title: Nanoplastic Treated Mice 4 - Left Ventricular Section

city: Singapore

first: Jeremy

last: Pang

address: 61 Biopolis Drive

country: Singapore

institute: A*STAR

description:
Library name: NP-4-D
NP4_D

data_processing:
Processed using scripts from https://github.com/singleron-RD/CeleScope (usage assay bulk_rna ).
Fastq file trimming and read filtering were performed using Celescope bulk_rna module
Spliced Transcripts Alignment to a Reference (STAR) aligner was used for mapping reads to reference geneome Mus_musculus_ensembl_99, implemented in the Celescope bulk_rna workflow
Feature count tool, part of Celecope bulk_rna workflow was used for gene quantification (UMI and genes).
Assembly: Mus_musculus_ensembl_99
Supplementary files format and content: tab-delimited text file which includes gene counts (count matrix)

source_name: Heart

extract_protocol:
Mouse hearts were perfused with cold PBS, sectioned accordingly to the sample labels, and homogenized for RNA isolation and purification using TRIZOL reagent.
Bulk RNA libraries were prepared using Singleron AccuraCode® RNA library construction kit, a plate-based high-throughput library construction kit, as per the manufacturer's instructions. Briefly, purified RNA sample was added into a well containing lysis buffer and magnetic oligo-dT beads to allow the release and capture of polyA RNA onto the beads. Subsequently, barcoded template-switching oligonucleotides (TSOs) were used to add well-specific barcodes to 5’-end of the RNA during reverse transcription. This barcoding step enables sample multiplexing after reverse transcription. Following the reverse transcription, the barcoded cDNA of all samples were pooled to streamline the downstream processing of cDNA amplification and bulk RNA sequencing library preparation. The generated NGS libraries were sequenced on an Illumina NovaSeq 6000 instrument (S4 V1.5) using a paired-end 150 bp approach

value: Heart

tag: tissue section

value: Left Ventricular Section

tag: treatment

value: Nanoplastics


title: Nanoplastic Treated Mice 4 - Atrial Section

status: Public on Apr 05 2026

type: SRA

description:
Library name: NP-4-B
NP4_B

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: Atrial Section


title: Kras_Q61R-d10_rep1_atac

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

country: USA

institute: Genentech, Inc.

description: Library name: Kras_Q61R-d10_rep1_atac

library_source: genomic single cell

data_processing:
. All snRNAseq and scATACseq datasets were pre-processed with 10X Cell Ranger ARC pipeline v.2.0.2, while all snRNAseq datasets were pre-processed with 10X Cell Ranger pipeline v.7.1.0. The genome was set to mm10-2020-A mouse genome reference, default parameters, and the platform set to 10x to Chromium Single Cell Multiome ATAC + Gene Expression kit or 10x Genomics v3.1 3’ scRNAseq kit. The 10X Cell Ranger pipeline performs read de-multiplexing, alignment, and unique molecular identifiers (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts in the case of RNAseq, and cells by unique fragments in the case of ATACseq.
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz

molecule: genomic DNA

source_name: Small intestine

extract_protocol:
Nuclei from cryo-preserved intestinal tissue was isolated using the Nuclei Isolation Kit (10x Genomics, 1000494). Briefly, tissue was cut on ice in lysis buffer supplemented with RNase inhibitor, transferred to a 1.5ml tube, further dissociated using a pestle, and lysed for 10 min. The remainder of the nuclei isolation was performed according to manufacturing instructions.
cDNA yield was quantified using High Sensitivity D5000 ScreenTape on a TapeStation (Agilent Technologies), library preparation was performed using Dual Index Plate TT (10x Genomics), followed by quantification on TapeStation (Agilent Technologies) and a Qubit fluorometer (Thermo Fisher Scientific). ATAC libraries were performed using Sample Index Plate N, Set A (10x Genomics, 3000427) by quantification on TapeStation (Agilent Technologies) and a Qubit fluorometer (Thermo Fisher Scientific) before submission for sequencing. The libraries were multiplexed and then sequenced on Illumina NovaSeq (Illumina) to generate at least 96M (expression) or 112M (ATAC) paired-end reads.

value: Small intestine

tag: genotype


title: Nanoplastic Treated Mice 4 - Right Ventricular Section

description:
Library name: NP-4-C
NP4_C

value: Right Ventricular Section


title: Apc_KO_Kras_G12D_rep1_atac

description: Library name: Apc_KO_Kras_G12D_rep1_atac

data_processing:
All snRNAseq and scATACseq datasets were pre-processed with 10X Cell Ranger ARC pipeline v.2.0.2, while all snRNAseq datasets were pre-processed with 10X Cell Ranger pipeline v.7.1.0. The genome was set to mm10-2020-A mouse genome reference, default parameters, and the platform set to 10x to Chromium Single Cell Multiome ATAC + Gene Expression kit or 10x Genomics v3.1 3’ scRNAseq kit. The 10X Cell Ranger pipeline performs read de-multiplexing, alignment, and unique molecular identifiers (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts in the case of RNAseq, and cells by unique fragments in the case of ATACseq.
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz, bam files, filtered_feature_bc_matrix.h5


title: Nanoplastic Treated Mice 3 - Left Ventricular Section

description:
Library name: NP-3-D
NP3_D


title: Apc_KO_Kras_WT_rep2_atac

description: Library name: Apc_KO_Kras_WT_rep2_atac


title: Apc_KO_Kras_Q61R_rep1_atac

description: Library name: Apc_KO_Kras_Q61R_rep1_atac


title: Nanoplastic Treated Mice 3 - Right Ventricular Section

description:
Library name: NP-3-C
NP3_C


title: Nanoplastic Treated Mice 2 - Left Ventricular Section

description:
Library name: NP-2-D
NP2_D


title: Apc_KO_Kras_Q61R_rep5

description: Library name: Apc_KO_Kras_Q61R_rep5

library_source: transcriptomic single cell

data_processing:
All snRNAseq data were pre-processed with 10X Cell Ranger ARC pipeline v.2.0.2, while all snRNAseq datasets were pre-processed with 10X Cell Ranger pipeline v.7.1.0. The genome was set to mm10-2020-A mouse genome reference, default parameters, and the platform set to 10x Genomics v3.1 3’ scRNAseq kit. The 10X Cell Ranger pipeline performs read de-multiplexing, alignment, and unique molecular identifiers (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5

molecule: nuclear RNA

extract_protocol:
Nuclei from cryo-preserved intestinal tissue was isolated using the Nuclei Isolation Kit (10x Genomics, 1000494). Briefly, tissue was cut on ice in lysis buffer supplemented with RNase inhibitor, transferred to a 1.5ml tube, further dissociated using a pestle, and lysed for 10 min. The remainder of the nuclei isolation was performed according to manufacturing instructions.
cDNA yield was quantified using High Sensitivity D5000 ScreenTape on a TapeStation (Agilent Technologies), library preparation was performed using Dual Index Plate TT (10x Genomics), followed by quantification on TapeStation (Agilent Technologies) and a Qubit fluorometer (Thermo Fisher Scientific). The libraries were multiplexed and then sequenced on Illumina NovaSeq (Illumina) to generate at least 96M  paired-end reads.


title: Nanoplastic Treated Mice 1 - Right Ventricular Section

description:
Library name: NP-1-C
NP1_C


title: Nanoplastic Treated Mice 3 - Atrial Section

description:
Library name: NP-3-B
NP3_B


title: Control Mice 2 - Left Ventricular Section

description:
Library name: UT-2-D
UT2_D

value: Control


title: Control Mice 3 - Atrial Section

description:
Library name: UT-3-B
UT3_B


title: Control Mice 1 - Left Ventricular Section

description:
Library name: UT-1-D
UT1_D


title: Control Mice 2 - Atrial Section

description:
Library name: UT-2-B
UT2_B


title: H42R_elSt_mut_rep3

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description:
Library name: RNA_Sample_78
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10
Supplementary files format and content: BigWig files created using the function qExportWig from the QuasR package for 100bp  tiles in the mm10 genome.

source_name: Testis

extract_protocol:
FACS-isolated populations of ScLZ, ScPD, rSt and elSt cells were pelleted at 2000g for 10 min at 4°C. Total RNA was extracted from cell pellets using the RNeasy Mini Kit (Qiagen 74104) according to manufacturer’s instructions. DNA removal was performed using on-column the RNase-Free DNase Set (Qiagen, 79254). RNA concentration was determined with Qubit RNA HS Assay Kit (Q32852). Quality of RNA was determined using Fragment Analyzer system
Libraries were prepared with the Illumina Stranded total RNA-seq protocol according to manufacturer’s instructions. Quality control of libraries was performed with Agilent 2100 Bioanalyzer System.  After passing the QC, sequencing was performed on Illumina NovaSeq platform (50 bp, paired end).

treatment_protocol: ScLZ, ScPD, rSt and elSt cells used for RNA-seq, we used a previously published protocol based on dual staining of DNA (Gill et al. 2024) on BD FACSAria II

value: Testis

tag: cell type

value: Elongating spermatids

tag: replicate


title: Nanoplastic Treated Mice 2 - Atrial Section

description:
Library name: NP-2-B
NP2_B


title: Control Mice 3 - Left Ventricular Section

description:
Library name: UT-3-D
UT3_D


title: H42R_rSt_het_rep3

description:
Library name: RNA_Sample_75
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution

value: Round spermatids

value: wt/-


title: Control Mice 2 - Right Ventricular Section

description:
Library name: UT-2-C
UT2_C


title: Nanoplastic Treated Mice 2 - Right Ventricular Section

description:
Library name: NP-2-C
NP2_C


title: H42R_elSt_mut_rep2

description:
Library name: RNA_Sample_72
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: Control Mice 1 - Atrial Section

description:
Library name: UT-1-B
UT1_B


title: H42R_elSt_wt_rep3

description:
Library name: RNA_Sample_74
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution

value: wt/wt


title: Nanoplastic Treated Mice 1 - Left Ventricular Section

description:
Library name: NP-1-D
NP1_D


title: H42R_elSt_het_rep2

description:
Library name: RNA_Sample_70
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: Control Mice 3 - Right Ventricular Section

description:
Library name: UT-3-C
UT3_C


title: Nanoplastic Treated Mice 1 - Atrial Section

description:
Library name: NP-1-B
NP1_B


title: H42R_rSt_mut_rep2

description:
Library name: RNA_Sample_71
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: Control Mice 1 - Right Ventricular Section

description:
Library name: UT-1-C
UT1_C


title: H42R_elSt_het_rep3

description:
Library name: RNA_Sample_76
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_rSt_wt_rep3

description:
Library name: RNA_Sample_73
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_rSt_mut_rep3

description:
Library name: RNA_Sample_77
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_rSt_het_rep2

description:
Library name: RNA_Sample_69
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_elSt_wt_rep2

description:
Library name: RNA_Sample_68
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_elSt_het_rep1

description:
Library name: RNA_Sample_64
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_rSt_wt_rep2

description:
Library name: RNA_Sample_67
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_rSt_het_rep1

description:
Library name: RNA_Sample_63
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: V24A_rSt_wt_rep3

description:
Library name: RNA_Sample_55
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_mut_rep3

description:
Library name: RNA_Sample_60
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_wt_rep3

description:
Library name: RNA_Sample_56
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_rSt_het_rep3

description:
Library name: RNA_Sample_57
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: H42R_rSt_mut_rep1

description:
Library name: RNA_Sample_65
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: V24A_elSt_wt_rep2

description:
Library name: RNA_Sample_50
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_mut_rep1

description:
Library name: RNA_Sample_48
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: H42R_elSt_mut_rep1

description:
Library name: RNA_Sample_66
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: H42R_rSt_wt_rep1

description:
Library name: RNA_Sample_61
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: V24A_rSt_het_rep2

description:
Library name: RNA_Sample_51
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: H42R_elSt_wt_rep1

description:
Library name: RNA_Sample_62
RNA-seq experiment to estimate the effect of the H3.4 to H3.4H42R substitution


title: V24A_rSt_mut_rep2

description:
Library name: RNA_Sample_53
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_rSt_wt_rep2

description:
Library name: RNA_Sample_49
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_mut_rep2

description:
Library name: RNA_Sample_54
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_het_rep3

description:
Library name: RNA_Sample_58
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_rSt_mut_rep3

description:
Library name: RNA_Sample_59
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_het_rep2

description:
Library name: RNA_Sample_52
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_rSt_wt_rep1

description:
Library name: RNA_Sample_43
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: H31_rSt_mut_rep4

description:
Library name: RNA_Sample_42
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Replicate 4


title: V24A_rSt_mut_rep1

description:
Library name: RNA_Sample_47
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_het_rep1

description:
Library name: RNA_Sample_46
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: H31_ScPD_mut_rep4

description:
Library name: RNA_Sample_41
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Pachytene/diplotene spermatocytes


title: V24A_rSt_het_rep1

description:
Library name: RNA_Sample_45
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: V24A_elSt_wt_rep1

description:
Library name: RNA_Sample_44
RNA-seq experiment to estimate the effect of the H3.4 to H3.4V24A substitution


title: H31_ScLZ_mut_rep4

description:
Library name: RNA_Sample_40
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Leptotene/zygotene spermatocytes


title: H31_rSt_het_rep4

description:
Library name: RNA_Sample_38
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: wt/ko


title: H31_elSt_het_rep4

description:
Library name: RNA_Sample_39
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: ORX_E12

city: Los Angeles

first: Aparna

last: Bhaduri

state: CA

address: 615 Charles E Young Dr S

institute: University of California Los Angeles

description:
Library name: Invivo_E12_ORX
invivo.rds

data_processing:
Cellranger v8
Assembly: GRCh38
Supplementary files format and content: Counts Matrix

source_name: Cortex

extract_protocol:
single-cell or single-nuclei purification
10X GEM-X or OCM

value: Cortex

value: Neural

value: ORX

tag: batch


title: H31_elSt_wt_rep3

description:
Library name: RNA_Sample_35
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Replicate 3


title: H31_rSt_wt_rep3

description:
Library name: RNA_Sample_34
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: Male, Donor3, Wild Type, Simulated Microgravity

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

description: Library name: CD36-SMG-M-WT-13-HM-061124_S25

data_processing:
Genes with a maximum read count below 10 were filtered out. The remaining data were normalized in sequential steps (Add:1.0, TMM, and log2 transformations). Differentially expressed genes (DEGs) were identified using the Limma-voom method with established p-value and fold change cutoffs. Data visualization, including principal component analysis (PCA), hierarchical clustering, Venn diagram construction, and gene set enrichment analyses, was performed within Partek® Flow®.
Assembly: mm39
Supplementary files format and content: CD36_ProcessedData_NormalizedCount.txt

source_name: Tissue-Meniscus

extract_protocol:
Meniscus tissue from three mice per group was used for bulk RNA sequencing. Immediately following the three-week mechanical stimulation, all four menisci from each mouse were pooled and preserved in TRIzol at −80°C, yielding one data point per mouse. Total RNA was extracted from ground tissue using the PuroSPIN™ NanoElute™ Total RNA Purification Kit (Luna Nanotech, Canada) according to the manufacturer’s instructions. Purified RNA samples were submitted to the University of British Columbia Biomedical Research Centre (UBC-BRC) for next-generation sequencing on the Illumina NextSeq 2000 platform. Sequencing reads were returned in FastQ format for downstream bioinformatics analyses.
Raw sequencing reads were processed in Partek® Flow® (version 12.5.0). A Phred quality score threshold of 20 was applie d to trim bases from the 3′ end. Trimmed reads were aligned to the mouse genome (mm39) using the STAR aligner (v2.7.8a), then quantified against mm39-GENCODE Genes (release M35) using the Partek E/M algorithm.

treatment_protocol: Four distinct experimental groups: 1.Female CD36 ko mice 2.Female C57Bl/6 control mice 3.Male CD36 ko mice 4.Male C57Bl/6 control mice.

value: Tissue-Meniscus

value: Wild Type

value: Simulated Microgravity


title: H31_ScPD_het_rep4

description:
Library name: RNA_Sample_37
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: H31_ScLZ_het_rep4

description:
Library name: RNA_Sample_36
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: NHEK, control, 24 h, n=1

type: RNA

city: Tokyo

first: Hitomi

last: Hagawa

address: 7-2-1 Hirai, Edogawa-ku

department: Research & Development Headquarters

country: Japan

institute: Lion Corporation

description: control

hyb_protocol: Biotin-labeled, fragmented cDNA was hybridized to Affymetrix/Thermo Fisher cartridge arrays using the GeneChip Hybridization, Wash and Stain Kit, according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned according to the manufacturer’s instructions described in the Affymetrix GeneChip Command Console User Manual (P/N 702569).

data_processing: Raw CEL files obtained from three independent samples per condition (n = 3) were imported into R software (version 4.3.2) and processed using the distribution-based Robust Multichip Analysis (RMA) algorithm, including background correction, normalization, and summarization to transcript cluster–level expression values.

label: biotin

organism: Homo sapiens

source_name: normal human epidermal keratinocytes (NHEKs)

label_protocol: The fragmented cDNA was then labeled with biotin using terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent.

growth_protocol: NHEKs were seeded and grown in six-well plates until they were subconfluent in a 37℃, 5% CO2 incubator.

extract_protocol: Total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality and quantity were evaluated using an Agilent 2100 Bioanalyzer.

treatment_protocol: The control samples (only the medium) and 2.0% hydrolyzed corn starch in the medium were added, and after cells were cultured for 24 h.

value: NHEKs


title: NHEK, control, 24 h, n=3

description: control


title: H31_elSt_mut_rep3

description:
Library name: RNA_Sample_31
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Testis


title: H31_ScLZ_mut_rep3

description:
Library name: RNA_Sample_28
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: H31_ScPD_mut_rep3

description:
Library name: RNA_Sample_29
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: NHEK, 2.0% Hydrolyzed corn starch, 24 h, n=3

description: NHEKs treated with 2.0% hydrolyzed corn starch for 24 h; total RNA used for Clariom S human array.

value: 2.0% Hydrolyzed corn starch


title: H31_rSt_het_rep3

description:
Library name: RNA_Sample_26
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Round spermatids


title: H31_ScLZ_wt_rep3

description:
Library name: RNA_Sample_32
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: Male, Donor2, Wild Type, Simulated Microgravity

description: Library name: CD36-SMG-M-WT-12-HM-061124_S24


title: DMSO_E12

description:
Library name: Invivo_E12_DMSO
invivo.rds

value: DMSO


title: H31_rSt_mut_rep3

description:
Library name: RNA_Sample_30
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: H31_elSt_het_rep3

description:
Library name: RNA_Sample_27
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Elongating spermatids


title: ORX_E15

description:
Library name: Invivo_E15_ORX
invivo.rds


title: H31_ScPD_het_rep3

description:
Library name: RNA_Sample_25
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: NHEK, 2.0% Hydrolyzed corn starch, 24 h, n=1


title: NHEK, control, 24 h, n=2

description: control


title: NHEK, 2.0% Hydrolyzed corn starch, 24 h, n=2


title: H31_ScPD_wt_rep3

description:
Library name: RNA_Sample_33
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: wt/wt


title: H31_ScLZ_het_rep3

description:
Library name: RNA_Sample_24
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: Male, Donor1, Wild Type, Simulated Microgravity

description: Library name: CD36-SMG-M-WT-11-HM-061124_S23


title: DMSO_E15

description:
Library name: Invivo_E15_DMSO
invivo.rds


title: H31_rSt_wt_rep2

description:
Library name: RNA_Sample_22
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Replicate 2


title: Female, Donor2, Knockout, Simulated Microgravity

description: Library name: CD36-SMG-M-KO-5-HM-061124_S33

value: CD36 Knockout


title: H31_elSt_wt_rep2

description:
Library name: RNA_Sample_23
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: H31_ScPD_wt_rep2

description:
Library name: RNA_Sample_21
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Pachytene/diplotene spermatocytes


title: H31_ScLZ_wt_rep2

description:
Library name: RNA_Sample_20
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Leptotene/zygotene spermatocytes


title: Female, Donor3, Wild Type, Simulated Microgravity

description: Library name: CD36-SMG-F-WT-9-HM-061124_S19


title: H31_rSt_mut_rep2

description:
Library name: RNA_Sample_18
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: EZ_T_rep3

city: Berlin

first: Teresa

last: Kowar

address: Königin-Luise-Str. 12-14

country: Germany

institute: Freie Universität Berlin

description: Library name: R353EZ_T

data_processing:
Reads were aligned to the C. merolae genome using the ENSEMBL genome sequence and genome annotation (Cunningham et al., 2022) and STAR aligner v2.7.9a (Dobin et al., 2013).
Reads were counted with FeatureCounts v2.0.1 (Liao et al., 2014) after exclusion of low-quality reads (MAPQ < 10).
Assembly: ASM9120v1.46
Supplementary files format and content: text file containing the raw counts for each protein-coding gene from FeatureCount, reanalyzed samples have the GSM-sampla accession number as column name

molecule: polyA RNA

organism: Cyanidioschyzon merolae

source_name: cell culture

growth_protocol: For experimental preparation, algae were grown in 2x Modified Allen’s (MA2) medium at 42 °C and constant light (90 µE) and ambient air supply for several days to an OD(750nm) = 1.0

extract_protocol:
RNA was extracted from the pelleted 2ml of cellculture using the innuPREP plant RNA kit (Analytik Jena) , adding 1% β-Mercaptoethanol to the lysis solution to increase RNA quality.
mRNA library was prepared using polyA enrichment and the NEBnext Ultra RNA Library Prep Kit producing unstranded data.

treatment_protocol: Cell culture tubes were heat stressed in 57°C for 30 min and/or 60°C for 15 min using a waterbath. When both stresses were applied the two treatments were divided by a 24h lag phase at 42°C.

value: cell culture

value: Cme(z)-1, 24h lag-phase in 42°C followed by 15min in 60°C, replicate 3


title: Female, Donor1, Knockout, Simulated Microgravity

description: Library name: CD36-SMG-M-KO-1-HM-061124_S26


title: EZ_PLT_rep3

description: Library name: R363EZ_PLT

value: Cme(z)-1, 30min in 57°C followed by 24h lag-phase in 42°C followed by 15min in 60°C, replicate 3


title: EZ_PL_rep3

description: Library name: R343EZ_PL

value: Cme(z)-1, 30min in 57°C followed by 24h lag-phase in 42°C, replicate 3


title: H31_ScPD_het_rep2

description:
Library name: RNA_Sample_14
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: wt/ko


title: Female, Donor1, Wild Type, Simulated Microgravity

description: Library name: CD36-SMG-F-WT-5-HM-061124_S18

value: Tissue-Meniscus

value: Wild Type

value: Simulated Microgravity


title: EZ_NL_rep3

description: Library name: R333EZ_NL

value: Cme(z)-1, naive after 24h lag-phase, replicate 3


title: Female, Donor2, Wild Type, Simulated Microgravity

description: Library name: CD36-SMG-F-WT-6-HM-061124_S32


title: Female, Donor3, Knockout, Simulated Microgravity

description: Library name: CD36-SMG-M-KO-10-HM-061124_S27


title: DD_mNeu

description:
Library name: 2D_directed_differentiation_mNeu
twodimensional_diff.rds

molecule: cytoplasmic RNA

source_name: Cell Culture

value: Cell Culture

tag: cell line

value: Neural


title: H31_elSt_mut_rep2

description:
Library name: RNA_Sample_19
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Testis

value: Elongating spermatids


title: H31_rSt_het_rep2

description:
Library name: RNA_Sample_15
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Round spermatids

value: Replicate 2


title: H31_ScLZ_mut_rep2

description:
Library name: RNA_Sample_16
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: H31_ScLZ_het_rep2

description:
Library name: RNA_Sample_13
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: Male, Donor3, Knockout, Simulated Microgravity

description: Library name: CD36-SMG-F-KO-15-HM-061124_S22

value: CD36 Knockout


title: H31_ScPD_mut_rep2

description:
Library name: RNA_Sample_17
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Pachytene/diplotene spermatocytes


title: DD_NbN

description:
Library name: 2D_directed_differentiation_NbN
twodimensional_diff.rds


title: WT_PLT_rep3

description: Library name: R303WT_PLT

value: cell culture

value: 10D wild type

value: 10D wild type, 30min in 57°C followed by 24h lag-phase in 42°C followed by 15min in 60°C, replicate 3


title: DD_NPC

description:
Library name: 2D_directed_differentiation_NPC
twodimensional_diff.rds


title: EZ_P_rep3

description: Library name: R323EZ_P

value: Cme(z)-1, 57°C for 30 min, replicate 3


title: H31_elSt_wt_rep1

description:
Library name: RNA_Sample_12
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: wt/wt

value: Replicate 1


title: Female, Donor4, Knockout, Simulated Microgravity

description: Library name: CD36-SMG-F-KO-5-HM-061124_S21

value: Tissue-Meniscus


title: WT_T_rep3

description: Library name: R293WT_T

value: 10D wild type, 24h lag-phase in 42°C followed by 15min in 60°C, replicate 3


title: DD_RGC

description:
Library name: 2D_directed_differentiation_RGC
twodimensional_diff.rds


title: H31_rSt_wt_rep1

description:
Library name: RNA_Sample_11
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: WT_PL_rep3

description: Library name: R283WT_PL

value: 10D wild type, 30min in 57°C followed by 24h lag-phase in 42°C, replicate 3


title: H31_ScPD_wt_rep1

description:
Library name: RNA_Sample_10
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: WT_NL_rep3

description: Library name: R273WT_NL

value: 10D wild type, naive after 24h lag-phase, replicate 3


title: Male, Donor1, Knockout, Simulated Microgravity

description: Library name: CD36-SMG-F-KO-3-HM-061124_S20

value: Simulated Microgravity


title: H31_ScLZ_wt_rep1

description:
Library name: RNA_Sample_9
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Testis

value: Leptotene/zygotene spermatocytes


title: Male, Donor3, Wild Type, Static

description: Library name: CD36-SC-M-WT-9-HM-061124_S31

value: Wild Type

value: Static


title: PPPi_inhibition_1.U6Wk12ORXplusRedox_2.KolfWk12ORXplusRibose_3.U1W12ORXplusRibose_4.U6W12ORXplusRibose

description:
Library name: PPPi_OCM_Lane6_withrescues
PPPiandRescue.rds

source_name: Cortical Organoid

value: Cortical Organoid

value: UCLA1, UCLA6, KOLF

value: Neural


title: Female, Donor3, Wild Type, Static

description: Library name: CD36-SC-F-WT-6-HM-061124_S30


title: PPPi_inhibition_1.U1Wk12ORX_2.U6Wk12ORX_3.KolfW12ORXplusRedox_4.U1W12ORXplusRedox

description:
Library name: PPPi_OCM_Lane5_withrescues
PPPiandRescue.rds


title: WT_P_rep3

description: Library name: R263WT_P

value: cell culture

value: 10D wild type

value: 10D wild type, 57°C for 30 min, replicate 3


title: H31_elSt_mut_rep1

description:
Library name: RNA_Sample_8
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Elongating spermatids


title: PPPi_inhibition_1.KolfWk12DMSO_2.U1Wk12DMSO_3.U6Wk12DMSO_4.KolfW12ORX

description:
Library name: PPPi_OCM_Lane4_v2
PPPiandRescue.rds


title: PPPi_inhibition_1.KolfWk12Ribose_2.KolfWk12Nucleotide_3.U1Wk12Nucleotide_4.U6Wk12Nucleotide

description:
Library name: Sufficiency_OCM_Lane3
Sufficiency.rds


title: Male, Donor2, Wild Type, Static

description: Library name: CD36-SC-M-WT-8-HM-061124_S34


title: PPPi_inhibition_1.KolfWk12ORXplusNuc_2.U1Wk12ORXplusNuc_3.U6Wk12ORXplusNuc_4.U1Wk12ORXplusNuc

description:
Library name: PPPi_OCM_Lane7_withrescues
PPPiandRescue.rds


title: Male, Donor1, Wild Type, Static

description: Library name: CD36-SC-M-WT-1-HM-061124_S35


title: EZ_T_rep2

description: Library name: R232EZ_T

value: Cme(z)-1, 24h lag-phase in 42°C followed by 15min in 60°C, replicate 2


title: EZ_PLT_rep2

description: Library name: R242EZ_PLT

value: Cme(z)-1, 30min in 57°C followed by 24h lag-phase in 42°C followed by 15min in 60°C, replicate 2


title: EZ_NL_rep2

description: Library name: R212EZ_NL

value: Cme(z)-1, naive after 24h lag-phase, replicate 2


title: Female, Donor2, Wild Type, Static

description: Library name: CD36-SC-F-WT-5-HM-061124_S29

value: Tissue-Meniscus


title: Female, Donor1, Wild Type, Static

description: Library name: CD36-SC-F-WT-1-HM-061124_S28


title: H31_ScLZ_mut_rep1

description:
Library name: RNA_Sample_5
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Replicate 1


title: H31_ScPD_mut_rep1

description:
Library name: RNA_Sample_6
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Pachytene/diplotene spermatocytes


title: WT_PL_rep2

description: Library name: R222EZ_PL

value: 10D wild type, 30min in 57°C followed by 24h lag-phase in 42°C, replicate 2


title: H31_elSt_het_rep1

description:
Library name: RNA_Sample_4
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Testis

value: wt/ko


title: embryo, Picrotoxin, rep2

city: Fujisawa

first: Masaki

last: Hachiman

state: Kanagawa

address: 5322 Endo

department: Graduate School of Media and Governance

institute: Keio University

description:
Library name: Picrotoxin, rep2
P2_S522

data_processing:
RaNA-Seq version 1.0 (https://ranaseq.eu/)
The Xenopus laevis v10.1 reference genome registered in NCBI was used for mapping (RefSeq ID: GCF_017654675.1).
Assembly: Xenopus_laevis_v10.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

organism: Xenopus laevis

source_name: embryo

extract_protocol:
RNA was harvested using  RNAiso (#9107, TaKaRa Bio Inc., Kusatsu, Shiga, Japan).
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Set (DNBSEQ-G400, MGI Tech Co., Shenzhen, China) following manufacturer's protocols.

value: embryo

tag: Stage

value: tail bud stage

tag: incubate time

value: 3 h

value: Picrotoxin


title: PPPi_inhibition_1.KolfW12untreated_2.U1Wk12untreated_3.U6Wk12untreated_4.KolfWk12Redox

description:
Library name: Sufficiency_OCM_Lane1
Sufficiency.rds

value: Cortical Organoid

value: UCLA1, UCLA6, KOLF

value: Neural


title: H31_ScPD_het_rep1

description:
Library name: RNA_Sample_2
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution


title: H31_rSt_het_rep1

description:
Library name: RNA_Sample_3
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Round spermatids


title: embryo, Control, rep2

description:
Library name: Control, rep2
C2_S520

value: Control


title: EZ_P_rep2

description: Library name: R202EZ_P

value: cell culture

value: Cme(z)-1, 57°C for 30 min, replicate 2


title: MCF7, Input

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description: Library name: MCF7_Input

library_source: genomic

data_processing:
FASTQ files were mapped to human genome (GRCh38) using Hisat2 (version 2.0.5) with default option.
The bigWig files were generated using deeptools (version 3.5.4) bamCoverage with the option "--binSize 100 --normalizeUsing CPM --smoothLength 1000".
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: Minimum Essential Medium (MEM) Alpha no phenol red containing 10 % FBS, 0.1 mM MEM Non-essential amino acids (NEAA), 1 mM Sodium pyruvate, and 10 µg/mL Insulin .

extract_protocol:
Cells were fixed with formaldehyde solution in the culture mediumfor 5 min. After cell lysis, chromatin was sonicated using a Branson 250 Sonifier (Branson Ultrasonics).
ChIP library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

value: Human metastatic mammary carcinoma cell line.

tag: chip antibody


title: H31_ScLZ_het_rep1

description:
Library name: RNA_Sample_1
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Leptotene/zygotene spermatocytes

value: Replicate 1


title: embryo, Picrotoxin, rep1

description:
Library name: Picrotoxin, rep1
P1_S521


title: WT_PLT_rep2

description: Library name: R182WT_PLT

value: 10D wild type

value: 10D wild type, 30min in 57°C followed by 24h lag-phase in 42°C followed by 15min in 60°C, replicate 2


title: MCF7, KPNA2-Abcam antibody, ChIP

description: Library name: MCF7_KPNA2_Abcam

value: KPNA2 (Abcam, rabbit pAb, ab84440)


title: WT_T_rep2

description: Library name: R172WT_T

value: 10D wild type, 24h lag-phase in 42°C followed by 15min in 60°C, replicate 2


title: EZ_PL_rep2

description: Library name: R162WT_PL

value: Cme(z)-1, 30min in 57°C followed by 24h lag-phase in 42°C, replicate 2


title: MCF7, KPNA2-BD antibody, ChIP

description: Library name: MCF7_KPNA2_BD

value: KPNA2 (BD Transduction. Mouse mAb, #610486)


title: ScPD_tg_Myc_rep2

description: Library name: ChIP_Sample_36

extract_protocol:
Conventional ChIP: ChIP-seq in post-replicative cell populations (ScPD and rSt) was performed as follows. Chromatin from FACS-isolated ScPD and rSt populations was prepared by incubating cells for 20 min on ice in lysis buffer (50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1% Triton X-100, 0.2% sodium deoxycholate, 5 mM CaCl2) containing 5 U MNase (Roche Nuclease S7 10107921001) per 1M cells. After incubation on ice, chromatin was digested for 10 min at 37°C. The MNAse reaction was stopped by adding EGTA to 50 mM final concentration. The IP reactions were performed overnight at 4ºC on a rotator in the following proportions. To profile H3 isoforms, chromatin from 50K ScPD or 200K rSt was incubated with 5 µl of antibodies (anti-MYC: Abcam ab9132, anti-H3.3: Cosmo Bio CE-040B). To profile H3K4me3 and H3K27me3 in ScPD cells, chromatin from 1200K ScPD was incubated with 3 µl of antibodies (anti-H3K4me3: Millipore 17-614, anti-H3K27me3: Cell Signaling #9733). Per sample, 25 µl of 1:1 mix of protein A:protein G Dynabeads (Thermo Fisher Scientific, 10001D and 10003D) was washed once with 25 µl lysis dilution buffer (50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1% Triton X-100, 0.2% sodium deoxycholate, 50 mM EGTA), then added to chromatin-antibody mix and incubated on a rotator for 4 h at 4ºC. The Chromatin-Antibody-Dynabeads complexes were washed twice with 200 µl of RIPA buffer (140 mM NaCl, 10 mM Tris-HCl (pH 8.0), 0.1% Sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 1 mM EDTA), once with 200 µl high salt buffer (140 mM NaCl, 10 mM Tris-HCl (pH 8.0), 0.1% Sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 1 mM EDTA), once with 200 µl LiCl wash buffer (250 mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, (pH 8.0)), and once with 200 µl TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Finally, chromatin was eluted and digested for 1 h at 63ºC in Elution buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.1% SDS, 300 mM NaCl). DNA from eluted material was purified by 2X volumes of Ampure XP DNA purification beads (Beckman Coulter, A63881) according to manufacturer’s instructions and resuspended in 9 µl of nuclease-free water. . ULI-ChIP: To profile the H3 isoforms, chromatin from 5K SgU or 10K SgD, ScLZ or ScPD cells were used with 0.5 µl of anti-H3.3 (Cosmo Bio CE-040B) or 0.5 µl anti-Myc (Abcam ab9132) antibodies per sample. ULI-ChIP-seq libraries were prepared from the eluted ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645L)
Conventional ChIP: The eluted ChIP DNA was used to prepare libraries using the NEB Ultra protocol according to the manufacturer’s instructions. The libraries were sequenced in a 50 pb single end mode on the Illumina HiSeq 2500 platform, according to the manufacturer’s instructions. ULI-ChIP: Libraries were sequenced in 50-bp paired-end mode with Illumina NovaSeq 6000 using the manufacturer’s instructions

treatment_protocol: for conventional ChIP-seq, ScPD and rSt samples were isolated using FACS according to a previously published protocol (Gill et al. 2024). For ULI (ultra-low input) experiments, SgU, SgD, ScLZ and ScPD populations were isolated according to a protocol published in Fanourgakis et al. 2025. All FACS experiments were done on BD FACSAria II.

value: Testis

tag: chip protocol

value: ULI (ultra-low input)

value: Pachytene/diplotene spermatocytes

value: MYC/wt

value: Replicate 2

tag: antibody

value: MYC-tag (abcam ab9132)


title: embryo, Control, rep1

description:
Library name: Control, rep1
C1_S519

value: embryo

value: tail bud stage

value: 3 h

value: Control


title: H31_rSt_mut_rep1

description:
Library name: RNA_Sample_7
RNA-seq experiment to estimate the effect of the H3.4 to H3.1 substitution

value: Round spermatids

value: Replicate 1


title: 2cpab_albino_3

city: Sevilla

first: Fernando

last: Rodríguez-Marín

state: Sevilla

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Library name: Sample9

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Assembly: tair10
Supplementary files format and content: comma-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

source_name: Six-day-old seedlings (albino seedlings)

extract_protocol:
RNA extraction was performed using Sure Prep kit (Fisher), following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina Stranded mRNA prep ligation kit (Illumina) were used for the construction of cDNA libraries.

value: 2cpab mutant

value: Six days in continuous light at 125 µE m−2 s−1 grown in MS with sucrose


title: WT_NL_rep2

description: Library name: R152WT_NL

value: cell culture

value: 10D wild type

value: 10D wild type, naive after 24h lag-phase, replicate 2


title: ScPD_tg_H3.3_rep2

description: Library name: ChIP_Sample_35

value: Testis

value: H3.3 (Cosmo Bio CE-040B)


title: 2cpab_albino_2

description: Library name: Sample8

value: Six-day-old seedlings (albino seedlings)


title: ScPD_wt_H3.3_rep2

description: Library name: ChIP_Sample_34

value: ULI (ultra-low input)

value: Pachytene/diplotene spermatocytes

value: wt/wt


title: 2cpab_albino_1

description: Library name: Sample7


title: EZ_T_rep1

description: Library name: R111EZ_T

value: Cme(z)-1, 24h lag-phase in 42°C followed by 15min in 60°C, replicate 1


title: WT_P_rep2

description: Library name: R142WT_P

value: 10D wild type, 57°C for 30 min, replicate 2


title: EZ_PLT_rep1

description: Library name: R121EZ_PLT

value: Cme(z)-1, 30min in 57°C followed by 24h lag-phase in 42°C followed by 15min in 60°C, replicate 1


title: PPPi_inhibition_1.U1Wk12Redox_2.U6Wk12Redox_3.U6Wk12Ribose_4.U1Wk12Ribose

description:
Library name: Sufficiency_OCM_Lane2
Sufficiency.rds

value: Cortical Organoid

value: UCLA1, UCLA6

value: Neural


title: 2cpab_green_3

description: Library name: Sample6

source_name: Six-day-old seedlings (green seedlings)

value: Six-day-old seedlings (green seedlings)

value: 2cpab mutant


title: ScPD_tg_H3.3_rep1

description: Library name: ChIP_Sample_32

value: MYC/wt

value: Replicate 1


title: EZ_PL_rep1

description: Library name: R101EZ_PL

value: cell culture

value: Cme(z)-1, 30min in 57°C followed by 24h lag-phase in 42°C, replicate 1


title: ScPD_wt_H3.3_rep1

description: Library name: ChIP_Sample_31

value: Testis

value: H3.3 (Cosmo Bio CE-040B)


title: 2cpab_green_1

description: Library name: Sample4

value: Six days in continuous light at 125 µE m−2 s−1 grown in MS with sucrose


title: adjacent normal bladder tissues_Rep2, SUP

city: Shanghai

first: Bo

last: Peng

address: 301 Yanchang Road

department: Department of Urology

country: China

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

description: raw data file: D50464-N.txt

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.

source_name: supernatant

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Obtaining samples after surgery

tag: sample id

tag: fraction

value: unmodified RNAs

value: adjacent normal bladder tissues


title: ScPD_tg_Myc_rep1

description: Library name: ChIP_Sample_33

value: ULI (ultra-low input)

value: Pachytene/diplotene spermatocytes

value: MYC-tag (abcam ab9132)


title: bladder cancer tissues_Rep2, SUP

description: raw data file: D50464-T.txt

value: bladder cancer tissues


title: ScLZ_tg_Myc_rep2

description: Library name: ChIP_Sample_30

value: Leptotene/zygotene spermatocytes

value: Replicate 2


title: 2cpab_green_2

description: Library name: Sample5

value: Six-day-old seedlings (green seedlings)


title: EZ_NL_rep1

description: Library name: R91EZ_NL

value: Cme(z)-1, naive after 24h lag-phase, replicate 1


title: bladder cancer tissues_Rep3, SUP

description: raw data file: D65756-T.txt


title: bladder cancer tissues_Rep1, SUP

description: raw data file: D45979-T.txt


title: adjacent normal bladder tissues_Rep3, SUP

description: raw data file: D65756-N.txt


title: EZ_P_rep1

description: Library name: R81EZ_P

value: 10D wild type, 57°C for 30 min, replicate 1


title: wt_3

description: Library name: Sample3

source_name: Six-day-old seedlings

value: Six-day-old seedlings


title: adjacent normal bladder tissues_Rep1, SUP

description: raw data file: D45979-N.txt


title: WT_PLT_rep1

description: Library name: R61WT_PLT

value: cell culture

value: 10D wild type

value: 10D wild type, 30min in 57°C followed by 24h lag-phase in 42°C followed by 15min in 60°C, replicate 1


title: wt_2

description: Library name: Sample2


title: ScLZ_tg_H3.3_rep2

description: Library name: ChIP_Sample_29

value: Testis

value: MYC/wt

value: H3.3 (Cosmo Bio CE-040B)


title: wt_1

description: Library name: Sample1

value: Six days in continuous light at 125 µE m−2 s−1 grown in MS with sucrose


title: WT_PL_rep1

description: Library name: R41WT_PL

value: 10D wild type, 30min in 57°C followed by 24h lag-phase in 42°C, replicate 1


title: WT_T_rep1

description: Library name: R51WT_T

value: 10D wild type, 24h lag-phase in 42°C followed by 15min in 60°C, replicate 1


title: ScLZ_wt_H3.3_rep2

description: Library name: ChIP_Sample_28

value: ULI (ultra-low input)

value: wt/wt


title: NTCP_Positive_B

city: Jerusalem

first: Johnny

last: Amer

address: Ein kerem

country: Israel

institute: Hadassah Hospital

description: Library name: NTCP_Positive_B

data_processing:
The counts data was generated with cellranger, v6.0.2, aligning against the human genome GRCh38 with gene annotations from Ensembl release 99. Default parameters were used with expected number of cells set to 10,000.
Single-cell analysis was performed via Seurat version 5.2.0 40 in R version 4.4.3.
Integration was conducted with default parameters, using SCT normalization, embedded within Seurat.
Assembly: GRCh38
Supplementary files format and content: For each of the samples, a cell barcodes file, a features file, and a UMI count matrix in Market Exchange format  are provided
Supplementary files format and content: The supplementary files per-series include the RNA counts of the integrated dataset (integrated_NKC__all4samples__RNA_count_matrix.txt) and selected metadata of the integrated dataset (integrated_NKC__all4samples__metadata.txt)

source_name: Blood

extract_protocol:
Isolation of NK cells from peripheral blood  Peripheral NK cells were isolated from two representative F3/F4 advanced liver fibrosis MASH patients (A and B) selected based on age and sex and were sorted on the basis of NTCP expression as described below.                                                                                Peripheral blood (20 mL) was obtained by venipuncture and collected into 5 mL sodium citrate tubes. Samples were diluted 1:1 with phosphate-buffered saline (PBS), gently mixed, and layered over an equal volume of Ficoll-Paque (GE17-1440-02; Merck) in a separate tube. Tubes were centrifuged at 515 × g for 20 minutes at room temperature without acceleration or braking. The lymphocyte-containing interface was collected under sterile conditions, transferred to a new tube, and washed with PBS or cell wash buffer by centrifugation at 515 × g for 10 minutes to remove residual contaminants.NK cells were isolated from the lymphocyte fraction using a Human NK Cell Isolation Kit (Catalog #17955; STEMCELL) via negative selection, following the manufacturer’s instructions. Briefly, non-NK cells included T cells, B cells, stem cells, dendritic cells, monocytes, granulocytes, and erythroid cells were magnetically labeled with a biotin-conjugated antibody cocktail (NK Cell RapidSpheres™) and removed, leaving untouched NK cells for downstream experiments. Following removal of dead cells via the Dead Cell Removal Kit (Miltenyi Biotec).                                                                                Fluorescence-activated cell sorting: NK cells [3X106/100 ul of PBS] were stained with 500 nM preS1(2-48)-myr-FITC with a cocktail of NTCP antibodies targeted for different extracellular epitopes, such as anti-NTCP (BS-1958R, Thermo), anti-NTCP (D-5) Alexa Fluor 488 (sc-518115, Santa Cruz Biotechnology), for 45 minutes at 4°C (these antibodies showed a fluorescent signal without NK permeabilization). NK cells were then sorted based on NTCP expression (NKNTCP- and NKNTCP+) via a FACSAria III Cell Sorter (BD FACSAria) for fluorescence-activated cell sorting (FACS). The cells that did not present NTCP-positive staining represented the NTCP-negative population. This was confirmed by comparable staining patterns following the use of isotype IgG labeled with the relevant fluorochrome [isotype negative control].
Approximately 10,000 cells from each NK cell subpopulation (NKNTCP+ and NKNTCP-) were loaded into the Chromium Controller system. The RNA libraries were subsequently prepared via the Chromium Single Cell 3’ Reagent Kit v.3 (10X Genomics) according to the manufacturer’s instructions.

value: Blood

value: Peripheral NK cells

tag: disease state

value: Liver fibrosis F4 score

value: FACS sorted NTCP+


title: ScLZ_tg_Myc_rep1

description: Library name: ChIP_Sample_27

value: Leptotene/zygotene spermatocytes

value: Replicate 1

value: MYC-tag (abcam ab9132)


title: adjacent normal bladder tissues_Rep3, IP

description: raw data file: D65756-N.txt

source_name: m6A immunoprecipitated

value: m6A modified RNAs

value: adjacent normal bladder tissues


title: NTCP_Negative_B

description: Library name: NTCP_Negative_B

value: FACS sorted NTCP-


title: ScLZ_tg_H3.3_rep1

description: Library name: ChIP_Sample_26

value: Testis

value: MYC/wt


title: adjacent normal bladder tissues_Rep2, IP

description: raw data file: D50464-N.txt


title: adjacent normal bladder tissues_Rep1, IP

description: raw data file: D45979-N.txt


title: ScLZ_wt_H3.3_rep1

description: Library name: ChIP_Sample_25

value: H3.3 (Cosmo Bio CE-040B)


title: bladder cancer tissues_Rep3, IP

description: raw data file: D65756-T.txt

value: bladder cancer tissues


title: WT_NL_rep1

description: Library name: R31WT_NL

value: cell culture

value: 10D wild type

value: 10D wild type, naive after 24h lag-phase, replicate 1


title: WT_P_rep1

description: Library name: R21WT_P

value: 10D wild type, 57°C for 30 min, replicate 1


title: SgD_tg_Myc_rep2

description: Library name: ChIP_Sample_24

value: ULI (ultra-low input)

value: Differentiating spermatogonia

value: Replicate 2


title: bladder cancer tissues_Rep2, IP

description: raw data file: D50464-T.txt


title: NTCP_Negative_A

description: Library name: NTCP_Negative_A

value: Blood

value: Peripheral NK cells

value: Liver fibrosis F4 score


title: NTCP_Positive_A

description: Library name: NTCP_Positive_A

value: FACS sorted NTCP+


title: SgD_wt_H3.3_rep2

description: Library name: ChIP_Sample_22

value: wt/wt


title: AKPS_iAPC_Divarasib_rep3

description: Library name: AKPS_iAPC_Divarasib_rep3

data_processing:
ENCODE ATAC-seq pipeline (v2.2.2)
Assembly: mm10
Supplementary files format and content: Bigwig fold-change
Supplementary files format and content: Bigwig p-value

source_name: AKPS-iAPC organoid

growth_protocol: Plate cells at 1×10^5 cells/ml in 80 μL Matrigel domes (12-well plate), grown for 3 days, then treated for 48 h with divarasib (10 nM), doxycycline (200 ng/ml) or their combination.

extract_protocol:
Cells were harvested, nuclei was isolated according to the ActiveMotif ATACseq protocol.
Libaries were constructed according ot the ActiveMotif ATACseq protocol.

value: AKPS-iAPC organoid

value: Diva


title: hiPSC day 0 rep 3

city: Manchester

first: Jacob

last: Sampson

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description: Library name: CM18_S18

data_processing:
Transcript expression quantification was carried out with RSEM v1.3.3, using GENCODE v47.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated table where each row corresponds to the TPM values for all samples (columns 4 onwards) for a unique GENCODE transcript_id (column 1), with the corresponding gene_id (column 2) and gene_name (column 3).

source_name: hiPSC - AD4

growth_protocol: Retinal organoid protocol based on Protocol based on Chichagova V, Dorgau B, Felemban M, Georgiou M, Armstrong L, Lako M. Differentiation of Retinal Organoids from Human Pluripotent Stem Cells. Curr Protoc Stem Cell Biol. 2019 Sep;50(1):e95. doi: 10.1002/cpsc.95.

extract_protocol:
Total RNA was extracted using Rneasy micro kit (Qiagen).
Sequencing libraries were generated using the Illumina® Stranded mRNA Prep. Ligation kit following manufacturer's instructions.

treatment_protocol: No treatment

value: hiPSC - AD4

value: Pluripotent stem cell

value: WT


title: SgD_tg_H3.3_rep2

description: Library name: ChIP_Sample_23

value: Testis

value: MYC/wt

value: H3.3 (Cosmo Bio CE-040B)


title: AKPS_iAPC_Divarasib_rep1

description: Library name: AKPS_iAPC_Divarasib_rep1


title: AKPS_iAPC_Divarasib_rep2

description: Library name: AKPS_iAPC_Divarasib_rep2


title: SgD_tg_Myc_rep1

description: Library name: ChIP_Sample_21

value: Replicate 1

value: MYC-tag (abcam ab9132)


title: bladder cancer tissues_Rep1, IP

description: raw data file: D45979-T.txt

value: m6A modified RNAs

value: bladder cancer tissues


title: AKPS_iAPC_GNE_7883_rep2

description: Library name: AKPS_iAPC_GNE_7883_rep2

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie (Pau and Reeder, 2012) in BioConductor (Huber et al., 2015) as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. The remaining reads were aligned to the reference genome mouse: GRCm38.p5 using GSNAP (PMID:20147302, 27008021) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes data base (GENCODE M15). To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
Assembly: GRCm38
Supplementary files format and content: The tab-delimited text file contains raw exonic RNA-seq counts for each sample.

growth_protocol: Plate cells at 1×10^5 cells/ml in 80 μL Matrigel domes (12-well plate), grown for 3days, then treated for 24 h with divarasib (10 nM), doxycycline (200 ng/ml), GNE-7883 (1 μM), or their combination.

extract_protocol:
RNA was isolated using RNAeasy kit (Qiagen) and on column DNA digestion.
Total RNA was quantified with Quant-iT RiboGreen RNA Kit (Thermo Fisher Scientific) on Victor X2 Multilabel Microplate Reader (PerkinElmer) and quality was assessed using High Sensitivity RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For sequencing library generation, the Illumina Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) on Victor X2 Multilabel Microplate Reader (PerkinElmer) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq X Plus (Illumina) to generate 30 millions single-end 50-base pair reads for each sample.


title: AKPS_iAPC_GNE_7883_rep1

description: Library name: AKPS_iAPC_GNE_7883_rep1


description: Library name: AKPS_iAPC_Divarasib_APC_restoration_rep3


title: hiPSC day 0 rep 2

description: Library name: CM17_S17


title: AKPS_iAPC_Divarasib_rep3

description: Library name: AKPS_iAPC_Divarasib_rep3


title: hiPSC day 0 rep 1

description: Library name: CM16_S16


title: SgD_tg_H3.3_rep1

description: Library name: ChIP_Sample_20

value: ULI (ultra-low input)

value: Differentiating spermatogonia


title: AKPS_iAPC_GNE_7883_rep3

description: Library name: AKPS_iAPC_GNE_7883_rep3


title: Retinal organoid day 150 batch 5

description: Library name: CM15_S15

source_name: Retinal organoid

value: Retinal organoid

value: Retinal differentiation


title: AKPS_iAPC_Divarasib_rep2

description: Library name: AKPS_iAPC_Divarasib_rep2


description: Library name: AKPS_iAPC_Divarasib_APC_restoration_rep2


title: AKPS_iAPC_Divarasib_rep1

description: Library name: AKPS_iAPC_Divarasib_rep1


description: Library name: AKPS_iAPC_Divarasib_APC_restoration_rep1


title: Retinal organoid day 150 batch 4

description: Library name: CM14_S14


title: SgU_tg_Myc_rep2

description: Library name: ChIP_Sample_18

source_name: Testis

value: Undifferentiated spermatogonia

value: Replicate 2


title: Retinal organoid day 120 batch 4

description: Library name: CM11_S11


title: AKPS_iAPC_Divarasib_GNE_7883_rep3

description: Library name: AKPS_iAPC_Divarasib_GNE_7883_rep3

value: AKPS-iAPC organoid


title: SgU_wt_H3.3_rep2

description: Library name: ChIP_Sample_16

value: wt/wt


title: SgD_wt_H3.3_rep1

description: Library name: ChIP_Sample_19


title: SgU_tg_Myc_rep1

description: Library name: ChIP_Sample_15


title: AKPS_iAPC_DMSO_rep3

description: Library name: AKPS_iAPC_DMSO_rep3

value: DMSO


title: AKPS_iAPC_Divarasib_GNE_7883_rep2

description: Library name: AKPS_iAPC_Divarasib_GNE_7883_rep2


title: AKPS_iAPC_DMSO_rep1

description: Library name: AKPS_iAPC_DMSO_rep1


title: Retinal organoid day 150 batch 2

description: Library name: CM13_S13

value: hiPSC - AD4

value: WT


title: Retinal organoid day 120 batch 5

description: Library name: CM12_S12


title: AKPS_iAPC_Divarasib_APC_restoration_rep3


title: AKPS_iAPC_DMSO_rep2

description: Library name: AKPS_iAPC_DMSO_rep2


title: SgU_tg_H3.3_rep2

description: Library name: ChIP_Sample_17

value: Testis

value: MYC/wt


title: AKPS_iAPC_Divarasib_GNE_7883_rep1

description: Library name: AKPS_iAPC_Divarasib_GNE_7883_rep1


title: AKPS_iAPC_APC_restoration_rep2

description: Library name: AKPS_iAPC_APC_restoration_rep2

value: Dox


title: AKPS_iAPC_APC_restoration_rep3

description: Library name: AKPS_iAPC_APC_restoration_rep3


title: Retinal organoid day 120 batch 2

description: Library name: CM10_S10


title: SgU_wt_H3.3_rep1

description: Library name: ChIP_Sample_13

value: Replicate 1

value: H3.3 (Cosmo Bio CE-040B)


title: Retinal organoid day 90 batch 5

description: Library name: CM9_S9


title: SgU_tg_H3.3_rep1

description: Library name: ChIP_Sample_14


title: AKPS_iAPC_Divarasib_APC_restoration_rep2


title: Retinal organoid day 90 batch 4

description: Library name: CM8_S8


title: Retinal organoid day 90 batch 2

description: Library name: CM7_S7


title: PANC-1, siHDAC5

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

description: Library name: Sample 3

data_processing:
Sequencing read quality was inspected using the fastqc v0.11.9. Adapter removal and read trimming were performed using fastp v0.23.3. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 20).
Alignment performed using bwa-mem2 2.2.1
deepTools v3.5.0 was used to generate bigWig files.
macs2 v2.2.7.1 was used to call peaks.
Assembly: hg38
Supplementary files format and content: BW (BigWig) files contain the genome data for each sample.

growth_protocol: DMEM,15% fetal bovine serum,2mM glutamine,1x penicillin/streptomycin..Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutesAfter auenching and cell livsis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Seq libraries were prepared using the KAPA HTP Library Preparaion Kit comoemented wih NEXTflex DNA Barcodes from Bioo Scientific. 10ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in lenath using Agencourt AlMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: human pancreatic cancer cells

value: MYC


title: AKPS_iAPC_APC_restoration_rep1

description: Library name: AKPS_iAPC_APC_restoration_rep1


title: BMDM 4 treated with 2.5uM bilirubin

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQ generated with bcl2fastq (version 2.20.0.422) files were processed using the nf-core/rnaseq pipeline (version 3.12, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCm39, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCm39
Supplementary files format and content: *_quant.sf.gz: Salmon transcript quantification file (tab-sparated text, https://salmon.readthedocs.io/en/latest/file_formats.html); to be used together with salmon_tx2gene.tsv by software accepting Salmon data

source_name: Bone-marrow derived macrophages (BMDM)

extract_protocol:
Bone marrow was flushed from the hind tibia and femurs of 8-week old female Balb/CJ mice using the protocol detailed in (doi: 10.3791/53936). After which bone marrow was filtered with at 40-micron filter and pelleted via centrifugation. Pellets were treated with 2 mLs ACK (150 mM Ammonium Chloride, 1 mM Potassium Bicarbonate, 0.1 mM EDTA, pH 7.4) to lyse red blood cells that was quenched with the addition of 10 mLs of HBSS. Cells were washed 2x with HBSS (400 mg/L KCl, 60 mg/L KH2PO4, 350 mg/L NaHCO3, 8000 mg/L NaCl, 48 ng/L Na2HPO4, 1,100 mg/L dextrose anhydrase) then resuspended in 10 mLs growth media (RMPI + 10% FBS + 1% pen/strep) and plated (~1.125-2 x 10^6 cells per petri dish). To differentiate cells into macrophages, they were treated with 25 ng/mL M-CSF (Shenandoah, 200-08) upon plating and again 2 days later. After 5 days, BMDM were treated with 2.5 uM bilirubin or DMSO control. After 48 hours treatment with bilirubin, mRNA was isolated from BMDM using TriZOL extraction as recommended by the manufacturer (FisherScientific, 15596-018).
Poly A selected total RNA library was prepared after mRNA extraction

value: Bone-marrow derived macrophages (BMDM)

tag: mouse pair

value: BMDM 4


description: Library name: AKPS_iAPC_Divarasib_APC_restoration_GNE_7883_rep3


title: PANC-1, siControl

description: Library name: Sample 2

value: siControl


title: Retinal organoid day 60 batch 2

description: Library name: CM4_S4

value: Retinal organoid

value: Retinal differentiation


title: BMDM 4 treated with vehicle control


title: conv_ScPD_H3K4me3

description: Library name: ChIP_Sample_41

value: conventional

value: Pachytene/diplotene spermatocytes

value: H3K4me3 (Millipore 17-614)


title: PANC-1, Input

description: Library name: Sample 1


description: Library name: AKPS_iAPC_Divarasib_APC_restoration_GNE_7883_rep2

value: AKPS-iAPC organoid


title: AKPS_iAPC_Divarasib_APC_restoration_rep1


title: BMDM 2 treated with 2.5uM bilirubin

value: BMDM 2


title: Retinal organoid day 60 batch 4

description: Library name: CM5_S5

value: hiPSC - AD4

value: WT


description: Library name: AKPS_iAPC_Divarasib_APC_restoration_GNE_7883_rep1


title: AKPS_iAPC_DMSO_rep3

description: Library name: AKPS_iAPC_DMSO_rep3

value: DMSO


title: Retinal organoid day 60 batch 5

description: Library name: CM6_S6


title: BMDM 3 treated with vehicle control

value: BMDM 3


title: conv_ScPD_H3K27me3

description: Library name: ChIP_Sample_40

value: Testis

value: wt/wt

value: Replicate 1

value: H2K27me3 (Cell Signaling 9733)


title: ScLZ_H3K27me3_rep1

description: Library name: ChIP_Sample_39

value: ULI (ultra-low input)

value: Leptotene/zygotene spermatocytes


title: BMDM 3 treated with 2.5uM bilirubin

value: Bone-marrow derived macrophages (BMDM)


title: AKPS_iAPC_DMSO_rep2

description: Library name: AKPS_iAPC_DMSO_rep2


title: Retinal organoid day 35 batch 2

description: Library name: CM1_S1

value: Retinal organoid

value: Retinal differentiation


title: ScPD_H3K4me3_rep1

description: Library name: ChIP_Sample_38

value: Pachytene/diplotene spermatocytes


title: BMDM 1 treated with 2.5uM bilirubin

value: BMDM 1


title: ScLZ_H3K4me3_rep1

description: Library name: ChIP_Sample_37

value: H3K4me3 (Millipore 17-614)


title: BMDM 1 treated with vehicle control


title: AKPS_iAPC_APC_restoration_rep2

value: AKPS-iAPC organoid

value: Dox


title: AKPS_iAPC_APC_restoration_rep3


title: Retinal organoid day 35 batch 4

description: Library name: CM2_S2

value: hiPSC - AD4

value: WT


title: AKPS_iAPC_DMSO_rep1

description: Library name: AKPS_iAPC_DMSO_rep1

value: DMSO


title: AKPS_iAPC_APC_restoration_rep1


title: PD_rep2_mut_Myc

description: Library name: ChIP_Sample_12

value: Testis

value: conventional

value: MYC/wt

value: Replicate 2

value: MYC-tag (abcam ab9132)


title: hearts, transduced with AAV-FGF17, rep4

city: Wenzhou

first: Chao

last: Niu

address: 109 Xueyuan West Road, Lucheng District

institute: Wenzhou Medical University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software(v0.11.7)
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt(v1.17)) were aligned to reference genome(GRCm38) using Hisat2 software(v2.1.0)
The transcript abundance for each sample was estimated with StringTie(v1.3.3), and the FPKM value for gene and transcript level was calculated with R package Ballgown(v2.10.0)
Assembly: GRCm38
Supplementary files format and content: the FPKM value of detected mRNA for each sample

source_name: Heart

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart


title: MDA PCa 189-1, scRNAseq

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description:
Library name: MDA PCa 189-1
10x Genomics

data_processing:
Since thes samples were derived from PDX models containing both human cancer cells and mouse cells (host), mouse cells were filtered out.  Briefly, the raw scRNAseq data were aligned to the combined human-mouse genomic reference (hg38-mm10) using the 10X Genomics Cell Ranger software (version 7.0.1) including introns to generate the barcode classification and the ‘cellranger count’ function to generate html QC metrics and fastq files for each sample. Further, the raw FASTQ data were aligned to human-only reference (hg38) by Cell Ranger.
Assembly: GRCm38/mm10, GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: prostate

extract_protocol:
Fresh tissue from  PDXs MDA PCa 177-B and MDA PCa 189-1PDXs was harvested and tissue dissociation to single cell suspension was performed using the enzymatic mix solution Accumax (Thermofisher, Cat. No.: 00-4666-56) for 20 min at 37°C under rotation. The cells were washed twice with PBS through cell strainer (70 μm) and centrifuged at 1,500 rpm for 5 min. The single cell suspensions were diluted in PBS with 0.4% BSA and transferred to the MDACC ATGC facility of MDACC for scRNA library processing using the Chromium Single Cell Gene Expression 10X Genomics protocol
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: baseline

value: tumor cells

value: prostate

tag: strain

value: PDX


title: MDA PCa 177-B, scRNAseq

description:
Library name: MDA PCa 177-B
10x Genomics


title: AKPS_iAPC_APC_restoration_GNE_7883_rep3

description: Library name: AKPS_iAPC_APC_restoration_GNE_7883_rep3

tag: treatment


title: H929, Treated rep3

description: Library name: SAR1nM_s3

data_processing:
Fastq files were processed using the nf-core/rnaseq pipeline (version 3.12.0, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the human transcriptome (GRCh38, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCh38
Supplementary files format and content: Txt file containg gene counts

growth_protocol: H929 cells were maintained at 1E6 cells million per 1mL and incubated at 37°C with 5% CO2 in RPMI 1640 medium with added 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin (ThermoFisher). Cell lines were validated using short tandem repeat polymorphism profile match analysis performed by the University of Colorado Cancer Center Cell Technologies Shared Research Core and checked for mycoplasma contamination annually using the MycoALert Detection Kit test (Lonza).

extract_protocol:
RNAeasy Plus Mini Kit (Qiagen). iScript cDNA Synthesis kit (BioRad) was used to convert RNA to cDNA for sequencing by the University of Colorado Cancer Center Genomics and Microarray Shared Resource Core.
A selected total RNA libraries were generated using the Universal Plus mRNA-Seq kit with NuQuant (Tecan).

treatment_protocol: Conditioned media was prepared with PBMC and H929 coculture with or without 1nM SAR442257. Conditioned media (supernatant) was extracted following

tag: tissue

value: Blood

value: myeloma

value: unmodified

value: SAR442257 (TCE) conditioned media


title: hearts, transduced with AAV-FGF17, rep3


title: PD_rep2_wt_H3_3

description: Library name: ChIP_Sample_10

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10
Supplementary files format and content: BigWig files created using the function qExportWig from the QuasR package for 100bp  tiles in the mm10 genome.

value: Pachytene/diplotene spermatocytes

tag: genotype

value: wt/wt

value: H3.3 (Cosmo Bio CE-040B)


title: hearts, transduced with AAV-FGF17, rep2


title: H929, Treated rep2

description: Library name: SAR1nM_s2

tag: cell type


title: AKPS_iAPC_APC_restoration_GNE_7883_rep2

description: Library name: AKPS_iAPC_APC_restoration_GNE_7883_rep2

value: AKPS-iAPC organoid


title: PD_rep2_mut_H3_3

description: Library name: ChIP_Sample_11

value: Testis

tag: replicate


title: hearts, transduced with AAV-FGF17, rep1


title: H929, Treated rep1

description: Library name: SAR1nM_s1


title: Kras_Q61R_vehicle_rep3

description: Library name: Kras_Q61R_vehicle_rep3

source_name: Small intestine

extract_protocol:
RNA was isolated using RNAeasy kit (Qiagen) and on column DNA digestion.
Total RNA was quantified with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies). For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pair reads for each sample.

treatment_protocol: Mice of both sexes, 6-12 weeks of age, were induced with 100mg/kg tamoxifen (Sigma-Aldrich T5648) dissolved in corn oil (Sigma-Aldrich C8267) by intraperitoneal injection with two doses, one day rest (0, 2d).

value: Small intestine

value: Kras Q61R

value: Vehicle

tag: batch


title: PD_rep1_mut_Myc

description: Library name: ChIP_Sample_9

value: conventional

value: MYC/wt

value: Replicate 1

value: MYC-tag (abcam ab9132)


title: PD_rep1_wt_H3_3

description: Library name: ChIP_Sample_7


title: hearts, transduced with control vector, rep3

value: Heart


title: PD_rep1_mut_H3_3

description: Library name: ChIP_Sample_8


title: H929, Untreated rep3

description: Library name: SAR1nM_u3

value: Blood

tag: cell line

value: untreated conditioned media


title: AKPS_iAPC_APC_restoration_GNE_7883_rep1

description: Library name: AKPS_iAPC_APC_restoration_GNE_7883_rep1


title: hearts, transduced with control vector, rep2


title: BMDM 2 treated with vehicle control

value: Bone-marrow derived macrophages (BMDM)

value: BMDM 2


title: Kras_Q61R_vehicle_rep2

description: Library name: Kras_Q61R_vehicle_rep2


title: hearts, transduced with control vector, rep4


title: H929, Untreated rep1

description: Library name: SAR1nM_u1

value: myeloma

value: unmodified


title: Kras_Q61R_vehicle_rep1

description: Library name: Kras_Q61R_vehicle_rep1


title: H929, Untreated rep2

description: Library name: SAR1nM_u2


title: hearts, transduced with control vector, rep1


title: rSt_rep2_mut_H3_3

description: Library name: ChIP_Sample_5

value: Round spermatids

value: Replicate 2

value: H3.3 (Cosmo Bio CE-040B)


title: L210-Mock

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: Library name: L210-Mock

data_processing:
Raw reads were evaluated by FastQC and adaptor sequences were trimmed using cutadapt.
Qualified reads were aligned to the human reference genome GRCh38 using STAR (v. 2.7.2)
Read counts for individual genes annotated based on GENCODE (v. 35) were subsequently determined using featureCounts
Assembly: GRCh38
Supplementary files format and content: Read count matrix

source_name: CD3+ effusion-infiltrating T cells

growth_protocol: The isolated CD3+ T cells were cultured in 24-well plates pre-coated with 1 μg/ml anti-CD3 (clone OKT3, BioLegend) and 1 μg/ml anti-CD28 (clone CD28.2, BioLegend) antibodies. Cells were maintained in complete RPMI-1640 medium supplemented with 90 IU/ml IL-2 (200-02, PeproTech). The complete RPMI-1640 medium consisted of 10% heat-inactivated fetal bovine serum, 1% L-glutamine, 1% non-essential amino acids, 1% penicillin-streptomycin, 1% MEM vitamin solution, and 1 mM sodium pyruvate.

extract_protocol:
Total cellular RNA was extracted using the PureLink RNA Mini Kit (12183018A, Invitrogen™) following the manufacturer's protocol.
mRNA-seq library was prepared for sequencing using standard Illumina protocol.

treatment_protocol: CD3+ T cells from malignant pleural effusions (MPE) were treated with 500 nM JQ1 for 72 hours followed by growing in drug-free medium for three days.

value: CD3+ effusion-infiltrating T cells

value: Mock


title: Retinal organoid day 35 batch 5

description: Library name: CM3_S3

value: Retinal organoid

value: hiPSC - AD4

value: WT

value: Retinal differentiation


title: hearts, 14 days post-MI treated with AAV-FGF17, rep3


title: Kras_Q61R_cobi_rep3

city: South San Francisco

first: Sandra

last: Melo

institute: Genentech, Inc.

description: Library name: Kras_Q61R_cobi_rep3

value: Small intestine

value: Kras Q61R

value: Cobimetinib


title: hearts, 14 days post-MI treated with AAV-FGF17, rep1

value: Heart


title: hearts, 14 days post-MI treated with AAV-FGF17, rep2


title: Kras_Q61R_cobi_rep2

description: Library name: Kras_Q61R_cobi_rep2


title: hearts, 14 days post-MI treated with control vector, rep3


title: rSt_rep1_mut_Myc

city: Basel

first: Antoine

last: Peters

institute: Friedrich Miescher Institute

description: Library name: ChIP_Sample_3

value: Testis

value: conventional

value: MYC/wt

value: Replicate 1

value: MYC-tag (abcam ab9132)


title: Kras_WT_rep3

description: Library name: Kras_WT_rep3

value: Kras WT

value: Day 10


title: L210-JQ1

description: Library name: L210-JQ1

value: CD3+ effusion-infiltrating T cells


title: L197-MOCK

description: Library name: L197-MOCK

value: Mock


title: rSt_rep1_wt_H3_3

description: Library name: ChIP_Sample_1

value: Round spermatids

value: wt/wt

value: H3.3 (Cosmo Bio CE-040B)


title: L204-Mock

description: Library name: L204-Mock


title: Kras_WT_rep2

description: Library name: Kras_WT_rep2


title: Kras_Q61R_cobi_rep1

description: Library name: Kras_Q61R_cobi_rep1


title: hearts, 14 days post-MI treated with control vector, rep2


title: rSt_rep2_mut_Myc

description: Library name: ChIP_Sample_6

value: Replicate 2


title: DLD1_iAPC_DMSO_rep3

description: Library name: DLD1_iAPC_DMSO_rep3

data_processing:
ENCODE ATAC-seq pipeline (v2.2.2)
Assembly: hg38
Supplementary files format and content: bigwig fold-change
Supplementary files format and content: bigwig p-value

growth_protocol: Cells were plated and then the following day were treated with doxycycline (250 ng/ml) or cobimetinib (1.3um) for 72h.

value: DMSO


title: L204-JQ1

description: Library name: L204-JQ1


title: rSt_rep2_wt_H3_3

description: Library name: ChIP_Sample_4


title: rSt_rep1_mut_H3_3

description: Library name: ChIP_Sample_2


title: Kras_WT_rep1

description: Library name: Kras_WT_rep1

value: Small intestine


title: L197-JQ1

description: Library name: L197-JQ1


title: hearts, 14 days post-MI treated with control vector, rep1


title: hearts, 3 days post-MI treated with AAV-FGF17, rep4


title: hearts, 3 days post-MI treated with AAV-FGF17, rep3


title: TP53INP2 rep2

city: Nanjing

first: yixuan

last: wang

state: Jiangsu

address: No.163, Xianlin Avenue

institute: Nanjing University

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

source_name: connective tissue

growth_protocol: SW872-S cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: connective tissue

value: liposarcoma cell

value: TP53INP2 OE


title: TP53INP2 rep1


title: Kras_Q61R_rep2

address: 1 DNA Way

description: Library name: Kras_Q61R_rep2

value: Kras Q61R


title: DLD1_iAPC_DMSO_rep1

description: Library name: DLD1_iAPC_DMSO_rep1


title: DLD1_iAPC_APC_restoration_rep3

description: Library name: DLD1_iAPC_APC_restoration_rep3

value: Dox


title: Kras_Q61R_rep3

description: Library name: Kras_Q61R_rep3


title: DLD1_iAPC_DMSO_rep2

description: Library name: DLD1_iAPC_DMSO_rep2


title: hearts, 3 days post-MI treated with AAV-FGF17, rep2

value: Heart


title: DLD1_iAPC_APC_restoration_rep2

description: Library name: DLD1_iAPC_APC_restoration_rep2


title: NC rep3

value: TP53INP2 NC


title: hearts, 3 days post-MI treated with AAV-FGF17, rep1


title: Kras_G12D_rep3

description: Library name: Kras_G12D_rep3

value: Kras G12D


title: DLD1_iAPC_APC_restoration_rep1

description: Library name: DLD1_iAPC_APC_restoration_rep1


title: Kras_G12D_rep2

description: Library name: Kras_G12D_rep2

value: Day 10


title: NC rep1


title: Kras_Q61R_rep1

description: Library name: Kras_Q61R_rep1


title: DLD1_DMSO_rep2

description: Library name: DLD1_DMSO_rep2


title: NC rep2


title: hearts, 3 days post-MI treated with control vector, rep2


title: Kras_G12D_rep1

description: Library name: Kras_G12D_rep1


title: DLD1_Cobimetinib_rep2

description: Library name: DLD1_Cobimetinib_rep2

value: Cobimetinib


title: hearts, 3 days post-MI treated with control vector, rep3


title: DLD1_DMSO_rep1

description: Library name: DLD1_DMSO_rep1


title: T24 cells, shBLACAT3, rep3

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Assembly: h19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human bladder cancer

growth_protocol: T24 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
RNA libraries for RNA-seq were prepared using ) KAPA Stranded RNA-Seq Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: T24 cells were respectively transfected with shControl and shBLACAT3 packaged by lentivirus, and the stably transfected cell strains were selected by puromycin.

value: human bladder cancer

value: bladder cancer cells

value: BLACAT3 knockdown

value: Cell transfection


title: hearts, sham-operated treated with control vector, rep4


title: T24 cells, shBLACAT3, rep1


title: DLD1_Cobimetinib_rep1

description: Library name: DLD1_Cobimetinib_rep1


title: Kras_Q61R_mouse_2_tumor_2

description: Library name: Kras_Q61R_mouse_2_tumor_2

data_processing:
Whole-exome data was processed using the WES somatic variant discovery workflow for mouse, utilizing "Functional Equivalence" pre-processing with GATK479 (https://gatk.broadinstitute.org/hc/en-us). Variant calling was performed with Strelka (v. 1.0.15). Functional annotations were provided by Ensembl VEP (Variant Effect Predictor; https://useast.ensembl.org/info/docs/tools/vep/index.html). Tumor/Normal pair confirmation was provided by NGS Checkmate (https://github.com/parklab/NGSCheckMate). FASTQ file quality checks were done by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The input for this pipeline consisted of paired-end FASTQ files. The output included a recalibrated BAM file with index, a VCF file with index for selected variant callers, and variant annotations file from VEP.
Assembly: mm10
Supplementary files format and content: strelka_snvs_VEP_out.txt

extract_protocol:
Genomic DNA was isolated using the QIAmp DNA FFPE Tissue Kit (Qiagen 56404). Exome capture was performed using 0.5ug of genomic DNA.
Exome capture was performed using 0.5mg of genomic DNA with the SureSelect XT mouse all exon kit according to manufacturer’s protocol (Agilent Technologies). The fragment size distribution of post-capture amplified libraries was determined with 2200 TapeStation using high sensitivity D1000 screen tape (Agilent Technologies). Concentration of the libraries was measured by a Qubit fluorometer (Thermo Fisher Scientific). Exome capture libraries were sequenced on HiSeq 4000 system (Illumina) to generate 50 million paired-end 75-base-pair reads.


title: Kras_Q61R_mouse_3_tumor_1

description: Library name: Kras_Q61R_mouse_3_tumor_1


title: Kras_Q61R_mouse_3_tumor_2

description: Library name: Kras_Q61R_mouse_3_tumor_2


title: T24 cells, shBLACAT3, rep2


title: hearts, 3 days post-MI treated with control vector, rep1


title: TP53INP2 rep3


title: T24 cells, shControl, rep3

value: WT


title: P145_CD8_JQ1

description: Library name: P145_CD8_JQ1

data_processing:
Adaptor sequences were removed using cutadapt and clean reads were aligned to the human genome GRCh38 using Burrows-Wheeler Alignment tool (BWA).
The duplicated reads were marked by GATK-Picard. Aligned reads that were improperly paired, had multiple hits, duplicates, or mapped to mitochondrial genome or ENCODE blacklisted regions were removed from further analysis and the position of aligned reads were shifted +4 and –5 bp for the positive and negative strands using alignmentSieve from deepTools.
Peaks were called using MACS2 with parameters -f BAMPE –keep-dup all and annotated by ChIPSeeker
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: CD8 T-cell

extract_protocol:
DNA sample preparation was performed as described in Corces et al., 2017.
ATAC-seq librarys was prepared for sequencing using Omni-ATAC protocol as described previously (Corces et al., 2017).

treatment_protocol: CD3+ T cells from malignant pleural effusions (MPE) were treated with 500 nM JQ1 for 24-72 hours followed by growing in drug-free medium until day 7.

value: CD8 T-cell


title: Kras_Q61R_mouse_2_tumor_1

description: Library name: Kras_Q61R_mouse_2_tumor_1

value: Small intestine


title: Kras_Q61R_mouse_1_tumor_1

description: Library name: Kras_Q61R_mouse_1_tumor_1


title: P145_CD8_Mock

description: Library name: P145_CD8_Mock

value: Mock


title: hearts, sham-operated treated with control vector, rep2


title: hearts, sham-operated treated with control vector, rep3


title: T24 cells, shControl, rep1


title: RAW,rep3

status: Public on Apr 04 2026

city: Hangzhou

first: Hengxing

last: Lu

state: Zhejiang

address: 1369 Wenyi West Road, Yuhang District

institute: Zhejiang University

description: Library name: RAW-3

data_processing:
Raw FASTQ reads were processed using fastp (v0.20.0) for quality control and adapter trimming. Parameters were set as follows: --qualified_quality_phred 20 --unqualified_percent_limit 40 --length_required 36 --n_base_limit 5 --trim_poly_g. Adapter sequences were automatically detected. Clean reads were then aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.2.1) with default parameters. Aligned reads in SAM format were converted to BAM format, sorted, and indexed using SAMtools (v1.10). RNA-seq quality metrics (including read distribution, insertion size, and coverage uniformity) were assessed using RSeQC (v2.6.4). Transcript assembly and quantification were performed using StringTie (v2.0.4) with default parameters. Gene-level and transcript-level expression abundances were calculated as transcripts per million (TPM) and raw read counts. Processed data files include gene/transcript expression matrices (TPM and raw counts) generated by StringTie.
Assembly: GRCm39.112
Supplementary files format and content: Raw counts of all samples

source_name: Cell line

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples with RNA integrity number (RIN) > 8.0 were used for library construction.
Sequencing libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001, Illumina, San Diego, CA, USA) starting with 1 µg of total RNA per sample. Library preparation followed the standard Illumina protocol, including poly-A selection, fragmentation, first- and second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, and PCR amplification.The resulting libraries were quantified by Qubit fluorometer and assessed for size distribution on a Bioanalyzer, then sequenced on an Illumina NovaSeq 6000 platform (or appropriate instrument) to generate 150 bp paired-end reads.

value: Cell line

value: Macrophage-like cell line


title: iMac,rep3

description: Library name: iMac-3

source_name: Cultured cells

value: Cultured cells

value: Differentiated macrophages

value: Macrophage


title: RAW,rep2

description: Library name: RAW-2


title: RAW,rep1

description: Library name: RAW-1


title: T24 cells, shControl, rep2


title: BMDM,rep2

description: Library name: BMDM-2

source_name: Primary cultured cells

value: Primary cultured cells

value: Bone marrow-derived macrophages


title: Kras_Q61R_adjacent_normal

description: Library name: Kras_Q61R_adjacent_normal

value: Kras Q61R


title: hearts, sham-operated treated with control vector, rep1

value: Heart


title: P110_CD8_JQ1

description: Library name: P110_CD8_JQ1


title: hearts, 3 days post-MI treated with control vector, rep4


title: P110_CD8_Mock

description: Library name: P110_CD8_Mock


title: iMac,rep2

description: Library name: iMac-2


title: BMDM,rep3

description: Library name: BMDM-3


title: iMono,rep1

description: Library name: iMono-1

value: Immortalized mouse monocytes

value: Monocyte


title: iMac,rep1

description: Library name: iMac-1


title: BMDM,rep1

description: Library name: BMDM-1


title: iMono,rep2

description: Library name: iMono-2


title: Volunteer 20, photoexposed skin, 6am (T06)

first: Qing-Jun

last: Meng

address: A.V. Hill Building, Oxford Road

department: Faculty of Biology, Medicine and Health

institute: The University of Manchester

description: Library name: 20H

data_processing:
Raw sequencing data is pre-processed or ‘trimmed’ to remove adapter sequences and low-quality reads.  Cleaned reads were aligned to the Homo sapiens GRCh38 reference genome using STAR aligner v2.5.2b with default parameters.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: raw_counts T00.csv, raw_counts T06.csv, raw_counts T12.csv, raw_counts T18.csv

source_name: 3 mm whole thickness skin

extract_protocol:
RNA was extracted and purified using QIAsymphony RNA (Cat no. 931636; Qiagen, Hilden, Germany)
100ng of RNA per sample was used for library preparation, performed by polyA selection-based mRNA enrichment, mRNA fragmentation, and random priming with subsequent first- and second-strand complementary DNA (cDNA) synthesis. Following that, end-repair 5′ phosphorylation and adenine nucleotide (dA)-tailing was performed. Last, adaptor ligation, polymerase chain reaction (PCR) enrichment, and Illumina NovaSeq technology–based sequencing was performed with 20M reads per sample using Trimmomatic v.0.36.

value: 3 mm whole thickness skin


title: Volunteer 20, photoexposed skin, midnight (T00)

description: Library name: 20F


title: Volunteer 20, photoprotected skin, 6am (T06)

description: Library name: 20G


title: Volunteer 19, photoprotected skin, 6am (T06)

description: Library name: 19G


title: Volunteer 20, photoprotected skin, midnight (T00)

description: Library name: 20E


title: Volunteer 20, photoexposed skin, noon (T12)

description: Library name: 20B


title: Volunteer 20, photoprotected skin, noon (T12)

description: Library name: 20A


title: Volunteer 19, photoprotected skin, midnight (T00)

description: Library name: 19E


title: Volunteer 19, photoexposed skin, 6pm (T18)

description: Library name: 19D


title: Volunteer 19, photoexposed skin, noon (T12)

description: Library name: 19B


title: Volunteer 19, photoprotected skin, noon (T12)

description: Library name: 19A


title: Volunteer 20, photoexposed skin, 6pm (T18)

description: Library name: 20D


title: Volunteer 19, photoexposed skin, 6am (T06)

description: Library name: 19H


title: Volunteer 19, photoexposed skin, midnight (T00)

description: Library name: 19F


title: Volunteer 18, photoprotected skin, 6am (T06)

description: Library name: 18G


title: Volunteer 19, photoprotected skin, 6pm (T18)

description: Library name: 19C


title: Volunteer 20, photoprotected skin, 6pm (T18)

description: Library name: 20C


title: Volunteer 18, photoexposed skin, midnight (T00)

description: Library name: 18F


title: Volunteer 18, photoexposed skin, 6am (T06)

description: Library name: 18H


title: Volunteer 18, photoexposed skin, 6pm (T18)

description: Library name: 18D


title: Volunteer 18, photoprotected skin, midnight (T00)

description: Library name: 18E


title: Volunteer 18, photoprotected skin, noon (T12)

description: Library name: 18A


title: Volunteer 18, photoexposed skin, noon (T12)

description: Library name: 18B


title: Volunteer 18, photoprotected skin, 6pm (T18)

description: Library name: 18C


title: Volunteer 17, photoexposed skin, 6am (T06)

description: Library name: 17H


title: Volunteer 17, photoexposed skin, midnight (T00)

description: Library name: 17F


title: Volunteer 17, photoprotected skin, 6am (T06)

description: Library name: 17G


title: Volunteer 17, photoexposed skin, noon (T12)

description: Library name: 17B


title: Volunteer 17, photoprotected skin, noon (T12)

description: Library name: 17A


title: Volunteer 16, photoprotected skin, midnight (T00)

description: Library name: 16E


title: Volunteer 16, photoexposed skin, midnight (T00)

description: Library name: 16F


title: Volunteer 16, photoexposed skin, noon (T12)

description: Library name: 16B


title: Volunteer 16, photoexposed skin, 6pm (T18)

description: Library name: 16D


title: Volunteer 15, photoprotected skin, 6am (T06)

description: Library name: 15G


title: Volunteer 16, photoprotected skin, 6pm (T18)

description: Library name: 16C


title: Volunteer 16, photoprotected skin, noon (T12)

description: Library name: 16A


title: Volunteer 17, photoprotected skin, 6pm (T18)

description: Library name: 17C


title: Volunteer 17, photoprotected skin, midnight (T00)

description: Library name: 17E


title: Volunteer 16, photoexposed skin, 6am (T06)

description: Library name: 16H


title: Volunteer 17, photoexposed skin, 6pm (T18)

description: Library name: 17D


title: Volunteer 16, photoprotected skin, 6am (T06)

description: Library name: 16G


title: Volunteer 15, photoexposed skin, 6am (T06)

description: Library name: 15H


title: Volunteer 15, photoexposed skin, 6pm (T18)

description: Library name: 15D


title: Volunteer 15, photoprotected skin, 6pm (T18)

description: Library name: 15C


title: Volunteer 15, photoexposed skin, midnight (T00)

description: Library name: 15F


title: Volunteer 15, photoexposed skin, noon (T12)

description: Library name: 15B


title: Volunteer 15, photoprotected skin, noon (T12)

description: Library name: 15A


title: Volunteer 14, photoexposed skin, 6pm (T18)

description: Library name: 14D


title: Volunteer 15, photoprotected skin, midnight (T00)

description: Library name: 15E


title: Volunteer 14, photoexposed skin, noon (T12)

description: Library name: 14B


title: Volunteer 14, photoexposed skin, 6am (T06)

description: Library name: 14H


title: Volunteer 14, photoprotected skin, midnight (T00)

description: Library name: 14E


title: Volunteer 13, photoexposed skin, midnight (T00)

description: Library name: 13F


title: Volunteer 13, photoexposed skin, 6am (T06)

description: Library name: 13H


title: Volunteer 13, photoprotected skin, 6am (T06)

description: Library name: 13G