5 min at 4 °C. Cells were resuspended in a hypotonic buffer (5 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl and 1x EDTA-free protease inhibitor cocktail) with 100 µg/ml CHX, 1 µM DTT and 100 U of RNAse inhibitor (recombinant RNasin® Ribonuclease Inhibitor, Promega, #N2515). Sodium deoxycholate and Triton X-100 were added to the lysis reaction to a final concentration of 0.5%. After 10 minutes incubation at 4 °C, lysates were centrifuged at 16,000 xg for 7 min at 4 °C. The supernatant was transferred to a new pre-chilled 1.5 ml tube. Samples were added on top of a sucrose density gradient (from 50 to 5% sucrose, containing 20 mM HEPES (pH 7.6), 0.1 M KCl, 5 mM MgCl2, 10 µg/ml cycloheximide, 1x EDTA-free protease inhibitor and 10 units/ml RNase inhibitor) in Ultra-clear centrifuge tubes (Beckman Coulter, #344057). Samples were ultracentrifuged in a Sorvall wX+ 80 (Thermo scientific, # 75000080) at 222,000 xg, for 2 h at 4 °C using an AH-650 rotor (Thermo-scientific, # 54294) without brakes. Fractions corresponding to the polysomes were pooled and 1 µg of 5EU-RNA of Drosophila melanogaster was added as spike-in. Then, the samples were diluted in TRIzol LS Reagent (Thermo Fisher Scientific, #10296010). RNA was purified according to the manufacturer protocol, using Monarch Total RNA purification columns (NEB, T2010S). The 5EU RNA was purified using Click-iT™ Nascent RNA Capture Kit (ThermoFisher Scientific, C10365) according to manufacturer protocol. The RNA was depleted of ribosomal RNA with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific, #A15015) according to the manufacturer's protocol. RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer protocol. Sequencing was performed on a NovaSeq X Plus (Oncogenomics Core Facility, SCCC, University of Miami) with 150 bp paired-end reads.

value: Actinomycin D


title: CRISPR screening, 786-O,CRISPRa, Day14, replicate 1


title: WT_DMSO_0J_exp_tript_rep1

description: Library name: WT_DMSO_0J_exp_tript_rep1


title: Blood, FF030BASO_B1

description:
Library name: sample4
10x Genomics


title: CRISPR screening, 786-O,CRISPRa, Day0, replicate 2


title: Blood, FF030BASO_A2

description:
Library name: sample2
10x Genomics


title: Poly_Purif_p300KO_ActD_rep2

description:
Library name: Poly_Purif_p300KO_ActD_rep2
Polysome Enriched fractions-5EU Purification


title: CRISPR screening, 786-O,CRISPRa, Day14, replicate 2


title: Poly_Purif_p300KO_20J_2h_rep4

description:
Library name: Poly_Purif_p300KO_20J_2h_rep4
Polysome Enriched fractions-5EU Purification


title: CRISPR screening, 786-O,CRISPRa, Day0, replicate 1


title: Poly_Purif_p300KO_20J_2h_rep3

description:
Library name: Poly_Purif_p300KO_20J_2h_rep3
Polysome Enriched fractions-5EU Purification


title: Skin, 6-OHDA, B3

description:
Library name: sample6
10x Genomics

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (v2.20). The FASTQ files were processed using the Cell Ranger pipeline (v6.1.1) for sample demultiplexing, barcode assignment, and single-cell 3′ gene counting. Data were aligned to the Ensembl v105 reference genome. The output from Cell Ranger was imported into Seurat (v3.1.1) for dimensionality reduction, clustering, and transcriptomic analysis.
Assembly: v105
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ear skin

extract_protocol:
Mouse ear skin was harvested from AD-like model mice, dissected into small pieces, and digested with Liberase™ TL (0.25 mg/mL; Roche) at 37°C with gentle agitation. The digested tissues were filtered through a 70-μm cell strainer to generate a single-cell suspension. Live CD45⁺ Lin⁻ cells were sorted using a FACSAria cell sorter (BD Biosciences) for downstream scRNA-seq.
A single-cell 3′ library was constructed using the 10x Genomics Chromium Single-Cell 3′ kit (v3). R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A- tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

treatment_protocol: All mice were treated with MC903, group B received 6-OHDA injection while control mice in group A were injected with vehicle.

value: Ear skin


title: CRISPR screening, 786-O,CRISPRi, Day21, replicate 2


title: Blood, FF030BASO_A3

description:
Library name: sample3
10x Genomics


title: Poly_Purif_p300KO_0J_rep4

description:
Library name: Poly_Purif_p300KO_0J_rep4
Polysome Enriched fractions-5EU Purification

value: Ctrl


title: Poly_Purif_p300KO_0J_rep3

description:
Library name: Poly_Purif_p300KO_0J_rep3
Polysome Enriched fractions-5EU Purification


title: DRB_5EU_NonFrag_p300KO_t0_0J

description: Library name: DRB_5EU_NonFrag_p300KO_t0_0J

treatment_protocol: For Polysome-enriched RNA purification, 10x10^6 cells for each condition (Control or 20J/m2 of UV irradiation) were incubated with 1 mM of 5EU for 30 minutes, 1 h and 30 min after UV irradiation for 2h, and 2 h and 30 min for 3 h. Then, cells were incubated with 100 µg/ml cycloheximide (CHX) in growth media for 5 min at 37 °C and 5% CO2. Subsequently, cells were washed twice with 10 ml of ice-cold 1x PBS containing 100 µg/ml CHX. Cells were gently scraped, collected with 5 ml of 100 µg/ml PBS-CHX, and centrifuged at 300 xg for 5 min at 4 °C. Cells were resuspended in a hypotonic buffer (5 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl and 1x EDTA-free protease inhibitor cocktail) with 100 µg/ml CHX, 1 µM DTT and 100 U of RNAse inhibitor (recombinant RNasin® Ribonuclease Inhibitor, Promega, #N2515). Sodium deoxycholate and Triton X-100 were added to the lysis reaction to a final concentration of 0.5%. After 10 minutes incubation at 4 °C, lysates were centrifuged at 16,000 xg for 7 min at 4 °C. The supernatant was transferred to a new pre-chilled 1.5 ml tube. Samples were added on top of a sucrose density gradient (from 50 to 5% sucrose, containing 20 mM HEPES (pH 7.6), 0.1 M KCl, 5 mM MgCl2, 10 µg/ml cycloheximide, 1x EDTA-free protease inhibitor and 10 units/ml RNase inhibitor) in Ultra-clear centrifuge tubes (Beckman Coulter, #344057). Samples were ultracentrifuged in a Sorvall wX+ 80 (Thermo scientific, # 75000080) at 222,000 xg, for 2 h at 4 °C using an AH-650 rotor (Thermo-scientific, # 54294) without brakes. Fractions corresponding to the polysomes were pooled and 1 µg of 5EU-RNA of Drosophila melanogaster was added as spike-in. Then, the samples were diluted in TRIzol LS Reagent (Thermo Fisher Scientific, #10296010). RNA was purified according to the manufacturer protocol, using Monarch Total RNA purification columns (NEB, T2010S). The 5EU RNA was purified using Click-iT™ Nascent RNA Capture Kit (ThermoFisher Scientific, C10365) according to manufacturer protocol. The RNA was depleted of ribosomal RNA with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific, #A15015) according to the manufacturer's protocol. RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer protocol. Sequencing was performed on a NovaSeq X Plus (Oncogenomics Core Facility, SCCC, University of Miami) with 150 bp paired-end reads. For 5EU RNAseq, cells were incubated with 1 mM 5‑EU for 10 minutes and then collected using Trizol. 5‑EU RNA from Drosophila melanogaster was used as a spike‑in. The RNA was purified using Monarch Total RNA Purification Columns (NEB, T2010S), and the 5‑EU RNA was further purified with the Click‑iT™ Nascent RNA Capture Kit (Thermo Fisher Scientific, C10365) according to the manufacturer's protocol. Ribosomal RNA was depleted using the RiboMinus Eukaryote System v2 (Thermo Fisher Scientific, #A15015) following the manufacturer's protocol. RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer's protocol. Sequencing was performed on a NovaSeq X Plus (Oncogenomics Core Facility, SCCC, University of Miami) with 150 bp paired‑end reads. For DRB‑5EUseq, samples were incubated with 100 µM DRB (5,6‑Dichlorobenzimidazole riboside) for 3 hours. Then, some cell groups were irradiated with 20 J/m², while others were left unirradiated (control groups). Immediately after irradiation, the cells were washed three times with warm PBS. Two mM 5‑EU was added 35 minutes after UV irradiation; 10 minutes later, the cells were harvested with Trizol. After purification, two protocols were followed: in one, the RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (E610S), and in the other, the RNA was left intact. The 5‑EU RNA purification and library preparation were performed as described for the 5EU RNAseq protocol.

value: human cervical cancer

value: Ctrl-DRB

tag: group


title: DRB_5EU_NonFrag_p300KO_t45min_20J

description: Library name: DRB_5EU_NonFrag_p300KO_t45min_20J

value: HeLa

value: UV (20J/m2)-DRB


title: DRB_5EU_Frag_No5EU_rep1

description:
Library name: DRB_5EU_Frag_No5EU_rep1
DRB_5EU_Frag_No5EU_merged.bw


title: DRB_5EU_NonFrag_No5EU

description: Library name: DRB_5EU_NonFrag_No5EU


title: CRISPR screening, 786-O,CRISPRi, Day21, replicate 1


title: DRB_5EU_Frag_WT_t45min_20J_rep2

description:
Library name: DRB_5EU_Frag_WT_t45min_20J_rep2
DRB_5EU_Frag_WT_20J_45min_merged.bw


title: Blood, FF030BASO_A1

description:
Library name: sample1
10x Genomics


title: Skin, 6-OHDA, B2

description:
Library name: sample5
10x Genomics


title: DRB_5EU_Frag_WT_t45min_20J_rep1

description:
Library name: DRB_5EU_Frag_WT_t45min_20J_rep1
DRB_5EU_Frag_WT_20J_45min_merged.bw


title: DRB_5EU_NonFrag_p300KO_t45min_0J

description: Library name: DRB_5EU_NonFrag_p300KO_t45min_0J


title: Skin, 6-OHDA, B1

description:
Library name: sample4
10x Genomics


title: DRB_5EU_Frag_WT_t45min_0J_rep1

description:
Library name: DRB_5EU_Frag_WT_t45min_0J_rep1
DRB_5EU_Frag_WT_0J_45min_merged.bw


title: DRB_5EU_Frag_WT_t45min_0J_rep2

description:
Library name: DRB_5EU_Frag_WT_t45min_0J_rep2
DRB_5EU_Frag_WT_0J_45min_merged.bw


title: CRISPR screening, 786-O,CRISPRi, Day14, replicate 1


title: CRISPR screening, 786-O,CRISPRi, Day14, replicate 2


title: Skin, vehicle, A3

description:
Library name: sample3
10x Genomics


title: DRB_5EU_Frag_WT_t0_0J_rep2

description:
Library name: DRB_5EU_Frag_WT_t0_0J_rep2
DRB_5EU_Frag_WT_0J_t0_merged.bw


title: DRB_5EU_Frag_p300KO_t45min_20J_rep1

description:
Library name: DRB_5EU_Frag_p300KO_t45min_20J_rep1
DRB_5EU_Frag_p300KO_20J_45min_merged.bw


title: DRB_5EU_Frag_WT_t0_0J_rep1

description:
Library name: DRB_5EU_Frag_WT_t0_0J_rep1
DRB_5EU_Frag_WT_0J_t0_merged.bw


title: CRISPR screening, 786-O,CRISPRi, Day0, replicate 2


title: 769P,H3K27ac

data_processing:
Bowtie2 to align the sequencing reads to the human genome (hg38)
SEACR (SEquencing-based Epigenetic Analysis for ChIP-seq Reads) to call peaks from the processed data.
Using samtools to sort and index a BAM file, then bamCoverage from deepTools to convert it into a BigWig file.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: 769-P human renal cell adenocarcinoma cell line (ATCC, CRL-1933) were all cultured in Roswell Park Memorial Institute (RPMI) 1640  supplemented with 10% fetal bovine serum. Cells were cultrued at 37℃ at 5% CO2.

extract_protocol:
The libraries were prepared by Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904).
The libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904). Sequencing was performed on the Illumina NovaSeq 6000 platform at Novogene, with biological replicates conducted twice to ensure reproducibility of the results.


title: DRB_5EU_Frag_p300KO_t45min_0J_rep1

description:
Library name: DRB_5EU_Frag_p300KO_t45min_0J_rep1
DRB_5EU_Frag_p300KO_0J_45min_merged.bw


title: CRISPR screening, 786-O,CRISPRi, Day0, replicate 1


title: APP/PS1 + OSK mPFC, replicate 4, snATACseq

city: Lausanne

first: Cesar

last: Sierra

address: SV 2513 (Bâtiment SV)

department: SV

country: Switzerland

institute: EPFL

library_source: genomic single cell

data_processing:
Single nuclei multimodal analysis. snRNA-seq and snATAC-seq libraries were processed with CellRanger-arc software (v. 2.0.0). Reads were aligned to a custom Mouse reference genome built from the mm10 genome and combined with the injected viral constructs for identification of infected GFP+ and OSK+ cells.
Assembly: mm10 genome combined with the injected viral constructs.
Supplementary files format and content: h5 file: contains both RNA-seq counts and ATAC-seq counts; tsv.gz: fragments file for ATAC-seq; tsv.gz.tbi: frangments file index for ATAC-seq

source_name: mPFC

extract_protocol:
Mice were sacrificed one day after the last recall session and the mPFC microdissected, flash-frozen in dry ice and finally stored in –80°C until processing. Nuclei were extracted as previously described (Misha). Briefly, tissue of individual animals was kept on ice throughout the protocol and first homogeneized in 600 µl of homogeneization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris⋅HCl, pH 7.4, 1 mM DTT, 1X protease inhibitor, 1 U/µl RiboLock RNAse inhibitor, 0.1% NP-40, in H20), gently filtered through a 40 µm cell strainer and washed with 1500 µl nuclei isolation medium (without NP-40). Samples were centrifuged for 8 min at 1000g and pellet resuspended in 210 µl of isolation medium and then added 290 µl of 50% iodixanol (optiprep, IDM 1X, 1 mM DTT, 1X protease inhibitor 50X, 1 U/µl RiboLock RNAse inhibitor). Nuclei suspension was carefully transferred to a Beckman tube (ref: 344090) and completed with 100 µl of nuclei isolation medium layered on top before ultracentrifugation at 10000g for 22 min using a SW 55 Ti rotor, for debris separation. The nuclei pellet was resuspended in 100 µl of permeabilization buffer (nuclei isolation medium plus 0.01%  Tween, 0.001% Digitonin, 0.01% NP-40, 0.5% BSA), kept on ice for 2 min at 4 °C and finally washed in 500 µl of nuclei isolation buffer plus 0.5% BSA. Samples were centrifuged at 1000g for 10 min at 4°C, pellets resuspended in diluted nuclei buffer (Chromium nuclei isolation kit, 10X Genomics) and nuclei filtered through a 40 µm Flowmi strainer before counting (average yield of 4000 nuclei/µl). Finally, nuclei were processed for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression sequencing
10X Multiome
snRNA-seq + snATAC-seq

value: mPFC

value: OSK


title: DRB_5EU_Frag_p300KO_t45min_20J_rep2

description:
Library name: DRB_5EU_Frag_p300KO_t45min_20J_rep2
DRB_5EU_Frag_p300KO_20J_45min_merged.bw


title: APP/PS1 + OSK mPFC, replicate 3, snATACseq


title: DRB_5EU_Frag_p300KO_t45min_0J_rep2

description:
Library name: DRB_5EU_Frag_p300KO_t45min_0J_rep2
DRB_5EU_Frag_p300KO_0J_45min_merged.bw


title: DRB_5EU_Frag_p300KO_t0_0J_rep2

description:
Library name: DRB_5EU_Frag_p300KO_t0_0J_rep2
DRB_5EU_Frag_p300KO_0J_t0_merged.bw


title: Skin, vehicle, A1

description:
Library name: sample1
10x Genomics


title: Skin, vehicle, A2

description:
Library name: sample2
10x Genomics


title: 5EU_WT_20J_rep2

description:
Library name: 5EU_WT_20J_rep2
Normalized_5EUseq.xlsx


title: CROP-seq,786-O,CRISPRa,scRNA

description: 10x Genomics

data_processing:
The raw sequencing data from 10x Genomics was initial processed with cell ranger-7.1.0 and resulting data were further filtered using Seurat v4.0.3.
Cells with mitochondrial percentage exceeding 10% or having less than 200 gene UMI were removed and genes that were expressed in less than 0.525% of cells were filtered out.
Droplets were also identified and removed using scDblFinder. Raw sequencing data of enriched sgRNA transcripts was also processed using cell ranger and reads that failed to align to the reference genome was extracted using Samtools to calculated the distribution of sgRNAs.
Assembly: hg38
Supplementary files format and content: filtered features matrix that contains cells and gene expression data.


title: CROP-seq,786-O,CRISPRi,scRNA

description: 10x Genomics


title: CROP-seq,Caki-1,CRISPRa,scRNA

description: 10x Genomics


title: DRB_5EU_Frag_p300KO_No5EU_rep1

description:
Library name: DRB_5EU_Frag_p300KO_No5EU_rep1
DRB_5EU_Frag_No5EU_merged.bw


title: 5EU_WT_20J_rep1

description:
Library name: 5EU_WT_20J_rep1
Normalized_5EUseq.xlsx


title: 5EU_WT_0J_rep2

description:
Library name: 5EU_WT_0J_rep2
Normalized_5EUseq.xlsx


title: APP/PS1 + OSK mPFC, replicate 1, snATACseq


title: APP/PS1 + OSK mPFC, replicate 2, snATACseq


title: 5EU_p300KO_20J_rep1

description:
Library name: 5EU_p300KO_20J_rep1
Normalized_5EUseq.xlsx


title: DRB_5EU_Frag_p300KO_t0_0J_rep1

description:
Library name: DRB_5EU_Frag_p300KO_t0_0J_rep1
DRB_5EU_Frag_p300KO_0J_t0_merged.bw


title: 5EU_p300KO_20J_rep2

description:
Library name: 5EU_p300KO_20J_rep2
Normalized_5EUseq.xlsx


title: APP/PS1 mPFC, replicate 3, snATACseq


title: 5EU_p300KO_0J_rep2

description:
Library name: 5EU_p300KO_0J_rep2
Normalized_5EUseq.xlsx


title: APP/PS1 mPFC, replicate 2, snATACseq


title: 5EU_WT_0J_rep1

description:
Library name: 5EU_WT_0J_rep1
Normalized_5EUseq.xlsx


title: CROP-seq,Caki-1,CRISPRi,scRNA

description: 10x Genomics


title: 5EU_p300KO_0J_rep1

description:
Library name: 5EU_p300KO_0J_rep1
Normalized_5EUseq.xlsx


title: 769P,ATACseq,rep2

data_processing:
The sequencing data was analyzed using the nf-core/atacseq pipeline
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
The libraries were prepared by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711)
The libraries were prepared by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711). Sequencing was performed on the Illumina NovaSeq 6000 platform at Novogene, with biological replicates conducted twice to ensure reproducibility of the results.


title: 769P,ATACseq,rep1


title: Poly_WT_20J_2h_rep1

description:
Library name: Poly_WT_20J_2h_rep1
Normalized_Polysomes_Total.xlsx

value: Polysome Enriched fractions


title: Poly_WT_20J_3h_rep2

description:
Library name: Poly_WT_20J_3h_rep2
Normalized_Polysomes_Total.xlsx


title: Poly_WT_0J_rep1

description:
Library name: Poly_WT_0J_rep1
Normalized_Polysomes_Total.xlsx


title: Poly_WT_20J_2h_rep2

description:
Library name: Poly_WT_20J_2h_rep2
Normalized_Polysomes_Total.xlsx


title: hPSC-Islet, EC protocol

city: Toronto

first: Maria

middle: Cristina

last: Nostro

address: 101 College Street

country: Canada

institute: McEwen Stem Cell Institute

description: 10x Genomics

data_processing:
Reads were demultiplexed, then aligned to the appropriate probe set reference, and transcripts were quantified
All analytic steps required to obtain the count matrices were done using CellRanger
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hPSC-Islets

growth_protocol: hPSCs were differentiated to NKX6-1-enhanced pancreatic progenitors, as delineated in the associated manuscript, and subsequently into islet-like cells with modifications according to the experimental condition

extract_protocol:
Approximately 8,000 cells per condition were sequenced after viability purification and fixation
Libraries were generated as per the protocol outlined for 10x genomics single cell fixed RNA profiling
Single Cell Fixed RNA profiling

treatment_protocol: hPSC-derived NKX6-1-enhanced pancreatic progenitors were patterned towards either islet or EC lineages

value: hPSC-Islets

value: hPSC-derived

value: Wild-type

value: EC patterning of NKX6-1-enhanced hPSC-PPs


title: APP/PS1 mPFC, replicate 1, snATACseq


title: RNAseq_Chr_p300KO_UV_08_rep2

data_processing:
RNA-seq FASTQ files were generated using BCL converter v4.2.7 (Illumina) for index identification. Sample quality was analyzed with FastQC v0.12.1. Reads were trimmed using Cutadapt v2.3 with the following parameters: -j 4 -m 18. Subsequently, reads were aligned to the hg19 genome using STAR 2.7.10a. Duplicate reads were removed using UMI-tools v1.1.4. FeatureCounts v2.0.3 was employed to calculate gene counts against either the human genome hg19 or the spike-in ERCC, using default parameters. Differential expression genes (DEGs) were identified using DESeq2 v1.34.0 and R v4.1.1, setting a q-value threshold of less than 0.05 and log2FC of 1.5. The geometric mean of the ERCC spike-in was used for sample normalization
Assembly: hg19
Supplementary files format and content: Tab-delimited tables with the comparision values between control and treatment using DESEQ2 and spike-in normalization

source_name: cell line

extract_protocol:
RNA was extracted using Trizol from chromatin-enriched or polysome-enriched fractions
RNAseq library were constructed using NEBNext Unique Dual Index UMI Adaptor and NEBNext Ultra II RNA Library Prep Kit for Illumina

value: cell line

value: p300 knock-out


title: Poly_Purif_WT_20J_2h_rep1

description:
Library name: Poly_Purif_WT_20J_2h_rep1
Normalized_WT_2h_Polysomes_Purified.xlsx

value: WT

value: Polysome Enriched fractions-5EU Purification


title: Poly_WT_20J_3h_rep1

description:
Library name: Poly_WT_20J_3h_rep1
Normalized_Polysomes_Total.xlsx


title: Poly_Purif_WT_0J_rep2

description:
Library name: Poly_Purif_WT_0J_rep2
Normalized_WT_2h_Polysomes_Purified.xlsx


title: Poly_Purif_WT_0J_rep1

description:
Library name: Poly_Purif_WT_0J_rep1
Normalized_WT_2h_Polysomes_Purified.xlsx


title: APP/PS1 + OSK mPFC, replicate 4, snRNAseq

molecule: nuclear RNA


title: hPSC-Islet, Islet protocol

description: 10x Genomics

value: Islet patterning of NKX6-1-enhanced hPSC-PPs


title: WT mPFC, replicate 3, snATACseq


title: WT mPFC, replicate 2, snATACseq


title: RNAseq_Chr_WT_UV_06_rep2


title: Poly_Purif_WT_20J_2h_rep2

description:
Library name: Poly_Purif_WT_20J_2h_rep2
Normalized_WT_2h_Polysomes_Purified.xlsx


title: Poly_WT_0J_rep2

description:
Library name: Poly_WT_0J_rep2
Normalized_Polysomes_Total.xlsx

value: Ctrl


title: Poly_Purif_p300KO_20J_3h_rep2

description:
Library name: Poly_Purif_p300KO_20J_3h_rep2
Normalized_p300KO_3h_Polysomes_Purified.xlsx

value: human cervical cancer


title: WT mPFC, replicate 1, snATACseq


title: APP/PS1 + OSK mPFC, replicate 3, snRNAseq


title: Poly_Purif_p300KO_20J_3h_rep1

description:
Library name: Poly_Purif_p300KO_20J_3h_rep1
Normalized_p300KO_3h_Polysomes_Purified.xlsx


title: Poly_Purif_p300KO_20J_2h_rep1

description:
Library name: Poly_Purif_p300KO_20J_2h_rep1
Normalized_p300KO_2h_Polysomes_Purified.xlsx


title: Poly_Purif_p300KO_0J_rep2

description:
Library name: Poly_Purif_p300KO_0J_rep2
Normalized_p300KO_2h_Polysomes_Purified.xlsx


title: RNAseq_Chr_p300KO_UV_04_rep1


title: RNAseq_Chr_p300KO_Ctrl_07_rep2


title: APP/PS1 + OSK mPFC, replicate 2, snRNAseq


title: RNAseq_Chr_WT_Ctrl_05_rep2


title: RNAseq_Chr_p300KO_Ctrl_03_rep1


title: Poly_Purif_p300KO_0J_rep1

description:
Library name: Poly_Purif_p300KO_0J_rep1
Normalized_p300KO_2h_Polysomes_Purified.xlsx


title: APP/PS1 + OSK mPFC, replicate 1, snRNAseq


title: Poly_Purif_p300KO_20J_2h_rep2

description:
Library name: Poly_Purif_p300KO_20J_2h_rep2
Normalized_p300KO_2h_Polysomes_Purified.xlsx


title: APP/PS1 mPFC, replicate 3, snRNAseq


title: RNAseq_Chr_WT_UV_02_rep1


title: APP/PS1 mPFC, replicate 2, snRNAseq


title: Poly_p300KO_20J_2h_rep1

description:
Library name: Poly_p300KO_20J_2h_rep1
Normalized_Polysomes_Total.xlsx


title: APP/PS1 mPFC, replicate 1, snRNAseq


title: Poly_p300KO_0J_rep2

description:
Library name: Poly_p300KO_0J_rep2
Normalized_Polysomes_Total.xlsx


title: Poly_p300KO_20J_2h_rep2

description:
Library name: Poly_p300KO_20J_2h_rep2
Normalized_Polysomes_Total.xlsx


title: RNAseq_Chr_WT_Ctrl_01_rep1


title: Poly_p300KO_0J_rep1

description:
Library name: Poly_p300KO_0J_rep1
Normalized_Polysomes_Total.xlsx


title: HeLa △P300, INPUT

description:
INPUT sample
P300_KO_INPUT

data_processing:
Single (or paired-end) read ChIP-seq fastq files were processed using the ENCODE-DCC/chip-seq-pipeline2 pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters and aligned to the hg19 genome. Peak calling was performed with MACS2 v2.2.4, and the peaks compared with each INPUT samples were used for subsequent analysis. DeepTools v3.3.1 was used to generate the ChIP-seq peak profiles for each sample. Bigwig output files were visualized in the UCSC genome browser (https://genome.ucsc.edu).
For strand-bias analysis, paired-end ChIPseq fastq files were aligned to the human genome hg19 using BWA-MEM v 0.7.17-r1188. The aligned files were converted to BAM files and sorted using Samtools v1.9. Duplicates reads were removed with Picard v3.00. Reads from each DNA strand (plus and minus) were split using Samtools. bamCoverage v3.3.1 using RPKM option was used to generate normalized ChIP-seq peak profiles for each sample.
For RNAPII mapping to CPD dimers, the same files utilized in the strand bias analysis were normalized to RPCG (1x genome coverage) using Deeptools v3.3.1. Dimer sites and flanking regions, extending 400 bases from both ends, were extracted from genes longer than 20 kb on chromosome 1 of the hg19 genome sequence in the positive strand of DNA. Read coverage for each sample were calculated using computeMatrix from Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig (Except for INPUT samples)

growth_protocol: DMEM (Gibco, #11965-092) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #10437-028), GlutaMAX (Gibco, #35050-061) and antibiotics (Penicillin-Streptomycin, Gibco, #15140-122).

extract_protocol:
Cells were cross-linked with ChIP Cross-link Gold (Diagenode, #C01019027). After incubation at room temperature for 30 min, the cells were fixed with a 1% formaldehyde solution (Thermo Fisher Scientific, #28908) for 10 min at room temperature. To stop the fixation, glycine was added to a final concentration of 125 mM and incubated for 5 min. The cells were then washed twice with PBS and harvested on ice using cell scrapers. The harvested cells were resuspended in ChIP lysis buffer supplemented with protease inhibitors (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.25% SDS) and sonicated on a Bioruptor Pico for 4 rounds of 10 cycles each at 4 °C with a short vortex between rounds to generate DNA fragments <500 bp.
Purified DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, #7370) following the manufacturer’s instructions.

value: human cervical cancer cell line (ATCC, #CCL-2)

value: P300 knockout

value: no-treatment

value: Rabbit monoclonal anti-Rbp1 NTD [clone D8L4Y], Cell Signaling Technology, #14958


title: HeLa, siUVSSA_DMSO_20J_rep2

description: Library name: siUVSSA_DMSO_20J_rep2

data_processing:
For strand-bias analysis, paired-end ChIPseq fastq files were aligned to the human genome hg19 using BWA-MEM v 0.7.17-r1188. The aligned files were converted to BAM files and sorted using Samtools v1.9. Duplicates reads were removed with Picard v3.00. Reads from each DNA strand (plus and minus) and split using Samtools. bamCoverage v3.3.1 using RPKM option was used to generate normalized ChIP-seq peak profiles for each sample. The resulting BigWig output files were visualized in the UCSC Genome Browser (https://genome.ucsc.edu). The Strand Specificity Index (SSI) was calculated based on the numbers of forward and reverse mapped reads, using the formula presented in Supplemental Figure 4E. Positive and negative SSI values indicate bidirectional gene orientation. Genes with fewer than 1 RPM were excluded from the analysis. The results were visualized with plotProfile from deepTools v 3.5.3. The lowest value among the profiles for each sample was used for graph normalization. In DRB-ChIP, samples were filtered with the IgG reads using bigwigCompare from deepTools v 3.5.3.
Assembly: hg19
Supplementary files format and content: Bigwig files with RPKM normalization with the reads of plus or minus DNA strand

value: HeLa

value: Human epithelial cell line derived from cervical cancer

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: HeLa WT, INPUT

description:
INPUT sample
WT_INPUT


title: HeLa, siUVSSA_DMSO_0J_rep2

description: Library name: siUVSSA_DMSO_0J_rep2


title: Poly_p300KO_20J_3h_rep1

description:
Library name: Poly_p300KO_20J_3h_rep1
Normalized_Polysomes_Total.xlsx

value: Polysome Enriched fractions


title: WO, HeLa WT, A485_WO, 20j3h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S24_A485WO_20j3h_rep2


title: HeLa, siUVSSA_DMSO_0J_rep1

description: Library name: siUVSSA_DMSO_0J_rep1


title: WT mPFC, replicate 2, snRNAseq

value: mPFC


title: HeLa, siUVSSA_DMSO_20J_rep1

description: Library name: siUVSSA_DMSO_20J_rep1


title: WT mPFC, replicate 3, snRNAseq


title: HeLa, siUVSSA_A485_20J_rep1

description: Library name: siUVSSA_A485_20J_rep1


title: HeLa, siUVSSA_A485_20J_rep2

description: Library name: siUVSSA_A485_20J_rep2


title: WT mPFC, replicate 1, snRNAseq


title: Lung, day-55-p.i.+glutamine, rep 4 [C1-15_Infection_D55+glutamine]

city: Newark

first: Ryan

last: Dikdan

state: NJ

address: 225 Warren St

department: Dept. of Medicine

institute: NJMS

description:
C1-15_Infection_D55+glutamine
V1_55vsC1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv

data_processing:
The resultant fastq files from transcriptomic sequencing were initially analyzed with Fastqc
The fastq files were then processed using fastp to trim adapters and filter based on quality
The processed fastq files were then aligned with the GENCODE GRCm39 primary assembly mouse genome using the STAR aligner. The GENCODE M31 gene annotations were used for gene counts.
Custom scripts in R were used to load the resulting gene counts from STAR into R. Transcripts per million (TPM) were calculated using a custom script along with genecode files and the samples’ raw counts were analyzed using DESeq2 and fGSEA for Differential Gene Expression (DGE) analysis and Gene Set Enrichment Analysis, respectively.
Assembly: GENCODE GRCm39 primary assembly
Supplementary files format and content: TPM and gene counts for each sample and differential gene expression data generated by DESeq2 across certain conditions are provided in csv files (as indicated in the corresponding sample description field)

source_name: lung

extract_protocol:
RNA was extracted from frozen lungs using RNAzol® RT Column Kit (Molecular research Center, Cincinnati, OH) following the manufacturer’s instruction
The library construction was performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA) and RNA sequencing by a NovaSeq S4 V1.5 (Illumina, California, USA).

treatment_protocol: Infected C57BL/6 mice were randomly assigned to two groups: (1) phosphate-buffered saline (PBS) or (2) glutamine supplementation. Glutamine was administered orally via gavage at a dosage of 500 mg/kg/day throughout the duration of the experiments. On days 12, 25, and 55 post-infection, both infected mice and uninfected control mice were sacrificed, and the lung tissues were collected and rapidly frozen in liquid nitrogen for subsequent RNA extraction and RNA-seq analysis.

value: lung


title: Poly_p300KO_20J_3h_rep2

description:
Library name: Poly_p300KO_20J_3h_rep2
Normalized_Polysomes_Total.xlsx


title: HeLa, siUVSSA_A485_0J_rep1

description: Library name: siUVSSA_A485_0J_rep1


title: WO, HeLa WT, A485_WO, 20j1h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S22_A485WO_20j1h_rep2


title: Lung, day-55-p.i.+glutamine, rep 3 [C1-14_Infection_D55+glutamine]

description:
C1-14_Infection_D55+glutamine
V1_55vsC1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: HeLa, sip62_DMSO_20J_rep2

description: Library name: sip62_DMSO_20J_rep2


title: WO, HeLa WT, A485_WO, Control, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S21_A485WO_Ctrl_rep2

value: A485_WO- Control


title: HeLa, sip62_DMSO_20J_rep1

description: Library name: sip62_DMSO_20J_rep1


title: Lung, day-55-p.i.+glutamine, rep 2 [C1-12_Infection_D55+glutamine]

description:
C1-12_Infection_D55+glutamine
V1_55vsC1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: HeLa, sip62_DMSO_0J_rep1

description: Library name: sip62_DMSO_0J_rep1


title: WO, HeLa WT, A485_WO, 20j2h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S23_A485WO_20j2h_rep2


title: WO, HeLa WT, A485_WO, 20j3h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S20_A485WO_20j3h_rep1


title: HeLa, sip62_A485_20J_rep1

description: Library name: sip62_A485_20J_rep1


title: HeLa, sip62_A485_20J_rep2

description: Library name: sip62_A485_20J_rep2


title: HeLa, siUVSSA_A485_0J_rep2

description: Library name: siUVSSA_A485_0J_rep2


title: Lung, day-55-p.i.+glutamine, rep 1 [C1-11_Infection_D55+glutamine]

description:
C1-11_Infection_D55+glutamine
V1_55vsC1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: Lung, day-55-p.i., rep 4 [V1-15_Infection_D55+H2O]

description:
V1-15_Infection_D55+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_55vsC1_55_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
UvsV1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: WO, HeLa WT, A485_WO, 20j2h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S19_A485WO_20j2h_rep1


title: HeLa, sip62_DMSO_0J_rep2

description: Library name: sip62_DMSO_0J_rep2


title: WO, HeLa WT, A485_WO, 20j1h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S18_A485WO_20j1h_rep1


title: HeLa, siCUL4A_DMSO_20J_rep2

description: Library name: siCUL4A_DMSO_20J_rep2


title: HeLa, sip62_A485_0J_rep1

description: Library name: sip62_A485_0J_rep1


title: HeLa, siCUL4A_DMSO_20J_rep1

description: Library name: siCUL4A_DMSO_20J_rep1


title: HeLa, sip62_A485_0J_rep2

description: Library name: sip62_A485_0J_rep2


title: HeLa, siCUL4A_DMSO_0J_rep2

description: Library name: siCUL4A_DMSO_0J_rep2


title: WO, HeLa WT, A485, 20j3h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S16_A485_20j3h_rep2


title: HeLa, siCUL4A_DMSO_0J_rep1

description: Library name: siCUL4A_DMSO_0J_rep1


title: Lung, day-55-p.i., rep 1 [V1-11_Infection_D55+H2O]

description:
V1-11_Infection_D55+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_55vsC1_55_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
UvsV1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: HeLa, siCUL4A_A485_20J_rep1

description: Library name: siCUL4A_A485_20J_rep1


title: HeLa, siCUL4A_A485_0J_rep2

description: Library name: siCUL4A_A485_0J_rep2


title: WO, HeLa WT, A485, 20j2h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S15_A485_20j2h_rep2


title: Lung, day-25-p.i.+ glutamine, rep 4 [C1-10_infection_D25_+_glutamine]

description:
C1-10_infection_D25_+_glutamine
V1_25vsC1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv

value: day-25-p.i.+ glutamine-4


title: HeLa, siCUL4A_A485_0J_rep1

description: Library name: siCUL4A_A485_0J_rep1

value: WT


title: Lung, day-55-p.i., rep 2 [V1-12_Infection_D55+H2O]

description:
V1-12_Infection_D55+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_55vsC1_55_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
UvsV1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: Lung, day-55-p.i., rep 3 [V1-14_Infection_D55+H2O]

description:
V1-14_Infection_D55+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_55vsC1_55_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
UvsV1_55_STAR_DESeq2.csv
C1_55vsV1_55_STAR_DESeq2.csv


title: WO, HeLa WT, A485_WO, Control, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S17_A485WO_Ctrl_rep1