title: MPP3, H3K4me3, infected, biol rep 1

description:
MPP3_H3K4me3_infected_1
MPP3_Diffbind_H3K4me3.csv
MPP3_H3K4me3_DBA_report_0.05.csv
MPP3_H3K4me3_GREAT_UP.tsv
MPP3_H3K4me3_infected_peaks.broadPeak
MPP3_H3K4me3_infected_1vsIgG_peaks.xls


title: subAR PAX_1122530_04

status: Public on Dec 01 2025

type: RNA

city: La Jolla

first: SUNIL

last: KURIAN

state: CA

address: 10666 N Torrey Pines Rd

country: USA

institute: Scripps Health

description:
subAR
GSM2869930

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC.

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC.

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Whole Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.

tag: tag

value: Subclinical acute rejection


title: TX PAX_1123067_04

description:
TX
GSM2869645

value: Well Functioning Transplant


title: MPP3, H3K27ac, infected, biol rep 1

type: SRA

city: Houston

first: Brandon

middle: T

last: Tran

email: Brandon.Tran@bcm.edu, brttran@gmail.com

state: Texas

address: 1 Moursund St

institute: Baylor College of Medicine

description:
MPP3_H3K27ac_infected_1
MPP_Diffbind_H3K27ac.csv
MPP3_H3K27ac_DBA_report_0.05.csv
MPP3_H3K27ac_GREAT_UP.tsv
MPP3_H3K27ac_infected_peaks.broadPeak
MPP3_H3K27ac_infected_1vsIgG_peaks.xls

library_source: genomic

data_processing:
FASTQ files were preprocessed using HTS stream
File alignment (BWA, samtools
Peakcalling done using MACS v2.2 in python, cut-off FDR < 0.01
Differential analysis using bioconductor package Diffbind in R, with cutoff FDR < 0.05.  GRanges generated as final object from Diffbind package
Granges exported as csv files for differential analysis
Gene ontology was performed on Granges using bioconductor rGREAT and GREAT v4.04 in Rstudio. Outputs were converted to dataframes and then exported as tsv files
Assembly: mm10
Supplementary files format and content: bigWig genomic tracks, broadpeak for peakcalling, xls files of identified peaks
Supplementary files format and content: csv files of differential analysis between infected vs naïve cell states, tsv files of GO analysis of both significantly  increased and decreased gene loci
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: Cell subpopulations (HSCs, MPP3s, GMPs, Macrophages) were isolated from whole bone marrwo from naïve or M. avium infected mice

extract_protocol:
tibias, femurs, and pelvic bones were isolated from mice and cell subpopulations (HSCs, MPP3s, GMPs, and Macrophages) were purified via FACS following cKit+ magnetic separation. Markers were for the following: HSCs (Lin-,cKit+, CD150+, CD48-), MPP3s (Lin-, cKit+, CD150-, CD48+, Flk2-, CD34+), GMPs (Lin-, ckit+, CD34+, CD16/32+), Macrophages (CD3-, B220-, NK1.1-, CD11b+, Ly6g-, Ly6c+). Cells were washed with wash buffer (50 mL  total, 20mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and a Roche Complete protein inhibitor tablet), incubated with Concanavalin A-coated magnetic beads (Bang Laboratories L200731C) for 15 minutes at room temperature. Samples slurries were then magnetically separated, washed once more, and then incubated in primary antibody at respective dilutions (1:50 dilution for all) in wash buffer added with 0.05% Digtonin (Digitonin Wash Buffer) at 4C overnight. Samples were washed with Digitonin Wash buffer three times then incubated with pAG-MNase (142.5 Digitonin Wash Buffer + pAG-MNase, Epicypher 15-1016) for 1 hour at 4C. Slurries were then magnetically separated and washed three more times and resuspended in 150 uL Digtonin Wash buffer. 1 uL of 100mM CaCl2 was added to activate enzymatic cleaving, to which samples were stored on ice in 4C for 45 minutes. After time, one equal volume of 2X Stop buffer ( 340mM NaCl, 20 mM EDTA, 4mM EGTA, 0.05 Digtonin, 0.05 mg/mL glycogen. 5ug/mL RNase A, 2pg/mL heterologus spike-in DNA) was added to end the reaction. Samples were incubated for 30 minutes at 37C to release CUT&RUN fragments and then magnetically separated. Supernatant was collected for DNA fragments, and DNA was purified through phenol-chloroform extraction and ethanol precipitation. Samples were resuspended in molecular grade water for frozen until library preparation.
DNA libraries were prepared for sequecning per standard Illumina protocols

treatment_protocol: Mice were systemically infected or sham treated with 1-month of M. avium, at 2.0e6 colony forming units of M. avium per mouse

tag: tissue

value: bone marrow

tag: cell type

value: murine multipotent progenitor 3

tag: genotype

value: wildtype

tag: strain

tag: treatment

value: M. avum infection, 4 weeks

tag: chip anitbody

value: H3K27ac (Cell Signaling Technologies, #8173)


title: MPP3, H3K27ac, infected, biol rep 2

description:
MPP3_H3K27ac_infected_2
MPP_Diffbind_H3K27ac.csv
MPP3_H3K27ac_DBA_report_0.05.csv
MPP3_H3K27ac_GREAT_UP.tsv
MPP3_H3K27ac_infected_peaks.broadPeak
MPP_H3K27ac_infected_2vsIgG_peaks.xls


title: MPP3, IgG, naive

description:
MPP3_IgG_naive
MPP3_Diffbind_H3K4me3.csv
MPP_Diffbind_H3K27ac.csv
MPP3_H3K4me3_DBA_report_0.05.csv
MPP3_H3K27ac_DBA_report_0.05.csv
MPP3_H3K4me3_naive_peaks.broadPeak
MPP3_H3K27ac_naive_peaks.broadPeak

value: naïve

value: IgG (Jackson ImmunoResearch 315-005-003)


title: TX PAX_1122218_04

description:
TX
GSM2869929


title: cAR PAX_1123535_04

description:
cAR
_

value: Clinical acute rejection


title: GMP, H3K27ac, naive, biol rep 2

description:
GMP_H3K27ac_naive_2
GMP_Diffbind_H3K27ac.csv
GMP_H3K27ac_DBA_report_0.05.csv
GMP_H3K27ac_GREAT_DOWN.tsv
GMP_H3K27ac_naive_peaks.broadPeak
GMP_H3K27ac_naive_2vsIgG_peaks.xls

value: murine granulocyte-monocyte progenitor


title: MPP3 ,H3K4me3, naive, biol rep 2

description:
MPP3_H3K4me3_naive_2
MPP3_Diffbind_H3K4me3.csv
MPP3_H3K4me3_DBA_report_0.05.csv
MPP3_H3K4me3_GREAT_UP.tsv
MPP3_H3K4me3_naive_peaks.broadPeak
MPP3_H3K4me3_naive_2vsIgG_peaks.xls

value: H3K4me3 (Cell Signaling Technologies, #9751)


title: MPP3, H3K4me3, naive, biol rep 1

description:
MPP3_H3K4me3_naive_1
MPP3_Diffbind_H3K4me3.csv
MPP3_H3K4me3_DBA_report_0.05.csv
MPP3_H3K4me3_GREAT_UP.tsv
MPP3_H3K4me3_naive_peaks.broadPeak
MPP3_H3K4me3_naive_1vsIgG_peaks.xls


title: MPP3, H3K27ac, naive, biol rep 2

description:
MPP3_H3K27ac_naive_2
MPP_Diffbind_H3K27ac.csv
MPP3_H3K27ac_DBA_report_0.05.csv
MPP3_H3K27ac_GREAT_UP.tsv
MPP3_H3K27ac_naive_peaks.broadPeak
MPP3_H3K27ac_naive_2vsIgG_peaks.xls


title: MPP3, H3K27ac, naive, biol rep 1

description:
MPP3_H3K27ac_naive_1
MPP_Diffbind_H3K27ac.csv
MPP3_H3K27ac_DBA_report_0.05.csv
MPP3_H3K27ac_GREAT_UP.tsv
MPP3_H3K27ac_naive_peaks.broadPeak
MPP3_H3K27ac_naive_1vsIgG_peaks.xls


title: TX PAX_1121663_04

description:
TX
GSM2869641


title: cAR PAX_1121662_05

description:
cAR
_


title: HSC, IgG, infected

description:
HSC_IgG_infected
HSC_Diffbind_H3K4me3.csv
HSC_H3K4me3_DBA_report_0.05.csv
HSC_H3K4me3_infected_peaks.broadPeak

value: murine hematopoietic stem cell


title: TX PAX_1121658_06

description:
TX
GSM2869639


title: HSC, H3K4me3, infected, biol rep 2

description:
HSC_H3K4me3_infected_2
HSC_Diffbind_H3K4me3.csv
HSC_H3K4me3_DBA_report_0.05.csv
HSC_H3K4me3_GREAT_UP.tsv
HSC_H3K4me3_infected_peaks.broadPeak
HSC_H3K4me3_infected_2vsIgG_peaks.xls


title: TX PAX_1121661_04

description:
TX
GSM2869640


title: TX PAX_1121521_04

description:
TX
GSM2869636


title: TX PAX_1121525_04

description:
TX
GSM2869637


title: subAR PAX_1121519_04

description:
subAR
GSM2869928


title: HSC, H3K4me3, naive, biol rep 2

description:
HSC_H3K4me3_naive_2
HSC_Diffbind_H3K4me3.csv
HSC_H3K4me3_DBA_report_0.05.csv
HSC_H3K4me3_GREAT_UP.tsv
HSC_H3K4me3_naive_peaks.broadPeak
HSC_H3K4me3_naive_2vsIgG_peaks.xls


title: HSC, IgG, naive

description:
HSC_IgG_naive
HSC_Diffbind_H3K4me3.csv
HSC_H3K4me3_DBA_report_0.05.csv
HSC_H3K4me3_naive_peaks.broadPeak


title: HSC, H3K4me3, infected, biol rep 1

description:
HSC_H3K4me3_infected_1
HSC_Diffbind_H3K4me3.csv
HSC_H3K4me3_DBA_report_0.05.csv
HSC_H3K4me3_GREAT_UP.tsv
HSC_H3K4me3_infected_peaks.broadPeak
HSC_H3K4me3_infected_1vsIgG_peaks.xls


title: TX PAX_1121112_04

description:
TX
GSM2869633


title: cAR PAX_1121131_06

description:
cAR
_


title: released_3

city: Leiden

first: Ramon

last: Arens

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

library_source: transcriptomic

data_processing:
Base calling software: RTA3 (Illumina NovaSeq 6000 system)
Alignment and read quantification using BIOWDL RNAseq pipeline v3.0.0
checking raw read QC: FastQC (v0.11.7)
adapter clipping (Cutadapt v2.4, default settings)
Read alignment software alignment using STAR 2.7.3a
deduplication: remove UMI detected sequences: umi_tools (v.0.5.5)
Supplementary files format and content: annotation: annotation.tsv
Supplementary files format and content: all sample fragments per gene: all_samples.fragments_per_gene.tsv

source_name: spleen

extract_protocol:
RNA was harvested using NucleoSpin Xs columns (Macherey-Nagel).
RNA libraries for RNA-seq were prepared using the Kap Hyperprep Kit, following manufacturerers protocols

value: spleen

value: CD8 T cells

value: WT

value: released


title: released_4


title: TX PAX_1120649_04

description:
TX
GSM2869630


title: TX PAX_1120663_06

description:
TX
GSM2869631


title: subAR PAX_1120289_05

description:
subAR
GSM2869927

value: Subclinical acute rejection


title: TX PAX_1121518_04

description:
TX
GSM2869635

value: Well Functioning Transplant


title: ADNR PAX_1120920_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: HSC, H3K3me3, naive, biol rep 1

description:
HSC_H3K4me3_naive_1
HSC_Diffbind_H3K4me3.csv
HSC_H3K4me3_DBA_report_0.05.csv
HSC_H3K4me3_GREAT_UP.tsv
HSC_H3K4me3_naive_peaks.broadPeak
HSC_H3K4me3_naive_1vsIgG_peaks.xls

value: bone marrow


title: released_1


title: TX PAX_1120019_05

description:
TX
GSM2869629


title: arrested_2

value: arrested


title: subAR PAX_1123023_06

description:
subAR
GSM2869931


title: arrested_3


title: TX PAX_1121271_04

description:
TX
GSM2869634


title: arrested_1


title: ADNR PAX_1120015_04

description:
ADNR
_


title: non-arrested_3

value: non-arrested


title: non-arrested_2


title: non-arrested_4


title: TX PAX_1119861_04

description:
TX
GSM2869627


title: released_2


title: ADNR PAX_1119791_04

description:
ADNR
_


title: non-arrested_1


title: cAR PAX_1119878_04

description:
cAR
_


title: unstimulated_4

value: unstimulated


title: arrested_4


title: ADNR PAX_1119738_06

description:
ADNR
_


title: unstimulated_3


title: TX PAX_1119869_04

description:
TX
GSM2869628


title: TX PAX_1119742_04

description:
TX
GSM2869625


title: unstimulated_2


title: TX PAX_1119860_06

description:
TX
GSM2869626


title: unstimulated_1


title: EdUseq_mESC_MSO_2hEdUHU

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

data_processing:
100-bp single end reads were aligned to the reference mouse genome Human GRCm38/mm10 using bwa v.0.7.17
Only the uniquely mapped reads with mapping quality > 30 Phred score were used as input to generate the coverage bigWig track in 1kb resolution by applying the bins per million mapped reads (BPM) normalization method and smoothing of 4kb.
Assembly: GRCm38/mm10
Supplementary files format and content: 1kb resolution bigWig signal files of EdUseq experiments
Library strategy: EdU-seq

source_name: Mouse cell line

growth_protocol: Mouse embryonic stem cells (mESCs) from 129/SVEV strain were purchased from Merck (CMTi-1, passage 11). They were thawed, amplified as per manufacturer instructions for three passages, aliquoted and frozen. This stock of cells was routinely used on gelatin plates (or flasks) for no more than 32 passages. For all experiments, mESC were grown in DMEM+Glutamax (Gibco, 61965-026), 10% ES-FBS (Gibco 16141-079), MEM NEAA (Gibco 11140-035), sodium pyruvate (Gibco, 11360-039), 1mM beta-mercaptoethanol (Gibco, 31350-010), penicillin/streptomycin (P/S, Gibco, 15140-122), 100ng/mL LIF (stocked at 1-2mg/mL; produced at the Protein Production and Purification Platform of the EPFL, Lausanne, Switzerland), 3µM GSK3 inhibitor (Sigma 361559) and MEK inhibitor (PD0325901, Selleckchem). ZHBTc4 68 and 2TSS2c 97 are tet-off mouse pluripotent cell lines which were obtained from Prof David Suter (EPFL, Switzerland). They were also grown in gelatine plates using the same media as mESCs. To deplete OCT4 (ZHBTc4), doxycycline was added to the growing media at the specified times. All cells were routinely checked for mycoplasma and only BM-MSCs tested positive.

extract_protocol:
Round cells were lifted by tapping the sides of the flasks and visually inspected. Depending on the conditions of the experiment, cell suspensions from different flasks were strained through a 40 µm mesh and pooled into 50 mL tubes, centrifuged at room temperature (400G, 5 minutes), washed once with 15 mL of PBS and centrifuged again. Pelleted cells were then carefully resuspended and plated. Commonly, the cells lifted from two T225 flasks would be seeded on one 10 cm plates (for EdU-seq and EU-seq) or on one 6 or 12 multi-well plate (if used for cell cycle analysis). Thymidine or aphidicolin synchronisation. Pluripotent cells (0.5-1x106 mESCs, ZHBTc4 or 2TS22c) or MEFs (1.5-2x106 cells) were seeded on 10 cm plates. 24 to 48 hours later 2mM thymidine or 4µM aphidicolin was added to the media for 10 to 12 hours. Cells were washed three to four times with PBS and released into fresh media. MEFs were also synchronised by 60 hours of serum starvation (DMEM, 0.1% FBS, P/S, L-glutamine) and released into fresh media.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina NovaSeq 6000 sequencer.

treatment_protocol: Mitotic shake-off was conducted on mESC, ZHBTc4 and 2TS22c as follows. Three to four million cells were seeded on T225 flasks using 40 mL of media. Two (mESCs or ZHBTc4) or three (2TS22c) days later, 100ng/mL nocodazole was added to the media for 4 to 6 hours. Media was then removed, and 15 mL of PBS were carefully added to the cells.

value: Mouse cell line

tag: cell line

value: mESC CMTi-1

value: Mouse Embryonic Stem Cells

tag: genetic modification

value: Synchronized with noco+MSO. Released in fresh media. EdU and HU were added for 2h before collection. Collected at 2h post MSO


title: 90 days post-IR treated with pilocarpine from 30 to 90 days, snRNAseq

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed via CellRanger (v7.0.1, RRID:SCR_017344) on 10x Genomics Cloud Analysis (https://www.10xgenomics.com/products/cloud-analysis) to map to the reference genome (GRCm38) and generate filtered gene-barcode matrices.
Assembly: GRCm38
Supplementary files format and content: tab separated value and matrix files

source_name: salivary gland

extract_protocol:
Single nuclei were isolated with Singulator S100 (S2 Genomics) from fresh frozen submandibular glands of non-IR, 93 days post-IR with saline and 93 days post-IR with pilocarpine treatments. The machine was set at nucleus mode with standard protocol. The isolated nuclei were then dyed with DAPI at 1:1000 and purified by flow cytometry.
Single nuclei were processed on the Chromium Controller (10x Genomics) using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) following the manufacturer’s instructions.
snRNA-seq

value: salivary gland

value: IR+pilocarpine


title: TX PAX_1119072_06

description:
TX
GSM2869624


title: ADNR PAX_1118900_04

description:
ADNR
_


title: TX PAX_1119052_04

description:
TX
GSM2869623


title: subAR PAX_1120921_04

description:
subAR
GSM2869632


title: 90 days post-IR, snRNAseq

description: 10x Genomics

value: IR+saline


title: subAR PAX_1119051_06

description:
subAR
GSM2869926


title: Non-IR, snRNA-seq

description: 10x Genomics

value: no treatment


title: M12

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

data_processing:
Raw data were analyzed for per base sequence quality (>30), per sequence GC content, adapter (universal Illumina adapter) removal using FASTQC v0.11.9.
The sequencing reads were mapped to the mouse reference genome (GRCm39 release 110 ) using HISAT2 v2.2.1 .
Aligned reads were counted using HTSeq v2.0.2, and the counts were then analyzed for differential gene expression using median-ratio-normalization with Deseq2 v1.38.3.
Assembly: mm39
Supplementary files format and content: tab-deliminated text file_including raw counts for each samples

source_name: Primary Chondrocytes

extract_protocol:
The mRNA was isolated using poly-T oligo-attached magnetic beads. mRNA quality was determined using an RNA Nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, CA, USA); only samples with an RNA integrity number (RIN) >6.8 were used for library preparation. The libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Biolabs. Ipswich, MA), and quality was determined by Qubit2.0 and Bioanalyzer 2100. Libraries were sequenced on an Illumina Nova 6000 platform, and 150 bp paired-end reads were generated with a read depth of ~20M per sample.
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. mRNA is captured with the PolyA enrichment method.

treatment_protocol: Primary mouse chondrocytes were transfected with either  Wildtype or SIRT5F101L mutant plasmids.

value: Primary Chondrocytes

value: Wild type

value: SIRT5F101L mutant


title: TX PAX_1118089_06

description:
TX
GSM2869620

value: Well Functioning Transplant


title: TX PAX_1118600_04

description:
TX
GSM2869622


title: TX PAX_1118086_06

description:
TX
GSM2869619


title: M11


title: M10


title: TX PAX_1117855_04

description:
TX
GSM2869618


title: M9


title: M8

value: WT


title: TX PAX_1118189_04

description:
TX
GSM2869621


title: TX PAX_1117852_04

description:
TX
GSM2869616


title: M7


title: TX PAX_1117854_04

description:
TX
GSM2869617


title: M6


title: ADNR PAX_1117583_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: TX PAX_1117182_04

description:
TX
GSM2869614


title: M5


title: M4

value: Control


title: TX PAX_1117179_04

description:
TX
GSM2869613


title: M3


title: M2


title: TX PAX_1117174_04

description:
TX
GSM2869611


title: TX PAX_1117176_06

description:
TX
GSM2869612


title: subAR PAX_1117054_05

description:
subAR
GSM2869924

value: Subclinical acute rejection


title: GMP, H3K4me3, naive, biol rep 1

description:
GMP_H3K4me3_naive_1
GMP_Diffbind_H3K4me3.csv
GMP_H3K4me3_DBA_report_0.05.csv
GMP_H3K4me3_GREAT_UP.tsv
GMP_H3K4me3_GREAT_DOWN.tsv
GMP_H3K4me3_naive_peaks.broadPeak
GMP_H3K4me3_naive_1vsIgG_peaks.xls

value: bone marrow

value: murine granulocyte-monocyte progenitor

value: wildtype

value: naïve

value: H3K4me3 (Cell Signaling Technologies, #9751)


title: TX PAX_1117046_04

description:
TX
GSM2869923


title: M1


title: EdUseq_mBMMSC_Aphi_30m

source_name: Mouse primary cell culture

value: Mouse primary cell culture

value: mBM-MSC

value: Mouse bone-marrow mesenchymal stem cells

value: Synchronized with 10-12h aphidicolin (4uM). Washed with PBS and released for 30' in the presence of EdU.


title: subAR PAX_1117048_04

description:
subAR
GSM2869610


title: EdUseq_MEF_Aphi_6h

value: MEF

value: Mouse Embryonic Fibroblasts

value: Synchronized with 10-12h aphidicolin (4uM). Washed with PBS and released for 6h. EdU was added for the last 30' before collection.


title: TX PAX_1117040_04

description:
TX
GSM2869608

value: Well Functioning Transplant


title: TX PAX_1117043_06

description:
TX
GSM2869609


title: EdUseq_MEF_Aphi_4h

value: Synchronized with 10-12h aphidicolin (4uM). Washed with PBS and released for 4h. EdU was added for the last 30' before collection.


title: cAR PAX_1116621_05

description:
cAR
_

value: Clinical acute rejection


title: TX PAX_1116617_04

description:
TX
GSM2869604


title: TX PAX_1116931_04

description:
TX
GSM2869606


title: EdUseq_ZHBTc4_24Dox_Thy_30R30E

value: Mouse Embryonic Stem Cells

value: Treated with doxycycline for 24h. Synchronized with thymidine, release for 1h with doxycycline, EdU added for the last 30'.


title: EdUseq_MEF_Aphi_2h

value: Synchronized with 10-12h aphidicolin (4uM). Washed with PBS and released for 2h. EdU was added for the last 30' before collection.


title: EdUseq_ZHBTc4_noDox_Thy_30R30E

value: Synchronized with thymidine, release for 1h with doxycycline, EdU added for the last 30'.


title: EdUseq_MEF_Aphi_1h

value: Synchronized with 10-12h aphidicolin (4uM). Washed with PBS and released for 1h. EdU was added for the last 30' before collection.


title: TX PAX_1117038_04

description:
TX
GSM2869607


title: EdUseq_ZHBTc4_18Dox_MSO_7h_rep2

value: Treated with doxycycline 18h pre-MSO. Synchronized with noco+MSO, released for 7h in the presence of doxycycline, EdU added the last 30'.


title: subAR PAX_1116616_04

description:
subAR
GSM2869603

value: Subclinical acute rejection


title: EdUseq_mBMMSC_Aphi_2h

value: Mouse primary cell culture


title: EdUseq_ZHBTc4_18Dox_MSO_7h_rep1


title: Whole Human Saphenous Veins, Patient 5, Day 7

city: Augusta

first: David

middle: S

last: Kim

state: GA

department: Vascular Biology Center

institute: Augusta University

description:
Library name: Sample 10
Column name in raw_counts.txt : S2D7

data_processing:
Reads were trimmed (Cutadapt v4.1) and aligned to GRCh38/hg38 using STAR v2.7.0. Gene counts were obtained with featureCounts v2.0.1.
Differential expression analysis was performed with DESeq2 (FDR<0.05), and visualization with ggplot2 and clusterProfiler.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited files include raw counts for combined samples

source_name: Human saphenous vein

growth_protocol: Human saphenous vein segments were obtained from CABG patients, washed in PBS with antibiotics, and cut into 3–5 mm rings. Samples were maintained in RPMI with 30% FBS and antibiotics at 37C with 5% CO2 for 7 days.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase treatment. 1ug of total RNA was used for construction of all libraries.
Libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold and sequenced on an Illumina HiSeq 2500 platform (150 bp paired-end; >35M reads/sample).

treatment_protocol: Baseline (Day 0) samples were processed immediately; cultured (Day 7) samples were maintained with media changes every 24-48 hours, then washed and collected for RNA extraction.

value: Human saphenous vein

value: Neointima proliferation

tag: time

value: Day 7


title: EdUseq_ZHBTc4_18Dox_MSO_4h_rep3

value: Treated with doxycycline 18h pre-MSO. Synchronized with noco+MSO, released for 4h in the presence of doxycycline, EdU added the last 30'.


title: Whole Human Saphenous Veins, Patient 6, Day 0

description:
Library name: Sample 11
Column name in raw_counts.txt : S3D0

value: Day 0


title: Whole Human Saphenous Veins, Patient 5, Day 0

description:
Library name: Sample 9
Column name in raw_counts.txt : S2D0


title: subAR PAX_1116615_04

description:
subAR
GSM2869922


title: subAR PAX_1116367_04

description:
subAR
GSM2869601


title: Whole Human Saphenous Veins, Patient 6, Day 7

description:
Library name: Sample 12
Column name in raw_counts.txt : S3D7


title: ADNR PAX_1116099_05

description:
ADNR
_

value: Acute dysfunction no rejection


title: Whole Human Saphenous Veins, Patient 4, Day 0

description:
Library name: Sample 7
Column name in raw_counts.txt : S1D0


title: Whole Human Saphenous Veins, Patient 3, Day 7

description:
Library name: Sample 6
Column name in raw_counts.txt : R3D7


title: EdUseq_ZHBTc4_18Dox_MSO_4h_rep2


title: TX PAX_1116095_04

description:
TX
GSM2869600

value: Well Functioning Transplant


title: Whole Human Saphenous Veins, Patient 3, Day 0

description:
Library name: Sample 5
Column name in raw_counts.txt : R3D0


title: EdUseq_ZHBTc4_18Dox_MSO_4h_rep1


title: Whole Human Saphenous Veins, Patient 2, Day 0

description:
Library name: Sample 3
Column name in raw_counts.txt : R2D0


title: TX PAX_1116093_04

description:
TX
GSM2869598


title: TX PAX_1116094_04

description:
TX
GSM2869599


title: subAR PAX_1116366_06

description:
subAR
GSM2869921


title: Whole Human Saphenous Veins, Patient 1, Day 0

description:
Library name: Sample 1
Column name in raw_counts.txt : R1D0


title: EdUseq_ZHBTc4_18Dox_MSO_2h_rep2

value: Treated with doxycycline 18h pre-MSO. Synchronized with noco+MSO, released for 2h in the presence of doxycycline, EdU added the last 30'.


title: EdUseq_ZHBTc4_18Dox_MSO_2h_rep1


title: HEK293T MELL3/14 KD, Torin-treated, RNA-Seq, rep2

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: Library name: dd_Mettl3_14_torin_RNA_2

data_processing:
Read quality control was performed with FastQC v0.11.5. The reads were trimmed with cutadapt v2.10 "--minimum-length 20 -q 20".
Read mapping was performed to the hg38 genome assembly using STAR v2.7.6a with default parameters and "--quantMode GeneCounts" to estimate the read counts per gene. The supplied genome annotation was GENCODE v38 with spike-in sequences as additional contigs.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files. File contents: the files contain the read counts per gene (including spike-ins) estimated by STAR.

molecule: cytoplasmic RNA

source_name: cell line

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, and 100 µg streptomycin.

extract_protocol:
Cells were chilled on ice and washed with PBS supplemented with cycloheximide (100 µg/ml), lysed with buffer containing 20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, and 25 U/ml TURBO DNase (Ambion). The lysate was divided into two parts for Ribo-Seq and RNA-Seq library preparation.
RNA-Seq libraries were constructed using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). The rRNA depletion was performed using a RiboMinus™ Eukaryote Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s recommendations.

treatment_protocol: Cells were treated with Torin1 (dissolved in DMSO, 250 nM; Tocris Bioscience, Bristol, UK) or with DMSO alone for 2 h.

value: cell line

value: Human Embryonic Kidney

value: METTL3 and METTL14 knockdown

value: 250 nM Torin1, 2h


title: HEK293T MELL3/14 KD, Torin-treated, RNA-Seq, rep3

description: Library name: dd_Mettl3_14_torin_RNA_3


title: HEK293T MELL3/14 KD, DMSO-treated, RNA-Seq, rep3

description: Library name: dd_Mettl3_14_RNA_3

value: DMSO, 2h


title: HEK293T MELL3/14 KD, DMSO-treated, RNA-Seq, rep2

description: Library name: dd_Mettl3_14_RNA_2


title: subAR PAX_1116087_04

description:
subAR
GSM2869597


title: Whole Human Saphenous Veins, Patient 4, Day 7

description:
Library name: Sampe 8
Column name in raw_counts.txt : S1D7


title: HEK293T, Torin1-treated, RNA-Seq, rep3

description: Library name: G6_torin_RNA_3

value: wt


title: TX PAX_1116372_04

description:
TX
GSM2869602


title: HEK293T MELL3/14 KD, Torin-treated, RNA-Seq, rep1

description: Library name: dd_Mettl3_14_torin_RNA_1


title: Whole Human Saphenous Veins, Patient 2, Day 7

description:
Library name: Sample 4
Column name in raw_counts.txt : R2D7


title: TX PAX_1116089_04

description:
TX
GSM2869918


title: EdUseq_ZHBTc4_12Dox_MSO_7h_rep2

value: Mouse Embryonic Stem Cells

value: Treated with doxycycline 12h pre-MSO. Synchronized with noco+MSO, released for 7h in the presence of doxycycline, EdU added the last 30'.


title: HEK293T MELL3/14 KD, DMSO-treated, RNA-Seq, rep1

description: Library name: dd_Mettl3_14_RNA_1


title: EdUseq_ZHBTc4_12Dox_MSO_7h_rep1


title: EdUseq_ZHBTc4_18Dox_MSO_2h_rep3


title: ADNR PAX_1116091_06

description:
ADNR
_


title: Whole Human Saphenous Veins, Patient 1, Day 7

description:
Library name: Sample 2
Column name in raw_counts.txt : R1D7


title: EdUseq_ZHBTc4_12Dox_MSO_4h_rep3

value: Treated with doxycycline 12h pre-MSO. Synchronized with noco+MSO, released for 4h in the presence of doxycycline, EdU added the last 30'.


title: HEK293T, Torin1-treated, RNA-Seq, rep2

description: Library name: G6_torin_RNA_2


title: HEK293T, Torin1-treated, RNA-Seq, rep1

description: Library name: G6_torin_RNA_1


title: HEK293T, DMSO-treated, RNA-Seq, rep2

description: Library name: G6_RNA_2


title: EdUseq_ZHBTc4_12Dox_MSO_4h_rep2


title: HEK293T, DMSO-treated, RNA-Seq, rep3

description: Library name: G6_RNA_3


title: TX PAX_1115735_04

description:
TX
GSM2869596


title: TX PAX_1115733_04

description:
TX
GSM2869594


title: subAR PAX_1115734_04

description:
subAR
GSM2869595

value: Subclinical acute rejection


title: EdUseq_ZHBTc4_12Dox_MSO_4h_rep1


title: ADNR PAX_1116083_04

description:
ADNR
_


title: HEK293T, DMSO-treated, RNA-Seq, rep1

description: Library name: G6_RNA_1


title: AR_GDC0941_DHT_posdox_chip

city: Baltimore

first: Yangzhenyu

last: Gao

state: MD

address: 2917 Saint Paul

department: Oncology

institute: johns hopkins university

description: Library name: AR_GDC0941_DHT_posdox_chip

data_processing:
Sequencing adaptors were removed using Trimmomatic v0.39. Trimmed reads were aligned to the hg38 human genome using Bowtie 2.4. Duplicate PCR and optical reads were removed using Picard MarkDuplicates v2.18.16. Aligned reads were extracted using SAMtools v1.9. Peaks were identified using a pipeline that adheres to standards set by ENCODE.  This includes initial peak calling with MACS2 v2.1.3 with a liberal p value threshold of 0.1 normalized to the input. Peak intensity was calculated using the countOverlaps function in the GenomicAlignments section of R. Peaks were annotated using ChIPseeker in the R package. The differential analysis of each condition compared to the control was done using DESeq2. For each pairwise comparison, only those peaks that were reproducible were considered for differential analysis. Moreover, peaks were required to have an FDR<0.05 (FDR, false discovery rate) to be considered statistically significantly different between comparisons. Normalized DESeq2 bigwig files were used for plotting tornado plots using DeepTools.
Assembly: hg38
Supplementary files format and content: fastq, bigwig

source_name: Prostate

growth_protocol: LNCaP cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin streptomycin in plates coated with 0.01% poly L-lysine.

extract_protocol:
Cells were crosslinked in adherent conditions with 1% paraformaldehyde.  After quenching and cell lysis, chromatin was sheared with a Covaris E220 ultrasonicator.
Illumina-compatible high diversity library primers were utilized

treatment_protocol: LNCaP cells were androgen deprived and cultured in DMSO or 1µg/ml doxycycline for 72h and treated with 10nM DHT and 1µM PI3K inhibitor GDC0941 for 8h, before crosslinking. AR antibody from Abcam (ab108341) was utilized.

value: Prostate

value: LNCaP

value: prostate cancer


title: ADNR PAX_1115395_06

description:
ADNR
_


title: EdUseq_ZHBTc4_12Dox_MSO_2h_rep2

value: Treated with doxycycline 12h pre-MSO. Synchronized with noco+MSO, released for 2h in the presence of doxycycline, EdU added the last 30'.


title: AR_GDC0941_DHT_negdox_Input

description: Library name: AR_GDC0941_DHT_negdox_Input


title: AR_GDC0941_DHT_negdox_chip

description: Library name: AR_GDC0941_DHT_negdox_chip


title: EdUseq_ZHBTc4_12Dox_MSO_2h_rep1


title: AR_GDC0941_DHT_posdox_Input

description: Library name: AR_GDC0941_DHT_posdox_Input


title: EdUseq_ZHBTc4_noDox_MSO_7h_rep3

value: Synchronized with noco+MSO, released for 7h, EdU added the last 30'.


title: AR_DHT_posdox_Input

description: Library name: AR_DHT_posdox_Input


title: EdUseq_ZHBTc4_noDox_MSO_7h_rep2


title: shKMT2D_H3K4me1_rep3

description: Library name: shKMT2D_H3K4me1_rep3

data_processing:
Sequencing reads were first quality-filtered and trimmed of adaptor sequences using fastq. The processed reads were aligned to the mouse reference genome (GRCm38) using Bowtie2 under the parameters: --local --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 800. Peak detection was carried out using MACS2 incorporating IgG controls for each antibody. Regions enriched for target of interest were identified using an FDR cutoff of 0.05 and a comprehensive peak atlas was constructed by merging peak regions across all samples. Read coverage across these union peaks were quantified with GenomicAlignments in R [software for computing]. Differential enrichment analysis was performed using DESeq2, with significant peaks defined as those with an absolute value of log2FoldChange > 0.5 and FDR < 0.05. For visualization, BigWig files from biological replicates were averaged and DeepTools was used to generate tornado plots summarizing signal distributions at differential sites.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
Extraction was performed as per the Epicypher CUTANA CUT&RUN v3 instructions.
Illumina-compatible high diversity, dual index library primers were utilized as per the Epicypher library preparation v1.1 protocol.

treatment_protocol: LNCaP cells were cultured in regular full media conditions and treated with 1µg/ml doxycycline for 72h. A validated Epicypher H3K4me1 antibody was used (Epicypher Cat# 13-0057).


title: AR_DHT_negdox_chip

description: Library name: AR_DHT_negdox_chip


title: AR_DHT_negdox_Input

description: Library name: AR_DHT_negdox_Input


title: AR_DHT_posdox_chip

description: Library name: AR_DHT_posdox_chip


title: EdUseq_ZHBTc4_noDox_MSO_7h_rep1


title: shKMT2D_H3K4me1_rep2

description: Library name: shKMT2D_H3K4me1_rep2


title: shKMT2D_H3K4me1_rep1

description: Library name: shKMT2D_H3K4me1_rep1


title: TX PAX_1115281_04

description:
TX
GSM2869591

value: Well Functioning Transplant


title: WT_H3K4me1_rep3

description: Library name: WT_H3K4me1_rep3


title: EdUseq_ZHBTc4_noDox_MSO_4h_rep2

value: Synchronized with noco+MSO, released for 4h, EdU added the last 30'.


title: TX PAX_1115282_04

description:
TX
GSM2869592


title: ADNR PAX_1115120_06

description:
ADNR
_

value: Acute dysfunction no rejection


title: TX PAX_1115005_04

description:
TX
GSM2869589


title: WT_H3K4me1_rep2

description: Library name: WT_H3K4me1_rep2


title: WT_H3K4me1_rep1

description: Library name: WT_H3K4me1_rep1


title: EdUseq_ZHBTc4_noDox_MSO_4h_rep1


title: ADNR PAX_1115394_04

description:
ADNR
_


title: FOSL1_DU145_shKMT2D_Rep3

description: Library name: FOSL1_DU145_shKMT2D_Rep3

data_processing:
Sequencing adaptors were removed using Trimmomatic v0.39. Trimmed reads were aligned to the hg38 human genome using Bowtie 2.4. Duplicate PCR and optical reads were removed using Picard MarkDuplicates v2.18.16. Aligned reads were extracted using SAMtools v1.9. Peaks were identified using a pipeline that adheres to standards set by ENCODE.  This includes initial peak calling with MACS2 v2.1.3 with a liberal p value threshold of 0.1 normalized to the input. Peak intensity was calculated using the countOverlaps function in the GenomicAlignments section of R. Peaks were annotated using ChIPseeker in the R package. The differential analysis of each condition compared to the control was done using DESeq2. For each pairwise comparison, only those peaks that were reproducible were considered for differential analysis. Moreover, peaks were required to have an FDR<0.05 (FDR, false discovery rate) to be considered statistically significantly different between comparisons. Normalized DESeq2 bigwig files were used for plotting tornado plots using DeepTools. Motif discovery on differentially enriched regions was conducted using HOMER.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: DU145 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

treatment_protocol: Cells were cultured in DMSO or 1µg/ml doxycycline for 72h, before crosslinking. FRA1/FOSL1 Antibody (Cell Signaling Technology Cat# 5281) was utilized for the ChIP-Seq.


title: TX PAX_1115731_04

description:
TX
GSM2869593


title: FOSL1_DU145_shKMT2D_Rep2

description: Library name: FOSL1_DU145_shKMT2D_Rep2


title: TX PAX_1115016_04

description:
TX
GSM2869590


title: EdUseq_ZHBTc4_noDox_MSO_2h_rep2

value: Synchronized with noco+MSO, released for 2h, EdU added the last 30'.


title: FOSL1_DU145_shKMT2D_Input

description: Library name: FOSL1_DU145_shKMT2D_Input


title: FOSL1_DU145_control_Rep3

description: Library name: FOSL1_DU145_control_Rep3


title: ADNR PAX_1114724_05

description:
ADNR
_


title: EdUseq_ZHBTc4_noDox_MSO_2h_rep1


title: FOSL1_DU145_control_Rep2

description: Library name: FOSL1_DU145_control_Rep2


title: FOSL1_DU145_control_Rep1

description: Library name: FOSL1_DU145_control_Rep1


title: FOSL1_DU145_control_Input

description: Library name: FOSL1_DU145_control_Input


title: cAR PAX_1114723_04

description:
cAR
_

value: Clinical acute rejection


title: EdUseq_mESC_MSO_TAK+ATRi_7h_merged

source_name: mESC CMTi-1

value: mESC CMTi-1

value: Synchronized with noco+MSO, released for 3h, treated for 4h with TAK-931 (1uM) and ATRi (100nM). Collected 7h post MSO.


title: LNCAP_shKMT2D_H3K4me2_rep2_input

description: Library name: LNCAP_shKMT2D_H3K4me2_rep2_input

data_processing:
Sequencing adaptors were removed using Trimmomatic v0.39. Trimmed reads were aligned to the hg38 human genome using Bowtie 2.4. Duplicate PCR and optical reads were removed using Picard MarkDuplicates v2.18.16. Aligned reads were extracted using SAMtools v1.9. Peaks were identified using a pipeline that adheres to standards set by ENCODE.  This includes initial peak calling with MACS2 v2.1.3 with a liberal p value threshold of 0.1 normalized to the input. Replicate peaks were then assessed using an irreproducible discovery rate (p value<0.05). Those peaks passing IDR were then merged to form a peak atlas. Peak intensity was calculated using the countOverlaps function in the GenomicAlignments section of R. Peaks were annotated using ChIPseeker in the R package. The differential analysis of each condition compared to the control was done using DESeq2. For each pairwise comparison, only those peaks that were reproducible were considered for differential analysis. Moreover, peaks were required to have an FDR<0.05 (FDR, false discovery rate) to be considered statistically significantly different between comparisons. Normalized DESeq2 bigwig files were used for plotting tornado plots using DeepTools.
Assembly: hg38
Supplementary files format and content: bam, bigwig

extract_protocol:
Cells were crosslinked in adherent conditions with 1% paraformaldehyde.  After quenching and cell lysis, chromatin was sheared with a Covaris E220 ultrasonicator.
Illumina-compatible high diversity, library primers were utilized

treatment_protocol: LNCaP cells were cultured in DMSO or 1µg/ml doxycycline for 72h before crosslinking. H3K4me2 antibody from Abcam (ab32356) was used.

value: Doxycycline


title: TX PAX_1114721_04

description:
TX
GSM2869917


title: EdUseq_mESC_MSO_TAK+ATRi+RO_7h_merged

value: Mouse Embryonic Stem Cells

value: Synchronized with noco+MSO, released for 3h, treated for 4h with TAK-931 (1uM), ATRi (100nM) and RO-3306 (9uM). Collected 7h post MSO.


title: TX PAX_1114715_04

description:
TX
GSM2869916


title: TX PAX_1114718_04

description:
TX
GSM2869588


title: EdUseq_mESC_MSO_TAK+RO_7h_merged

value: Synchronized with noco+MSO, released for 3h, treated for 4h with TAK-931 (1uM) and RO-3306 (9uM). Collected 7h post MSO.


title: LNCAP_shKMT2D_H3K4me2_rep1_input

description: Library name: LNCAP_shKMT2D_H3K4me2_rep1_input


title: FOSL1_DU145_shKMT2D_Rep1

description: Library name: FOSL1_DU145_shKMT2D_Rep1


title: LNCAP_control_H3K4me2_rep2_chip

description: Library name: LNCAP_control_H3K4me2_rep2_chip

value: DMSO, H3K4me2 antibody


title: LNCAP_shKMT2D_H3K4me2_rep1_chip

description: Library name: LNCAP_shKMT2D_H3K4me2_rep1_chip

value: Prostate

value: Doxycycline, H3K4me2 antibody


title: EdUseq_mESC_MSO_Nuc_7h

value: Treated with Embyomax (0.5x). Synchronized with noco+MSO, released and collected 7h post MSO.


title: LNCAP_control_H3K4me2_rep1_input

description: Library name: LNCAP_control_H3K4me2_rep1_input

value: LNCaP

value: prostate cancer

value: DMSO


title: LNCAP_control_H3K4me2_rep1_chip

description: Library name: LNCAP_control_H3K4me2_rep1_chip


title: TX PAX_1114714_04

description:
TX
GSM2869587

value: Well Functioning Transplant


title: LNCAP_control_H3K4me2_rep2_input

description: Library name: LNCAP_control_H3K4me2_rep2_input


title: EdUseq_mESC_MSO_Nuc_4h

value: Treated with Embyomax (0.5x). Synchronized with noco+MSO, released and collected 4h post MSO.


title: EdUseq_mESC_MSO_Nuc_2h

value: Treated with Embyomax (0.5x). Synchronized with noco+MSO, released and collected 2h post MSO.


title: EdUseq_mESC_MSO_10TAK_60mR_30mEdUHU

value: Synchronized with noco+MSO, treated with TAK-931 for 10h. Released for 60'; EdU+HU added for 30' and collected.


title: LNCAP_KMT2D_GDC0941_rep2_chip

description: Library name: LNCAP_KMT2D_GDC0941_rep2_chip

data_processing:
Sequencing adaptors were removed using Trimmomatic v0.39. Trimmed reads were aligned to the hg38 human genome using Bowtie 2.4. Duplicate PCR and optical reads were removed using Picard MarkDuplicates v2.18.16. Aligned reads were extracted using SAMtools v1.9. Peaks were identified using a pipeline that adheres to standards set by ENCODE.  This includes initial peak calling with MACS2 v2.1.3 with a liberal p value threshold of 0.1 normalized to the input. Replicate peaks were then assessed using an irreproducible discovery rate (p value<0.05). Those peaks passing IDR were then merged to form a peak atlas. Peak intensity was calculated using the countOverlaps function in the GenomicAlignments section of R. Peaks were annotated using ChIPseeker in the R package. The differential analysis of each condition compared to the control was done using DESeq2. For each pairwise comparison, only those peaks that were reproducible were considered for differential analysis. Moreover, peaks were required to have an FDR<0.05 (FDR, false discovery rate) to be considered statistically significantly different between comparisons. Normalized DESeq2 bigwig files were used for plotting tornado plots using DeepTools.
Assembly: hg38
Supplementary files format and content: fastq, bigwig

growth_protocol: LNCaP cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin in plates coated with 0.01% poly L-lysine.

treatment_protocol: LNCaP cells were treated with 1μM PI3K inhibitor GDC0941 for 8 hours before crosslinking. KMT2D antibody from Sigma Aldrich (Cat# HPA035977) was used.

value: GDC0941, KMT2D antibody


title: LNCAP_KMT2D_GDC0941_rep1_input

description: Library name: LNCAP_KMT2D_GDC0941_rep1_input


title: LNCAP_KMT2D_GDC0941_rep1_chip

description: Library name: LNCAP_KMT2D_GDC0941_rep1_chip


title: LNCAP_KMT2D_DMSO_rep2_input

description: Library name: LNCAP_KMT2D_DMSO_rep2_input


title: ADNR PAX_1114361_05

description:
ADNR
_

value: Acute dysfunction no rejection


title: EdUseq_mESC_MSO_12Thy_60mR_30mEdUHU

value: mESC CMTi-1

value: Synchronized with noco+MSO, treated with thymidine for 12h. Released for 60'; EdU+HU added for 30' and collected.


title: ADNR PAX_1114713_04

description:
ADNR
_


title: LNCAP_shKMT2D_H3K4me2_rep2_chip

description: Library name: LNCAP_shKMT2D_H3K4me2_rep2_chip


title: EdUseq_mESC_CDC7i_7h

value: Mouse Embryonic Stem Cells

value: Synchronized with noco+MSO, released for 3h, treated for 4h with CDC7i (5uM). EdU+HU were added for the last 30'. Collected 7h post MSO.


title: LNCAP_KMT2D_DMSO_rep2_chip

description: Library name: LNCAP_KMT2D_DMSO_rep2_chip

value: DMSO, KMT2D antibody


title: TX PAX_1114350_04

description:
TX
GSM2869584


title: LNCAP_KMT2D_GDC0941_rep2_input

description: Library name: LNCAP_KMT2D_GDC0941_rep2_input

value: Prostate


title: LNCAP_shKMT2D_FOXA1_rep2_input

description: Library name: LNCAP_shKMT2D_FOXA1_rep2_input

treatment_protocol: LNCaP cells were cultured in DMSO or 1µg/ml doxycycline for 72h before crosslinking. FOXA1 antibody from Abcam (ab23738) was used.

value: Doxycycline


title: ADNR PAX_1114207_04

description:
ADNR
_


title: LNCAP_shKMT2D_FOXA1_rep2_chip

description: Library name: LNCAP_shKMT2D_FOXA1_rep2_chip

value: Doxycycline, FOXA1 antibody


title: LNCAP_shKMT2D_FOXA1_rep1_input

description: Library name: LNCAP_shKMT2D_FOXA1_rep1_input

value: LNCaP


title: EdUseq_mESC_MSO_TAK_4h_merged

value: Synchronized with noco+MSO, released for 3h, treated for 1h with TAK-931 (1uM). Collected 4h post MSO.


title: LNCAP_shKMT2D_FOXA1_rep1_chip

description: Library name: LNCAP_shKMT2D_FOXA1_rep1_chip

value: prostate cancer


title: LNCAP_control_FOXA1_rep2_input

description: Library name: LNCAP_control_FOXA1_rep2_input

value: DMSO


title: TX PAX_1114354_04

description:
TX
GSM2869586

value: Well Functioning Transplant


title: TX PAX_1114204_05

description:
TX
GSM2869583


title: EdUseq_mESC_MSO_1hATRi_7h_rep2

value: Synchronized with noco+MSO, collected 7h post MSO having been treated with ATRi (100nM) for the last 1h.


title: LNCAP_KMT2D_DMSO_rep1_input

description: Library name: LNCAP_KMT2D_DMSO_rep1_input


title: LNCAP_control_FOXA1_rep2_chip

description: Library name: LNCAP_control_FOXA1_rep2_chip

value: DMSO, FOXA1 antibody


title: EdUseq_mESC_MSO_lowHU+Ai_8h

value: Synchronized with noco+MSO, treated with HU (100uM) + ATRi (100nM) and collected 8h post MSO.


title: TX PAX_1114351_04

description:
TX
GSM2869585


title: EdUseq_mESC_MSO_lowHU+Ai_6h

value: Synchronized with noco+MSO, treated with HU (100uM) + ATRi (100nM) and collected 6h post MSO.


title: LNCAP_KMT2D_DMSO_rep1_chip

description: Library name: LNCAP_KMT2D_DMSO_rep1_chip


title: cAR PAX_1114018_04

description:
cAR
_

value: Clinical acute rejection


title: TMD8_JIB04_500nM_Rep2

city: Boston

first: Mohamad Ali

last: Najia

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: TMD8_JIB04_500nM_Rep2

data_processing:
Paired-end RNA-seq reads were pseudoaligned to the hg19 reference transcriptome with  Kallisto (version 0.46.0) in order to quantify transcriptome-wide gene expression. Transcript-level estimates were summed using the tximport package (version 1.28.0) in R (version 4.3.1). Differential expression was performed using the DESeq2 package (version 1.40.2) on the estimated counts matrix from Kallisto. Statistically significant genes varying between two conditions were identified using an FDR-based P value adjustment method and alpha = 0.05. We defined genes as significantly differentially expressed if P adjusted < 0.05 and log2(fold-change) > 1 or log2(fold-change) < -1.
Assembly: hg19
Supplementary files format and content: Kallisto counts matrix in tab-separated text format
Supplementary files format and content: Kallisto transcripts-per-million (TPM) matrix in tab-separated text format

growth_protocol: OCI-Ly1 cells were cultured in IMDM + 10% FBS + Penicillin-Streptomycin. TMD8 cells were cultured in RPMI 1640 + 10% FBS + Penicillin-Streptomycin.

extract_protocol:
Total RNA from JIB-04 or DMSO treated OCI-Ly1 and TMD8 cells were isolated using the RNeasy Plus Micro kit (Qiagen cat. no. 74034) per the manufacturer’s protocol.
Purified RNA was subjected to ribosomal depletion, using the NEBNext rRNA Depletion Kit (New England Biolabs cat. no. E7770L). RNA-Seq libraries were prepared in technical triplicate using the NEBNext Ultra RNA II Library Prep Kit (New England Biolabs cat. no. E6310L) and paired-end sequenced with 101 cycles each read on an Illumina HiSeq.

treatment_protocol: Cells were treated with various doses of JIB-04 (Stem Cell Technologies cat. no. 73212) or 0.01% DMSO as a vehicle control.


title: subAR PAX_1114017_04

description:
subAR
GSM2869914

value: Subclinical acute rejection


title: subAR PAX_1114001_04

description:
subAR
GSM2869913


title: EdUseq_mESC_MSO_TAK_7h_merged

value: mESC CMTi-1

value: Mouse Embryonic Stem Cells

value: Synchronized with noco+MSO, released for 3h, treated for 4h with TAK-931 (1uM). Collected 7h post MSO.


title: TMD8_JIB04_500nM_Rep1

description: Library name: TMD8_JIB04_500nM_Rep1


title: TX PAX_1114000_04

description:
TX
GSM2869582


title: TX PAX_1113998_04

description:
TX
GSM2869580


title: TMD8_JIB04_150nM_Rep3

description: Library name: TMD8_JIB04_150nM_Rep3


title: TMD8_JIB04_150nM_Rep2

description: Library name: TMD8_JIB04_150nM_Rep2


title: LNCAP_control_FOXA1_rep1_input

description: Library name: LNCAP_control_FOXA1_rep1_input

value: Prostate


title: TMD8_JIB04_150nM_Rep1

description: Library name: TMD8_JIB04_150nM_Rep1


title: EdUseq_mESC_MSO_1hATRi_7h_rep1


title: EdUseq_mESC_MSO_Ai_10h

value: Synchronized with noco+MSO, treated with 100nM ATRi and collected 10h post MSO.


title: TMD8_DMSO_Rep3

description: Library name: TMD8_DMSO_Rep3


title: EdUseq_mESC_MSO_lowHU+Ai_4h

value: Synchronized with noco+MSO, treated with HU (100uM) + ATRi (100nM) and collected 4h post MSO.


title: TMD8_JIB04_500nM_Rep3

description: Library name: TMD8_JIB04_500nM_Rep3


title: OCI-Ly1_JIB04_500nM_Rep3

description: Library name: OCI-Ly1_JIB04_500nM_Rep3


title: TMD8_DMSO_Rep1

description: Library name: TMD8_DMSO_Rep1


title: TX PAX_1113997_04

description:
TX
GSM2869579


title: TMD8_DMSO_Rep2

description: Library name: TMD8_DMSO_Rep2


title: EdUseq_mESC_MSO_Ai_8h

value: Synchronized with noco+MSO, treated with 100nM ATRi and collected 8h post MSO.


title: LNCAP_control_FOXA1_rep1_chip

description: Library name: LNCAP_control_FOXA1_rep1_chip

value: LNCaP


title: EdUseq_mESC_MSO_Ai_6h

value: Synchronized with noco+MSO, treated with 100nM ATRi and collected 6h post MSO.


title: OCI-Ly1_JIB04_500nM_Rep2

description: Library name: OCI-Ly1_JIB04_500nM_Rep2


title: OCI-Ly1_JIB04_500nM_Rep1

description: Library name: OCI-Ly1_JIB04_500nM_Rep1


title: OCI-Ly1_JIB04_150nM_Rep3

description: Library name: OCI-Ly1_JIB04_150nM_Rep3


title: EdUseq_mESC_MSO_Ai_4h

value: Synchronized with noco+MSO, treated with 100nM ATRi and collected 4h post MSO.


title: OCI-Ly1_JIB04_150nM_Rep2

description: Library name: OCI-Ly1_JIB04_150nM_Rep2


title: TX PAX_1113512_04

description:
TX
GSM2869577

value: Well Functioning Transplant


title: subAR PAX_1113513_04

description:
subAR
GSM2869912


title: OCI-Ly1_JIB04_150nM_Rep1

description: Library name: OCI-Ly1_JIB04_150nM_Rep1


title: OCI-Ly1_DMSO_Rep3

description: Library name: OCI-Ly1_DMSO_Rep3

value: DMSO


title: OCI-Ly1_DMSO_Rep2

description: Library name: OCI-Ly1_DMSO_Rep2


title: EdUseq_mESC_MSO_lowHU_10h

value: Synchronized with noco+MSO, treated with 100uM HU and collected 10h post MSO.


title: TX PAX_1113516_04

description:
TX
GSM2869578


title: EdUseq_mESC_MSO_lowHU_8h_rep2

value: Synchronized with noco+MSO, treated with 100uM HU and collected 8h post MSO.


title: OCI-Ly1_DMSO_Rep1

description: Library name: OCI-Ly1_DMSO_Rep1


title: TX PAX_1113332_04

description:
TX
GSM2869576


title: ADNR PAX_1113325_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: EdUseq_mESC_MSO_Ai_2h

value: Synchronized with noco+MSO, treated with 100nM ATRi and collected 2h post MSO.


title: MycCaP sHR 24hr rep3

city: Chicago

first: Mihai

middle: Ioan

last: Truica

state: Illinois

address: 303 E Superior

department: Urology

institute: Northwestern University

description: Library name: Sample 12

data_processing:
Raw FASTQ files were processed using the Ceto next‑generation sequencing analysis pipeline developed in the Bartom laboratory (Elizabeth Bartom; https://github.com/ebartom/NGSbartom). Briefly, Ceto’s RNA‑seq module performed initial quality control on raw reads, adapter and quality trimming, after which cleaned paired‑end reads were aligned to the GRCh38 or GRCm39 reference genome using the splice‑aware aligner STAR v2.7.11b with a genome index built from the corresponding GTF gene annotation, followed by generation of gene‑level count tables from uniquely mapped reads. The pipeline produced per‑sample quality metrics (including read quality, mapping statistics, and duplication estimates) and a matrix of raw gene counts that was used for downstream normalization and differential expression analysis in R.
Gene‑level counts were obtained from the STAR‑generated BAM files using featureCounts (Subread), counting properly paired fragments overlapping exons and accounting for strand specificity when applicable
The resulting raw count matrix was used as input for downstream normalization and differential expression analysis in R ( using DESeq2), including filtering of lowly expressed genes, library size and dispersion estimation, and statistical testing for differential expression between conditions
Assembly: GRCh38 and GRCmm39 (for mouse line MycCaP)
Supplementary files format and content: tab-delimited text file includes raw counts for each file

molecule: polyA RNA

growth_protocol: PC-3 and A549 cells were grown in F12K (Gibco) medium and MycCaP cells in DMEM medium (Gibco), all supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco). All cells were cultured in 1% Penicillin-Streptomycin (10,000U/ml, Life Technologies) and 5% CO2 in a humidified incubator at 37 °C.

extract_protocol:
Total RNA was extracted from cell pellet using Qiagen RNeasy Plus kit. 1 μg of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare sequencing libraries. The Kit procedure was performed without modifications. This procedure includes rRNA depletion, remaining RNA purification and fragmentation, cDNA synthesis, end preparation, Illumina adapter ligation, library PCR amplification and validation.

treatment_protocol: All 3 different cell lines were treated with either 5µM HYDRAC or 5 µM scramble control for 24 hours. PC3 cells were also treated with siMYC or siCNT as per the siRNA protocol:  cells were seeded at 3 × 10^5 cells per well in a 6-well plate in 2 mL of antibiotic-free complete medium and allowed to attach for 24 hours. siRNA targeting MYC (siEP300, M-003282-07-0005, Horizon Discovery Biosciences) or a control siRNA (siCTL, D-001210-01-05, Horizon Discovery Biosciences) were reconstituted in nuclease-free water to a final concentration of 10 μM. Transfection was performed using DharmaFect transfection reagent 1 (Horizon Discovery Biosciences) according to the manufacturer’s protocol. After 72 hours of incubation, cells were harvested, and knockdown efficiency was evaluated by Western blot analysis of MYC protein levels.

value: MycCaP

value: mouse prostate epithelial cancer cells

value: WT

value: non-targeting degrading copolymer


title: MycCaP sHR 24hr rep2

description: Library name: Sample 11


title: EdUseq_mESC_MSO_lowHU_8h_rep1

value: mESC CMTi-1

value: Mouse Embryonic Stem Cells


title: EdUseq_mESC_MSO_lowHU_6h_rep1

value: Synchronized with noco+MSO, treated with 100uM HU and collected 6h post MSO.


title: MycCaP HYDRAC 24hr rep3

description: Library name: Sample 9

value: MYC-targeting degrading copolymer


title: ADNR PAX_1113028_04

description:
ADNR
_


title: EdUseq_mESC_MSO_lowHU_6h_rep2


title: MycCaP HYDRAC 24hr rep1

description: Library name: Sample 7


title: BMDM_Rosa_2

city: Shanghai

first: Guofang

last: Xia

address: NO. 600 Yishan road

country: China

institute: Shanghai Jiaotong University School of Medicine Affiliated Sixth People's Hospital

description: Library name: Rosa_2

data_processing:
Expression levels of transcripts were estimated using StringTie and FPKM calculation. The identification of differentially expressed mRNAs was conducted using the edgeR R package, with |log2fold change| > 1 and a p-value < 0.05.
Assembly: The fastp software was utilized for quality filtering, and HISAT2 was utilized to align the reads to the Mus musculus GRCm39 reference genome. Mapped reads were assembled with StringTie. The assembly of all transcriptomes was undertaken using GffCompare.
Supplementary files format and content: gene_count_matrix.txt: Tab-delimited text file includes gene counts for each sample.

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma Aldrich, US) from BMDMs.
The integrity of the RNA was confirmed using a Bioanalyzer 2100 (RIN > 7.0) and agarose gel electrophoresis. Poly (A) RNA was purified using Dynabeads Oligo (dT) 25 and fragmented with the Magnesium RNA Fragmentation Module. Reverse transcription was then performed with SuperScript™ II. Adapter ligation to A-tailed cDNA fragments was performed following end repair, and size selection was conducted using AMPure XP beads. The ligated products were then amplified via PCR, and the final cDNA library had an average insert size of 300 ± 50 bp.

value: bone marrow

value: bone marrow-derived macrophages

value: macrophages

value: Rosa-targeted CRISPR-CAS9 lentivirus transfection

tag: batch


title: BMDM_Adcy7KO_1

description: Library name: Adcy7KO_1

value: Adcy7-targeted CRISPR-CAS9 lentivirus transfection


title: MycCaP HYDRAC 24hr rep2

description: Library name: Sample 8


title: BMDM_Adcy7KO_2

description: Library name: Adcy7KO_2


title: TX PAX_1112643_04

description:
TX
GSM2869573

value: Well Functioning Transplant


title: EdUseq_mESC_MSO_lowHU_4h_rep2

value: Synchronized with noco+MSO, treated with 100uM HU and collected 4h post MSO.


title: BMDM_Rosa_1

description: Library name: Rosa_1


title: EdUseq_mESC_MSO_lowHU_4h_rep1


title: ADNR PAX_1112641_06

description:
ADNR
_

value: Acute dysfunction no rejection


title: MycCaP sHR 24hr rep1

description: Library name: Sample 10


title: subAR PAX_1113026_06

description:
subAR
GSM2869911

value: Subclinical acute rejection


title: EdUseq_mESC_MSO_lowHU_2h

value: Synchronized with noco+MSO, treated with 100uM HU and collected 2h post MSO.


title: TX PAX_1112642_04

description:
TX
GSM2869572


title: EdUseq_mESC_MSO_CDC7i+HU_8h

value: Synchronized with noco+MSO, released for 3h, CDC7i foor 3h, released for 1.5h, EdU+HU added for 30'


title: fPA1B_H4K12pr

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: Library name: 23L009852

data_processing:
Paired-end sequencing reads were trimmed by cutadapt  (version 3.5) with the parameters -a CTGTCTCTTATA -A CTGTCTCTTATA -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=20 and mapped to the reference genome (Mus musculus GRCm38 dna primary assembly) using bowtie2  (version 2.5.1). Reads were filtered by samtools  (version 1.17) with the parameter -q 12.
ChIP-seq coverage (bigwig) files created in R (version 4.1.2) using the Bioconductor packages ShortRead (version 1.52.0) and rtracklayer (version 1.54.0) on the unique fragments (read pairs). Coverages were normalized by the total number of fragments and multiplied by a million.
ChIP-seq peaks were called using Homer  (version 4.10) findPeaks with parameters -style histone -fragLength 150 -inputFragLength 150 using input libraries as control. Peaks overlapping black list regions were filtered out using bedtools (version 2.31.0) and the black list (mm10-blacklist.v2 ).
Assembly: GRCm38
Supplementary files format and content: BED peak files
Supplementary files format and content: BW bigwig coverage

source_name: liver

growth_protocol: WT and hypomorphic Pcca-/- (A138T) mice (FVB background) were maintained on standard chow diet in a temperature-controlled environment on a 12/12 h light-dark cycle. Food and water were available ad libitum.

extract_protocol:
We used a native ChIP approach. For this 40-60 mg of frozen liver tissue was homogenized via a tissue grinder. After lysis, the nuclei pellet was digested with 20 U MNase for 15 min at 20 °C.
Libraries from purified DNA were prepared using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s instructions. After PCR enrichment of adaptor-ligated DNA, libraries were size selected at 150-700 bp in length using AMPure XP beads (Beckman Coulter) following the instructions of SPRIselect User Guide. Libraries were controlled via BioAnalyzer (Agilent) measurements using the High Sensitivity DNA

value: liver

tag: Sex

value: female

tag: age

value: 11 weeks

value: PA

tag: antibody

value: H4K12pr (PTM Bio, PTM-206)

tag: chip input


title: TX PAX_1112553_04

description:
TX
GSM2869571

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf


title: fPA2B_H4K12pr

description: Library name: 23L009855


title: EdUseq_mESC_Aphi_60mR_30mEdUHU_rep2

value: mESC CMTi-1

value: Mouse Embryonic Stem Cells

value: Synchronized with aphidicolin (4uM), washed with PBS, , release for 60', EdU and HU were added for 30'.


title: fWT2B_H4K12ac

description: Library name: 23L009847

value: WT

value: H4K12ac (abcam, ab46983)


title: fPA1B_H4K5pr

description: Library name: 23L009850

value: H4K5pr (PTM Bio, PTM-219RM)


title: subAR PAX_1112550_04

description:
subAR
GSM2869910


title: subAR PAX_1112548_05

description:
subAR
GSM2869909


title: fWT2B_H4K12pr

description: Library name: 23L009848


title: fWT2B_H4K5pr

description: Library name: 23L009846


title: fWT1B_H4K12pr

description: Library name: 23L009844


title: EdUseq_mESC_Thy_60mR_30mEdUHU_rep2

value: Synchronized with thymidine, washed with PBS, release for 60', EdU and HU were added for 30'.


title: fPA2B_H4K12ac

description: Library name: 23L009854


title: TX PAX_1112544_05

description:
TX
GSM2869569

value: Well Functioning Transplant


title: fWT1B_H4K5pr

description: Library name: 23L009842


title: EdUseq_mESC_Thy_60mR_30mEdUHU_rep1


title: Tet2mut, ATAC, sample5

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

description: Library name: Tet2mut_sample5

data_processing:
ATAC-Seq: fastQC, preprocessing with PRINSEQ-lite, alignment against mouse reference genome mm10 with BWA, further processing with SAMtools, peakcalling with MACS2
Assembly: mm10
Supplementary files format and content: ATAC: coverage as bigWig files and peaks as bed files

source_name: murine Cebpap30/p30

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 µg of total RNA was used for construction of sequencing libraries. gDNA for ATAC-Seq was harvested from 50.000 cells with Nextera DNA Library Preparation Kit (Illumina).
RNA libraries were constructed using QUANTseq 3' mRNA-Seq Library Prep Kit (Lexogen). ATAC libraries were generated at the Biomedical Sequencing Facility of CeMM, using custom Nextera Library Adaptors.

value: murine Cebpap30/p30


title: fPA1B_H4K12ac

description: Library name: 23L009851


title: EdUseq_mESC_MSO_12h_rep2

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 12h post MSO


title: TX PAX_1112542_04

description:
TX
GSM2869568


title: fPA1B_H4K5ac

description: Library name: 23L009836

value: H4K5ac (abcam, ab51997)


title: fPA2B_H4K5pr

description: Library name: 23L009840


title: fPA2B_H4K5ac

description: Library name: 23L009839


title: fWT1B_H4K5ac

description: Library name: 23L009830


title: EdUseq_mESC_Aphi_60mR_30mEdUHU_rep1


title: TX PAX_1112545_04

description:
TX
GSM2869570


title: fWT2B_H4K5ac

description: Library name: 23L009833


title: EdUseq_mESC_MSO_12h_rep1


title: TX PAX_1112259_04

description:
TX
GSM2869565


title: TX PAX_1112453_04

description:
TX
GSM2869567


title: MC38_220822_64 Obese SDX

city: WESTON

first: Pierre

middle: Jean

last: Dufour

address: 273 CONANT RD.

institute: SynDevRx, Inc

description:
Library name: 220822_64
Obese SDX Cohort

data_processing:
The sequencing library was clustered on one lane of a flowcell and loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The sample was sequenced using a 2x150bp Paired End (PE) configuration.
Raw sequence data (.bcl files) generated were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Raw RNA-sequence reads were aligned to the mouse reference genome (GRCm38/mm10) with Gencode vM10 annotations using STAR v2.7.5c.
Principal component analysis (PCA) was performed using the PCA function within the python package scikit-learn.
Assembly: GRCm38/mm10
Supplementary files format and content: txt files include gene TPM for each cohort and gene counts for each sample.

source_name: subcutaneous MC38 tumors

extract_protocol:
Total RNA from MC38 tumors was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen). The RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies) and RNA integrity was checked using TapeStation (Agilent Technologies).
The RNA sequencing library was prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs), validated on TapeStation (Agilent Technologies), and quantified by Qubit 2.0 Fluorometer (Invitrogen) and quantitative PCR (KAPA Biosystems).

value: subcutaneous MC38 tumors

value: male

value: tumor cells

value: Wild type

tag: background

tag: dose

value: 6 mg/kg

tag: diet

value: High Fat 60% Diet

tag: d0 body_weight_(g)

tag: d17 body_weight_(g)

tag: d0 tumor_volume_(mm^3)

tag: d17 tumor_volume_(mm^3)


title: EdUseq_mESC_MSO_10h_rep3

data_processing:
100-bp single end reads were aligned to the reference mouse genome Human GRCm38/mm10 using bwa v.0.7.17
Only the uniquely mapped reads with mapping quality > 30 Phred score were used as input to generate the coverage bigWig track in 1kb resolution by applying the bins per million mapped reads (BPM) normalization method and smoothing of 4kb.
Assembly: GRCm38/mm10
Supplementary files format and content: 1kb resolution bigWig signal files of EdUseq experiments
Library strategy: EdU-seq

value: mESC CMTi-1

tag: cell type

tag: treatment

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 10h post MSO


title: MC38_220822_63 Obese SDX

description:
Library name: 220822_63
Obese SDX Cohort

tag: tissue

tag: genotype


title: fWT1B_H4K12ac

description: Library name: 23L009843

value: liver

value: female

value: 11 weeks


title: MC38_220822_52 Obese SDX

description:
Library name: 220822_52
Obese SDX Cohort


title: MC38_220822_51 Obese SDX

description:
Library name: 220822_51
Obese SDX Cohort


title: EdUseq_mESC_MSO_10h_rep2

tag: cell line

value: Mouse Embryonic Stem Cells

tag: genetic modification


title: MC38_220822_55 Obese Veh

description:
Library name: 220822_55
Obese Veh Cohort

tag: Sex

value: Vehicle


title: subAR PAX_1112456_04

description:
subAR
GSM2869908

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.

tag: tag

value: Subclinical acute rejection


title: EdUseq_mESC_MSO_10h_rep1


title: cAR PAX_1112196_06

description:
cAR
_

value: Clinical acute rejection


title: MC38_220822_28 Lean SDX

description:
Library name: 220822_28
Lean SDX Cohort

value: Lean 10% Diet


title: EdUseq_mESC_MSO_8h_rep2

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 8h post MSO


title: MC38_220822_43 Obese Veh

description:
Library name: 220822_43
Obese Veh Cohort

value: subcutaneous MC38 tumors


title: MC38_220822_53 Obese Veh

description:
Library name: 220822_53
Obese Veh Cohort

value: male


title: EdUseq_mESC_MSO_8h_rep1


title: MC38_220822_22 Lean SDX

description:
Library name: 220822_22
Lean SDX Cohort

value: tumor cells


title: TX PAX_1112256_04

description:
TX
GSM2869564

value: Well Functioning Transplant


title: TX PAX_1112069_04

description:
TX
GSM2869563


title: TX PAX_1112068_04

description:
TX
GSM2869562


title: S. cerevisiae WT RNA004 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA004)

library_source: other

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

molecule: other

organism: Saccharomyces cerevisiae

source_name: haploid

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: haploid

value: BY4741 parent


title: EdUseq_mESC_MSO_7h_rep4

value: mESC CMTi-1

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 7h post MSO


title: TX PAX_1112066_04

description:
TX
GSM2869561


title: S. cerevisiae WT RNA002 chemistry

description: tRNA sequencing (RNA002)


title: EdUseq_mESC_MSO_7h_rep3


title: MC38_220822_13 Lean SDX

description:
Library name: 220822_13
Lean SDX Cohort

value: Wild type

value: 6 mg/kg


title: S. cerevisiae pus2∆ RNA004 chemistry

description: tRNA sequencing (RNA004)

value: BY4741 pus2{delta}


title: S. cerevisiae pus1∆ RNA004 chemistry

description: tRNA sequencing (RNA004)

value: BY4741 pus1{delta}


title: EdUseq_mESC_MSO_7h_rep2

value: Mouse Embryonic Stem Cells


title: EdUseq_mESC_MSO_7h_rep1


title: MC38_220822_25 Lean Veh

description:
Library name: 220822_25
Lean Veh Cohort

value: Vehicle


title: S. cerevisiae petite cells RNA004 chemistry

description: tRNA sequencing (RNA004)

value: S288C petite


title: TX PAX_1112061_05

description:
TX
GSM2869907


title: EdUseq_mESC_MSO_6h_rep3

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 6h post MSO


title: MC38_220822_5 Lean Veh

description:
Library name: 220822_5
Lean Veh Cohort

value: Lean 10% Diet


title: S. cerevisiae grande cells RNA004 chemistry

description: tRNA sequencing (RNA004)

value: S288C grande


title: MC38_220822_3 Lean Veh

description:
Library name: 220822_3
Lean Veh Cohort

value: subcutaneous MC38 tumors

value: male


title: MC38_220822_20 Lean SDX

description:
Library name: 220822_20
Lean SDX Cohort

value: tumor cells


title: EdUseq_mESC_MSO_6h_rep2


title: TX PAX_1112052_05

description:
TX
GSM2869558

value: Well Functioning Transplant


title: EdUseq_mESC_MSO_6h_rep1bc


title: D. melanogaster, RNA004 chemistry

description: tRNA sequencing (RNA004)

organism: Drosophila melanogaster


title: TX PAX_1112057_04

description:
TX
GSM2869560


title: TX PAX_1112053_04

description:
TX
GSM2869559


title: cAR PAX_1112064_04

description:
cAR
_

value: Clinical acute rejection


title: D. melanogaster, RNA002 chemistry

description: tRNA sequencing (RNA002)


title: brain, MCMV-infected,P7,rep5

city: WUHAN

first: Meng-Jie

last: MEI

address: Golden Dragon Street

institute: Wuhan Institute of Virology, Chinese Academy of Sciences

description: Library name: FKDL202607613

data_processing:
The BD WTA Rhapsody Analysis Pipeline Version 1.9.1 was used to process the fastq files of the sequencing raw data.
We used HISAT to map the single-cell reads to the joint reference genome that including the GENCODE comprehensive mm10 reference and MCMV strain K181 genome (NCBI:txid69156).
Cell labels and molecular indices were identified, and gene identity was determined by alignment against the joint genome.
The gene-barcode matrix was then obtained following the Seurat (version 5.1.0) pipeline in R software (version 4.4.0, R-Foundation, Vienna, Austria).
Low-quality cells (minimum expression cells > 3, gene numbers < 200, and mitochondrial genes > 15%) were filtered and the rest of cells were employed for bioinformatic analysis.
Assembly: Mouse: genome build mm10;  Murine cytomegalovirus (strain K181)
Supplementary files format and content: comma separated values (CSV) file. Each file includes the number of UMIs obtained for each cell for all genes.

source_name: Brain

growth_protocol: All mice were bred and housed at  A2 animal lab with a 12-h light/12-h dark cycle

extract_protocol:
RNA was harvest for reverse transcrition to cDNA using the BD Rhapsody system.  A single-cell suspension of ~10,000 cells was captured from every sample, without selection, on an array of > 200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell.  After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads.  Beads were retrieved into a single tube for reverse transcription.
RNA libraies for scRNA-seq were prepared using BD Rhapsody™ Single-Cell Analysis System Instrument User Guide

treatment_protocol: 2 μL of MCMV-K181-eGFP (100 pfu) was injected into the lateral ventricle of fetuses at E13.5, while the same volume of DMEM was injected in the same manner as mock-infected control.

value: Brain

value: MCMV-Intracranial-lateral intraventricular injection in utero


title: cAR PAX_1111873_06

city: La Jolla

first: SUNIL

last: KURIAN

institute: Scripps Health

description:
cAR
_


title: ADNR PAX_1111890_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: EdUseq_mESC_MSO_6h_rep1a

extract_protocol:
Round cells were lifted by tapping the sides of the flasks and visually inspected. Depending on the conditions of the experiment, cell suspensions from different flasks were strained through a 40 µm mesh and pooled into 50 mL tubes, centrifuged at room temperature (400G, 5 minutes), washed once with 15 mL of PBS and centrifuged again. Pelleted cells were then carefully resuspended and plated. Commonly, the cells lifted from two T225 flasks would be seeded on one 10 cm plates (for EdU-seq and EU-seq) or on one 6 or 12 multi-well plate (if used for cell cycle analysis). Thymidine or aphidicolin synchronisation. Pluripotent cells (0.5-1x106 mESCs, ZHBTc4 or 2TS22c) or MEFs (1.5-2x106 cells) were seeded on 10 cm plates. 24 to 48 hours later 2mM thymidine or 4µM aphidicolin was added to the media for 10 to 12 hours. Cells were washed three to four times with PBS and released into fresh media. MEFs were also synchronised by 60 hours of serum starvation (DMEM, 0.1% FBS, P/S, L-glutamine) and released into fresh media.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina NovaSeq 6000 sequencer.

value: mESC CMTi-1


title: brain, MCMV-infected,P7,rep4

description: Library name: FKDL202607612


title: MC38_220822_7 Lean Veh

description:
Library name: 220822_7
Lean Veh Cohort

value: Wild type


title: brain, MCMV-infected,P7,rep3

description: Library name: FKDL202607611


title: EdUseq_mESC_MSO_5h_rep2

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 5h post MSO


title: subAR PAX_1111872_05

description:
subAR
GSM2869906

value: Subclinical acute rejection


title: uninfected_10, run 2

city: Ann Arbor

first: Marc

middle: B

last: Hershenson

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pediatric Pulmonology

institute: Michigan Medicine

description: Library name: 13215-JK-13

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCh38 (ENSEMBL 109), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20 (Ewels et al., 2016).
Assembly: GRCh38 (ENSEMBL 109)
Supplementary files format and content: Tab-deliminated text file includes a complete matrix of gene expected count totals for all samples.

source_name: nasal epithelium

extract_protocol:
Total RNA from nasal swab samples was prepared using Trizol extraction. RNA was purified using RNEasy spin columns and enriched for mRNA using a Poly(A) mRNA Magnetic Isolation Module.
A TruSeq-based Takara kit was used during library preparation. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan.

value: nasal epithelium

tag: host viral_infection

value: uninfected

tag: library batch


title: uninfected_9, run 2

description: Library name: 13215-JK-12


title: TX PAX_1111870_04

description:
TX
GSM2869557

source_name: Peripheral Whole Blood


title: EdUseq_mESC_MSO_5h_rep1

value: Mouse Embryonic Stem Cells


title: brain, MCMV-infected,P7,rep2

description: Library name: FKDL202607610


title: uninfected_2, run 3

description: Library name: 13215-JK-11


title: subAR PAX_1111869_04

description:
subAR
GSM2869905


title: uninfected_1, run 3

description: Library name: 13215-JK-10


title: brain, MCMV-infected,P7,rep1

description: Library name: FKDL202607609


title: EdUseq_mESC_MSO_4h_rep2

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 4h post MSO


title: EdUseq_mESC_MSO_4h_rep1


title: brain, Mock-infected,P7,rep3

description: Library name: FKDL202607608

value: DMEM-Intracranial-lateral intraventricular injection in utero


title: TX PAX_1111867_04

description:
TX
GSM2869556


title: EdUseq_mESC_MSO_2h_rep2

value: Synchronized with noco+MSO. Resleased in fresh media. EdU was added for the last 30' before collection. Collected at 2h post MSO


title: uninfected_13, run 1

description: Library name: 13215-JK-9


title: brain, Mock-infected,P7,rep2

description: Library name: FKDL202607607


title: MC38_220822_47 Obese Veh

description:
Library name: 220822_47
Obese Veh Cohort

value: subcutaneous MC38 tumors

value: male

tag: background

value: Vehicle

value: High Fat 60% Diet


title: ADNR PAX_1111866_04

description:
ADNR
_


title: uninfected_12, run 1

description: Library name: 13215-JK-8


title: EdUseq_mESC_MSO_2h_rep1


title: brain, Mock-infected,P7,rep1

description: Library name: FKDL202607606

value: Brain


title: Euseq_MEF_G2_M

data_processing:
100-bp single end reads were aligned to the reference mouse genome Human GRCm38/mm10 using bwa v.0.7.17
Only the uniquely mapped reads with mapping quality > 30 Phred score were used as input to generate the coverage bigWig track in 1kb resolution by applying the bins per million mapped reads (BPM) normalization method and smoothing of 4kb.
Assembly: GRCm38/mm10
Supplementary files format and content: 1kb resolution bigWig signal files of Euseq experiments
Library strategy: EU-seq

source_name: MEF

growth_protocol: Mouse embryonic stem cells (mESCs) from 129/SVEV strain were purchased from Merck (CMTi-1, passage 11). They were thawed, amplified as per manufacturer instructions for three passages, aliquoted and frozen. This stock of cells was routinely used on gelatin plates (or flasks) for no more than 32 passages. For all experiments, mESC were grown in DMEM+Glutamax (Gibco, 61965-026), 10% ES-FBS (Gibco 16141-079), MEM NEAA (Gibco 11140-035), sodium pyruvate (Gibco, 11360-039), 1mM beta-mercaptoethanol (Gibco, 31350-010), penicillin/streptomycin (P/S, Gibco, 15140-122), 100ng/mL LIF (stocked at 1-2mg/mL; produced at the Protein Production and Purification Platform of the EPFL, Lausanne, Switzerland), 3µM GSK3 inhibitor (Sigma 361559) and MEK inhibitor (PD0325901, Selleckchem). MEF were grown in DMEM with 10% FBS, l-glutamine, pyruvate and penicillin/streptomycin. All cells were routinely checked for mycoplasma.

extract_protocol:
RNA samples were then precipitated by adding 350 µL of water, 16 µL of 5M NaCl, 1 µL of glycogen and 832 µL of cold ethanol, incubating the mix at -70ºC and centrifuging for 30-60 minutes at 4ºC, 16000 G. The RNA pellet was washed twice in a cold solution of 75% ethanol/water, centrifuged and the pellet resuspended in 400 µL of water. Biotinylated RNA was captured using 200 µL of Dynabeads MyOne streptavidin C1 (Invitrogen, 65001) per sample. The beads had been previously washed thrice in buffer W1x (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.5% Tween-20), twice in Solution A (0.1M NaOH, 0.05M NaCl in water) and twice in Solution B (0.1M NaCl in water). The volume of solutions used for washing the beads was calculated as 200 µL per sample and scaled up depending on the total number of samples. After the last wash, the beads were removed from the magnet and resuspended in buffer W2x (same as W1x but two times concentrated) in two times the original volume (400 µL per sample). 400 µL of this washed bead mix were added to each biotinylated RNA sample and incubated 30 minutes at room temperature on a rotating wheel. Afterwards, the bead-RNA samples were washed three times with 800 µL of buffer W1x. Each Biotinylated-RNA sample was eluted by resuspending the beads in a solution containing 55 µL of 10mM Tris pH 8 and 1.1 µL of 2-mercaptoethanol and incubating them for one hour at room temperature.
RNA libraries were generated without the ribodepletion step and sequenced at the Genomics platform of the University of Geneva.

treatment_protocol: For the synchronized 2h EU-seq, two T225 flasks were each seeded with three million mESCs. Two days after, nocodazole was added in the morning and mitotic-shake-off was performed 6 hours later. The lifted cells were seeded on a 10 cm gelatine plate. EU (5-ethynil-uridine, Jena Biosciences, Cat. No. CLK-N002-10) was added at a concentration of 0.5 mM for 30 minutes before collection, which took place two hours after seeding. For FACS sorted EU-seq, one million mESCs or 3 million MEFs were seeded in 10 cm plates and, the following day, EU was added at a concentration of 0.5 mM for 30 minutes before collection by trypsinization. For all experiments, the samples were then processed as in 59, but with certain modifications. Briefly, cell pellets were resuspended in 600 µL of Trizol and total RNA was extracted through chloroform purification and ethanol precipitation. 10-15 µg of EU-labelled RNA were processed with the Click-iT Nascent RNA Capture Kit (Invitrogen, Cat. No. C-10365) but substituting the biotin-azide from the kit with cleavable biotin-azide (Azide-PEG(3+ 3)-S-S-biotin) (Jena Biosciences, CLK-A2112-10). The click reaction took place on a volume of 50 µL for 30 minutes at room temperature.

value: MEF

value: Mouse Embryonic Fibroblasts

value: Asynchronous cells. FACS sorted according to cell cycle. 6th of six fractions.


title: RV (untyped)_5, run 1

description: Library name: 13215-JK-6

value: RV (untyped)


title: uninfected_11, run 1

description: Library name: 13215-JK-7


title: cAR PAX_1111863_05

description:
cAR
_

value: Clinical acute rejection


title: MC903_HTO

city: ILLKIRCH

first: Mei

last: Li

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

description:
HTO strored in Custom matrix in the processed data file
BFP_MC903_barcodes.tsv.gz
BFP_MC903_features.tsv.gz
BFP_MC903_matrix.mtx.gz

data_processing:
After sequencing, reads were processed using Cell Ranger count (10X Genomics) version 3.1.0 on a hybrid reference consisting of the Mus musculus genome assembly GRCm38 (mm10) and the BFP sequence to generate count matrices for RNA and HTO.
Assembly: genome assembly GRCm38 (mm10) with BFP sequence
Supplementary files format and content: barcodes, features, and matrix files. Matrix contain counts for each barcodes and genes.

molecule: protein

source_name: Ear-draining lymph node

extract_protocol:
At D5, BFP+ and BFP- migDC (B220- CD11cint MHCIIhi) from NT and MC903-treated EDLN were enriched by FACS. NT/BFP+ (5000 cells) and NT/BFP- (7000 cells) migDCs cells were then labelled with anti-bodies (anti-CD45/anti-MHC-I) tagged with hashtag oligonucleotide (HTO), TotalSeq™ barcoded antibody A0301 Hashtag1 (H1)and A0302 Hashtag2 (H2) respectively. MC903/BFP+ (5000 cells) and MC903/BFP- (7000 cells) migDCs were labeled with A0303 Hashtag3 (H3) and A0304 Hashtag4 (H4), respectively.
NT cells (H1 and H2 labelled cells) and MC903 cells (H3 and H4 labelled cells) were then submitted respectively to 3’mRNAseq library preparation using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (16 rxns PN-1000075) following the guidelines of 10X Genomics User Manual "CG000185 RevB", and the Biolegend protocol TotalSeq™-A Anti-bodies and Cell Hashing. Single cell suspensions were processed on the 10X Genomics Chromium Controller. Amplification of cDNA was carried out using 11 cycles of PCR. Construction of single index HTO and 3' gene expression libraries was performed with 12 cycles of amplification during sample index PCR. Final libraries quantification and quality control were completed using Bioanalyzer 2100 (Agilent Technologies, Les Ulis, France) before sequencing using the Illumina HiSeq 4000 platform as paired-end 2x100 base reads (NT and MC903 cells were sequenced in two different lanes).

treatment_protocol: Ears of Tnfsf4KI/+ mice were either untreated (NT) or treated at D0, D2 and D4 with MC903.

value: Ear-draining lymph node

value: migDC


title: RV (untyped)_4, run 1

description: Library name: 13215-JK-5

value: nasal epithelium


title: TX PAX_1111864_06

address: 10666 N Torrey Pines Rd

description:
TX
GSM2869555

value: Well Functioning Transplant


title: MC903_GEX

description:
GEX stored in Gene Expression matrix in the processed data file
BFP_MC903_barcodes.tsv.gz
BFP_MC903_features.tsv.gz
BFP_MC903_matrix.mtx.gz


title: untreated_HTO

description:
HTO strored in Custom matrix in the processed data file
BFP_NT_barcodes.tsv.gz
BFP_NT_features.tsv.gz
BFP_NT_matrix.mtx.gz


title: EUseq_MEF_S3

city: Geneva

first: Vasilis

last: Dionellis

institute: University of Geneva

value: Asynchronous cells. FACS sorted according to cell cycle. 4th of six fractions.


title: RV (untyped)_3, run 1

description: Library name: 13215-JK-4


title: EUseq_MEF_S2

value: Asynchronous cells. FACS sorted according to cell cycle. 3rd of six fractions.


title: RV (untyped)_2, run 1

description: Library name: 13215-JK-3


title: TX PAX_1110968_04

description:
TX
GSM2869553


title: TX PAX_1110971_06

description:
TX
GSM2869554


title: RV (untyped)_1, run 1

description: Library name: 13215-JK-1


title: EUseq_MEF_S1

value: Asynchronous cells. FACS sorted according to cell cycle. 2nd of six fractions.


title: fPA2_RNA

data_processing:
STAR index was prepared by rsem-prepare-reference (RSEM version 1.3.3).
Paired-end RNA-seq reads were aligned to the reference genome (Mus musculus GRCm38 dna primary assembly) by STAR (version 2.7.6a) with the annotation (GRCm38.101.gtf) and with the parameter –quantMode GeneCounts.
Transcript per million (TPM) was calculated by rsem-calculate-expression with the parameters --paired-end --strandedness none.
Assembly: GRCm38
Supplementary files format and content: ReadsPerGene.out.tab
Supplementary files format and content: rsem.genes.results

extract_protocol:
Total RNA was extracted from 20 mg of frozen liver tissue using the Quick-RNA Miniprep Kit (Zymo Research), following the manufacturer’s protocol. RNA concentration was determined with the Qubit RNA Broad Range assay kit (Thermo Fisher), and RNA integrity was assessed using the Bioanalyzer 6000 Nano Chip (Agilent).
RNA libraries were prepared using the NEBNext RNA Library Prep Kit for Illumina sequencing.

value: liver

value: female

tag: age

value: 11 weeks

value: PA


title: subAR PAX_1110965_04

description:
subAR
GSM2869904

value: Subclinical acute rejection


title: TX PAX_1110792_04

description:
TX
GSM2869552


title: TX PAX_1110785_04

description:
TX
GSM2869551


title: EUseq_MEF_G1

value: MEF

value: Asynchronous cells. FACS sorted according to cell cycle. 1st of six fractions.


title: fPA1_RNA


title: EUseq_MEF_S4

value: Mouse Embryonic Fibroblasts

value: Asynchronous cells. FACS sorted according to cell cycle. 5th of six fractions.


title: fWT2_RNA

value: WT


title: Euseq_mESC_G2_M_rep1

value: mESC CMTi-1

value: Mouse Embryonic Stem Cells


title: fWT1_RNA


title: Euseq_mESC_G2_M_rep2


title: uninfected_8, run 1

description: Library name: 11119-JK-45

value: nasal epithelium

value: uninfected


title: uninfected_10, run 1

description: Library name: 11119-JK-47


title: TX PAX_1110674_04

description:
TX
GSM2869550

value: Well Functioning Transplant


title: uninfected_7, run 1

description: Library name: 11119-JK-44


title: cAR PAX_1110393_06

description:
cAR
_

value: Clinical acute rejection


title: fWT2B_Nr5H4K16pr

data_processing:
Paired-end sequencing reads were trimmed by cutadapt (version 3.5) with the parameters -a CTGTCTCTTATA -A CTGTCTCTTATA -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=20 and mapped to the reference genome (Mus musculus GRCm38 dna primary assembly) using bowtie2 (version 2.5.1). Reads were filtered by samtools (version 1.17) with the parameter -q 12.
ChIP-seq coverage (bigwig) files created in R (version 4.1.2) using the Bioconductor packages ShortRead (version 1.52.0) and rtracklayer (version 1.54.0) on the unique fragments (read pairs). Coverages were normalized by the total number of fragments and multiplied by a million.
ChIP-seq peaks were called using Homer (version 4.10) findPeaks with parameters -style histone -fragLength 150 -inputFragLength 150 using input libraries as control. Peaks overlapping black list regions were filtered out using bedtools (version 2.31.0) and the black list (mm10-blacklist.v2).
Assembly: GRCm38
Supplementary files format and content: BED peak files
Supplementary files format and content: BW bigwig coverage

tag: antibody

value: H4K16pr (in-house)

tag: chip input


title: ADNR PAX_1110532_06

description:
ADNR
_

value: Acute dysfunction no rejection


title: untreated_GEX

description:
GEX stored in Gene Expression matrix in the processed data file
BFP_NT_barcodes.tsv.gz
BFP_NT_features.tsv.gz
BFP_NT_matrix.mtx.gz

value: Ear-draining lymph node

value: migDC


title: TX PAX_1110320_06

description:
TX
GSM2869548


title: EUseq_mESC_S4_rep1


title: fWT1B_Nr5H4K16pr

value: liver

value: female

value: 11 weeks


title: uninfected_6, run 2

description: Library name: 11119-JK-43


title: EUseq_mESC_S3_rep2

value: Asynchronous cells. FACS sorted according to cell cycle. 4th of six fractions.


title: uninfected_9, run 1

description: Library name: 11119-JK-46


title: uninfected_5, run 2

description: Library name: 11119-JK-42


title: EUseq_mESC_S3_rep1


title: fPA1B_TermoH4K16pr

value: PA

value: H4K16pr (Thermo Fisher, #PA5-112557)


title: fPA2B_TermoH4K16pr


title: EUseq_mESC_S4_rep2

value: Asynchronous cells. FACS sorted according to cell cycle. 5th of six fractions.


title: EUseq_mESC_S2_rep2

value: mESC CMTi-1

value: Asynchronous cells. FACS sorted according to cell cycle. 3rd of six fractions.


title: TX PAX_1110313_04

description:
TX
GSM2869547


title: TX PAX_1110321_04

description:
TX
GSM2869549


title: RSV_12, run 1

description: Library name: 11119-JK-40

value: nasal epithelium

value: RSV


title: TX PAX_1110275_04

description:
TX
GSM2869545

value: Well Functioning Transplant


title: fWT2B_TermoH4K16pr

value: WT


title: EUseq_mESC_S2_rep1

value: Mouse Embryonic Stem Cells


title: fWT1B_TermoH4K16pr


title: EUseq_mESC_S1_rep2

value: Asynchronous cells. FACS sorted according to cell cycle. 2nd of six fractions.


title: RSV_10, run 1

description: Library name: 11119-JK-38


title: fPA2B_input


title: TX PAX_1109801_04

description:
TX
GSM2869542


title: EUseq_mESC_S1_rep1


title: TX PAX_1110268_04

description:
TX
GSM2869544


title: RSV_9, run 1

description: Library name: 11119-JK-37


title: uninfected_4, run 2

description: Library name: 11119-JK-41

value: uninfected


title: fPA1B_input


title: fWT2B_input


title: RVC_30, run 1

description: Library name: 11119-JK-36

value: RV-C


title: TX PAX_1109293_04

description:
TX
GSM2869903


title: cAR PAX_1109694_04

description:
cAR
_

value: Clinical acute rejection


title: fWT1B_input

value: liver

value: female


title: RVA_16, run 1

description: Library name: 11119-JK-35

value: RV-A


title: EUseq_mESC_G1_rep1

value: Asynchronous cells. FACS sorted according to cell cycle. 1st of six fractions.


title: TX PAX_1109291_04

description:
TX
GSM2869541


title: RSV_11, run 1

description: Library name: 11119-JK-39


title: RVC_29, run 1

description: Library name: 11119-JK-34


title: fPA2A_H4K16bu

value: 11 weeks

value: PA

value: H4K16bu (in-house)


title: Repliseq_mBMMSC_S3

data_processing:
100-bp single end reads were aligned to the reference mouse genome Human GRCm38/mm10 using bwa v.0.7.17
Only the uniquely mapped reads with mapping quality > 30 Phred score were used as input to generate the coverage bigWig track in 1kb resolution by applying the bins per million mapped reads (BPM) normalization method and smoothing of 4kb.
Assembly: GRCm38/mm10
Supplementary files format and content: 1kb resolution bigWig signal files of RepliSeq experiments
Library strategy: Repli-Seq

source_name: mBM-MSC

growth_protocol: Mouse embryonic stem cells (mESCs) from 129/SVEV strain were purchased from Merck (CMTi-1, passage 11). They were thawed, amplified as per manufacturer instructions for three passages, aliquoted and frozen. This stock of cells was routinely used on gelatin plates (or flasks) for no more than 32 passages. For all experiments, mESC were grown in DMEM+Glutamax (Gibco, 61965-026), 10% ES-FBS (Gibco 16141-079), MEM NEAA (Gibco 11140-035), sodium pyruvate (Gibco, 11360-039), 1mM beta-mercaptoethanol (Gibco, 31350-010), penicillin/streptomycin (P/S, Gibco, 15140-122), 100ng/mL LIF (stocked at 1-2mg/mL; produced at the Protein Production and Purification Platform of the EPFL, Lausanne, Switzerland), 3µM GSK3 inhibitor (Sigma 361559) and MEK inhibitor (PD0325901, Selleckchem). Cells were seeded in T225 flasks and grown for 48 hours after which EdU (40 µM) was added for 30 minutes.

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina NovaSeq 6000 sequencer.

treatment_protocol: We should aim to collect at least have at least 20 million cells. Cells were collected by trypsinization, pelleted, resuspended in PBS, fixed in methanol added drop-wise (final concentration 90%) and stored at -20ºC until further processing. Cells were centrifuged at 4ºC, 400G for 10’, washed with 2-5 mL PBS and pelleted again, permeabilized in 5 mL 2% triton/PBS for 30 minutes. Cells were pelleted, washed in PBS and passed into a 5 mL low bind tube. They were centrifuged, resuspended in 1-5 mL of Biotin-Azide Reaction cocktail (as in EdU-seq) and incubated for 30 minutes at room temperature. Cells were then centrifuged, washed once in PBS and resuspended in PBS containing 500µg/mL propidium iodide and 500-100U of RNaseA (Thermo EN0531). The sample was incubated for 30 minutes at 37ºC and kept at 4ºC until the day after. The cells were then sorted in six fractions according to the cell cycle PI profile on a MOFLO Astrios EQ (Beckman Coulter) at the Cytometry platform of the University of Geneva. At least one million cells per fraction were sorted directly into low bind centrifuge tubes, which were later centrifuged and processed as in the EdU-seq protocol.

value: mBM-MSC

value: Asynchronous cells. FACS sorted according to cell cycle. 4th of six fractions.


title: Repliseq_mBMMSC_S4

value: Asynchronous cells. FACS sorted according to cell cycle. 5th of six fractions.


title: fPA1A_H4K16bu


title: TX PAX_1109290_04

description:
TX
GSM2869540

value: Well Functioning Transplant


title: RVC_28, run 1

description: Library name: 11119-JK-32

value: nasal epithelium


title: RVC_27, run 1

description: Library name: 11119-JK-31


title: fWT2A_H4K16bu

value: WT