title: HELA-319A

description: Library name: HELA-319A


title: kidney biopsy_NH125

status: Public on Jan 16 2026

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, Santa Clara, CA).

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr/mixed, no abmr/mixed)

value: ABMR/Mixed

tag: tissue

value: kidney biopsy


title: shControl_Control_H3K36me3_Rep4

type: SRA

city: New Haven

first: Don

last: Nguyen

state: Connecticut

address: 310 Cedar Street

department: Pathology

country: USA

institute: Yale University

description: Library name: CK233

library_source: genomic

data_processing:
All samples were quality controlled using FastQC (Babraham Bioinformatics).
Narrow peaks (H3K27Ac, FLAG-KDM2A) were trimmed with TrimGalore (Babraham Bioinformatics) and FLAG-KDM2A reads were cleaned with SMARTCleaner. Broad peaks (H3K36me) were trimmed Trimmomatic. Experiments were aligned against hg38 using Bowtie2.
Peak calling was done using MACS2 (narrow) and MACS3 (broad).
Average coverage files were generated using deepTools tools: bamCoverage, bigwigAverage, and bigwigCompare. Prior to generation, optical duplicates were removed using Picard Tools (Broad Institute), and poor-quality reads filtered using samTools20. All coverage files were normalized for sequencing depth using the counts per million (CPM) method, and averaged using bigwigAverage.
Assembly: hg38
Supplementary files format and content: Average BigWig files of CPM normalized reads for each methylation IP  are provided. MACS2 called peaks are provided for FLAG samples.

molecule: genomic DNA

growth_protocol: H2030-BrM3 cells were grown  under cluster forming conditions in the presence of doxycycline for 5 days.

extract_protocol:
H3K27Ac: Samples were sent to Active Motif (Carlsbad, CA) for ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed basic data analysis. In brief, cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Qubit. Extrapolation to the original chromatin volume allowed determination of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ug of antibody against H3K27Ac (Active Motif, catalog number 39133, lot number 06921014). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.   FLAG and H3K36Me: FLAG-KDM2A samples were double-fixed using 2mM ethylene glycol bis(scuccinimidyl succinate) (EGS) (Thermo Scientific cat. 21565) for 1h followed by 1% formaldehyde for ten minutes.  H3K36 methylation samples were fixed with 1% formaldehyde alone.  Reactions were quenched with glycine to a final concentration of 0.125M. Pellets were washed with PBS and lysed in complete sonication buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5mM EGTA, 1x protease inhibitors (Roche), 0.5% SDS, and 0.5mM PMSF) prior to sonication with a QSonica Q800. Fragment size (200-500bp) from extracted DNA was confirmed by agarose gel and quantified by Qubit. Input was aliquoted from 20% of total material, and chromatin samples were subsequently pre-cleared for 1 hour at 4ºC with immunoprecipitation (IP) buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5% Triton X-100, 150mM NaCl, and 10% Glycerol) and Protein A/G beads. IP for proteins of interest was conducted using protein A/G beads and 10µg of antibody. For H3K36 methylation IPs Drosophila spike-in chromatin (100ng)  (Active Motif cat. 53083) and spike-in antibody (5μg) (Active Motif cat. 61686)were added. IPs were washed then eluted in a buffer of 100mM NaHC03, 1% SDS. Both IP and input samples were proteinase K treated, reverse crosslinked, and purified by phenol-chloroform extraction with ethanol precipitation.
H3K27Ac: Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides described by Bentley et al., 2008)) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500  (75 nt reads, single end).  FLAG and H3K36Me: Samples were checked by Agilent Bioanalyzer, and libraries were prepared by the using ThruPlex DNA Seq (Takara Bio. cat. R400674) for H3K36 libraries, and DNA SMART ChiP-Seq (Takara Bio.cat. 634865) for FLAG libraries. Libraries were barcoded, pooled, and sequenced (PE) on Illumina NovaSeq X and NovaSeq 6000 machines. Please note, H3K36 methylation libraries were  initially sequenced on the NovaSeq 6000 then subsequently on the NovaSeq X  for additional coverage depth. Fastq files from these runs were concatinated head to tail prior to any anaylsis, and these pooled files are provided here for convenience. Files from each individual sequencing run are available upon request.

tag: cell line

tag: cell type

value: Human metastatic lung adenocarcinoma


title: CAPAN1_WT_TP1_R2_S2_R1_001

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
FASTQ files were counted and analyzed using MAGeCK version 0.5.6, using RRA and total read count normalization, with default settings
Supplementary_files_format_and_content: counts_table_CRIPSR.csv

source_name: CAPAN1 cell line

growth_protocol: sgRNA containing lentiviruses were transduced into Cas9 expressing PDA cell lines (HPAFII, PATU8988S, CAPAN1, KP4, PANC1 and PK45H) in duplicates (in presence of 8ug/ml polybrene) with estimated MOI 0.2 - 0.3. Next day the lentivirus containing media was removed, cells washed with PBS and puromycin containing media (2ug/ml) was added to the cells for 48-72h until the control cells (no virus) were dead. The first timepoint of the screen was done immediately after this. At all times the cells were maintained at >1500 cells per guide through the 33-day screens

extract_protocol:
After the screen, the genomic DNA from the first and the last timepoint were extracted by using Blood and Cell culture DNA Maxi kits (Qiagen)
Library preparations were done as (PMID 30202008).
The resulting products of 290 bp were gel purified (GeneJet), pooled together and sequenced with a custom primer (CRISPRSeq) and the i5 and i7 index primers by running 20 + 6 + 6 cycles on the Illumina HiSeq2500, where i7 reads the RSL and i5 the illumina sample index.

value: PDA tumor

tag: treatment

value: Time point 1 / Replicate 2


title: shControl_Control_H3K36me3_Rep3

description: Library name: CK193


title: CAPAN1_WT_TP1_R1_S1_R1_001

value: Time point 1 / Replicate 1


title: shControl_Control_H3K36me3_Rep2

description: Library name: CK113


title: PB Isotype

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: Library name: PB_Ctrl

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of sequencing runs were performed using the 10X Cell Ranger (Version 5.0.0) pipeline .
Assembly: GRCh38_and_mm10-2020-A
Supplementary files format and content: Count matrix

source_name: Peripheral blood

extract_protocol:
SK-MEL-5 tumors were dissected from humanized mice treated with either isotype control antibody or anti-LILRB2 antibody and single-cell suspensions were obtained. Live, single, tumor-infiltrating immune cells were enriched by FACS.
Cells were counted and loaded onto the Chromium Controller (10x Genomics, RRID: SCR_019326). Samples were processed as per manufacturer’s instruction and sequenced on an Illumina NextSeq 500 sequencer (RRID:SCR_014983).

value: Peripheral blood

value: Human CD45 cells

value: Immune cells

value: Isotype


title: kidney biopsy_NH124

value: No ABMR/Mixed


title: PB LILRB2 treatment

description: Library name: PB_anti_B2


title: ND tumor Isotype

description: Library name: ND_Ctrl

source_name: tumor

value: tumor


title: CAPAN1_WT_TP_last_R2_S4_R1_001

value: Last time point / Replicate 2


title: Wild-type - biol rep 2

city: Stanford

first: Julika

last: Huber

state: CA

address: 257 Campus Drive

institute: Stanford University

description:
Library name: wt-3_S3
Column name in raw_counts_All_Samples.csv: wt.3_S3

library_source: transcriptomic

data_processing:
Sequencing data in FASTQ format were aligned in HISAT2 and assembled in String Tie using the mm10 reference genome.
Counts matrices were ported to edgeR, filtered for lowly expressed genes, normalized by total counts, dispersion-estimated, and log-transformed using the standard package pipeline 74.
Differential expression was identified by the Exact Test methodology for two groups of negative-binomially distributed counts 74
Assembly: mm10
Supplementary files format and content: raw counts for each sample

organism: Mus musculus

source_name: skull bone

extract_protocol:
Total RNA was isolated using TRIzol method.
Libraries were prepped using ClonTech Low Input Library Rep Kit v2

value: skull bone

tag: genotype

value: WT

tag: time

value: postnatal day 15


title: shControl_Control_H3K36me3_Rep1

description: Library name: CK13


title: Sh3Pxd2bnee-/- - biol rep 2

description:
Library name: mutant_4_S4
Column name in raw_counts_All_Samples.csv: mutant_4_S4


title: shKDM2A_Cluster_H3K36me2_Rep4

description: Library name: CK222


title: Wild-type - biol rep 1

description:
Library name: wt-1_S1
Column name in raw_counts_All_Samples.csv: wt.1_S1


title: PK45H OVOL2 3

data_processing:
Single end PLATE-Seq reads were pseudoaligned to the GRCh38 transcriptome (mRNA and ncRNA) and quantified using kallisto version 0.44.0 (kallisto citation) with sequence-specific bias correction. Transcript-level counts were collapsed to entrez-id gene-level counts using the tximport package in R (tximport citation). The biomaRt package in R (biomaRt citations) was used to map transcript-level Ensembl-ids to gene-level entrez-ids
Assembly: GRCh38
Supplementary files format and content: Table containing reads count of each gene (row) in each sample (column)

source_name: Human PDA cell line - PK45H

growth_protocol: Each ORF containing lentivirus was transduced to Morphogenic cell lines with MOI 2 in triplicates (6 well format in the presence of 8ug/ml polybrene). In another set of triplicates lentiviral ORFs were co-transduced with M2rtTA (FUW-M2rtTA, addgene #20342), which acts as transcriptional amplifier in tetracyclin inducible systems. The following day after the viral transductions, the media was changed and puromycin (2.5ug/ml) and doxocycline (0.6ug/ml) was added to the cells.

extract_protocol:
Cells were incubated in total 6 days
Total RNA was collected by Direct-zol RNA MiniPrep Plus kit (Zymo Research)
Samples were sequenced by the PlateSeq approach (PMID: 28740083) from 100ng total RNA starting amount.

value: Human PDA cell line - PK45H

value: OVOL2 overexpression


title: ND tumor LILRB2 treatment

description: Library name: ND_anti_B2


title: kidney biopsy_NH122

value: kidney biopsy


title: PK45H mCHERRY 1

value: mCherry ORF (negative control)


title: shKDM2A_Cluster_H3K36me2_Rep3

description: Library name: CK102

value: Human metastatic lung adenocarcinoma


title: Sh3Pxd2bnee-/- - biol rep 1

description:
Library name: mutant_2_S2
Column name in raw_counts_All_Samples.csv: mutant_2_S2


title: kidney biopsy_NH123


title: shKDM2A_Cluster_H3K36me2_Rep2

description: Library name: CK182


title: PANC1 mCHERRY + M2RTTA 2

source_name: Human PDA cell line - PANC1

value: Human PDA cell line - PANC1

value: mCherry ORF co-transduced with M2RTTA (negative control)


title: kidney biopsy_NH121


title: kidney biopsy_NH120

value: ABMR/Mixed


title: WT TML, Tcf7+, S9

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
9_Wp
S9_Wp

data_processing:
Purity-filtered reads were trimmed to remove adapters and low-quality bases with Cutadapt (v. 1.8). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). The remaining reads were further filtered to remove low complexity reads with reaper (v. 15-065).
Reads were aligned against the Mus musculus (GRCm38.92) genome using STAR (v. 2.5.3a). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) using the Mus musculus (GRCm38.92) gene annotation.
The raw count matrix was imported into R (v. 3.5.3). Genes were filtered to retain only the ones detected at 1 count per million (cpm) in at least 1 sample, yielding 13,303 retained genes. Normalization factors were calculated using the weighted trimmed mean of M-values (TMM) method implemented in the edgeR package (v. 3.24.3). Gene counts were next transformed to log2(cpm) and the mean-variance modeling was performed using the voom function implemented in the limma package (v. 3.38.3).
Assembly: mm10 (GRCm38.92)
Supplementary files format and content: The supplementary files are tab-delimited text files. One contains htseq-count output, with raw counts summarized per gene (in rows) per sample (in columns). The other file contains log2(normalized counts) for retained genes only (we removed lowly expressed genes). In each file, the first 3 columns contain gene annotation. The first column labelled "gene_id" contains the Ensembl gene ID, the second column labelled  "gene_name" contains the gene symbols, and the third column is labelled with "gene_biotype". The following 16 columns correspond to the counts per sample. The column names of the samples correspond to the sample description.

molecule: polyA RNA

source_name: splenocytes

extract_protocol:
Sorted cells were lysed and stored in Trizol before extraction of total cellular RNA using the Direct-zol RNA MiniPrep kit (Zymo Research). RNA quality was assessed on a Fragment Analyzer (Agilent Technologies) and all RNAs had an RQN ≥ 8.7. From 50 ng total RNA, mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module. RNA-seq libraries were then prepared from the mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
NEBNext Ultra II RNA Library Prep Kit (non-strand specific library preparation)

value: splenocytes

value: P14 CD8 T cells Tcf7GFP+

value: Tcf7GFP tg/+ TCRLCMV327 tg/+

tag: strain

value: LCMV cl13


title: KP4 OVOL2 M2RTTA 3

source_name: Human PDA cell line - KP4

value: Human PDA cell line - KP4

value: OVOL2 overexpression (with M2RTTA)


title: kidney biopsy_NH119

value: No ABMR/Mixed


title: KP4 mCHERRY M2RTTA 1


title: shKDM2A_Cluster_H3K36me2_Rep1

description: Library name: CK42


title: aPD-L1 TML, Tcf7+, S7

description:
7_aPD1p
S7_aPD1p

value: LCMV cl13 + a PDL-1


title: shControl_Cluster_H3K36me2_Rep4

description: Library name: CK212


title: PK45H OVOL2 2


title: kidney biopsy_NH118


title: PANC1 OVOL2 + M2RTTA 3


title: PATU8988S NORMAL 2

source_name: Human PDA cell line - PATU8988S

value: Human PDA cell line - PATU8988S

value: Untreated


title: aPD-L1 TEX, Tcf7-, S8

description:
8_aPD1n
S8_aPD1n

value: P14 CD8 T cells Tcf7GFP-


title: aPD-L1 TEX, Tcf7-, S6

description:
6_aPD1n
S6_aPD1n


title: shControl_Cluster_H3K36me2_Rep2

description: Library name: CK172


title: PD-1 KO naive, Tcf7+, S4

description:
4_K_naive
S4_K_naive

value: PD1 -/-  Tcf7GFP tg/+ TCRLCMV327 tg/+


title: shControl_Cluster_H3K36me2_Rep1

description: Library name: CK22


title: aPD-L1 TML, Tcf7+, S5

description:
5_aPD1p
S5_aPD1p


title: PANC1 mCHERRY + M2RTTA 1


title: shKDM2A_Control_H3K36me2_Rep3

description: Library name: CK202


title: shKDM2A_Control_H3K36me2_Rep4

description: Library name: CK242


title: shControl_Cluster_H3K36me2_Rep3

description: Library name: CK92


title: kidney biopsy_NH116

value: kidney biopsy


title: kidney biopsy_NH114


title: shKDM2A_Control_H3K36me2_Rep1

description: Library name: CK32

value: Human metastatic lung adenocarcinoma


title: kidney biopsy_NH117


title: KP4 OVOL2 M2RTTA 2


title: PD-1 KO TEX, Tcf7-, S16

description:
16_Kn
S16_Kn


title: shKDM2A_Control_H3K36me2_Rep2

description: Library name: CK122


title: WT naive, Tcf7+, S2

description:
2_W_naive
S2_W_naive


title: shControl_Control_H3K36me2_Rep4

description: Library name: CK232


title: KP4 mCHERRY 3

value: mCherry ORF (negative control)


title: PD-1 KO naive, Tcf7+, S3

description:
3_K_naive
S3_K_naive


title: PD-1 KO TML, Tcf7+, S15

description:
15_Kp
S15_Kp


title: PATU8988S NORMAL 1


title: kidney biopsy_NH115


title: kidney biopsy_NH112


title: PD-1 KO TEX, Tcf7-, S14

description:
14_Kn
S14_Kn


title: kidney biopsy_NH113


title: PK45H OVOL2 1

value: Human PDA cell line - PK45H

value: OVOL2 overexpression


title: shControl_Control_H3K36me2_Rep3

description: Library name: CK192


title: kidney biopsy_NH109


title: kidney biopsy_NH110


title: shControl_Control_H3K36me2_Rep2

description: Library name: CK112


title: PD-1 KO TML, Tcf7+, S13

description:
13_Kp
S13_Kp

value: splenocytes


title: kidney biopsy_NH108

value: ABMR/Mixed


title: PANC1 OVOL2 + M2RTTA 2

value: Human PDA cell line - PANC1


title: WT TEX, Tcf7-, S12

description:
12_Wn
S12_Wn

value: Tcf7GFP tg/+ TCRLCMV327 tg/+

value: LCMV cl13


title: shControl_Control_H3K36me2_Rep1

description: Library name: CK12


title: PANC1 mCHERRY 3


title: WT TML, Tcf7+, S11

description:
11_Wp
S11_Wp

value: P14 CD8 T cells Tcf7GFP+


title: kidney biopsy_NH107


title: shKDM2A_Cluster_H3K36me1_Rep3

description: Library name: CK101


title: kidney biopsy_NH111

value: No ABMR/Mixed


title: KP4 OVOL2 M2RTTA 1

value: Human PDA cell line - KP4

value: OVOL2 overexpression (with M2RTTA)


title: WT TEX, Tcf7-, S10

description:
10_Wn
S10_Wn


title: KP4 mCHERRY 2


title: shKDM2A_Cluster_H3K36me1_Rep4

description: Library name: CK221


title: PK45H mCHERRY + M2RTTA 3

value: mCherry ORF co-transduced with M2RTTA (negative control)


title: shKDM2A_Cluster_H3K36me1_Rep1

description: Library name: CK41


title: shKDM2A_Cluster_H3K36me1_Rep2

description: Library name: CK181


title: WT naive, Tcf7+, S1

description:
1_W_naive
S1_W_naive


title: kidney biopsy_NH106


title: K14-Ctrl, LC, replicate 5

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
For the analysis of the RNA-seq reads, Nextpresso v2 was used, as follows:
UMI sequences within reads were extracted with UMItools. The resulting FASTQ files were processed with bbduk (https://sourceforge.net/projects/bbmap/) for the extraction of adapters, polyA and rRNA sequences. Read quality was verified with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The derived FASTQ files were aligned to the mouse genome (GRCm39) with Hisat2. The obtained BAM files were sorted with SAMtools, and the UMItools were employed once again for read deduplication. Htseq-count was used to count the number of reads that aligned within genes, using the Gencode vM29 gene annotation. ComBat-seq was then used to adjust the batch effect. Differential expression was performed with DESeq2, keeping only those genes with more than 10 counts across the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAStandard was used to perform gene set enrichment analysis for the selected gene signatures, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: TSV file with raw counts

source_name: mammary gland

extract_protocol:
Fresh mamamry glands were mechanically dissected by scissor chopping after draining lymph nodes were removed and enzymatically digested with digestium medium (Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Biowest, #L0093-500ml), 0.6 U/ml collagenase A (Sigma-Aldrich, #1108879300), 2.85U/mL dispase II (ThermoFisher Scientific, #17105041), 2% HEPES (ThermoFisher Scientific, #H8357-100ml) and 1% penicillin–streptomycin(ThermoFisher Scientific, #15140-122)) for 1h rocking (50 rpm) at 37°C. Samples were washed with CO2 independent media (ThermoFisher Scientific, # 18045088) supplemented with 2mM glutamax (Gibco, #35050-061). Single cells were isolated by sequential treatments with 0.25%trypsin/0.1% EDTA solution (Sigma-Aldrich, #T3924-100ml) for 1min at RT and dispaseII/DNAseI (ThermoFisher Scientific, #17105041 / Roche, #10104159001) at 37°C for 5 min. Enzymatic digestions were blocked by adding CO2 independent media (ThermoFisher Scientific, #18045088) supplemented with 2mM glutamax (Gibco, #35050-061) and 5% FBS (ThermoFisher Scientific, #F7524-500ml). Erythrocytes were eliminated by treating samples with cold (4°C) ammonium chloride solution (STEMCELL Technologies, #7008) for 1min at RT. Cell aggregates were removed by filtering the cell suspension with a 40μm strainer and single epithelial cells were counted manually using a Neubauer chamber. Single cells were blocked with blocking buffer (PBS + 0.5% Bovine Serum Albumin (Sigma-Aldrich, #13391+ 2mM EDTA) for 20min on ice. Single cells were incubated for 40 min on ice with the corresponding surface antibodies (CD24-AlexaFluor700 (564237, BD Pharmingen™, 1μg/ml), CD49f-AlexaFluor647 (562473, BD Pharmingen™,1.25 μg/ml), CD31-PECy7 (102417, Biolegend, 0.25 μg/ml), and CD45-PECy7 (103113, Biolegend, 0.125 μg/ml)). Prior sorting, single cells solution was filtered by a 70μm strainer. Cell sorting was performed using a BD FACSAriaTM cell sorter.Sorted cells were directly collected into the lysis buffer from RNeasy micro kit (Qiagen, #74004). Samples were mechanically homogenized by passing through 30G syringe 5-times, and RNA extracted according to the manufacturer’s instructions.
Total RNA samples were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, whereby random primers featured a 6 nt long Unique Molecular Identifier 5' tag to be addressed at data analysis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina NextSeq550 by following manufacturer's protocols.

treatment_protocol: 1 mg/ml doxycycline + 20mg/ml sucrose, ad libitum in the drinking water for 4 weeks

value: mammary gland

value: Luminal cells

tag: Sex

value: female

value: 1mg/ml doxycicline


title: K14-Ctrl, BC, replicate 5

value: Basal Cells


title: kidney biopsy_NH103

value: kidney biopsy


title: KP4 NORMAL 3

value: Untreated


title: kidney biopsy_NH104


title: shControl_Cluster_H3K36me1_Rep4

description: Library name: CK211

value: Human metastatic lung adenocarcinoma


title: kidney biopsy_NH102


title: kidney biopsy_NH101


title: kidney biopsy_NH105


title: shControl_Cluster_H3K36me1_Rep3

description: Library name: CK91


title: K14-Ctrl, LC, replicate 4


title: K14-Ctrl, BC, replicate 4


title: shControl_Cluster_H3K36me1_Rep1

description: Library name: CK21


title: shControl_Cluster_H3K36me1_Rep2

description: Library name: CK171


title: PANC1 OVOL2 + M2RTTA 1


title: KP4 OVOL2 3

value: OVOL2 overexpression


title: shKDM2A_Control_H3K36me1_Rep4

description: Library name: CK241


title: K14-Ctrl, BC, replicate 3


title: K14-Rank, LC, replicate 4


title: KP4 mCHERRY 1

value: mCherry ORF (negative control)


title: shKDM2A_Control_H3K36me1_Rep3

description: Library name: CK201


title: K14-Ctrl, LC, replicate 3


title: K14-Rank, BC, replicate 4


title: KP4 NORMAL 2


title: kidney biopsy_NH99


title: PANC1 OVOL2 3

value: Human PDA cell line - PANC1


title: kidney biopsy_NH100


title: PANC1 mCHERRY 2


title: PK45H mCHERRY + M2RTTA 2

value: Human PDA cell line - PK45H


title: kidney biopsy_NH97


title: kidney biopsy_NH98


title: shKDM2A_Control_H3K36me1_Rep1

description: Library name: CK31


title: K14-Rank, LC, replicate 3


title: K14-Rank, BC, replicate 3


title: kidney biopsy_NH95


title: kidney biopsy_NH94


title: shControl_Control_H3K36me1_Rep4

description: Library name: CK231


title: KP4 OVOL2 2


title: kidney biopsy_NH96


title: shKDM2A_Control_H3K36me1_Rep2

description: Library name: CK121


title: PANC1 mCHERRY 1


title: shControl_Control_H3K36me1_Rep1

description: Library name: CK11


title: shControl_Control_H3K36me1_Rep2

description: Library name: CK111


title: K14-Rank, BC, replicate 2


title: kidney biopsy_NH93


title: PK45H NORMAL 3


title: kidney biopsy_NH92


title: K14-Rank, LC, replicate 2


title: shControl_Control_H3K36me1_Rep3

description: Library name: CK191


title: kidney biopsy_NH90


title: kidney biopsy_NH91

value: ABMR/Mixed


title: K14-Rank, BC, replicate 1


title: KP4 NORMAL 1


title: PK45H OVOL2 + M2RTTA 3


title: K14-Rank, LC, replicate 1


title: PANC1 OVOL2 2


title: PANC1 NORMAL 3


title: ChIP-sequencing analysis of O-glycosylated Notch1 intracellular domain (Input)

city: Chongqing

first: Lei

last: Liu

address: 1 Youyi Road, Yuanjiagang, Yuzhong District

department: Department of Breast and Thyroid Surgery

country: China

institute: The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

description: Library name: O-Glc NICD1, Input

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al., 2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
The interaction between transcript factor or chromatin histone modification and DNA were not random, while they show some specific sequence preference. Homer (Heinz et al., 2010) was used to detect the denovo sequence motif and the matched known motifs.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker (Yu et al., 2015) was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak-related genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways.
Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Assembly: hg38
Supplementary files format and content: bigWig, bedgraph (except for Input sample)

source_name: notochord

growth_protocol: medium containing Iscove's Modified Dulbecco's Medium (IMDM): RPMI-1640 Medium (4:1), 10% fetal bovine serum (FBS), and additional 1% L-glutamine

extract_protocol:
ChIP DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA).
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: MUG-Chor1 cells treated with or without PUGNAc+GlcNAc, then pull down with Notch1 antibody.

value: notochord

value: Human mesenchymal like cells


title: ChIP-sequencing analysis of Notch1 intracellular domain (ChIP)

description: Library name: NICD1, ChIP


title: PK45H mCHERRY + M2RTTA 1


title: K14-Ctrl, BC, replicate 2


title: ChIP-sequencing analysis of Notch1 intracellular domain (Input)

description: Library name: NICD1, Input


title: KP4 OVOL2 1

value: Human PDA cell line - KP4


title: PK45H NORMAL 2


title: kidney biopsy_NH86

value: No ABMR/Mixed


title: K14-RankD/D, LC, replicate 4

value: mammary gland


title: ChIP-sequencing analysis of O-glycosylated Notch1 intracellular domain (ChIP)

description: Library name: O-Glc NICD1, ChIP


title: K14-RankD/D, BC, replicate 5


title: kidney biopsy_NH87


title: K14-Ctrl, LC, replicate 2

value: Luminal cells


title: FIL_RNASeq_REP3

city: Austin

first: TASLIMA

middle: E.

last: HAQUE

address: J.T. Patterson Laboratories Bldg, 2415 Speedway

department: Department of Integrative Biology

institute: University of Texas at Austin

description:
Library name: FIL_RNASeq_REP3
TAGSeq_Control

data_processing:
TAGseq data was processed as descripedin Bhaskara et al. (2016).After marking duplicated reads, bigwig file was generated at 10 bp bin normalized as CPM.
For each ATACSeq library, raw reads were trimmed using Trimmomatic v0.39 for NexteraPE (2:30:10) based on clipping leading and trailing bases below quality thresholds (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15). Reads with a minimum length of 36 bp with proper pairs were retained. The reference genomes of the two study ecotypes were masked for non-mappable regions and known repeats. To identify mappable regions, the target genome was simulated by in silico fragmentation into 100 bp fragments which were mapped to reference. Only uniquely mapped regions were considered as mappable. Trimmed reads of each ATAC-Seq library were mapped against the corresponding masked reference genome using bowtie2 v2.4.4 (-X 1000 –very-sensitive –no-mixed –no-discordant), filtered for mapping quality or mapped at organelle genomes and sorted by coordinate using SAMtools v1.13. Clonal duplicates were removed by Picard v2.25. bigwig file was generated at 10 bp bin without any normalization
Assembly: var. hallii HAL2 reference genome v2.2: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=591/ and var. filipes FIL2 reference genome v3.2: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=495/
Supplementary files format and content: For TAGSeq data: bigwig file. Coverage was generated using CPM normalization at 10 bp bin
Supplementary files format and content: ForA TAGSeq data: bigwig file. Coverage was generated without normalization at 10 bp bin

organism: Panicum hallii var. filipes

source_name: Leaf

growth_protocol: Seeds of inland (var. hallii; HAL2 genotype) and coastal (var. filipe; FIL2 genotype) ecotypes of P. hallii were stratified and germinated in sand for each temporal block separately. Seedlings were transferred to individual 4-inch pots filled with potting media (6:1:1 homogenous mixture of Promix: Turface: Profile) on the fourth day after germination. Plants were grown in a controlled growth chamber at 28/25°C for 12hr/12hr day/night cycle and pots were arrayed in a randomized design with four replicates in each cohort.One replicate from each ecotype from a given cohort was randomly chosen for library preparation. Leaves of a whole seedling were harvested after two weeks to prepare TAGSeq and corresponding ATAC-Seq library for that given replicate

extract_protocol:
Tissue samples were flash-frozen in liquid nitrogen, stored at -80°C and later were ground into a fine powder. RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific; Cat # 15596018) following the manufacturer’s instructions.
ATAC-Seq libraries were prepared as described by Lu et al. (2016). TAGSeq libraries were prepared from 1 μg of total RNA following the protocol described by Weng et al. (2019)

value: Leaf

value: Panicum hallii var. filipes

value: Control


title: TC-1-NC

city: Beijing

first: Yueyue

last: Yan

state: Beijing

address: No. 1 ShuaiFuyuan Road, Dongcheng District

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: TC-1-NC

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKMvalues for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) from roots tissue of Scutellaria baicalensis Georgi according to protocol. Then, electrophoresis on a denaturing agarose gel and NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) were used for separating and measuring total RNA. Approximately 2 µg of total RNA with a concentration of 200 ng/µl from equal amount of RNA samples.
RNA libraries created with the QIAseq miRNA Library Kit (Qiagen, Valencia, CA, USA) from total RNA following manufacturer's protocols.


title: HPAFII NORMAL 3

source_name: Human PDA cell line - HPAFII

value: Human PDA cell line - HPAFII


title: FIL_RNASeq_REP2

description:
Library name: FIL_RNASeq_REP2
TAGSeq_Control


title: FIL_RNASeq_REP1

description:
Library name: FIL_RNASeq_REP1
TAGSeq_Control


title: PK45H OVOL2 + M2RTTA 2

value: OVOL2 overexpression (with M2RTTA)


title: kidney biopsy_NH85

value: kidney biopsy


title: K14-Ctrl, LC, replicate 1

value: female

value: 1mg/ml doxycicline


title: K14-RankD/D, BC, replicate 4

value: Basal Cells


title: kidney biopsy_NH89


title: TC-1-319A

description: Library name: TC-1-319A


title: kidney biopsy_NH88


title: kidney biopsy_NH84


title: PK45H mCHERRY 3

value: Human PDA cell line - PK45H

value: mCherry ORF (negative control)


title: genomic_DNAmethylation_204936250027_R06C01

type: genomic

city: Boston

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

description: Genomic DNA from 204936250027_R06C01

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to manufacturer's protocol

scan_protocol: iScan system according to manufacturer's protocol

data_processing: Quantile and noob normalization, filtering to remove probes with detection p-values > 0.01 in at least one sample, sites mapping to the X and Y chromosomes, sites with annotated probe SNPs, and cross-reactive probes identified by Chen et al. (2013) and Pidsley et al. (2016).

label: Cy3 and Cy5

source_name: spina bifida

label_protocol: Standard Illumina protocol

extract_protocol: Blood and buccal: Qiagen QIAsymphony DSP DNA Midi Kit. Dural tissue: treated with EtOH to remove OCT gel, DNA extracted with Qiagen DNeasy Blood and Tissue Kit.

value: buccal swab

tag: source

value: Genomic DNA from 01-1178-C

tag: basename

value: F


title: K14-Ctrl, BC, replicate 1


title: KP4 mCHERRY M2RTTA 3

value: Human PDA cell line - KP4

value: mCherry ORF co-transduced with M2RTTA (negative control)


title: K14-RankD/D, LC, replicate 3

value: mammary gland

value: Luminal cells


title: kidney biopsy_NH81

value: No ABMR/Mixed


title: K14-RankD/D, BC, replicate 2


title: kidney biopsy_NH82


title: kidney biopsy_NH80


title: PANC1 OVOL2 1

value: Human PDA cell line - PANC1

value: OVOL2 overexpression


title: K14-RankD/D, BC, replicate 3


title: genomic_DNAmethylation_204316970040_R02C01

description: Genomic DNA from 204316970040_R02C01

value: Genomic DNA from 01-1173-C


title: genomic_DNAmethylation_204936250027_R01C01

description: Genomic DNA from 204936250027_R01C01

value: Genomic DNA from 01-1165-C


title: K14-RankD/D, LC, replicate 2

value: female


title: kidney biopsy_NH83

value: kidney biopsy


title: PK45H NORMAL 1

value: Untreated


title: PANC1 NORMAL 2


title: genomic_DNAmethylation_204316970040_R06C01

description: Genomic DNA from 204316970040_R06C01

value: Genomic DNA from 01-1160-C


title: K14-RankD/D, BC, replicate 1

value: Basal Cells

value: 1mg/ml doxycicline


title: kidney biopsy_NH77


title: HPAFII NORMAL 2

value: Human PDA cell line - HPAFII


title: K14-RankD/D, LC, replicate 1


title: kidney biopsy_NH79

value: ABMR/Mixed


title: kidney biopsy_NH78


title: PK45H mCHERRY 2

value: Human PDA cell line - PK45H

value: mCherry ORF (negative control)


title: genomic_DNAmethylation_204930640032_R03C01

description: Genomic DNA from 204930640032_R03C01

value: buccal swab

value: Genomic DNA from 01-1159-C

value: F


title: kidney biopsy_NH76

value: No ABMR/Mixed


title: PK45H OVOL2 + M2RTTA 1

value: OVOL2 overexpression (with M2RTTA)


title: genomic_DNAmethylation_204316970116_R01C01

description: Genomic DNA from 204316970116_R01C01

value: Genomic DNA from 01-1155-C


title: kidney biopsy_NH74


title: Ewt sample 1

first: Rui

last: Sun

address: No.19, Xinjiekouwai St

department: School of Environment

institute: Beijing Normal University

description: Library name: Ewt_1

data_processing:
Raw sequencing reads (in fastq format) were processed using the fastp tool (version 0.20.1).
Adapter sequences, poly-N regions, and low-quality reads were filtered out to generate clean data.
The quality of the cleaned data was assessed by calculating quality control metrics, including Q20, Q30, and GC content. Only high-quality clean reads were retained for subsequent analyses.
Assembly: The clean reads were aligned to the reference genome (GCF_000005845.2) using Bowtie2 (version 2.5.4), a tool optimized for prokaryotic genomes. The reference genome and corresponding gene annotation files were obtained from the NCBI database.
Supplementary files format and content: excel files include FPKM value for each sample
Supplementary files format and content: excel files include count value for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655

growth_protocol: Strains were grown in LB medium at 37  °C with shaking at 180 rpm in the dark.

extract_protocol:
Total RNA was extracted from the selected biological samples using an RNA extraction kit (manufacturer details), following the manufacturer’s protocol. RNA quantity and quality were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The RNA integrity number (RIN) was verified to be above 8.0, ensuring suitability for downstream sequencing.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. Ribosomal RNA was depleted from the total RNA, followed by RNA fragmentation. First-strand cDNA synthesis was carried out using random hexamer primers. In the second-strand cDNA synthesis, dTTPs replaced dUTPs. After end repair, A-tailing, adapter ligation, size selection, amplification, and purification with Agencourt AMPure XP beads (Beckman Coulter, USA), the libraries were quantified using a Qubit fluorometer, and their quality was validated with the Agilent Bioanalyzer.

treatment_protocol: Escherichia coli was cultured in LB medium at 37°C, 180 rpm, in the dark, until the stationary phase (20 h). A 1 mL cell suspension (108 CFU/mL) was collected and exposed to 30 mg/L AgNPs, 20 mg/L CuNPs, or 10 mg/L ZnO NPs. Another 1 mL cell suspension (107 CFU/mL) was collected and exposed to 100 mg/L Fe3O4 NPs, 100 mg/L CeO2 NPs, or 100 mg/L SiO2 NPs separately. The cells were then incubated in the dark for 4 h. After incubation, 100 μL of the mixture was transferred into 10 mL of fresh LB medium for a subsequent 20-h growth phase, completing one cycle. A total of 14 cycles were conducted. After 14 days of exposure to different NPs, the strains were named EAgNPs, ECuNPs, EZnO NPs, EFe3O4 NPs, ECeO2 NPs, and ESiO2 NPs. The ppk gene was knocked out in the EAgNPs strain, which was subsequently named EAgNPs(△ppk). Ewt represents the untreated control with no NP exposure.

value: Escherichia coli MG1655

value: WT

value: control


title: genomic_DNAmethylation_204316970165_R06C01

description: Genomic DNA from 204316970165_R06C01

value: Genomic DNA from 01-1157-C

value: M


title: KP4 mCHERRY M2RTTA 2

value: Human PDA cell line - KP4

value: mCherry ORF co-transduced with M2RTTA (negative control)


title: Ewt sample 3

description: Library name: Ewt_3


title: PANC1 NORMAL 1

value: Human PDA cell line - PANC1

value: Untreated


title: genomic_DNAmethylation_204936250101_R03C01

description: Genomic DNA from 204936250101_R03C01

value: Genomic DNA from 01-1139-C


title: Ewt sample 2

description: Library name: Ewt_2


title: PATU8988S NORMAL 3

value: Human PDA cell line - PATU8988S


title: EAgNPs(ppk gene knockout) sample3

description: Library name: Eppk_3

value: ppk gene knockout

value: WT was cyclically exposed to AgNPs for 14 days, followed by ppk gene knockout, sample3


title: genomic_DNAmethylation_204936250102_R01C01

description: Genomic DNA from 204936250102_R01C01

value: buccal swab

value: Genomic DNA from 01-1136-C


title: genomic_DNAmethylation_204936250060_R02C01

description: Genomic DNA from 204936250060_R02C01

value: Genomic DNA from 01-1152-C

value: F


title: kidney biopsy_NH72

value: No ABMR/Mixed

value: kidney biopsy


title: genomic_DNAmethylation_204316970116_R03C01

description: Genomic DNA from 204316970116_R03C01

value: Genomic DNA from 01-1164-C


title: genomic_DNAmethylation_204316970030_R03C01

description: Genomic DNA from 204316970030_R03C01

value: Genomic DNA from 01-1149-C


title: EAgNPs(ppk gene knockout) sample1

description: Library name: Eppk_1

value: Escherichia coli MG1655

value: WT was cyclically exposed to AgNPs for 14 days, followed by ppk gene knockout, sample1


title: kidney biopsy_NH71


title: kidney biopsy_NH73

value: ABMR/Mixed


title: EAgNPs(ppk gene knockout) sample2

description: Library name: Eppk_2

value: WT was cyclically exposed to AgNPs for 14 days, followed by ppk gene knockout, sample2


title: PATU8988S_TARGET_CELL_LINE_2

data_processing:
Single end PLATE-Seq reads were pseudoaligned to the GRCh38 transcriptome (mRNA and ncRNA) and quantified using kallisto version 0.44.0 (kallisto citation) with sequence-specific bias correction. Transcript-level counts were collapsed to entrez-id gene-level counts using the tximport package in R (tximport citation). The biomaRt package in R (biomaRt citations) was used to map transcript-level Ensembl-ids to gene-level entrez-ids
PLATE-Seq samples were sequenced across four lanes of the sequencer (L001, L002, L003, L004). Data from each lane were aligned individually, and then summed the read counts from each lane to get the final read counts matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Table containing reads count of each gene (row) in each sample (column)

growth_protocol: Each ORF containing lentivirus was transduced to KP4 morphogenic cell line with MOI 2 in triplicates (6 well format in the presence of 8ug/ml polybrene). In another set of triplicates lentiviral ORFs were co-transduced with M2rtTA (FUW-M2rtTA, addgene #20342), which acts as transcriptional amplifier in tetracyclin inducible systems. The following day after the viral transductions, the media was changed and puromycin (2.5ug/ml) and doxocycline (0.6ug/ml) was added to the cells.

tag: tumor

value: PDA tumor

value: Untreated


title: HPAFII NORMAL 1

value: Human PDA cell line - HPAFII


title: genomic_DNAmethylation_204936250102_R05C01

description: Genomic DNA from 204936250102_R05C01

value: Genomic DNA from 01-1132-C

value: M


title: ESiO2NPs  sample 2

description: Library name: ESiO2_2

value: WT

value: WT was subjected to 14-day cyclic exposure to SiO2 NPs, sample 2


title: ESiO2NPs  sample 3

description: Library name: ESiO2_3

value: WT was subjected to 14-day cyclic exposure to SiO2 NPs, sample 3


title: PATU8988S_TARGET_CELL_LINE_3


title: genomic_DNAmethylation_204930640094_R02C01

description: Genomic DNA from 204930640094_R02C01

value: buccal swab

value: Genomic DNA from 01-1130-C


title: PATU8988S_TARGET_CELL_LINE_1


title: kidney biopsy_NH68

value: kidney biopsy


title: genomic_DNAmethylation_204930640032_R07C01

description: Genomic DNA from 204930640032_R07C01

value: Genomic DNA from 01-1135-C

value: F


title: PANC1 mCHERRY + M2RTTA 3

value: Human PDA cell line - PANC1

value: mCherry ORF co-transduced with M2RTTA (negative control)


title: ECeO2NPs  sample 3

description: Library name: ECeO2_3

value: Escherichia coli MG1655

value: WT was subjected to 14-day cyclic exposure to CeO2NPs, sample 3


title: genomic_DNAmethylation_204930640093_R08C01

description: Genomic DNA from 204930640093_R08C01

value: Genomic DNA from 01-1129-C


title: KP4_OVOL2_M2RTTA_2

value: PDA tumor

value: OVOL2 overexpression (with M2RTTA)


title: KP4_OVOL2_M2RTTA_1


title: KP4_OVOL2_3

value: OVOL2 overexpression


title: kidney biopsy_NH70

value: ABMR/Mixed


title: genomic_DNAmethylation_204936250027_R02C01

description: Genomic DNA from 204936250027_R02C01

value: Genomic DNA from 01-1126-C

value: M


title: KP4_OVOL2_M2RTTA_3


title: kidney biopsy_NH69


title: kidney biopsy_NH67

value: No ABMR/Mixed


title: EFe3O4NPs  sample 2

description: Library name: EFe3O4_2

value: WT

value: WT was subjected to 14-day cyclic exposure to Fe3O4 NPs, sample 2


title: EFe3O4NPs  sample 3

description: Library name: EFe3O4_3

value: WT was subjected to 14-day cyclic exposure to Fe3O4 NPs, sample 3


title: ESiO2NPs  sample 1

description: Library name: ESiO2_1

value: WT was subjected to 14-day cyclic exposure to SiO2 NPs, sample 1


title: genomic_DNAmethylation_204316970040_R04C01

description: Genomic DNA from 204316970040_R04C01

value: buccal swab

value: Genomic DNA from 01-1123-C

value: F


title: genomic_DNAmethylation_204930640032_R05C01

description: Genomic DNA from 204930640032_R05C01

value: Genomic DNA from 01-1120-C


title: KP4_OVOL2_1


title: genomic_DNAmethylation_204936250027_R08C01

description: Genomic DNA from 204936250027_R08C01

value: Genomic DNA from 01-1128-C


title: ECeO2NPs  sample 2

description: Library name: ECeO2_2

value: Escherichia coli MG1655

value: WT was subjected to 14-day cyclic exposure to CeO2NPs, sample 2


title: kidney biopsy_NH66

value: kidney biopsy


title: kidney biopsy_NH62


title: kidney biopsy_NH60


title: genomic_DNAmethylation_204316970165_R03C01

description: Genomic DNA from 204316970165_R03C01

value: Genomic DNA from 01-1127-C


title: ECeO2NPs  sample 1

description: Library name: ECeO2_1

value: WT was subjected to 14-day cyclic exposure to CeO2NPs, sample 1


title: EZnONPs  sample 2

description: Library name: EZnO_2

value: WT was subjected to 14-day cyclic exposure to ZnO NPs, sample 2


title: genomic_DNAmethylation_204930640032_R01C01

description: Genomic DNA from 204930640032_R01C01

value: Genomic DNA from 01-1115-C

value: M


title: EZnONPs  sample 1

description: Library name: EZnO_1

value: WT

value: WT was subjected to 14-day cyclic exposure to ZnO NPs, sample 1


title: genomic_DNAmethylation_204936250101_R02C01

description: Genomic DNA from 204936250101_R02C01

value: Genomic DNA from 01-1114-C


title: kidney biopsy_NH65

value: No ABMR/Mixed


title: ECuNPs  sample 3

description: Library name: ECu_3

value: WT was subjected to 14-day cyclic exposure to CuNPs, sample 3


title: kidney biopsy_NH64


title: kidney biopsy_NH59


title: genomic_DNAmethylation_204936250060_R01C01

description: Genomic DNA from 204936250060_R01C01

value: buccal swab

value: Genomic DNA from 01-1110-C


title: KP4_OVOL2_2

value: PDA tumor

value: OVOL2 overexpression


title: kidney biopsy_NH63


title: KP4_NR2F6_2

value: NR2F6 overexpression


title: EAgNPs sample 3

description: Library name: EAgNPs_3

value: Escherichia coli MG1655

value: WT was subjected to 14-day cyclic exposure to AgNPs, sample 3


title: EZnONPs  sample 3

description: Library name: EZnO_3

value: WT was subjected to 14-day cyclic exposure to ZnO NPs, sample 3


title: genomic_DNAmethylation_204316970116_R07C01

description: Genomic DNA from 204316970116_R07C01

value: Genomic DNA from 01-1119-C


title: ECuNPs  sample 1

description: Library name: ECu_1

value: WT was subjected to 14-day cyclic exposure to CuNPs, sample 1


title: KP4_NR2F6_M2RTTA_3

value: NR2F6 overexpression (with M2RTTA)


title: genomic_DNAmethylation_204930640032_R06C01

description: Genomic DNA from 204930640032_R06C01

value: dural tissue

value: Genomic DNA from 01-1178-C

value: F


title: KP4_NR2F6_M2RTTA_2


title: EFe3O4NPs  sample 1

description: Library name: EFe3O4_1

value: WT

value: WT was subjected to 14-day cyclic exposure to Fe3O4 NPs, sample 1


title: ECuNPs  sample 2

description: Library name: ECu_2

value: WT was subjected to 14-day cyclic exposure to CuNPs, sample 2


title: KP4_NR2F6_M2RTTA_1


title: genomic_DNAmethylation_204930640094_R04C01

description: Genomic DNA from 204930640094_R04C01

value: buccal swab

value: Genomic DNA from 01-1111-C

value: M


title: kidney biopsy_NH58

value: No ABMR/Mixed

value: kidney biopsy


title: kidney biopsy_NH53


title: KP4_NR2F6_3

value: PDA tumor

value: NR2F6 overexpression


title: E12.5 KO epithelial cells rep 1

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

description: Library name: E12pt5_KO_01

data_processing:
Alignment to mm10 and count quantification with nf-core/rnaseq pipeline (STAR + salmon)
Normalization and differential expression testing with pyDEseq2
Assembly: mm10
Supplementary files format and content: Anndata object containing raw, normalized, and VST-transformed gene expression values for all samples.

source_name: lung

extract_protocol:
Live, EPCAM+ cells were sorted by FACS from freshly dissociated E12.5 lungs of individual mice directly into lysis buffer before freezing.
Thawed lysate was depleted of ribosomal RNAs before paired-end sequencing library construction.

value: lung

value: epithelial cells

value: Shh-Cre/+ x Brd4fl/fl


title: kidney biopsy_NH61

source_name: kidney biopsy


title: kidney biopsy_NH52

value: ABMR/Mixed


title: KP4_NR2F6_1


title: kidney biopsy_NH75


title: kidney biopsy_NH56


title: KP4_NORMAL_CELL_LINE_1

value: untreated


title: kidney biopsy_NH51


title: KP4_mCHERRY_M2RTTA_2

value: mCherry ORF co-transduced with M2RTTA (negative control)


title: EAgNPs sample 1

description: Library name: EAgNPs_1

value: Escherichia coli MG1655

value: WT was subjected to 14-day cyclic exposure to AgNPs, sample 1


title: genomic_DNAmethylation_204936250101_R08C01

description: Genomic DNA from 204936250101_R08C01

value: Genomic DNA from 01-1101-C

value: F


title: kidney biopsy_NH55


title: genomic_DNAmethylation_204316970165_R02C01

description: Genomic DNA from 204316970165_R02C01

value: dural tissue

value: Genomic DNA from 01-1165-C


title: EAgNPs sample 2

description: Library name: EAgNPs_2

value: WT

value: WT was subjected to 14-day cyclic exposure to AgNPs, sample 2


title: kidney biopsy_NH54

value: kidney biopsy


title: KP4_mCHERRY_M2RTTA_1

value: PDA tumor


title: genomic_DNAmethylation_204316970116_R08C01

description: Genomic DNA from 204316970116_R08C01

value: Genomic DNA from 01-1160-C


title: KP4_mCHERRY_M2RTTA_3


title: genomic_DNAmethylation_204936250060_R03C01

description: Genomic DNA from 204936250060_R03C01

value: Genomic DNA from 01-1173-C


title: KP4_NORMAL_CELL_LINE_2


title: kidney biopsy_NH57


title: kidney biopsy_NH49

value: No ABMR/Mixed


title: E12.5 HET epithelial cells rep 0

description: Library name: E12pt5_HET_00

value: lung

value: epithelial cells

value: Shh-Cre/+ x Brd4fl/+


title: E12.5 KO epithelial cells rep 0

description: Library name: E12pt5_KO_00

value: Shh-Cre/+ x Brd4fl/fl


title: KP4_mCHERRY_3

value: mCherry ORF (negative control)


title: genomic_DNAmethylation_204930640094_R03C01

description: Genomic DNA from 204930640094_R03C01

value: Genomic DNA from 01-1164-C

value: M


title: genomic_DNAmethylation_204930640093_R06C01

description: Genomic DNA from 204930640093_R06C01

value: Genomic DNA from 01-1157-C


title: kidney biopsy_NH48


title: E12.5 WT epithelial cells rep 1

description: Library name: E12pt5_WT_01


title: kidney biopsy_NH50

value: ABMR/Mixed


title: genomic_DNAmethylation_204936250060_R08C01

description: Genomic DNA from 204936250060_R08C01

value: dural tissue

value: Genomic DNA from 01-1159-C

value: F


title: genomic_DNAmethylation_204316970116_R06C01

description: Genomic DNA from 204316970116_R06C01

value: Genomic DNA from 01-1152-C


title: E12.5 WT epithelial cells rep 0

description: Library name: E12pt5_WT_00


title: KP4_mCHERRY_1

value: PDA tumor


title: K14-Rank, B/L hybrid, replicate 3

first: Jaime

last: Redondo-Pedraza

state: Madrid

address: Melchor Fernandez Almagro 3, CNIO

department: Molecular Oncology

data_processing:
Tags were aligned to mouse genome (mm9) using Bowtie2
Genome tracks have been generated using bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPKM normalization (bin size of 50 bps and 300 bps read extension).
Assembly: mm9
Supplementary files format and content: bigWig (Coverage files)

extract_protocol:
Fresh mamamry glands were mechanically dissected by scissor chopping after draining lymph nodes were removed and enzymatically digested with digestium medium (Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Biowest, #L0093-500ml), 0.6 U/ml collagenase A (Sigma-Aldrich, #1108879300), 2.85U/mL dispase II (ThermoFisher Scientific, #17105041), 2% HEPES (ThermoFisher Scientific, #H8357-100ml) and 1% penicillin–streptomycin(ThermoFisher Scientific, #15140-122)) for 1h rocking (50 rpm) at 37°C. Samples were washed with CO2 independent media (ThermoFisher Scientific, # 18045088) supplemented with 2mM glutamax (Gibco, #35050-061). Single cells were isolated by sequential treatments with 0.25%trypsin/0.1% EDTA solution (Sigma-Aldrich, #T3924-100ml) for 1min at RT and dispaseII/DNAseI (ThermoFisher Scientific, #17105041 / Roche, #10104159001) at 37°C for 5 min. Enzymatic digestions were blocked by adding CO2 independent media (ThermoFisher Scientific, #18045088) supplemented with 2mM glutamax (Gibco, #35050-061) and 5% FBS (ThermoFisher Scientific, #F7524-500ml). Erythrocytes were eliminated by treating samples with cold (4°C) ammonium chloride solution (STEMCELL Technologies, #7008) for 1min at RT. Cell aggregates were removed by filtering the cell suspension with a 40μm strainer and single epithelial cells were counted manually using a Neubauer chamber. Single cells were blocked with blocking buffer (PBS + 0.5% Bovine Serum Albumin (Sigma-Aldrich, #13391+ 2mM EDTA) for 20min on ice. Single cells were incubated for 40 min on ice with the corresponding surface antibodies (CD24-AlexaFluor700 (564237, BD Pharmingen™, 1μg/ml), CD49f-AlexaFluor647 (562473, BD Pharmingen™,1.25 μg/ml), CD31-PECy7 (102417, Biolegend, 0.25 μg/ml), and CD45-PECy7 (103113, Biolegend, 0.125 μg/ml)). Prior sorting, single cells solution was filtered by a 70μm strainer. Cell sorting was performed using a BD FACSAriaTM cell sorter.For ATAC-seq, 25000 FACs-isolated cells were washed in cold PBS (500g, 5’, 4ºC) and lysed in 50ul lysis buffer (10 mM TrisHCl pH7,5, 10 mM NaCl, 3 mM MgCl2, 0,1% NP40, 0,1% Tween 20, 0,01% Digitonin and 1x Complete Protease Inhibitor Cocktail) for 5 minutes on ice. Nuclei were isolated by centrifugation (500g, 10 min, 4ºC) and treated with transposase Tn5 (, Illumina, Nextera DNA Library Preparation Kit, #FC-131-1024). DNA was purified using MinElute PCR Purification Kit (Qiagen, #28004).
Libraries were prepared using NEBNext HF Polymerase with indexing primers from Nextera and sequenced using Illumina Novaseq

treatment_protocol: Treat 4 week old female mice with 1 mg/ml doxycycline + 20mg/ml sucrose, ad libitum in the drinking water for 4 weeks Then, treat females when 6 week old  with 50mg/ml MPA pellet (Innovative Research of America #NP-161) for 21 days.

value: mammary gland

value: Basal-luminal hybrid cells

tag: age

value: 9 weeks

value: 50mg/pellet MPA (#NP-161) (21 days)


title: genomic_DNAmethylation_204930640032_R02C01

description: Genomic DNA from 204930640032_R02C01

value: Genomic DNA from 01-1149-C


title: genomic_DNAmethylation_204316970116_R02C01

description: Genomic DNA from 204316970116_R02C01

value: Genomic DNA from 01-1155-C


title: KP4_mCHERRY_2


title: E12.5 HET epithelial cells rep 1

description: Library name: E12pt5_HET_01

value: lung

value: epithelial cells

value: Shh-Cre/+ x Brd4fl/+


title: KP4_HNF1A_M2RTTA_2

value: HNF1A overexpression (with M2RTTA)


title: K14-Rank, BC, replicate 3

value: Basal Cells


title: kidney biopsy_NH46

value: No ABMR/Mixed

value: kidney biopsy


title: kidney biopsy_NH44


title: genomic_DNAmethylation_204316970040_R08C01

description: Genomic DNA from 204316970040_R08C01

value: dural tissue

value: Genomic DNA from 01-1136-C

value: M


title: KP4_HNF1A_M2RTTA_1

value: PDA tumor


title: KP4_HNF1A_M2RTTA_3


title: K14-Rank, LC, replicate 3

value: mammary gland

value: Luminal cells


title: genomic_DNAmethylation_204316970165_R08C01

description: Genomic DNA from 204316970165_R08C01

value: Genomic DNA from 01-1135-C

value: F


title: genomic_DNAmethylation_204316970030_R01C01

description: Genomic DNA from 204316970030_R01C01

value: Genomic DNA from 01-1139-C


title: kidney biopsy_NH42


title: kidney biopsy_NH47


title: KP4_HNF1A_3

value: HNF1A overexpression


title: kidney biopsy_NH43


title: KP4_NORMAL_CELL_LINE_3

value: untreated


title: K14-Rank, B/L hybrid, replicate 2

value: Basal-luminal hybrid cells

value: 9 weeks

value: 50mg/pellet MPA (#NP-161) (21 days)


title: genomic_DNAmethylation_204936250101_R01C01

description: Genomic DNA from 204936250101_R01C01

value: Genomic DNA from 01-1132-C


title: KP4_HNF1A_1


title: K14-Ctrl, LC, replicate 3


title: K14-Rank, BC, replicate 2

value: Basal Cells


title: KP4_HNF1A_2


title: kidney biopsy_NH45

value: No ABMR/Mixed

value: kidney biopsy


title: genomic_DNAmethylation_204936250027_R04C01

description: Genomic DNA from 204936250027_R04C01

value: dural tissue

value: Genomic DNA from 01-1130-C


title: KP4_FOXA3_M2RTTA_3

value: PDA tumor

value: FOXA3 overexpression (with M2RTTA)


title: genomic_DNAmethylation_204936250102_R02C01

description: Genomic DNA from 204936250102_R02C01

value: Genomic DNA from 01-1129-C

value: M


title: kidney biopsy_NH41


title: genomic_DNAmethylation_204930640109_R01C01

description: Genomic DNA from 204930640109_R01C01

value: Genomic DNA from 01-1128-C


title: K14-Ctrl, BC, replicate 3

value: mammary gland


title: kidney biopsy_NH40


title: KP4_FOXA3_M2RTTA_1


title: KP4_FOXA3_M2RTTA_2


title: K14-Rank, LC, replicate 2

value: Luminal cells


title: genomic_DNAmethylation_204930640109_R02C01

description: Genomic DNA from 204930640109_R02C01

value: Genomic DNA from 01-1126-C


title: genomic_DNAmethylation_204936250102_R06C01

description: Genomic DNA from 204936250102_R06C01

value: Genomic DNA from 01-1127-C


title: KP4_FOXA3_3

value: FOXA3 overexpression


title: genomic_DNAmethylation_204930640109_R03C01

description: Genomic DNA from 204930640109_R03C01

value: Genomic DNA from 01-1123-C

value: F


title: K14-Ctrl, LC, replicate 2

value: 9 weeks

value: 50mg/pellet MPA (#NP-161) (21 days)


title: KP4_FOXA3_1


title: K14-Rank, B/L hybrid, replicate 1

value: Basal-luminal hybrid cells


title: kidney biopsy_NH39

value: No ABMR/Mixed

value: kidney biopsy


title: kidney biopsy_NH35

value: ABMR/Mixed


title: K14-Rank, LC, replicate 1


title: KP4_FOXA2_M2RTTA_3

value: PDA tumor

value: FOXA2 overexpression (with M2RTTA)


title: K14-Ctrl, BC, replicate 1

value: Basal Cells


title: kidney biopsy_NH37


title: KP4_FOXA3_2


title: kidney biopsy_NH36


title: kidney biopsy_NH38


title: genomic_DNAmethylation_204930640094_R08C01

description: Genomic DNA from 204930640094_R08C01

value: dural tissue

value: Genomic DNA from 01-1120-C

value: M


title: kidney biopsy_NH34


title: genomic_DNAmethylation_204930640093_R02C01

description: Genomic DNA from 204930640093_R02C01

value: Genomic DNA from 01-1119-C


title: K14-Rank, BC, replicate 1

value: mammary gland


title: KP4_FOXA2_M2RTTA_2


title: genomic_DNAmethylation_204936250060_R07C01

description: Genomic DNA from 204936250060_R07C01

value: Genomic DNA from 01-1115-C


title: genomic_DNAmethylation_204316970030_R06C01

description: Genomic DNA from 204316970030_R06C01

value: Genomic DNA from 01-1111-C


title: K14-Ctrl, LC, replicate 1

value: Luminal cells


title: HAL_RNASeq_REP3

description:
Library name: HAL_RNASeq_REP3
TAGSeq_Control

organism: Panicum hallii var. hallii

value: Leaf

value: Panicum hallii var. Hallii

value: Control


title: kidney biopsy_NH33


title: genomic_DNAmethylation_204930640094_R06C01

description: Genomic DNA from 204930640094_R06C01

value: Genomic DNA from 01-1114-C


title: HAL_RNASeq_REP2

description:
Library name: HAL_RNASeq_REP2
TAGSeq_Control


title: kidney biopsy_NH32

value: kidney biopsy


title: KP4_FOXA2_M2RTTA_1


title: kidney biopsy_NH31

value: ABMR/Mixed


title: KP4_FOXA2_1

value: PDA tumor

value: FOXA2 overexpression


title: genomic_DNAmethylation_204316970030_R05C01

description: Genomic DNA from 204316970030_R05C01

value: Genomic DNA from 01-1101-C

value: F


title: K14-Ctrl, BC, replicate 2

value: Basal Cells

value: 9 weeks

value: 50mg/pellet MPA (#NP-161) (21 days)


title: HAL_RNASeq_REP1

description:
Library name: HAL_RNASeq_REP1
TAGSeq_Control


title: kidney biopsy_NH30


title: KP4_ETV4_M2RTTA_3

value: ETV4 overexpression (with M2RTTA)


title: KP4_FOXA2_3


title: genomic_DNAmethylation_204930640109_R04C01

description: Genomic DNA from 204930640109_R04C01

value: dural tissue

value: Genomic DNA from 01-1110-C


title: kidney biopsy_NH27

value: No ABMR/Mixed


title: genomic_DNAmethylation_204930640093_R01C01

description: Genomic DNA from 204930640093_R01C01

value: whole blood

value: Genomic DNA from 01-1178-C


title: kidney biopsy_NH28


title: HAL_ATACSeq_REP2

description:
Library name: HAL_ATACSeq_REP2
ATACSeq_Control

value: Leaf

value: Panicum hallii var. Hallii

value: Control


title: KP4_FOXA2_2


title: KP4_ETV4_M2RTTA_2


title: genomic_DNAmethylation_204316970030_R04C01

description: Genomic DNA from 204316970030_R04C01

value: Genomic DNA from 01-1173-C


title: HAL_ATACSeq_REP1

description:
Library name: HAL_ATACSeq_REP1
ATACSeq_Control


title: KP4_ETV4_M2RTTA_1

value: PDA tumor


title: genomic_DNAmethylation_204936250102_R03C01

description: Genomic DNA from 204936250102_R03C01

value: Genomic DNA from 01-1165-C


title: rat retina, postnatal day 90, treated with hNPCs, rep 2

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Library name: 15_rat_retina_p90_treated_2

data_processing:
Sample demultiplexing was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core.  Raw data were delivered as multiple gzipped fastq files.
Rat samples:  demultiplexed fastq files were run via CellRanger v7.1 using the "cellranger count" command using a CellRanger reference sequence previously complied using the "cellranger mkref" command and reference sequence Rnor_6.0.102
Human samples:  demultiplexed fastq files were run via CellRanger v6.1.2 using the "cellranger count" command using the 10x-provided reference GRCh38-2020-A
Assembly: Human: GRCh38, Rat: Rnor6.0.102
Supplementary files format and content: Rat:  CellRanger output filtered_feature_bc_matrix.h5 files
Supplementary files format and content: Human:  CellRanger output filtered_feature_bc_matrix directory (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)

organism: Rattus norvegicus

source_name: retina

growth_protocol: hNPC vials were rapidly thawed in a 37 °C water bath after removal from liquid nitrogen, followed by resuspension in prewarmed Stemline medium (Sigma, St. Louis, Missouri) supplemented with rhEGF (100 ng/mL; Millipore, Billerica, MA) and rhLIF (100 ng/mL; Millipore). The cell suspension was centrifuged at 200g for 5 minutes, and the pellet was resuspended in Balanced salt solution (BSS, Alcon). Cells were then labeled using PKH26 Red Fluorescent Cell Linker Kits (Sigma, St. Louis, Missouri) according to the manufacturer's protocol, and finally resuspended at a concentration of 30,000 cells/μL in BSS. Cells were kept on ice until transplantation.

extract_protocol:
Rats retinas were pooled, digested with papain, and dissociated into single-cell suspensions by manual trituration in ovomucoid solution. Single-cell suspensions from hNPC-treated and untreated retinas were labeled with DAPI. PKH26-labeled hNPCs, along with hNPC-treated and untreated retinal cells, were sorted using a FACS sorter and collected into 1.7 mL RNase-free tubes containing 2% BSA in PBS.
Library preparation was performed using the 10x Chromium v3 single-cell reagent kit, following the manufacturer's protocol.

treatment_protocol: 2 μL of the hNPC suspension (6 × 10^4 cells/eye) was injected into the subretinal space of both left and right eyes through a small scleral incision using a fine glass pipette (internal diameter 75-150μm) attached via tubing to a 25-μL syringe (Hamilton). To reduce intraocular pressure and minimize cell efflux, the cornea was punctured prior to injection. Immediately after injection, the fundus was examined for retinal damage or signs of vascular distress. Animals showing such issues were excluded from further study.

value: retina

value: Royal College of Surgeons

value: hNPC

tag: time point


title: kidney biopsy_NH26

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

value: ABMR/Mixed

value: kidney biopsy


title: KP4_ETV4_3

value: ETV4 overexpression


title: HAL_ATACSeq_REP3

description:
Library name: HAL_ATACSeq_REP3
ATACSeq_Control


title: rat retina, postnatal day 90, treated with hNPCs, rep 1

description: Library name: 14_rat_retina_p90_treated_1


title: genomic_DNAmethylation_204316970030_R02C01

description: Genomic DNA from 204316970030_R02C01

value: Genomic DNA from 01-1164-C

value: M


title: KP4_ETV4_2


title: genomic_DNAmethylation_204930640094_R01C01

description: Genomic DNA from 204930640094_R01C01

value: Genomic DNA from 01-1160-C

value: F


title: kidney biopsy_NH29

value: No ABMR/Mixed


title: rat retina, postnatal day 90, untreated disease control, rep 1

description: Library name: 13_rat_retina_p90_untreated_1


title: kidney biopsy_NH25


title: genomic_DNAmethylation_204930640093_R07C01

description: Genomic DNA from 204930640093_R07C01

value: whole blood

value: Genomic DNA from 01-1159-C


title: KP4_ESRRA_M2RTTA_3

value: ESRRA overexpression (with M2RTTA)


title: KP4_ETV4_1


title: genomic_DNAmethylation_204936250101_R06C01

description: Genomic DNA from 204936250101_R06C01

value: Genomic DNA from 01-1155-C


title: genomic_DNAmethylation_204316970040_R07C01

description: Genomic DNA from 204316970040_R07C01

value: Genomic DNA from 01-1157-C


title: kidney biopsy_NH23


title: KP4_ESRRA_M2RTTA_2

value: PDA tumor


title: kidney biopsy_NH24


title: KP4_ESRRA_M2RTTA_1


title: rat retina, postnatal day 60, treated with hNPCs, rep 2

description: Library name: 11_rat_retina_p60_treated_2

value: retina


title: genomic_DNAmethylation_204930640094_R07C01

description: Genomic DNA from 204930640094_R07C01

value: Genomic DNA from 01-1152-C


title: kidney biopsy_NH22


title: kidney biopsy_NH19


title: kidney biopsy_NH21


title: genomic_DNAmethylation_204936250027_R05C01

description: Genomic DNA from 204936250027_R05C01

value: Genomic DNA from 01-1149-C


title: kidney biopsy_NH20


title: KP4_ESRRA_3

value: ESRRA overexpression


title: genomic_DNAmethylation_204316970165_R05C01

description: Genomic DNA from 204316970165_R05C01

value: Genomic DNA from 01-1139-C


title: rat retina, postnatal day 60, untreated disease control, rep 2

description: Library name: 08_rat_retina_p60_untreated_2

value: Royal College of Surgeons


title: rat retina, postnatal day 60, untreated disease control, rep 1

description: Library name: 07_rat_retina_p60_untreated_1


title: KP4_ESRRA_2


title: rat retina, postnatal day 60, treated with hNPCs, rep 3

description: Library name: 12_rat_retina_p60_treated_3

value: hNPC


title: rat retina, postnatal day 60, untreated disease control, rep 3

description: Library name: 09_rat_retina_p60_untreated_3


title: rat retina, postnatal day 60, treated with hNPCs, rep 1

description: Library name: 10_rat_retina_p60_treated_1


title: genomic_DNAmethylation_204936250102_R07C01

description: Genomic DNA from 204936250102_R07C01

value: Genomic DNA from 01-1135-C


title: genomic_DNAmethylation_204930640093_R04C01

description: Genomic DNA from 204930640093_R04C01

value: Genomic DNA from 01-1136-C

value: M


title: kidney biopsy_NH18

value: No ABMR/Mixed

value: kidney biopsy


title: KP4_ESRRA_1


title: Cryoablation day 7 Xenium slide 3

city: Würzburg

first: Andy

middle: Shing Fung

last: Chan

address: Gebäude E6,, Versbacher Str. 9

country: Germany

institute: Institute for Systems Immunology, University of Würzburg

description: formalin-fixed paraffin-embedded tissue sections, in situ sequencing

hyb_protocol: Gene panel targeting 475 genes was applied to the sample in 10nM, which targeted mRNA molecules of the 475 target genes. In addition to the gene panel, two negative controls were added, to assess non-specific binding and ensure the signals were from binding to RNA but not to genomic DNA. Hybridization was performed at 50°C overnight, followed by a washing step to remove unhybridized probes. Additionally, barcode oligo-conjugated antibodies (ATP1A1, E-Cadherin, CD45, aSMA, Vimentin and 18S rRNA marker) labeling the cell boundaries and interior proteins were added to label cellular structures. Samples were then ligated at 37°C for 2h, for annealing of rolling circle amplification (RCA) primer, followed by circularized probe amplification at 4°C for 1h, and 37°C for 2h, resulting in amplification of the gene-specific barcode for each RNA binding probe, enhancing the signal-to-noise ratio. Background fluorescence was chemically quenched.   Sections were placed in an imaging cassette and loaded onto the Xenium Analyzer instrument combining a high numerical aperture and a fast area scan camera with a low read noise sensor (achieving a lateral resolution of 200nm per pixel). Images were acquired in sequential hybridization-imaging cycles. In each cycle, unique fluorescently labeled secondary probes targeting RCA-amplified probe-RNA complexes were hybridized, and visualized in combination with 4′,6-diamidino-2-phenylindole (DAPI) staining. Stained samples were imaged, followed by stripping off the secondary probe and starting of another round of hybridization and imaging. Z-stacks were acquired at a 0.75μm step size across the tissue thickness.   Images were pre-processed with the built-in pipeline, where low quality signals were filtered out, and the identities of transcripts were decoded using a Xenium codebook. For quality scoring, a Phred-style Q-Score was assigned to each decoded transcript, reflecting confidence in transcript identity. Q-Scores were calibrated using negative control codewords, probes targeting non-biological sequences, and unassigned codewords. Only transcripts with a Q-Score ≥20 were included in downstream analyses.   Multimodal cell segmentation was also performed by the Xenium in-built pipeline where cells were segmented based on nuclear (DAPI), cell boundary and interior RNA signals.

scan_protocol: OTHER: Spatial Transcriptomics (in situ sequencing)

data_processing:
Raw imaging data were processed using 10x Xenium built-in pipeline to obtain cell coordinates and gene counts
NiCo was used to annotate cell type identities of segmented cells, using scRNA-seq from this study as reference data
This method is imaging-based, no genome assembly is required
cells.csv.gz: coordinates of segmented cells
matrix.mtx.gz: gene expression count data
barcodes.tsv.gz: list of segmented cell barcodes
features.tsv.gz: list of gene IDs
nico_annotation_cluster.csv.gz: annotated cluster numbers of segmented cells
nico_annotation_ct_name.csv.gz: cluster number and cell type/state

source_name: heart left ventricles

extract_protocol: tissue preparation protocol: All experimental steps followed the guideline of the Xenium workflow. Briefly, 5μm formalin-fixed paraffin-embedded tissue sections (transverse plane of the LV) were mounted on a Xenium slide within the desired imaging region. The mRNA was exposed by deparaffinization and permeabilization.

value: heart left ventricles

value: Wild type

value: Cryoablation


title: genomic_DNAmethylation_204930640094_R05C01

description: Genomic DNA from 204930640094_R05C01

value: whole blood

value: Genomic DNA from 01-1130-C


title: Cryoablation day 28 Xenium slide 3


title: KP4_ELF3_M2RTTA_3

value: PDA tumor

value: ELF3 overexpression (with M2RTTA)


title: kidney biopsy_NH16

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

value: ABMR/Mixed


title: kidney biopsy_NH17


title: genomic_DNAmethylation_204936250027_R07C01

description: Genomic DNA from 204936250027_R07C01

value: Genomic DNA from 01-1132-C


title: KP4_ELF3_M2RTTA_1


title: KP4_ELF3_M2RTTA_2


title: KP4_ELF3_3

value: ELF3 overexpression


title: genomic_DNAmethylation_204930640093_R05C01

description: Genomic DNA from 204930640093_R05C01

value: Genomic DNA from 01-1129-C


title: Cryoablation day 28 Xenium slide 2


title: Cryoablation day 7 Xenium slide 2


title: Sham day 7 Xenium slide 2

value: Sham


title: kidney biopsy_NH15


title: Sample_0014553_Region3

description: Raw data file contains the full output produced by Xenium Analyzer/Xenium Onboard Analysis package

scan_protocol: Imaging-based Spatial Transcriptomic (iST profiling) was performed following the manufacturer’s standard workflow

data_processing:
The Xenium onboard analysis processes raw instrument images by first segmenting cell nuclei using DAPI stain, then decoding fluorescent probes to build a precise 3D map of individual RNA transcripts, and finally uses these transcript locations to refine the cell boundaries before generating the final data outputs. Raw image data generated by the Xenium Analyzer was processed using the Xenium Onboard Analysis package (10x Genomics)
processed data includes: raw gene expression values

source_name: human pancreatic cancer

label_protocol: To identify PDA malignant cell states, in addition to the Xenium Human Multi-Tissue and Cancer Gene Expression panel (n=377 genes), we generated a custom panel of 100 genes predictive of the three pancreatic ductal lineages (PDLs) and the MAPK-high cell state

growth_protocol: Eight fresh frozen OCT-embedded tissue blocks from untreated human pancreatic cancer patients were obtained from the Molecular Pathology Shared Resource (MPSR) at Columbia University

extract_protocol: The Xenium Analyzer performed iterative rounds of hybridization, washing, and imaging to decode the spatial location and identity of each mRNA molecule

treatment_protocol: Tissue sections of 5 µm were sectioned and mounted onto Xenium slides (10x Genomics)  and processed following manufacturer’s instructions

value: human pancreatic cancer


title: genomic_DNAmethylation_204316970165_R04C01

description: Genomic DNA from 204316970165_R04C01

value: Genomic DNA from 01-1127-C


title: KP4_ELF3_2


title: genomic_DNAmethylation_204316970040_R05C01

description: Genomic DNA from 204316970040_R05C01

value: Genomic DNA from 01-1128-C

value: M


title: KP4_EGFP_M2RTTA_3

value: EGFP ORF co-transduced with M2RTTA (negative control)


title: kidney biopsy_NH13

value: No ABMR/Mixed

value: kidney biopsy


title: kidney biopsy_NH12


title: kidney biopsy_NH14


title: KP4_ELF3_1


title: genomic_DNAmethylation_204930640109_R07C01

description: Genomic DNA from 204930640109_R07C01

value: Genomic DNA from 01-1123-C

value: F


title: kidney biopsy_NH11


title: Sample_0014553_Region1


title: genomic_DNAmethylation_204936250101_R07C01

description: Genomic DNA from 204936250101_R07C01

value: whole blood

value: Genomic DNA from 01-1126-C


title: Sample_0014553_Region2


title: Sample_0014553_Region4


title: genomic_DNAmethylation_204936250027_R03C01

description: Genomic DNA from 204936250027_R03C01

value: Genomic DNA from 01-1119-C


title: Sample_0014524_Region3


title: kidney biopsy_NH9


title: kidney biopsy_NH8

value: ABMR/Mixed


title: Sample_0014524_Region4


title: KP4_EGFP_3

value: PDA tumor

value: EGFP ORF (negative control)


title: KP4_EGFP_M2RTTA_2


title: KP4_EGFP_2


title: genomic_DNAmethylation_204936250102_R04C01

description: Genomic DNA from 204936250102_R04C01

value: Genomic DNA from 01-1120-C


title: genomic_DNAmethylation_204316970116_R04C01

description: Genomic DNA from 204316970116_R04C01

value: Genomic DNA from 01-1115-C


title: genomic_DNAmethylation_204936250101_R05C01

description: Genomic DNA from 204936250101_R05C01

value: Genomic DNA from 01-1114-C


title: Sample_0014524_Region2

value: human pancreatic cancer


title: kidney biopsy_NH7


title: kidney biopsy_NH10


title: KP4_EGFP_M2RTTA_1


title: kidney biopsy_NH6


title: kidney biopsy_NH5


title: genomic_DNAmethylation_204936250060_R06C01

description: Genomic DNA from 204936250060_R06C01

value: Genomic DNA from 01-1111-C


title: Sample_0014524_Region1


title: kidney biopsy_NH4


title: HPAFII_TARGET_CELL_LINE_2

value: HPAFII

value: untreated


title: HPAFII_TARGET_CELL_LINE_3


title: KP4_EGFP_1


title: 11dpf, replicate 3, scRNA-seq

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

description: Library name: sample_11dpf_3

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification. Briefly, reads with low-quality barcodes and UMIs were filtered out and then mapped to the reference genome. Reads uniquely mapped to the transcriptome and intersecting an exon at least 50% were considered for UMI counting.Before quantification, the UMI sequences would be corrected for sequencing errors, and valid barcodes were identified based on the EmptyDrops method.The cell by gene matrices were produced via UMI counting and cell barcodes calling.The cell by gene matrices for each sample were individually imported to Seurat  for downstream analysis.Quality control, removing doublets, empty droplets, and cells with higher mitochondrial containment, was performed by utilizing the Seurat (v. 4.3.0) package in R with the thresholds calculated by scuttle::isOutlier function
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

organism: Danio rerio

source_name: brain

extract_protocol:
At 3, 6, and 11 dpf, zebrafish larvae were anesthetized in the E3 medium, and brain tissues were isolated within 30 min. 1500-2000 brain tissues were isolated from the above zebrafish at the corresponding time point and incubated at 37℃ with tissue digestion solution containing 2 mg/L of papain for about 25 min. Then the tissues were incubated with DMEM containing 5% fetal bovine serum (FBS) to terminate the digestion. Cell suspensions were centrifugated at 500 g for 30 min at 4℃ and resuspended with DMEM medium containing 5% FBS. Then cell suspensions were filtered through 70 μm, 40 μm cell strainer to prepare single cell suspensions. All filtration procedures were performed on ice to preserve cell viability. eGFP positive cells were sorted by FACS aril III and collected with DMEM medium containing 5% FBS.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

value: brain

value: primary cell

value: endothelial cell

value: Wild Type


title: kidney biopsy_NH3

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

value: kidney biopsy


title: 6dpf, replicate 2, scRNA-seq

description: Library name: sample_6dpf_2


title: genomic_DNAmethylation_204930640032_R04C01

description: Genomic DNA from 204930640032_R04C01

value: whole blood

value: Genomic DNA from 01-1101-C

value: F


title: HPAFII_TARGET_CELL_LINE_1

value: PDA tumor


title: genomic_DNAmethylation_204930640109_R08C01

description: Genomic DNA from 204930640109_R08C01

value: Genomic DNA from 01-1110-C


title: WT BMDMs treated with DMSO vehicle for 8 hours [WTBMDM_VEH_T2]

status: Public on Jan 15 2026

first: Peter

middle: G

last: Kim

address: 360 Longwood Ave, LC8202

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
Library name: WTBMDM_VEH_T2
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv

data_processing:
For single cell RNAseq, demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger 9.0.1 (10x Genomics), and further analyzed using Seurat v3. For BMDM RNAseq, files were trimmed using Trimmomatic-0.39 for adapters, aligned to the mm10 genome using RSEM-1.3.1 and STAR-2.7.2b.
Assembly: Mouse mm10
Supplementary files format and content: counts.csv
Supplementary files format and content: tab separated value, barcode, and matrix files

source_name: blood

extract_protocol:
For single cell RNAseq, cells were sorted using the Sony MA900 sorter based on the expression of BFP or RFP expression, which measures sgRNA transduction. 15000 cells were isolated per sample. RNA was encapsulated using 10x Genomics 5' reagent kit. For BMDMs, bone marrow cells were crushed, filtered, and differentiated using 20ng/ml of MCSF in DMEM/10% FCS/PSG for 10 days. BMDM RNA was extracted using Qiagen RNEasy RNA extraction kit.
scRNA library was prepared using the single cell 5' reagent kit (10x Genomics) according to manufacturer's instructions. Library was sequenced on an Illumina Novaseq SP. BMDM RNAseq library was prepared using NEBNext Ultra II RNA Library Prep Kit according to manufacturer's instructions after poly(A) selection module or via Novogene.

treatment_protocol: For single cell RNAseq, Cas9 WT or Tet2 HSPCs were transduced with control, Ogt, Acly gRNAs and myeloid cells including Ly6C monocytes were sorted 4-weeks post-transplantation from two mice per arm. For ZPugNAc treatments, after differentiation, BMDMs were treated with DMSO or ZPugNAc (50uM) for 8 hours in DMEM/10%FCS/PSG with 20ng/ml of MCSF. For glucose treatments, BMDMs were differentiated in DMEM/10%FCS/PSG with 20ng/ml of MCSF, grown in serum free defined media consisting of DMEM without glucose or glutamine (Thermo A1443001), supplemented with ITS-X (Thermo), 20ng/ml M-CSF, HEPES (10mM), and glucose 5.5mM for 24 hours, then challenged with vehicle or glucose (55mM) for 18 hours.

value: blood

value: bone marrow derived macrophages

value: WT

value: DMSO for 8 hours


title: WT BMDMs treated with DMSO vehicle for 8 hours [WTBMDM_VEH_T1]

description:
Library name: WTBMDM_VEH_T1
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv


title: kidney biopsy_NH2

institute: University of Alberta

value: ABMR/Mixed


title: WT BMDMs treated with 50 uM ZPugNAc for 8 hours [WTBMDM_ZPUG_T2]

description:
Library name: WTBMDM_ZPUG_T2
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv

value: 50 uM ZPugNAc for 8 hours


title: Tet2 KO BMDMs treated with 50 uM ZPugNAc for 8 hours [TETBMDM_ZPUG_T1]

description:
Library name: TETBMDM_ZPUG_T1
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv

value: Tet2 KO


title: Tet2 KO BMDMs treated with DMSO vehicle for 8 hours [TETBMDM_VEH_T2]

description:
Library name: TETBMDM_VEH_T2
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv


title: Tet2 KO BMDMs treated with DMSO vehicle for 8 hours [TETBMDM_VEH_T1]

description:
Library name: TETBMDM_VEH_T1
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv


title: WT BMDMs treated with 50 uM ZPugNAc for 8 hours [WTBMDM_ZPUG_T1]

description:
Library name: WTBMDM_ZPUG_T1
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv


title: Tet2 KO BMDMs treated with 50 uM ZPugNAc for 8 hours [TETBMDM_ZPUG_T2]

description:
Library name: TETBMDM_ZPUG_T2
RNA-seq using NEBNext Ultra II RNA Library Prep Kit
Zpug.genes.counts.csv


title: shControl_Control_Rep2

first: Don

last: Nguyen

address: 310 Cedar Street

institute: Yale University

description: Library name: KP0023

data_processing:
Read quality was checked using FastQC (Babraham Bioinformatics), adaptors trimmed with TrimGalore (Babraham Bioinformatics), and reads were aligned to hg38 using HISAT2. Reads were filtered using Picard Tools (Broad Institute), transcripts assembled using String Tie with Gencode v27, and counts generated using Ballgown. Differential expression was determined using DESeq2
Assembly: hg38
Supplementary files format and content: Normalized counts are provided for all libraries

growth_protocol: H2030-BrM3 cells expressing either shControl or shKDM2A-1 were grown either under control or cluster forming conditions in the presence of doxycycline for 5 days.

extract_protocol:
Samples were washed with PBS prior to lysis in RLT buffer, homogenization using QIAShredder columns (Qiagen cat. 79656), and RNA extracted with the RNeasy kit (Qiagen cat. 74016) using a 15 minute DNAse treatment ( Qiagen cat. 79254).
RNA quality was confirmed by Agilent Bioanalyzer, and TruSeq PolyA enriched libraries were generated (Illumina).Samples were sequenced on an Illumina HiSeq 4000 to generate a minimum of 25M paired-end reads.

value: Human metastatic lung adenocarcinoma


title: shControl_Control_Rep3

description: Library name: KP0027


title: shKDM2A_Control_Rep2

description: Library name: KP0024


title: shKDM2A_Cluster_Rep2

description: Library name: KP0026


title: shControl_Cluster_Rep2

description: Library name: KP0025


title: shKDM2A_Control_Rep1

description: Library name: KP0020


title: shControl_Cluster_Rep1

description: Library name: KP0021


title: Preadipocytes Proliferating High Ox 2

city: Belmont

first: Azucena

last: Rocha

state: Massachusetts

address: 42 Alma Avenue

department: MCB

institute: Brown University

description: Library name: PAP29

data_processing:
counts tables were generated using HTSeq
Assembly: hg38
Supplementary files format and content: .txt files, counts tables

source_name: Cell Culture

growth_protocol: Cells were maintained in Ham’s F-10 nutrient mixture media (Gibco) supplemented with 15% fetal bovine serum (FBS) and antibiotics for LF1 cells and in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics for all other cell lines, in humidified atmosphere with 5% CO2 at 37C. High Ox cells were maintained at ~20% O2, Low Ox cells were maintained at ~3% O2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. For LF1 samples, Total RNA was extracted from early passage, SW-induced quiescent, early and late senescent cells. Cells were washed with PBS and harvested using Trizol reagent (Invitrogen), after which Total RNA was harvested using the Qiagen Rneasy kit.
Libraries were constructed by Azenta. For LF1 samples, NEBNext ultra II directional RNA library prep kit for Illumina along with the NEBNext Poly(A) mRNA magnetic bead isolation module was used to make isolated mRNA and cDNA libraries. Strand specific cDNA libraries were sent to Azenta for paired-end sequencing

treatment_protocol: Contact inhibition was induced by allowing cells to reach 100%confluency for 3 days. Serum withdrawal was induced with DMEM media supplimented with 0.01% FBS for 3 days and for LF1 cells, with Ham’s F-10 nutrient mixture media (Gibco) supplemented with 0.01% fetal bovine serum (FBS; Corning), and antibiotics for 5 days for LF1 cells. Replicatively senescent LF1 cells were attained by serial passaging until cell division ceased.  1 month after cells entered senescence, LF1 cells were harvested for the early replicative senescent cell state timepoint, and late replicative senescent cells were harvested 4 months after entry into senescence.

value: Cell Culture

value: Primary Preadipocytes

value: Preadipocytes

value: Proliferating

tag: batch


title: Pradipocytes Serum Withdrawal High Ox 1

description: Library name: PASW34

value: Serum Withdrawal


title: kidney biopsy_NH1

value: No ABMR/Mixed

value: kidney biopsy


title: Preadipocytes Proliferating High Ox 3

description: Library name: PAP30


title: shControl_Control_Rep1

description: Library name: KP0019


title: Preadipocytes Contact inhibition High Ox 3

description: Library name: PACI33

value: Contact Inhibition


title: shControl_Cluster_Rep3

description: Library name: KP0029


title: shKDM2A_Control_Rep3

description: Library name: KP0028


title: Preadipocytes Contact inhibition High Ox 1

description: Library name: PACI31


title: IMR90 Serum Withdrawal Low Ox 3

description: Library name: ILSW18

value: Fibroblasts


title: IMR90 Serum Withdrawal Low Ox 1

description: Library name: ILSW16


title: IMR90 Proliferating Low Ox 3

description: Library name: ILP12


title: IMR90 Proliferating Low Ox 1

description: Library name: ILP10


title: Preadipocytes Proliferating High Ox 1

description: Library name: PAP28


title: Preadipocytes Contact inhibition High Ox 2

description: Library name: PACI32


title: shKDM2A_Cluster_Rep3

description: Library name: KP0030


title: IMR90 Contact inhibition Low Ox 1

description: Library name: ILCI13


title: IMR90 Serum Withdrawal Low Ox 2

description: Library name: ILSW17


title: IMR90 Proliferating Low Ox 2

description: Library name: ILP11


title: Pradipocytes Serum Withdrawal High Ox 2

description: Library name: PASW35


title: IMR90 Serum Withdrawal High Ox 2

description: Library name: IHSW8


title: IMR90 Proliferating High Ox 2

description: Library name: IHP2


title: IMR90 Contact Inhibition High Ox 3

description: Library name: IHCI6


title: IMR90 Contact Inhibition High Ox 2

description: Library name: IHCI5


title: BJ Serum Withdrawal High Ox 1

description: Library name: BSW25

value: BJ


title: IMR90 Contact inhibition Low Ox 3

description: Library name: ILCI15


title: BJ Contact Inhibition High Ox 3

description: Library name: BCI24


title: IMR90 Contact inhibition Low Ox 2

description: Library name: ILCI14


title: IMR90 Serum Withdrawal High Ox 3

description: Library name: IHSW9


title: IMR90 Serum Withdrawal High Ox 1

description: Library name: IHSW7


title: PB bulk, 9107A

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

institute: University Health Network

data_processing:
Data was mapped with Bowtie2 and peak called with MACS2
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: peripheral blood

extract_protocol:
Nuclei were isolated using digitnnin-containing buffer from viable frozen peripheral blood cells from AML patients and then incubated with Illumina Transposase for 30min at 37 C.
Libraries were amplified using per-sample determined PCR cycles

tag: disease state

value: Acute Myeloid Leukemia

value: peripheral blood

value: bulk


title: IMR90 Proliferating High Ox 1

description: Library name: IHP1


title: PB bulk, 90793


title: BJ Serum Withdrawal High Ox 2

description: Library name: BSW26


title: IMR90 Contact Inhibition High Ox 1

description: Library name: IHCI4


title: PB bulk, 90575


title: PB bulk, 854081_A


title: BJ Proliferating High Ox 3

description: Library name: BP21


title: PB bulk, 849910_B


title: PB bulk, 8362B


title: BJ Serum Withdrawal High Ox 3

description: Library name: BSW27


title: BJ Proliferating High Ox 1

description: Library name: BP19


title: BJ Contact Inhibition High Ox 1

description: Library name: BCI22


title: PB bulk, 827875_A


title: BJ Contact Inhibition High Ox 2

description: Library name: BCI23


title: PB bulk, 90272


title: PB bulk, 80401


title: PB bulk, 780325_A


title: PB bulk, 90783


title: PB bulk, 800919_A


title: BJ Proliferating High Ox 2

description: Library name: BP20


title: PB bulk, 801529_A


title: PB bulk, 8565


title: PB bulk, 838712_B


title: PB bulk, 811325_A


title: PB bulk, 5553


title: PB bulk, 5684


title: PB bulk, 804372_B


title: Pradipocytes Serum Withdrawal High Ox 3

description: Library name: PASW36


title: PB bulk, 6471_B


title: PB bulk, 5700


title: PB bulk, 5717


title: PB bulk, 5679


title: PB bulk, 8278


title: PB bulk, 5511A


title: PB bulk, 4306_A


title: PB bulk, 4371


title: PB bulk, 331020_A


title: PB bulk, 316382_B


title: PB bulk, 322659_A


title: PB bulk, 303168_B


title: PB bulk, 313631_B


title: PB bulk, 313030_B


title: PB bulk, 320145_A


title: PB bulk, 290174_A


title: PB bulk, 289034_B


title: PB bulk, 291925_A


title: PB bulk, 326377_B


title: PB bulk, 296112_A


title: PB bulk, 282068_A


title: PB bulk, 282210_A


title: PB bulk, 747762B


title: PB bulk, 5494B


title: PB bulk, 253192_A


title: PB bulk, 271542_A


title: PB bulk, 265138B


title: PB bulk, 260845_B


title: PB bulk, 248309_A


title: PB bulk, 274116_A


title: PB bulk, 2_6


title: PB bulk, 293018_B


title: PB bulk, 229434_A


title: PB bulk, 280508_B


title: PB bulk, 194785_A


title: PB bulk, 211554_A


title: PB bulk, 162122_A


title: PB bulk, 320789_A


title: PB bulk, 162218_B


title: PB bulk, 162089_B