title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate2

city: Aurora

first: Christopher

last: Ng

state: Colorado

address: 12800 East 19th Ave

institute: University of Colorado - Anschutz Medical Campus

description:
Library name: D4V60F2
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4

data_processing:
Each sample had 10M reading pairs per 20M total reads. RNA-seq analysis was conducted using Salmon and edgeR-based quantification to generate raw counts and CPM matrices
Assembly: GrCh38
Supplementary files format and content: Salmon Quantification Exports, (.sf) files.

source_name: HUVEC

growth_protocol: Human umbilical vein cells (HUVECs), Human Pulmonary Artery Endothelial Cells (HPAEC), and Human Lung Microvascular Endothelial Cells (HMVEC) primary cells were purchased from Lonza (Portsmouth, NH). All endothelial cells used for experimentation were passaged no more than 7 time. Endothelial cells were sustained in EBM2-MV (Lonza) supplemented with 10% fetal Bovine serum (FBS). Experiments were orchestrated to ensure similar passage across cell lines.

extract_protocol:
After relevant experimentation, RNA was extracted using miRNeasy Mini Kit and direct cellular lysis in the slide
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries

treatment_protocol: Cells were harvested and reseeded into a µ-Slide I Luer (IBIDI 80166) at density of 60,000 cells/cm2 or 100,000 cells/cm2.  After 24hr, the cells were washed with PBS and a total of 120µL of fresh medium was added to the cells. For control samples, the slide was placed back in the incubator and medium was changed every 24 hours until the conclusion of the experiment. For flow samples, the slide was connected to 100cm of tubing on each end of the slide. 0.5mm diameter tubing was used to create the 1dynes/cm2 flow condition, 0.8mm dimeter tubing was used to create the 4dynes/cm2 flow condition, and 1.6mm diameter tubing to create the 10 dynes/cm2 flow condition. One end of the tubing was then connected to a reservoir of medium that was kept inside of the incubator with the slide and the other end of the tubing was connected to a syringe outside of the incubator. The syringe was then attached to the Standard Infuse/Withdraw PHD ULTRA™ Syringe Pumps (Harvard Apparatus 70-3007). The desired flow rate was input into the device and flow was started. Flow was applied to the cells for a total of 24 or 48 hours and every 22 minutes the direction of flow was changed from infuse to withdraw.

value: HUVEC

value: commercial endothelial cells

value: WT

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:4


title: kidney biopsy N209

status: Public on Jul 23 2025

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

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

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

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

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

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

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

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: NR


title: kidney biopsy N58


title: kidney biopsy N290

value: ABMR


title: kidney biopsy N77

value: Mixed


title: ChIP, Nanog, eG1-2, rep1

type: SRA

city: Lausanne

first: David

middle: Michael

last: Suter

address: Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

library_source: genomic

data_processing:
Sequencing libraries were aligned to the Mus musculus mm10 genome (GRCm38 release M25) and to the Drosophila Melanogaster genome (BDGP6 release 28) using STAR 2.7.0e (Dobin et al., 2013). Duplicated reads were removed with Picard (Broad Institute), and indexed using SAMTools 1.10 (Li et al., 2009). ChIP-seq samples were spike-in-normalized based on the sample with the lowest abundance of Drosophila reads (Bonhoure et al., 2014; Orlando et al., 2014) using SAMTools. For replicates, bam files were merged using SAMTools, and BigWig files were computed using the deepTools 3.5.1 (Ramírez et al., 2016) function bamCoverage with the setting “--normalizeUsing RPKM”. Peaks were called using MACS 2.2.4 (Zhang et al., 2008) with settings “-f BAMPE -g mm”, and merged using awk. Blacklisted peaks (Dunham et al., 2012) were removed with BEDTools (Quinlan and Hall, 2010) using the setting “-v”.
Assembly: mm10
Supplementary files format and content: bigWig file includes RPKM normalized reads
Supplementary files format and content: bed file containing peaks (except for input)
Supplementary files format and content: bigWig file includes TMM normalized reads (except for input)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: CGR8 WT, 2TS22C, ZHBTc4, and 44iN cells in GMEM supplemented with 10% inactivated ESC qualified fetal bovine serum, 1% nonessential amino acids, 2 mM L-glutamine, 2 mM sodium pyruvate, 100µM 2-mercaptoethanol, 1% penicillin and streptomycin, leukemia inhibitory factor (made in-house), 3 µM CHIR99021 and 0.8 µM PD184352. Cdt-MD cells were neurobasal Medium and DMEM/F-12, supplemented with B-27, N-2, 2 mM L-glutamine, 1% penicillin and streptomycin, 100µM 2-mercaptoethanol, 3 µM CHIR99021, 1 µM PD184352, and leukemia inhibitory factor. All cell lines were cultured on 0.1% gelatin-coated Petri dishes at 37°C and 5% CO2.

extract_protocol:
Briefly, cells were collected after trypsinization and fixed with 2 mM DSG in PBS for 50 min at room temperature on a rotating platform. Subsequently, cells were pelleted, and fixed for 10 min with 1 % formaldehyde on a rotating platform. The reaction was stopped using 200 mM Tris-HCl pH 8.0 for 10 min on a rotating platform. Tubes were filled with 1 % FBS in PBS and cells were spun down. Nuclei were extracted by resuspending the cell pellet twice in LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100), incubated for 10 min at 4°C and with gentle shaking at 100 rpm, and pelleted. The nuclei were then resuspended in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), incubated for 10 min at 4°C and with gentle shaking at 100 rpm, and spun down. To wash nuclei, SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS) was added twice without disturbing the pellet, the tube was rolled to rinse the walls and spun down. All buffers were supplemented with a 1:100 dilution of protease inhibitor cocktail. Chromatin was sheared for 20 min at 5% duty, 140 W, 200 cycles, or for samples with 50,000 cells for 10 min, 10% duty, 75 W, 200 cycles in a Covaris E220 focused ultrasonicator. To remove the insoluble material, chromatin was spun down and the supernatant was transferred to a new tube. As total input control and to evaluate the sonication efficiency, a few microliters of chromatin were incubated with 1X TE buffer pH 8.0 and 10 ng/µl RNAse A at 37°C for 30 min. Proteinase K was added at 400 ng/µl and the reaction was incubated for another 30 min at 55°C and shaking at 1100 rpm. Finally, 200 mM NaCl was added to reverse the crosslinks at 65°C for 16 h and shaking at 1100 rpm. The chromatin was purified using a MinElute PCR purification kit (Qiagen, 28004) and quality-checked on a 1 % agarose gel. Next steps were performed using the ChIP-IT High Sensitivity kit (Active motif, 53040) with a few modifications highlighted below. For immunoprecipitation of samples made from at least 1 million cells, 3.5 µg chromatin were used unless stated otherwise, and for samples made from 50,000 cells, all extracted chromatin was used. The following antibodies were used: anti-OCT4A (Cell Signaling Technology, 5677S) at 3.1 µl per 3.5 µg chromatin, anti-SOX2 (Cell Signaling Technology, 23064) at 3.1 µl per 3.5 µg chromatin, and anti-NANOG (Cell Signaling Technology, 8822) at 1.55 µl per 3.5 µg chromatin. To obtain quantitative ChIP-seq results, drosophila spike-in chromatin and spike-in antibody (Active motif, 61686) were used according to the manufacturer’s recommendations. Before binding the immunoprecipitated chromatin to the beads, the beads were washed once with ChIP buffer. For cross-link reversal, 2 µl proteinase K was added, the reaction was incubated at 55°C for 30 min and the temperature increased to 65°C and shaking at 1100 rpm for 16 h. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L), and sequenced on a NextSeq 500 using 75-nucleotide read length paired-end sequencing.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L)

treatment_protocol: 44iN cells were maintained in culture with 1 µg/ml doxycycline or left untreated for 24h, 2TS22C and ZHBTc4 were treated with 1 µg/ml doxycycline or left untreated for 26h (2TS22C) or 24h (ZHBTc4), Cdt-MD cells untreated

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: chip antibody

value: Nanog (CST, #8822)


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate3

country: USA

description:
Library name: 48V60F3
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10

library_source: transcriptomic

molecule: polyA RNA

tag: genotype

tag: treatment

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:10

tag: batch


title: kidney biopsy N33


title: ChIP, Nanog, eG1-1, rep1


title: ChIP, Nanog, eG1-1, rep3


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate2

description:
Library name: 48V60F2
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate1

description:
Library name: D4V60F3
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate3

description:
Library name: D4V60F1
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4


title: kidney biopsy N166


title: kidney biopsy N78


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate1

description:
Library name: 48V60F1
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate7

description:
Library name: D4V60C2
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:0


title: ChIP, Nanog, 54K, eG1-1, rep1


title: kidney biopsy N199


title: kidney biopsy N174


title: ChIP, Input, eG1-4, rep4


title: kidney biopsy N132


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate6

description:
Library name: D4V60C4
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Input, eG1-4, rep3


title: kidney biopsy N297


title: kidney biopsy N176


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate5

description:
Library name: D4V60C5
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Input, eG1-4, rep2


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate4

description:
Library name: D4V60C6
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Nanog, 54K, rep1


title: kidney biopsy N218


title: ChIP, Input, eG1-4, rep1


title: kidney biopsy N296


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate3

description:
Library name: 48V60C3
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Input, eG1-3, rep4


title: kidney biopsy N256


title: ChIP, Input, eG1-3, rep3


title: kidney biopsy N300


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate1

description:
Library name: 48V60C1
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Input, eG1-3, rep2


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes: 4, replicate1

description:
Library name: D4V60C1
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes: 4


title: ChIP, Input, eG1-2, rep4


title: HUVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate1

description:
Library name: 24V60F
HUVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:10

value: Time:24hrs, Seeding density (cells/cm2):60,000, Dynes:10


title: HUVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate1

description:
Library name: 24V60C
HUVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:0

value: Time:24hrs, Seeding density (cells/cm2):60,000, Dynes:0


title: ChIP, Input, eG1-2, rep3


title: kidney biopsy N131

value: pABMR


title: kidney biopsy N230


title: HUVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:10, replicate1

description:
Library name: 24V100F
HUVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:10

value: Time:24hrs, Seeding density (cells/cm2):100,000, Dynes:10


title: ChIP, Input, eG1-2, rep2


title: kidney biopsy N124


title: HUVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:0, replicate1

description:
Library name: 24V100C
HUVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:0

value: Time:24hrs, Seeding density (cells/cm2):100,000, Dynes:0


title: ChIP, Input, eG1-2, rep1


title: kidney biopsy N201

value: TCMR


title: ChIP, Input, eG1-1, rep4


title: kidney biopsy N153


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate2

description:
Library name: 48V60C2
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0

value: HUVEC


title: kidney biopsy N161


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate4

description:
Library name: D4A60F1
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4

source_name: HPAEC

value: HPAEC

value: commercial endothelial cells


title: ChIP, Input, eG1-1, rep3


title: ChIP, Input, eG1-3, rep1


title: kidney biopsy N27


title: kidney biopsy N145


title: kidney biopsy N269


title: kidney biopsy N139


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate2

description:
Library name: D4A60F3
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4

value: WT

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:4


title: ChIP, Input, eG1-1, rep2


title: ChIP, Input, eG1-1, rep1


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate3

description:
Library name: 48A60F3
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: ChIP, Sox2, SOX2ON, rep2

value: +DOX


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate2

description:
Library name: 48A60F2
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: ChIP, Sox2, SOX2ON, rep1


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate3

description:
Library name: D4A60F2
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate1

description:
Library name: 48A60F1
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: ChIP, Sox2, SOX2OFF, rep2


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate9

description:
Library name: D4A60C1
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N55

value: NR


title: ChIP, Sox2, SOX2OFF, rep1

value: mouse embryonic stem cells


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate8

description:
Library name: D4A60C3
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Sox2, OCT4ON, rep2


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate1

description:
Library name: D4A60F4
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate6

description:
Library name: D4A60C5
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N39


title: ChIP, Sox2, OCT4ON, rep1


title: ChIP, Sox2, OCT4OFF, rep2


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate5

description:
Library name: D4A60C6
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N53

value: Mixed


title: ChIP, Sox2, OCT4OFF, rep1


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate4

description:
Library name: D4A60C7
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N134


title: ChIP, Sox2, NANOGON, rep2


title: kidney biopsy N5


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate3

description:
Library name: 48A60C3
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Sox2, NANOGON, rep1


title: kidney biopsy N46

value: ABMR


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate2

description:
Library name: 48A60C2
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:0


title: kidney biopsy N232


title: kidney biopsy N206


title: kidney biopsy N76


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate7

description:
Library name: D4A60C4
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N87


title: kidney biopsy N223


title: ChIP, Sox2, NANOGOFF, rep2


title: kidney biopsy N247


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate1

description:
Library name: 48A60C1
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Sox2, NANOGOFF, rep1


title: kidney biopsy N149


title: HPAEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate1

description:
Library name: 24A60F
HPAEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:10

value: Time:24hrs, Seeding density (cells/cm2):60,000, Dynes:10


title: ChIP, Oct4, OCT4ON, rep2


title: HPAEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes: 0, replicate1

description:
Library name: 24A60C
HPAEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes: 0

value: Time:24hrs, Seeding density (cells/cm2):60,000, Dynes:0


title: ChIP, Oct4, OCT4ON, rep1


title: HPAEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:10, replicate1

description:
Library name: 24A100F
HPAEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:10


title: ChIP, Oct4, OCT4OFF, rep2


title: kidney biopsy N138


title: HPAEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:0, replicate1

description:
Library name: 24A100C
HPAEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:0


title: ChIP, Oct4, OCT4OFF, rep1


title: kidney biopsy N217


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate2

description:
Library name: D4M60F2
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4

source_name: HMVEC

value: HMVEC


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate1

description:
Library name: D4M60F3
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4


title: ChIP, Oct4, NANOGOFF, rep2


title: ChIP, Oct4, NANOGON, rep1


title: ChIP, Oct4, NANOGON, rep2


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4, replicate3

description:
Library name: D4M60F1
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:4


title: ChIP, Oct4, NANOGOFF, rep1


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate3

description:
Library name: 48M60F3
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:10


title: ChIP, Nanog, SOX2ON, rep2

value: Nanog (CST, #8822)


title: ChIP, Nanog, SOX2ON, rep1


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate1

description:
Library name: 48M60F1
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate2

description:
Library name: 48M60F2
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: kidney biopsy N281


title: kidney biopsy N73

value: TCMR


title: kidney biopsy N273


title: kidney biopsy N180


title: ChIP, Nanog, SOX2OFF, rep2


title: kidney biopsy N37


title: kidney biopsy N13


title: kidney biopsy N70


title: kidney biopsy N194


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate6

description:
Library name: D4M60C2
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N129


title: kidney biopsy N268


title: ChIP, Nanog, OCT4ON, rep2


title: kidney biopsy N213


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate5

description:
Library name: D4M60C3
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Nanog, OCT4ON, rep1


title: kidney biopsy N95


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate4

description:
Library name: 48M60C4
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N246


title: kidney biopsy N222


title: ChIP, Nanog, OCT4OFF, rep2


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate3

description:
Library name: 48M60C3
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: ChIP, Nanog, OCT4OFF, rep1


title: kidney biopsy N152


title: ChIP, Nanog, NANOGON, rep2


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate7

description:
Library name: D4M60C1
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate2

description:
Library name: 48M60C2
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N208


title: kidney biopsy N21


title: ChIP, Nanog, NANOGON, rep1


title: ChIP, Nanog, NANOGOFF, rep2


title: HMVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate1

description:
Library name: 24M60C
HMVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate1

description:
Library name: 48M60C1
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: HMVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate1

description:
Library name: 24M60F
HMVEC,Time: 24hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: HMVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:10, replicate1

description:
Library name: 24M100F
HMVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:10

value: Time:24hrs, Seeding density (cells/cm2):100,000, Dynes:10


title: ChIP, Input, OCT4ON, rep2


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10, replicate4

description:
Library name: 48M60F4
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:10


title: kidney biopsy N119


title: kidney biopsy N151


title: ChIP, Input, OCT4ON, rep1


title: ChIP, Nanog, NANOGOFF, rep1


title: ChIP, Input, OCT4OFF, rep2


title: biol rep 2, EVTs, Day 6

city: Alphen aan den Rijn

first: Qing

last: Yong

address: Emmalaan

country: Netherlands

institute: LUMC

description:
Library name: sample 9
Column name in CPMs_All_Samples.txt: s104902.001.009

data_processing:
RNA-Seq FASTQ files were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 developed at the LUMC. This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, and read expression quantification FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings. RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome. The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=yes”. The gene annotation used for quantification was Ensembl version 104. Using the gene read count matrix, CPM was calculated per sample on all annotated genes. Genes with a CPM higher than 1 in at least 25% of all samples are kept for downstream analysis.
Assembly: GRCh38 human reference genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: human trophoblasts

growth_protocol: CTBs were cultured on plates coated with 5 µg/mL of collagen IV in CTB medium, which was DMEM/F12 supplemented with 0.05 mM 2-mercaptoethanol, 0.2% FBS, 1% penicillin/streptomycin (p/s), 0.3% bovine serum albumin (BSA), 0.5% Knockout Serum Replacement (KSR), 1% Insulin-Transferrin-Selenium (ITS)-X, 1.5 µg/mL of Lascorbic acid, 50 ng/mL of epithelial growth factor (EGF), 2 µM CHIR-99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM Valproic acid, and 5 µM Y-27632. Collagen IV was incubated for 90 min at 37℃. Then 0.5*106 CTBs were plated in 2 mL of CTB medium. During culturing, the medium was refreshed every 2-3 days.

extract_protocol:
RNA was extracted from cells using TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: For EVTs differentiation, 0.75*105 CTBs were transferred to plates coated with 1 µg/mL of collagen IV and incubated in 2 mL of EVT medium, which included DMEM/F-12 medium supplemented with 0.1 mM 2-mercaptoethanol, 1% p/s, 0.3% BSA, 1% ITS-X, 7.5 µM A 83-01, 2.5 µM Y-27632, 100 ng/mL of Neuregulin 1 (NRG1), and 4% KSR. Finally, 2% Matrigel® was added to cells with EVT medium. After three days, the medium was replaced with the same content but without NRG1 and with a Matrigel concentration of 0.5%. On day 3 and 6, cells were harvested for mRNA measurement separetely.

value: human trophoblasts

value: EVT differentiation


title: biol rep 2, CTBs, Day 0

description:
Library name: sample 7
Column name in CPMs_All_Samples.txt: s104902.001.007

source_name: first trimester placenta

tag: tissue

value: first trimester placenta


title: ChIP, Nanog, SOX2OFF, rep1


title: ChIP, Input, OCT4OFF, rep1


title: biol rep 2, EVTs, Day 3

description:
Library name: sample 8
Column name in CPMs_All_Samples.txt: s104902.001.008


title: ChIP, Input, NANOGON, rep2


title: HMVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:0, replicate1

description:
Library name: 24M100C
HMVEC,Time: 24hrs, Seeding density (cells/cm2): 100,000, Dynes:0

value: commercial endothelial cells

value: WT

value: Time:24hrs, Seeding density (cells/cm2):100,000, Dynes:0


title: biol rep 1, EVTs, Day 3

description:
Library name: sample 5
Column name in CPMs_All_Samples.txt: s104902.001.005


title: ChIP, Input, NANOGON, rep1

value: mouse embryonic stem cells

value: +DOX


title: ChIP, Input, NANOGOFF, rep2


title: biol rep 1, CTBs, Day 0

description:
Library name: sample 4
Column name in CPMs_All_Samples.txt: s104902.001.004


title: ChIP, Input, NANOGOFF, rep1


title: SU6-DTHIB

city: Guangzhou

first: Yu

last: Fang

state: State...

address: 107th Yanjiangxi Road

country: China

institute: Sun Yat-Sen Memorial Hospital

description: Library name: Sample 4

data_processing:
Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5%  (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Assembly: hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary files format and content: excel files include normalize values for each Sample

source_name: lymphoma

growth_protocol: SU-DHL-2 and SU-DHL-6 cells were cultured in RPMI 1640 medium (Gibco, Carlsbad, California, USA) supplemented with 10% fetal bovine serum and 1% penicillin‒streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SU-DHL-2 or SU-DHL-6 cells were treated with DMSO or DTHIB (8 μM) for 36 hours.

value: lymphoma

value: diffuse large B-cell lymphoma cells

value: DTHIB


title: SU6-DMSO

description: Library name: Sample 3

value: Negetive control


title: kidney biopsy N75

value: NR


title: EVTs, Day 6

description:
Library name: sample 3
Column name in CPMs_All_Samples.txt: s104902.001.003


title: kidney biopsy N97


title: SU2-DTHIB

description: Library name: Sample 2


title: kidney biopsy N205


title: kidney biopsy N165

value: pTCMR


title: EVTs, Day 3

description:
Library name: sample 2
Column name in CPMs_All_Samples.txt: s104902.001.002


title: SU2-DMSO

description: Library name: Sample 1


title: ATAC, eG1-4, N2B27, rep1

data_processing:
Sequencing libraries were aligned to the Mus musculus mm10 genome (GRCm38 release M25) using STAR 2.7.0e (Dobin et al., 2013). Duplicated reads were removed with Picard (Broad Institute), and indexed using SAMTools 1.10 (Li et al., 2009). ATAC-seq samples were scaled to the same number of reads in each file using SAMTools. For replicates, bam files were merged using SAMTools, and BigWig files were computed using the deepTools 3.5.1 (Ramírez et al., 2016) function bamCoverage with the setting “--normalizeUsing RPKM”. Peaks were called using MACS 2.2.4 (Zhang et al., 2008) with settings “-f BAMPE -g mm”, and merged using awk. Blacklisted peaks (Dunham et al., 2012) were removed with BEDTools (Quinlan and Hall, 2010) using the setting “-v”.
Assembly: mm10
Supplementary files format and content: bigWig file includes RPKM normalized reads
Supplementary files format and content: bed file containing peaks

growth_protocol: 44iN cells were cultured in GMEM supplemented with 10% inactivated ESC qualified fetal bovine serum, 1% nonessential amino acids, 2 mM L-glutamine, 2 mM sodium pyruvate, 100µM 2-mercaptoethanol, 1% penicillin and streptomycin, leukemia inhibitory factor (made in-house), 3 µM CHIR99021 and 0.8 µM PD184352. Cdt-MD cells were cultured in neurobasal Medium and DMEM/F-12, supplemented with B-27, N-2, 2 mM L-glutamine, 1% penicillin and streptomycin, 100µM 2-mercaptoethanol, 3 µM CHIR99021, 1 µM PD184352, and leukemia inhibitory factor. All cell lines were cultured on 0.1% gelatin-coated Petri dishes at 37°C and 5% CO2.

extract_protocol:
Briefly, 50,000 cells were sorted or collected after trypsinization. Cells were then pelleted, washed once with cold PBS, and kept on ice. Subsequently, cells were resuspended in 50 µl cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40), and centrifuged. For the transposition reaction, pelleted nuclei were resuspended in 50 µl of 0.5 µM Tn5 (in-house produced according to (Chen et al., 2017)) in TAPS-DMF buffer (10  mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. During the reaction, the tubes were flicked gently several times, and DNA was immediately purified using the DNA Clean & Concentrator kit (Zymo Research, D4003) with a binding buffer to sample ratio of  5:1. Transposed DNA was diluted in 10 µl DNA elution buffer, and amplified in a solution containing 0.5 mM Ad1.1 universal primer, 0.5 mM of Ad2.X indexing primer, 0.6X SYBR Green I and 1X NEBNext High-Fidelity 2X PCR Master Mix at 72°C for 5 min, 98°C for 30 s, and 5 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. The PCR reaction was monitored to stop the amplification before saturation by sampling 10 µl of amplified DNA and analyzing it by qPCR. The number of cycles to add was determined by the time at which the fluorescence was still in the rising phase. The remaining DNA was further amplified at 98°C for 30 s, and 4-7 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Next, the library was purified using the DNA Clean & Concentrator kit with a binding buffer-to-sample ratio of 5:1. The purified library was further size-selected using a 0.55X and 1.2X ratio of AMPure XP beads. Library concentrations were determined by Qubit, analyzed on a fragment analyzer, and sequenced on an Illumina NextSeq 500 using 75 nucleotide read-length paired-end sequencing.
Libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix

treatment_protocol: 44iN cells were maintained in culture with 1 µg/ml doxycycline or left untreated for 24h, Cdt-MD cells are untreated


title: kidney biopsy N298


title: kidney biopsy N225

value: ABMR


title: kidney biopsy N116

value: TCMR


title: CTBs, Day 0

description:
Library name: sample 1
Column name in CPMs_All_Samples.txt: s104902.001.001


title: PIM411

city: Houston

first: Jeffrey

address: 6431 Fannin St

institute: University of Texas

description: Library name: PIM411

data_processing:
The gene expression data was sequenced in six separate batches and preprocessed using the same pipeline.
We processed the data using the BETSY system, which aligned the reads to the hg19 genome with STAR estimated the transcript abundance as transcripts per million (TPM) with RSEM.
We applied ComBat to log_2 TPM values for batch effect normalization.
Assembly: hg19
Supplementary files format and content: expression.counts.txt.  Read counts for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.tpm.txt.  Transcripts per million for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.combat.txt.  ComBat normalized transcripts per million.  Includes only genes with positive variance in all batches before correction.  Tab-delimited text file.

source_name: patient-derived xenograft (PDX) model of TNBC from tumor

growth_protocol: The fourth mammary fat pads of 4-to-8-week-old female NOD/SCID mice were implanted with 500,000 PDX tumor cells suspended in 30 µL of a 50:50 mixture of DMEM/F12 media and Matrigel. Cells in Matrigel were maintained on ice until engraftment.

extract_protocol:
The RNA was extracted using PicoPure RNA isolation kit and RNA concentration was quantified by Nanodrop.
Whole transcriptome RNA-seq libraries were prepared using RNA HyperPrep kit with RiboErase following the manufacturer's instructions. Paired-end sequencing was performed on Illumina instruments, which varied across batches.

treatment_protocol: Patients were treated with neoadjuvant chemotherapy.  Tumors were extracted and engrafted into xenograft mouse models before (pre), during (mid), and after (post) treatment.

value: tumor

value: doxorubicin + cyclophosphamide

tag: time point

value: recur


title: ATAC, eG1-3, N2B27, rep2


title: K-562 cells, Martinostat 24h, 1 μM. Biol rep 3

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.txt: M-1-3

data_processing:
Sequence reads were trimmed for adaptor sequences and low-quality bases using Trim Galore v0.6.10.
Trimmed reads were mapped to the hg38 reference genome using HISAT2 v2.2.1.
Mapped SAM files were converted to BAM format and sorted using Samtools v1.21.
Read quantification: Gene-level read counts were obtained using featureCounts v1.5.3 with the GENCODE v38 annotation
Assembly: hg38
Supplementary files format and content: txt file include raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: K-562 cells were cultured and maintained in RPMI-1640 medium (Lonza, Basel, Switzerland) containing 1% antibiotics (streptomycin and penicillin), antimycotics (Lonza, Walkersville, MD, USA) and 10 % of heat-inactivated fetal bovine serum (FBS; Biowest, Riverside, MO, USA) at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was isolated using TRIzol™ reagent (Invitrogen) and assessed for quality using an Agilent 2100 Bioanalyzer. RNA quantification was performed using an ND-2000 Spectrophotometer (Thermo Inc.).
RNA libraries were prepared using the NEBNext Ultra II Directional RNA-Seq Kit (NEB). mRNA was isolated using the Poly(A) RNA Selection Kit (Lexogen).

treatment_protocol: K-562 cells were treated by HDACi martinostat for 24 h with different concentrations (0.15, 0.25, 0.5 and 1 μM).

value: Bone marrow

value: Myelogenous leukemia cell


title: PIM407

description: Library name: PIM407

value: post


title: ATAC, eG1-4, N2B27, rep2


title: kidney biopsy N64


title: K-562 cells, Martinostat 24h, 1 μM. Biol rep 2

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.txt: M-1-2


title: ATAC, eG1-2, N2B27, rep2


title: kidney biopsy N93


title: PIM404

description: Library name: PIM404


title: K-562 cells, Martinostat 24h, 1 μM. Biol rep 1

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.txt: M-1-1


title: ATAC, eG1-2, N2B27, rep1


title: PIM402

description: Library name: PIM402

value: mid


title: K-562 cells, Martinostat 24h, 0.5 μM. Biol rep 3

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.txt: M-0-5-3


title: ATAC, eG1-1, N2B27, rep2

value: mouse embryonic stem cells


title: kidney biopsy N52


title: ATAC, eG1-3, N2B27, rep1


title: K-562 cells, Martinostat 24h, 0.5 μM. Biol rep 2

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.txt: M-0-5-2


title: ATAC, eG1-1, N2B27, rep1


title: kidney biopsy N137


title: PIM393

description: Library name: PIM393


title: K-562 cells, Martinostat 24h, 0.5 μM. Biol rep 1

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.txt: M-0-5-1


title: PIM388

description: Library name: PIM388

value: pre


title: ATAC, NANOGON, rep2

value: +DOX


title: kidney biopsy N26


title: K-562 cells, Martinostat 24h, 0.25 μM. Biol rep 3

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt: M-0-25-3


title: kidney biopsy N99


title: PIM397

description: Library name: PIM397


title: PIM384

description: Library name: PIM384


title: kidney biopsy N272


title: K-562 cells, Martinostat 24h, 0.25 μM. Biol rep 1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: M-0-25-1


title: ATAC, NANOGOFF, rep1


title: PIM373

description: Library name: PIM373


title: K-562 cells, Martinostat 24h, 0.15 μM. Biol rep 3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: M-0-15-3


title: kidney biopsy N211


title: PIM371

description: Library name: PIM371


title: K-562 cells, Martinostat 24h, 0.15 μM. Biol rep 2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: M-0-15-2


title: ATAC, NANOGON, rep1


title: PIM387

description: Library name: PIM387


title: Purified CD4+ lymphocytes, sample HD2

city: Ferrara

first: Cristian

last: Bassi

state: Ferrara

address: Via Fossato di Mortara 70

department: Medicina Traslazionale e per la Romagna

country: Italy

institute: Università di Ferrara

description: Library name: HD2

data_processing:
Base calling was performed by Illumina Real-Time Analysis software and NextSeq Control Software.The raw RNA-seq reads from all samples were quality assessed using FastQC v. 0.11.5 a quality control tool available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc. We obtained a median of 43.5 million 74 bp paired end reads per sample. To assess the presence of variants we used the GATK Best Practices workflow for SNP and indel calling on RNA-seq data. Briefly, after the alignment, reads were split into exon segments and hard-clipped to remove any sequence overhanging into the intronic region. A base quality score recalibration algorithm adjusted the base quality scores of each base call in the data. Single Nucleotide Variants (SNVs) were called using the HaplotypeCaller tool (Calling Variants in RNA-seq: Methods and Workflows. https://www.broadinstitute.org/gatk/guide/article?id=3891). Variants were filtered by excluding clusters of at least 3 SNPs within a window of 35 bases (using the parameters -window 35 -cluster 3) and based on quality metrics, removing those with Fisher Strand values (FS) > 30.0, which indicate a high probability of strand bias at the site, and Qual By Depth values (QD) < 2.0. Resulting variants were subsequently filtered to retain only those with a Variant Allele Frequency (VAF) greater than 15% and a sequencing depth higher than 20x. To identify pathogenic variations, mutations also occurring in healthy donors’ samples were filtered out.
Assembly: GRCh37
Supplementary files format and content: The file contains the normalized gene expression data and the chromosomal coordinates of the genes

source_name: CD4+ lymphocytes

extract_protocol:
Isolation of CD4+ cells from peripheral blood (PB) was performed using the untouched human CD4+ T Cell Isolation Kit (Miltenyi Biotech, Germany) following the manufacturer instructions. Purity of samples measured by FACS assessed >90% of CD4+ T cells for each patient analyzed in this study. Direct-zol RNA Miniprep (Zymo Research) obtained high-quality total RNA according to the manufacturer's instructions.
An equimolar libraries, measured by Bioanalyzer High Sensitivity DNA 1000 Assay and Qubit® RNA HS Assay Kit, was loaded onto Illumina NextSeq 500 platform according to the manufacturer's recommendations. To obtain a high percentage of sequencing reads, we pooled 8 library samples per run into a High Output Kit v2.5 cartridge (paired-end sequencing with about 50 million clusters per sample).

value: CD4+ lymphocytes

tag: time

value: Normal


title: Purified CD4+ lymphocytes, sample HD3

description: Library name: HD3


title: K-562 cells, Martinostat 24h, 0.25 μM. Biol rep 2

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt: M-0-25-2


title: kidney biopsy N196


title: ATAC, NANOGOFF, rep2


title: kidney biopsy N259


title: kidney biopsy N271


title: kidney biopsy N170


title: kidney biopsy N221


title: kidney biopsy N150


title: kidney biopsy N62


title: Purified CD4+ lymphocytes, sample HD1

description: Library name: HD1


title: biol rep 1, EVTs, Day 6

description:
Library name: sample 6
Column name in CPMs_All_Samples.txt: s104902.001.006

value: human trophoblasts

value: EVT differentiation


title: kidney biopsy N294

value: pABMR


title: kidney biopsy N173

value: NR


title: kidney biopsy N83

value: TCMR


title: kidney biopsy N283


title: PIM359

description: Library name: PIM359

value: tumor


title: K-562 cells, Martinostat 24h, 0.15 μM. Biol rep 1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: M-0-15-1


title: K-562 cells, untreated, biol rep 3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: M-0-3


title: Purified CD4+ lymphocytes, sample 94T2

description: Library name: 94T2


title: PIM358

description: Library name: PIM358


title: PIM356

description: Library name: PIM356

value: doxorubicin + cyclophosphamide


title: Purified CD4+ lymphocytes, sample 94T1

description: Library name: 94T1


title: Purified CD4+ lymphocytes, sample 92T2

description: Library name: 92T2


title: K-562 cells, untreated, biol rep 1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: M-0-1


title: PIM350

description: Library name: PIM350


title: PIM369

description: Library name: PIM369


title: Purified CD4+ lymphocytes, sample 92T1

description: Library name: 92T1


title: NHDF, MOI5 96hr, H3K9me3, Rep2

city: Chicago

first: Derek

last: Walsh

state: Illinois

address: 303 East Chicago Avenue, Ward 6165

department: Microbiology Immunology

institute: Northwestern University

description: Library name: CR15

data_processing:
Samples were processed using nf-core/cutandrun pipeline (v3.2.2) and aligned with bowtie2 to a hg38 (GCA_000001405.15_GRCh38) and TB40E (MW439039) concatinated genome.
Assembly: hg38+TB40E
Supplementary files format and content: bigwig (.bigWig) processed files
Library strategy: CUT&Run

source_name: NHDF

growth_protocol: Cells used in this study were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Fisher Scientific) supplemented 2 mM L-glutamine, penicillin/streptomycin and 5% Fetal Bovine Serum (FBS) and incubated at 37°C and 5% CO2. Single donor primary normal human dermal fibroblasts (NHDFs) were isolated from human male neonatal foreskin (Lonza: CC-2509).

extract_protocol:
Cells were dislodged from plate using 0.05% trypsin and resuspending in 5% FBS media for further processing. Approximately 500,000 cells per CUT&RUN experiment were used.
Libraries were made following Epicypher's CUTANA CUT&RUN Library Prep kit ( (#14-1048) including E.coli spike-in controls. Antibodies used were CST Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9751, Di-Methyl-Histone H3 (Lys9) (D85B4) XP Rabbit mAb #4658, and Epicypher kit provided IgG control. Libraries were sequenced 2x150bp.

treatment_protocol: Cells were either mock infected or infected at an MOI of 5 with TB40E-UL99-mCherry for designated timepoints.

value: MOI 5

value: NHDF

value: normal human fibroblasts

value: WT

tag: antibody

value: H3K9me3, MOI5


title: PIM346

description: Library name: PIM346


title: PIM339

description: Library name: PIM339


title: Purified CD4+ lymphocytes, sample 88T2

description: Library name: 88T2


title: PIM344

description: Library name: PIM344


title: NHDF, MOI5 96hr, IgG, Rep2

description: Library name: CR13

value: IgG, MOI5


title: Purified CD4+ lymphocytes, sample 88T1

description: Library name: 88T1


title: NHDF, Mock 96hr, H3K9me3, Rep2

description: Library name: CR11

value: Mock


title: PIM334

description: Library name: PIM334

value: pre


title: K-562 cells, untreated, biol rep 2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: M-0-2

value: Bone marrow

value: Myelogenous leukemia cell


title: Purified CD4+ lymphocytes, sample 87T1

description: Library name: 87T1

value: CD4+ lymphocytes


title: NHDF, Mock 96hr, H3K4me3, Rep2

description: Library name: CR10


title: Purified CD4+ lymphocytes, sample 87T2

description: Library name: 87T2


title: PIM332

description: Library name: PIM332


title: NHDF, Mock 96hr, IgG, Rep2

description: Library name: CR09

value: IgG


title: PIM333

description: Library name: PIM333


title: NHDF, MOI5 96hr, H3K9me3, Rep1

description: Library name: CR07


title: NHDF, MOI5 96hr, H3K4me3, Rep2

description: Library name: CR14

value: H3K4me3, MOI5


title: Purified CD4+ lymphocytes, sample 85T1

description: Library name: 85T1


title: kidney biopsy N86

value: Mixed


title: PIM328

description: Library name: PIM328

value: post


title: kidney biopsy N128


title: NHDF, MOI5 96hr, H3K4me3, Rep1

description: Library name: CR06


title: PIM326

description: Library name: PIM326

value: tumor


title: Purified CD4+ lymphocytes, sample 84T2

description: Library name: 84T2


title: kidney biopsy N188

value: TCMR


title: NHDF, MOI5 96hr, IgG, Rep1

description: Library name: CR05

value: MOI 5


title: kidney biopsy N291

value: NR


title: Purified CD4+ lymphocytes, sample 84T1

description: Library name: 84T1


title: kidney biopsy N12

value: ABMR


title: kidney biopsy N252


title: Purified CD4+ lymphocytes, sample 85T2

description: Library name: 85T2


title: NHDF, Mock 96hr, H3K9me3, Rep1

description: Library name: CR03

value: NHDF

value: normal human fibroblasts

value: WT


title: PIM311

description: Library name: PIM311

value: doxorubicin + cyclophosphamide


title: kidney biopsy N81


title: Purified CD4+ lymphocytes, sample 83T1

description: Library name: 83T1


title: kidney biopsy N242


title: kidney biopsy N210


title: kidney biopsy N103


title: NHDF, Mock 96hr, IgG, Rep1

description: Library name: CR01

value: Mock


title: kidney biopsy N198


title: PIM291

description: Library name: PIM291


title: Purified CD4+ lymphocytes, sample 81T2

description: Library name: 81T2


title: PIM300

description: Library name: PIM300

value: pre


title: NHDF, MOI5, siATAT1-B 72hr matchedTT Rep1

description: Library name: TR24

data_processing:
Reads were trimmed (trimmomatic v0.39) and aligned to a concatinated genome of hg38 (GCA_000001405.15_GRCh38) and TB40E (MW439039) using STAR (v2.7.5). Duplicates were marked and removed by STAR and samtools respectively. Gene counts were generated by htseq-count (v2.0.3) with parameters for stranded libraries.
Assembly: hg38+TB40E
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: coverage normalized bigwig (.bw) file

extract_protocol:
For matched TTseq RNA, 4sU labeled RNA was taken prior to biotin enrichment step, all RNA samples were TRIzol extracted. rRNA was depleted prior to library prep using the NEBNext rRNA Depletion Kit v2 (#E7400).
Libraries were generated using NEB Ultra II Directional library prep kit (#E7760).  Libraries were sequenced 2x150bp.

treatment_protocol: For siRNA experiments, cells were either mock infected or infected at an MOI of 5 with TB40E-UL99-mCherry 12hrs before first siRNA treatment. For timepoints 96 and 120, a second round of siRNA knock-down was performed at 72hrs.

value: siATAT1-B, MOI5


title: kidney biopsy N80


title: NHDF, MOI5, siATAT1-A, 72hr matchedTT Rep1

description: Library name: TR23

value: siATAT1-A, MOI5


title: Purified CD4+ lymphocytes, sample 83T2

description: Library name: 83T2

value: CD4+ lymphocytes


title: Purified CD4+ lymphocytes, sample 78T2

description: Library name: 78T2


title: kidney biopsy N48


title: PIM284

description: Library name: PIM284

value: mid


title: Purified CD4+ lymphocytes, sample 78T1

description: Library name: 78T1


title: kidney biopsy N263


title: PIM283

description: Library name: PIM283


title: NHDF, MOI5, siSUN1-A, 72hr matchedTT Rep1

description: Library name: TR21

value: siSUN1-A, MOI5


title: PIM269

description: Library name: PIM269


title: Purified CD4+ lymphocytes, sample 81T1

description: Library name: 81T1


title: Purified CD4+ lymphocytes, sample 77T2

description: Library name: 77T2


title: NHDF, MOI5, siControl-B, 72hr matchedTT Rep1

description: Library name: TR20

value: siControl-B, MOI5


title: PIM263

description: Library name: PIM263

value: tumor


title: kidney biopsy N267

value: Mixed


title: kidney biopsy N251


title: NHDF, MOI5, siControl-A, 72hr matchedTT Rep1

description: Library name: TR19

value: siControl-A, MOI5


title: PIM321

description: Library name: PIM321

value: post


title: kidney biopsy N179

value: NR


title: PIM262

description: Library name: PIM262


title: NHDF, Mock, siControl-B, 72hr matchedTT Rep1

description: Library name: TR18

value: NHDF

value: siControl-B


title: NHDF, Mock 96hr, H3K4me3, Rep1

description: Library name: CR02

value: normal human fibroblasts

value: WT


title: Purified CD4+ lymphocytes, sample 76T1

description: Library name: 76T1


title: PIM254

description: Library name: PIM254


title: Purified CD4+ lymphocytes, sample 69T2

description: Library name: 69T2


title: PIM245

description: Library name: PIM245


title: Purified CD4+ lymphocytes, sample 77T1

description: Library name: 77T1


title: kidney biopsy N51


title: NHDF, MOI5, siATAT1-B 96hr matchedTT Rep2

description: Library name: TR16


title: Purified CD4+ lymphocytes, sample 69T1

description: Library name: 69T1


title: PIM244

description: Library name: PIM244


title: Purified CD4+ lymphocytes, sample 76T2

description: Library name: 76T2


title: kidney biopsy N200

value: ABMR


title: kidney biopsy N262

value: pTCMR


title: PIM242

description: Library name: PIM242

value: pre


title: Purified CD4+ lymphocytes, sample 67T3

description: Library name: 67T3


title: NHDF, MOI5, siATAT1-A, 96hr matchedTT Rep2

description: Library name: TR15

value: siATAT1-A, MOI5


title: NHDF, MOI5, siSUN1-B, 96hr matchedTT Rep2

description: Library name: TR14

value: siSUN1-B, MOI5


title: kidney biopsy N216


title: kidney biopsy N24


title: PIM239

description: Library name: PIM239


title: kidney biopsy N15


title: kidney biopsy N178


title: Purified CD4+ lymphocytes, sample 67T1

description: Library name: 67T1

value: CD4+ lymphocytes


title: NHDF, MOI5, siSUN1-A, 96hr matchedTT Rep2

description: Library name: TR13

value: siSUN1-A, MOI5


title: PIM231

description: Library name: PIM231

value: doxorubicin + cyclophosphamide

value: mid


title: NHDF, MOI5, siControl-B, 96hr matchedTT Rep2

description: Library name: TR12

value: siControl-B, MOI5


title: Purified CD4+ lymphocytes, sample 63T2

description: Library name: 63T2


title: PIM228

description: Library name: PIM228

value: tumor


title: Purified CD4+ lymphocytes, sample 63T1

description: Library name: 63T1


title: Purified CD4+ lymphocytes, sample 67T2

description: Library name: 67T2


title: NHDF, Mock, siControl-B, 96hr matchedTT Rep2

description: Library name: TR10


title: kidney biopsy N19


title: PIM226

description: Library name: PIM226


title: PIM225

description: Library name: PIM225


title: Purified CD4+ lymphocytes, sample 60T2

description: Library name: 60T2


title: kidney biopsy N169

value: pABMR


title: Purified CD4+ lymphocytes, sample 60T1

description: Library name: 60T1


title: NHDF, Mock, siControl-A, 96hr matchedTT Rep2

description: Library name: TR09

value: siControl-A


title: PIM224

description: Library name: PIM224


title: NHDF, MOI5, siControl-A, 96hr matchedTT Rep2

description: Library name: TR11

value: NHDF

value: siControl-A, MOI5


title: NHDF, Mock, siControl-A, 72hr matchedTT Rep1

description: Library name: TR17

value: normal human fibroblasts


title: PIM215

description: Library name: PIM215


title: NHDF, MOI5, siATAT1-B 96hr matchedTT Rep1

description: Library name: TR08

value: WT

value: siATAT1-B, MOI5


title: Purified CD4+ lymphocytes, sample 50T3

description: Library name: 50T3


title: Purified CD4+ lymphocytes, sample 50T2

description: Library name: 50T2


title: PIM214

description: Library name: PIM214


title: kidney biopsy N261

value: pTCMR


title: NHDF, MOI5, siATAT1-A, 96hr matchedTT Rep1

description: Library name: TR07


title: Purified CD4+ lymphocytes, sample 45T2

description: Library name: 45T2


title: NHDF, MOI5, siSUN1-B, 96hr matchedTT Rep1

description: Library name: TR06


title: kidney biopsy N136

value: NR


title: PIM195

description: Library name: PIM195

value: pre


title: kidney biopsy N204

value: ABMR


title: PIM201

description: Library name: PIM201


title: kidney biopsy N3


title: Purified CD4+ lymphocytes, sample 45T1

description: Library name: 45T1

value: CD4+ lymphocytes


title: kidney biopsy N192


title: NHDF, MOI5, siSUN1-A, 96hr matchedTT Rep1

description: Library name: TR05

value: siSUN1-A, MOI5


title: kidney biopsy N220


title: Purified CD4+ lymphocytes, sample 32T2

description: Library name: 32T2


title: NHDF, MOI5, siControl-B, 96hr matchedTT Rep1

description: Library name: TR04


title: kidney biopsy N156


title: PIM191

description: Library name: PIM191


title: kidney biopsy N202


title: Purified CD4+ lymphocytes, sample 32T1

description: Library name: 32T1


title: NHDF, Mock, siControl-B, 96hr matchedTT Rep1

description: Library name: TR02

value: siControl-B


title: GSC_pooled_input

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1301 Morris Park Avenu

department: Computational and Systems Biology

institute: Albert Einstein College of Medicine

description: Library name: Sample7

data_processing:
For RNA pol2 and H3K27ac, 75-nucleotide sequence reads were obtained using the Illumina NextSeq 500 system, resulting in over 30 million reads for each library, and aligned to the genome using the Burrows-Wheeler Alignment (BWA) algorithm.
The 3’ end of aligned reads (tags) were extended in silico to 150-250 bp and the density of these extended fragments was quantified for the entire genome, which was divided into 32-nucleotide bins. The detection of peaks, genomic regions with significant local enrichment for tags, was performed using the MACS and SICER algorithms.
Tag number across multiple libraries was normalized by being reduced to the number of tags in the smallest library through random sampling, in order to preserve site-specific and global differences between libraries.
For further processing, We focus on the +/- 2.5 kilo base-pairs (kbp) flanking region of the transcription start site (TSS) for each gene and divide it into 50 bins, with each bin representing 100 base pairs.
To prepare the genomic data for ML modeling, we create a 50 x 4 matrix with rows representing bins and columns for epigenetic features for each of the 20,015 genes, and each bin contains summarized counts.
Assembly: GRCh38/hg38
Supplementary files format and content: csv file

source_name: Glioblastoma

growth_protocol: The IRB of Rhode Island Hospital has approved the collection of patient-derived glioblastoma multiforme (GBM) tissue. All collections were performed with patient consent and in completely de-identified manner. Primary hGSC spheres were cultured from human glioma samples as previously described (Galli et al., 2004) All hGCs used in this study were authenticated by ATCC using short tandem repeat (STR) analysis. All human primary cells used were between passages 5 and 30. GSCs were cultured either as spheres or as attached on fibronectin-coated plates (10ug/ml, Millipore Sigma) in a medium of 1X Neurobasal Medium (Fisher Scientific), B27 serum-free supplement, minus Vitamin A (Fisher Scientific), 100X Glutamax (Fisher Scientific), 1mg/ml Heparin (STEMCELL Technologies), 20 ng/ml epidermal growth factor (Peprotech), 20ng/ml basic-fibroblast growth factor (Peprotech), and 1% Antibiotic-Antimycotic (Fisher Scientific).

extract_protocol:
For CTCF, 3 million cells were crosslinked and lysed using the truCHIP Chromatin Shearing Kit (Covaris). For RNA pol2 and H3K27ac, For each biological replicate, 5 million cells were pelleted and sent to Active Motif for chromatin immunoprecipitation, library preparation, and bioinformatic analysis.
For CTCF, Immunoprecipitation for CTCF and ChIP-seq library preparation was performed using the ChIP-IT High Sensitivity Kit (Active Motif) and Next Gen DNA Library Kit (Active Motif), following the manufacturer’s instructions.

value: Glioblastoma

value: Glioblastoma stem cells

value: glioblastoma stem cells

value: non-treated


title: PIM182

description: Library name: PIM182

value: tumor


title: NHDF, Mock, siControl-A, 96hr matchedTT Rep1

description: Library name: TR01

value: NHDF

value: siControl-A


title: GSC2_Stem_CTCF

description:
Library name: Sample6
During processing, bam file was merged

value: Glioblastoma stem cells 2


title: PIM181

description: Library name: PIM181


title: PIM180

description: Library name: PIM180


title: GSC1_Stem_CTCF

description:
Library name: Sample5
During processing, bam file was merged

value: Glioblastoma stem cells 1


title: NHDF, MOI5, siATAT1-B 72hr Rep1

description:
Library name: TT24
4sU labeled RNA

library_source: other

data_processing:
Reads were trimmed (trimmomatic v0.39) and aligned to a concatinated genome of hg38 (GCA_000001405.15_GRCh38) and TB40E (MW439039) using STAR (v2.5.6). Duplicates were marked and removed by STAR and samtools respectively. Gene counts were generated by htseq-count (v09.1) with parameters for stranded libraries.
Assembly: hg38+TB40E
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigwig (.bw) coverage tracks

molecule: other

extract_protocol:
Following labeling, cells were lysed with TRIzol and RNA phenol-chloroform extracted. Total RNA was fragmented using the NEBNext RNA Fragmentation Module and labelled with MTSEA-biotin-XX. 4sU labeled RNA was enriched wirth Streptavidin beads. The NEBNext rRNA Depletion Kit v2 was used prior to library prperation.
Libraries were generated using NEB Ultra II Directional library prep kit (#E7760).  Libraries were sequenced 2x150bp.

treatment_protocol: For siRNA experiments, cells were either mock infected or infected at an MOI of 5 with TB40E-UL99-mCherry 12hrs before first siRNA treatment. For timepoints 96 and 120, a second round of siRNA knock-down was performed at 72hrs. For 4sU labeling, media was replaced with media containing 500 µM 4-thiouridine prewarmed to 37° C and incubated for 1hr prior to timepoint collection.

value: normal human fibroblasts

value: WT

value: siATAT1-B, MOI5


title: NHDF, MOI5, siATAT1-A, 72hr Rep1

description:
Library name: TT23
4sU labeled RNA

value: siATAT1-A, MOI5


title: NHDF, MOI5, siControl-A, 96hr matchedTT Rep1

description: Library name: TR03

value: siControl-A, MOI5


title: NHDF, MOI5, siSUN1-B, 72hr Rep1

description:
Library name: TT22
4sU labeled RNA

value: siSUN1-B, MOI5


title: kidney biopsy N233

value: NR


title: PIM190

description: Library name: PIM190

value: pre


title: GSC1_Stem_RNApol2

description: Library name: Sample3

value: Glioblastoma


title: PIM173

description: Library name: PIM173


title: kidney biopsy N287


title: GSC2_Stem_RNApol2

description: Library name: Sample4


title: NHDF, MOI5, siSUN1-A, 72hr Rep1

description:
Library name: TT21
4sU labeled RNA

value: siSUN1-A, MOI5


title: GSC2_Stem_H3K27ac

description: Library name: Sample2

value: glioblastoma stem cells


title: PIM172

description: Library name: PIM172

value: doxorubicin + cyclophosphamide

value: mid


title: kidney biopsy N31


title: GSC1_Stem_H3K27ac

description: Library name: Sample1

value: non-treated


title: NHDF, MOI5, siControl-B, 72hr Rep1

description:
Library name: TT20
4sU labeled RNA

value: NHDF

value: siControl-B, MOI5


title: MDAMB468, Resistant, Sample1

city: Oslo

first: Eivind Valen

last: Egeland

address: Ullernchausseen 70

department: Department of Tumor Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
Library name: S11
col S11 in raw_data_mdamb468.txt

data_processing:
Fastq files were cropped to longest common read length, 75 bp, with Trimmomatic (v0.38).
Trimmed samples were aligned to grch38 with STAR (v2.7.8a), and transcript reference (UCSC KnownGene downloaded March 7th 2022) using default parameters.
Gene counts were retrieved with featureCounts from Subread.
Assembly: hg38
Supplementary files format and content: tab-delimited txt-file containes raw-counts from all Samples

source_name: TNBC

growth_protocol: The human TNBC cell line MDA-MB-468 (RRID:CVCL_0419) was obtained from the American Type Culture Collection (ATCC) (Manassas, VA, USA). Cells were cultured in high glucose DMEM containing GlutaMAX (Gibco, Life Technologies, Carlsbad, CA, USA) and supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol:
RNA was extracted with AllPrep DNA/RNA/miRNA Unviersal kit (Qiagen).
Libraries were prepared with Kapa RNA HyperPrep with dual index to generate cDNA, followed by Twist Human Comprehensive Exome for the mRNA capturing according to manufacturer's protocol. Amount of starting material 100 ng total RNA.

value: TNBC

value: Untreated


title: NHDF, MOI5, siControl-A, 72hr Rep1

description:
Library name: TT19
4sU labeled RNA

value: normal human fibroblasts

value: WT


title: PIM166

description: Library name: PIM166

value: tumor


title: NHDF, Mock, siControl-B, 72hr Rep1

description:
Library name: TT18
4sU labeled RNA

value: siControl-B


title: MDAMB468, Ctr, Sample1

description:
Library name: S10
col S10 in raw_data_mdamb468.txt


title: PIM165

description: Library name: PIM165


title: kidney biopsy N102

value: ABMR


title: PIM285

description: Library name: PIM285


title: NHDF, Mock, siControl-A, 72hr Rep1

description:
Library name: TT17
4sU labeled RNA

value: siControl-A


title: PIM164

description: Library name: PIM164

value: pre


title: kidney biopsy N109

value: Mixed


title: donor with cataract surgery history, female-4, 73yr

city: Augusta

first: Xingjun

last: Fan

state: GA

address: 1460 Laney Walker Blvd, Room CB1119

department: Cellular Biology and Anatomy

institute: Augusta University

description: Library name: FXJ33

data_processing:
We performed gene alignment, quantification, and differential expression analysis using the Partek Cloud computing service. Briefly, we used STAR (version 2.7.8a) to align sequencing reads to the human reference genome (hg19). We then quantified gene expression using the Partek E/M annotation model, followed by normalization with the median ratio method for DESeq2-based differential expression analysis. Additionally, gene expression levels were quantified in transcripts per million (TPM) for expression analysis. DESeq2 was used to compare post-cataract surgery tissue to non-cataract controls in the differential expression analysis. Normalized counts were utilized for principal component analysis (PCA). To improve accuracy, we applied base trimming to remove low-quality nucleotides and implemented a noise reduction filter before transcript count normalization.
Assembly: human reference genome (hg19)
Supplementary files format and content: xlsx file

source_name: Lens capsule

extract_protocol:
To purify total RNA from lens tissues pre-treated with RNAlater, samples were homogenized using a FastPrep-24 5G homogenizer (MPBio, Santa Ana, CA), followed by total RNA extraction using the mirVana miRNA Isolation Kit (AM1560, ThermoFisher, Waltham, MA). RNA quality was assessed using a Bioanalyzer, and only high-quality samples with distinct rRNA peaks were selected for poly(A) RNA sequencing.
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760, New England BioLabs) with 11 PCR cycles.

value: Lens capsule

tag: subject

value: donor with cataract surgery history

tag: Sex

value: female

tag: age


title: NHDF, MOI5, siATAT1-B 96hr Rep2

description:
Library name: TT16
4sU labeled RNA

value: siATAT1-B, MOI5


title: donor with cataract surgery history, male-2, 66yr

description: Library name: FXJ32

value: male


title: PIM171

description: Library name: PIM171


title: PIM163

description: Library name: PIM163


title: kidney biopsy N177

value: NR


title: NHDF, MOI5, siSUN1-B, 72hr matchedTT Rep1

description: Library name: TR22

value: NHDF

value: siSUN1-B, MOI5


title: kidney biopsy N90


title: kidney biopsy N219


title: kidney biopsy N118


title: NHDF, MOI5, siATAT1-A, 96hr Rep2

description:
Library name: TT15
4sU labeled RNA

value: siATAT1-A, MOI5


title: kidney biopsy N164


title: PIM161

description: Library name: PIM161


title: donor with cataract surgery history, female, 78yr

description: Library name: FXJ30


title: kidney biopsy N61


title: kidney biopsy N234


title: NHDF, MOI5, siSUN1-B, 96hr Rep2

description:
Library name: TT14
4sU labeled RNA

value: normal human fibroblasts


title: kidney biopsy N79


title: NHDF, MOI5, siSUN1-A, 96hr Rep2

description:
Library name: TT13
4sU labeled RNA

value: WT

value: siSUN1-A, MOI5


title: donor with cataract surgery history, male-1, 66yr

description: Library name: FXJ29


title: PIM137

description: Library name: PIM137

value: tumor


title: PIM147

description: Library name: PIM147


title: NHDF, MOI5, siControl-B, 96hr Rep2

description:
Library name: TT12
4sU labeled RNA

value: siControl-B, MOI5


title: kidney biopsy N162


title: PIM135

description: Library name: PIM135


title: donor with cataract surgery history, female-2, 73yr

description: Library name: FXJ24


title: kidney biopsy N284


title: PIM114

description: Library name: PIM114

value: doxorubicin + cyclophosphamide

value: post


title: NHDF, MOI5, siControl-A, 96hr Rep2

description:
Library name: TT11
4sU labeled RNA

value: siControl-A, MOI5


title: kidney biopsy N191


title: NHDF, Mock, siControl-B, 96hr Rep2

description:
Library name: TT10
4sU labeled RNA

value: siControl-B


title: PIM106

description: Library name: PIM106

value: pre


title: NHDF, Mock, siControl-A, 96hr Rep2

description:
Library name: TT09
4sU labeled RNA

value: siControl-A


title: donor with cataract surgery history, male-2, 76yr

description: Library name: FXJ22

value: Lens capsule

value: donor with cataract surgery history


title: PIM099

description: Library name: PIM099


title: kidney biopsy N245

value: NR


title: donor with cataract surgery history, male, 71yr

description: Library name: FXJ28

value: male


title: kidney biopsy N49


title: NHDF, MOI5, siATAT1-B 96hr Rep1

description:
Library name: TT08
4sU labeled RNA

value: NHDF

value: siATAT1-B, MOI5


title: donor with cataract surgery history, female-3, 73yr

description: Library name: FXJ25

value: female


title: donor with cataract surgery history, female, 79yr

description: Library name: FXJ23


title: NHDF, MOI5, siATAT1-A, 96hr Rep1

description:
Library name: TT07
4sU labeled RNA

value: normal human fibroblasts

value: WT

value: siATAT1-A, MOI5


title: donor with cataract surgery history, female-1, 73yr

description: Library name: FXJ19


title: PIM097

description: Library name: PIM097

value: tumor


title: donor with cataract surgery history, female, 88yr

description: Library name: FXJ14


title: PIM091

description: Library name: PIM091


title: kidney biopsy N125

value: ABMR


title: PIM084

description: Library name: PIM084


title: kidney biopsy N187

value: TCMR


title: donor with cataract surgery history, female, 71yr

description: Library name: FXJ13


title: NHDF, MOI5, siSUN1-A, 96hr Rep1

description:
Library name: TT05
4sU labeled RNA

value: siSUN1-A, MOI5


title: NHDF, MOI5, siSUN1-B, 96hr Rep1

description:
Library name: TT06
4sU labeled RNA

value: siSUN1-B, MOI5


title: donor with cataract surgery history, female-2, 75yr

description: Library name: FXJ11


title: kidney biopsy N226


title: kidney biopsy N243


title: kidney biopsy N98


title: PIM073

description: Library name: PIM073

value: pre


title: PIM068

description: Library name: PIM068


title: kidney biopsy N241

value: pABMR


title: donor with cataract surgery history, female-1, 75yr

description: Library name: FXJ5

value: Lens capsule


title: NHDF, MOI5, siControl-B, 96hr Rep1

description:
Library name: TT04
4sU labeled RNA

value: siControl-B, MOI5


title: NHDF, MOI5, siControl-A, 96hr Rep1

description:
Library name: TT03
4sU labeled RNA

value: siControl-A, MOI5


title: PIM066

description: Library name: PIM066


title: kidney biopsy N56

value: NR


title: donor with cataract surgery history, male, 70yr

description: Library name: FXJ2

value: donor with cataract surgery history

value: male


title: kidney biopsy N30


title: donor with cataract surgery history, female, 76yr

description: Library name: FXJ1

value: female


title: NHDF, Mock, siControl-B, 96hr Rep1

description:
Library name: TT02
4sU labeled RNA

value: NHDF

value: normal human fibroblasts

value: siControl-B


title: NHDF, Mock, siControl-A, 96hr Rep1

description:
Library name: TT01
4sU labeled RNA

value: WT

value: siControl-A


title: donor with cataract surgery history, male-1, 76yr

description: Library name: FXJ3


title: kidney biopsy N175


title: PIM053

description: Library name: PIM053

value: tumor


title: Non-cataract donor, female-2, 57yr

description: Library name: FXJ37

value: Non-cataract donor


title: PIM050

description: Library name: PIM050

value: doxorubicin + cyclophosphamide

value: mid


title: 35ac_scp

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

library_source: transcriptomic single cell

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Human reads were aligned to reference genome GRCh38, rhesus macaque reads were aligned to reference genome Mmul_10, and Olive Baboon reads with aligned to refernce genome Panubis1.0.
Assembly: GRCh38, Mmul_10, and Panubis1.0
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each sample.

source_name: brain (amygdala)

extract_protocol:
For human samples, the amygdala was dissected from fresh frozen postmortem human tissue and 100 micron coronal sections of amygdala from fresh frozen postmortem human tissue were obtained by cryosectioning. For nonhuman primates, coronal brain blocks were flash-frozen immediately prior to tissue punches localized to specific amygdala subregions. All nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing

value: brain (amygdala)


title: Non-cataract donor, male, 66yr

description: Library name: FXJ35

value: Lens capsule


title: 34ac_scp


title: PIM048

description: Library name: PIM048

value: pre


title: kidney biopsy N227

value: ABMR


title: PIM056

description: Library name: PIM056


title: 4c-AMYBLA


title: Non-cataract donor, male, 60yr

description: Library name: FXJ31


title: PIM028

description: Library name: PIM028


title: 3c-AMYBLA


title: Non-cataract donor, male-2, 68yr

description: Library name: FXJ27


title: CD8+ Tcells, RB208_1

city: Daejeon

first: YEO

last: JINHEE

address: 291 Daehak-ro

institute: Korea Advanced Institute of Science and Technology

description: Library name: 5_GEx_8

data_processing:
All single-cell sequencing data were aligned to the GRCh38 reference genome, and processed using the CellRanger pipeline with default parameters. The filtered feature-barcode count matrices and TCR V(D)J annotation files passed quality control in the CellRanger pipeline, and were analysed using the Seurat R package. For additional quality control, all subsequent analyses excluded cells with <200 or >2,000 detected genes, and cells with >10% mitochondrial gene expression in RNA UMI counts. We also filtered out cells with detected protein expression of <100 or >10,000 in ADT UMI counts, to avoid antibody aggregation and ensure sufficient cell-surface protein expression data. TCR annotation was conducted using the 10× Cell Ranger V(D)J pipeline, as described above. The TCR clonotype was considered successfully assembled when it comprised paired TCR alpha and beta chains, with either αβ or ααβ configurations. Cells having both the same configuration and CDR3 nucleotide sequences in all chains were considered the same TCR clone. To identify tumour-specific clonotypes in single-cell data, tumour-specific cells were defined as those containing CDR3 amino acid sequences of the TCR beta chain that matched tumour-specific clonotypes identified in the above-described bulk TCR sequencing data. To classify virus-specific clonotypes in the single-cell data, we defined virus-specific cells as those containing CDR3 amino acid sequences of the TCR beta chain specific to human cytomegalovirus (hCMV), Epstein-Barr virus (EBV), and influenza A, with matched HLA genotype in a public VDJ database (VDJdb)4. To ensure reliability of the analysis, we only extracted clonotypes having frequencies of two or more cells. HLA class I genotyping was predicted from scRNA-seq data of each patient using the Optitype tool.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TCR informations for each cell
Supplementary files format and content: tab-delimited text file includes raw ADT counts for each cell

source_name: peripheral blood

extract_protocol:
From single-cell suspensions of tumours and PBMCs, CCR7-CD45RA- and CCR7-CD45RA+ CD8+ T cells were sorted and stained with antibody-derived tags (ADTs) and hashtags. Next, these cells were loaded onto the 10× Genomics Chromium Single Cell platform, and the manufacturer’s protocol was followed to perform a comprehensive analysis of the transcriptome, cell-surface protein, and T-cell antigen receptor repertoire at the individual single-cell level.
Libraries for 5' transcriptome (RNA), ADT, and T-cell receptor (TCR) V(D)J sequences were constructed, following the standard manufacturer’s protocol from the 10× Genomics Single Cell Immune Profiling Kit, and were sequenced using Illumina HiSeq systems.

value: peripheral blood

tag: histology

value: clear cell

tag: tumor stage

value: IV


title: 9811 mDC

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
Juicer pipeline was applied to covert raw fastq files to Hi-C maps binned at resolutions of 5K and 10K
The processed data files are binary files generated from the Juicer pipeline using the raw fastq files from sequencing. We further use these hic files for loop calling
Chromatin loops were identified by MUSTACHE using Hi-C maps binned at resolutions of 5K or 10K, respectively
Chromatin loops identified at two resolutions were further merged using hicMergeLoops
Assembly: hg19
Supplementary files format and content: the final processed data were in bedpe format, with information of the chromosomes and positions of both ends of the chromotin loops

source_name: blood

growth_protocol: PBMCs were Ficoll-Hypaque purified, decorated with CD1c+ magnetic beads (CD1c (BDCA-1) Dendritic Cell Isolation Kit, 130-119-475), and passed over an MS column. The retained myeloid cells were then decorated with the antibody cocktail Lineage 1 with FITC (BD 340546), CD11c with PE-CF594 (BD 562393) and HLA-DR with APC/Cy7 (Biolegend 307618) and underwent the flow sorting to get the purified myeloid dendritic cells (lin1-CD11c+HLA-DR+).

extract_protocol:
The cells were crossinglinked using Arima crosslinking-low input protocol (A160134).
HiC-seq libraries were prepared using the Arima-HiC Kit (A510008)  follwing the Swift Accel-NGS 2S DNA Library Kit per Arima-HiC low input protocol.

treatment_protocol: NO

value: blood

tag: disease

value: psoriasis unaffected

value: primary cells

value: myeloid dendritic


title: Non-cataract donor, male-1, 68yr

description: Library name: FXJ26

value: male


title: PIM049

description: Library name: PIM049


title: CD8+ Tcells, RB183_2

description: Library name: 5_GEx_5

value: III


title: kidney biopsy N121

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

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

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: NR


title: Non-cataract donor, male-2, 64yr

description: Library name: FXJ21

value: Non-cataract donor


title: G6/7R TNF-NTF CART, +THP1, donor 3

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

data_processing:
Illumina NovaSeq 6000 was used for base calling.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.1.0).
Read counts for genes were calculated by featureCounts of the Subread package (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Calculated raw read counts for individual genes are shown in a tab-delimited text file.

source_name: CD8+ T cells

growth_protocol: Human T cells were stimulated by K562 cells that express anti-CD3 mAb (clone OKT3)-derived scFV linked to the transmembrane and cytoplasmic domain of CD8a, and CD80 (K562-OKT3/CD80) (day 0). The stimulated T cells were knocked out of the TNF gene (day1), then transduced with anti-TNF-NTF CAR or anti-TNF-NTF CAR and G6/7R on day 2. The CAR-T cells were expanded in vitro with RPMI media supplemented with 10% FBS and 100 IU/ml human recombinant IL-2.

extract_protocol:
The CD8+ CAR-T cell populaiton was isolated by an MA900 Cell Sorter (SONY) on day 10. Total RNA was isolated from the purified CD8+ CAR-T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
Library preparation was conducted by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: Control or G6/7R expressing TNF-NTF CAR-T cells were cultured in cytokine-free media overnight (day 8) and stimulated by NALM-6 TNF-NTF or THP1 cells for 24h on day 9.

value: CD8+ T cells

value: TNF KO+G6/7R

value: THP1 coculture


title: kidney biopsy N22

source_name: kidney biopsy


title: Non-cataract donor, female-1, 57yr

description: Library name: FXJ34

value: Lens capsule

value: female


title: kidney biopsy N250

value: TCMR


title: CD8+ Tcells, RT183_4.RB183_3

description: Library name: 5_GEx_6

source_name: kidney/peripheral blood

value: kidney/peripheral blood


title: 5c-AMYBLA

value: brain (amygdala)


title: kidney biopsy N231


title: kidney biopsy N104


title: Non-cataract donor, male, 72yr

description: Library name: FXJ20


title: kidney biopsy N224

value: Mixed


title: kidney biopsy N154


title: kidney biopsy N229


title: 4443 mDC

value: blood

value: psoriasis affected

tag: cell line


title: G6/7R TNF-NTF CART, +THP1, donor 2

tag: cell type


title: Non-cataract donor, male, 69yr

description: Library name: FXJ18


title: PIM177

description: Library name: PIM177

value: tumor

value: pre


title: CD8+ Tcells, RB183_1

description: Library name: 5_GEx_4

value: peripheral blood

value: clear cell

value: male


title: Non-cataract donor, female, 76yr

description: Library name: FXJ16

value: Non-cataract donor


title: kidney biopsy N92


title: G6/7R TNF-NTF CART, +THP1, donor 1

value: CD8+ T cells


title: CD8+ Tcells, RT208_3

description: Library name: 5_GEx_208_3

source_name: kidney

value: kidney

value: IV


title: CD8+ Tcells, RT183_3

description: Library name: 5_GEx_3

value: III


title: TNF-NTF CART, +THP1, donor 3

value: TNF KO

value: THP1 coculture


title: kidney biopsy N67

value: NR


title: Non-cataract donor, male, 75yr

description: Library name: FXJ15

value: Lens capsule


title: CD8+ Tcells, RT208_1

description: Library name: 5_GEx_208_1


title: Non-cataract donor, male-1, 64yr

description: Library name: FXJ10


title: Non-cataract donor, male, 53yr

description: Library name: FXJ9


title: CD8+ Tcells, RT208_2

description: Library name: 5_GEx_208_2


title: TNF-NTF CART, +THP1, donor 2


title: TNF-NTF CART, +THP1, donor 1


title: CD8+ Tcells, RT183_2

description: Library name: 5_GEx_2


title: G6/7R TNF-NTF CART, +NALM6 TNF-NTF, donor 3

value: TNF KO+G6/7R

value: NALM6 TNF-NTF coculture


title: Non-cataract donor, female, 66yr

description: Library name: FXJ8

value: female


title: CD8+ Tcells, RT199_3

description: Library name: 5_GEx_199_3


title: Non-cataract donor, male, 76yr

description: Library name: FXJ7


title: CD8+ Tcells, RT199_2

description: Library name: 5_GEx_199_2


title: Non-cataract donor, male, 73yr

description: Library name: FXJ6


title: G6/7R TNF-NTF CART, +NALM6 TNF-NTF, donor 1


title: G6/7R TNF-NTF CART, +NALM6 TNF-NTF, donor 2


title: TNF-NTF CART, +NALM6 TNF-NTF, donor 3


title: CD8+ Tcells, RT199_1

description: Library name: 5_GEx_199_1


title: Non-cataract donor, male, 78yr

description: Library name: FXJ4


title: TNF-NTF CART, +NALM6 TNF-NTF, donor 2


title: CD8+ Tcells, RT183_1

description: Library name: 5_GEx_1


title: kidney biopsy N17

value: Mixed


title: kidney biopsy N44


title: kidney biopsy N8

value: TCMR


title: TNF-NTF CART, +NALM6 TNF-NTF, donor 1


title: kidney biopsy N197


title: PDAC-CA-Tumor-31

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

description: Library name: 63_B10_S6

data_processing:
Adapter sequences and low quality reads were trimmed from fastq files using trim_galore.
With HISAT, trimmed raw read sequences were mapped to Homo sapiens reference genome (hg38)
The aligned reads were sorted via samtools (Version: 1.3.1). HTSeq-count (version 0.6.0) was used to obtain raw read counts for each annotated human gene. Differential expression analysis was carried out using DESeq2.  Genes with an adjusted p-value <0.05 and a log2-fold change >= 1 or <= -1 were considered significantly differentially expressed
Assembly: hg38
Supplementary files format and content: tab delimited text file include normalized read counts for each sample from DESeq.

source_name: Pancreas

extract_protocol:
Total RNA (including small RNAs) was extracted from FFPE tissue sections using Qiagen AllPrep DNA/RNA FFPE kits (Cat #80234), following the manufacturer’s protocol. RNA integrity and quantification were assessed using the Agilent TapeStation instrument with High Sensitivity RNA ScreenTapes (Cat #5067-5579) and Qubit RNA assay kits (Cat#: Q32855, Invitrogen, Thermo Fisher).
Library preparation from input RNA was performed using SureSelectXT Low Input Library Preparation and Target Enrichment Kits (Cat #5190-9686). Final pooled libraries (12-plex) were run to obtain 30M read depth for single-end reads using NextSeq 500/550 High Output Reagent Cartridge v2 (Cat # 15057934) on an Illumina NextSeq 500/550 instrument.

value: Pancreas

tag: race

value: Caucasian

tag: condition

value: Tumor


title: kidney biopsy N28


title: kidney biopsy N69


title: kidney biopsy N249


title: kidney biopsy N123


title: cre_negative_9535

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

description:
Library name: creNeg_9535
10x Genomics scRNAseq

data_processing:
Demultiplexing, and mapping of reads to feature barcode matrices was performed using the cellranger v.9.0.0 pipeline from 10x Genomics using the mm10 genome.
Downstream analysis was performed using the seurat package (v5) within the R statistical computing environment (v4.4.0). Ambient RNA was calculated and corrected using SoupX and high quality cells expressing less than 7,000 gene features, between 800-40,000 UMIs and less than 10 percent mitochondrial content were retained. Doublets were detected and removed from the analysis and the filtered dataset was normalized, scaled while regressing out mitochondrial content, and clustered using a resolution of 0.8 using the seurat standard workflow. Cell types were annotated using publicly available lung scRNAseq datasets and literature sources for key marker genes.
Assembly: mouse mm10
Supplementary files format and content: mapped count matrices from cellranger pipeline

source_name: lung

extract_protocol:
Lungs were harvested on day 8 post-infection (from IAV), flash frozen, and sent to Azenta for nuclear extraction and processing for sn-RNAseq.
Next-generation sequencing libraries were prepared using the 10x Genomics single cell 3' v4 (polyA) reagent kit following manufacturer's protocol. Libraries were uniquely indexed, pooled, and sequenced on an Illumina sequencer. Libraries were sequenced in a paired-end, dual index sequencing run targeting 20,000 mean reads per cell.

value: lung

value: multiple

tag: genotype

tag: infection

value: IAV


title: PDAC-CA-Tumor-30

description: Library name: 62_D7_S5

tag: tissue


title: end_6

first: Andrea

last: Facciabene

state: PA

address: 3400 Civic Center Bulevard

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq datasets were quality checked and pre-processed using FastQC and Cutadapt. Alignment of the trimmed sequencing reads was conducted against the Homo sapiens (version GRCh38) genome using the STAR aligner.
Isoform-level quantification was performed using RSEM and expected counts for each gene were extracted for downstream analysis.
Trimmed mean of M-values (TMM) normalization was applied to RSEM read counts and differential expression analysis was conducted using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files that includes raw counts for each sample

source_name: PBMCs

extract_protocol:
Total RNA was extracted using standard trizol protocol, following RNA concentrations were measured with Qubit Flourometric Quantification (Theromo Fisher Scientific), RNA integrity number (RIN) was determined with Bioanalyzer on RNA 6000 Nano Kit (Agilent Technologies), all samples were high quality with RIN > 9.
RNA-seq libraries were generated using NEBNext Poly(A) + ultra–Directional RNA library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s instructions.  For sequencing (150 bp paired-end) at Genewiz NJ, USA

treatment_protocol: SBRT was administered per institutional guidelines for peripheral or centrally located tumors under 5 cm. Treatment was delivered as 50 Gy across 4 or 5 fractions on non-consecutive days. Patient setup involved 4D CT simulation with upper and lower vaclok bags for reproducibility and a compression belt for tumors in the lower lobe to reduce motion. Treatment volumes were defined using the 4D CT images to create an IGTV, with an isotropic 5 mm margin added to form the PTV. Established dose constraints from previous publications were followed

value: PBMCs

tag: treatment

value: RT

value: end


title: GSC2_atac

description:
Library name: Sample2
Libraries were analyzed by GENEWIZ using the Illumina HiSeq 2500 system to acquire 150 bp paired-end sequence reads. 200 million genomic reads per sample were obtained to detect open vs. closed chromatin regions.

data_processing:
For further processing, We focus on the +/- 2.5 kilo base-pairs (kbp) flanking region of the transcription start site (TSS) for each gene and divide it into 50 bins, with each bin representing 100 base pairs.
To prepare the genomic data for ML modeling, we create a 50 x 4 matrix with rows representing bins and columns for epigenetic features for each of the 20,015 genes, and each bin contains summarized counts.
Assembly: GRCh38/hg38
Supplementary files format and content: csv file

extract_protocol:
For each biological replicate, 50,000 cells were used to prepare ATAC-seq libraries in accordance with the protocol used in Ackermann et al. for alpha and beta cells, which was adapted with some modifications from the original protocol from Buenrostro et al. and the Omni-ATAC protocol.
Samples with low viability (85%) were treated with DNase (Worthington) at a concentration of 200 U/mL for 30 minutes at 37° C. Double-sided bead purification to remove primer dimers and large 1,000 bp fragments was carried out using Agencourt AMPure XP beads (Beckman Coulter). Quality control was performed before sequencing using a Fragment Analyzer (Agilent) and the KAPA Library Quantification Kit (Roche).

value: Glioblastoma

value: Glioblastoma stem cells 2

value: glioblastoma stem cells

value: Non-treated


title: cre_negative_5769

description:
Library name: creNeg_5769
10x Genomics scRNAseq

tag: time


title: start_6

value: start


title: PDAC-CA-Tumor-28

description: Library name: 58_F9_S4


title: kidney biopsy N74

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

institute: University of Alberta

value: NR


title: GSC1_atac

description:
Library name: Sample1
Libraries were analyzed by GENEWIZ using the Illumina HiSeq 2500 system to acquire 150 bp paired-end sequence reads. 200 million genomic reads per sample were obtained to detect open vs. closed chromatin regions.

value: Glioblastoma stem cells 1


title: vancomycin_baseline_6

value: RT + Vancomycin

value: baseline


title: kidney biopsy N54


title: PDAC-CA-Tumor-27

description: Library name: 55_B9_S4

value: Pancreas

value: Caucasian


title: vancomycin_end_5


title: GSC2

description: Library name: Sample2

data_processing:
Sequence reads were aligned to the hg38 assembly of the human genome with hisat2 (Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).
Sequence-read summarization was done with featureCounts (Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014) using refSeq exon coordinates extracted from the refGene.txt file (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz)
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated text file with raw counts for refseq protein-coding genes.

extract_protocol:
RNA was harvested using the Trizol reagent and the RNeasy mini kit (Qiagen)
Completed with Genewiz (RNA with PolyA selection)


title: PDAC-CA-Tumor-26

description: Library name: 53_F6_2_S3

value: Tumor


title: kidney biopsy N112

value: ABMR


title: GSC1

description: Library name: Sample1


title: PDAC-CA-Tumor-25

description: Library name: 52_C11_S3


title: vancomycin_start_5


title: MOLM13_shNS_Ribo_rep2

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description: Ribosome-profiling

data_processing:
The raw reads (R1 only) were adapter trimmed by Cutadapt with parameters: -m 25 -M 40 -a AGATCGGAAGAGCACACGTCT. The human tRNA, rRNA and snoRNA sequences were removed from trimmed reads by using Bowtie software. Then the clean reads were mapped to human transcriptome (hg38 version + GENCODE v37) by utilizing STAR software. The reads counts and TPM on gene level were estimated by RSEM.
Assembly: hg38
Supplementary files format and content: tab-seperated results from RSEM, containing gene expression information
Library strategy: Ribo-seq

growth_protocol: MOLM13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
The ribosomes from the cell lysates were separated in the sugrose gredient by ultracentrifugation and were collected. ribosome protecting RNA fracgments were recovered from polyacrylamide TBE-Urea gel. The end structures of the RNA fragments were repaired by T4 polynucleotide kinase (T4 PNK, M0201S, New England Biolabs): (1) 3’ end healing reaction (10 μl): 7 μl RNA sample, 1 μl 10×T4 PNK buffer, 1 μl T4 PNK, and 1 μl SUPERase In RNase Inhibitor were mixed and incubated for 1 h at 37 ℃; (2) 5’-end phosphorylation: 1 μl 10 mM ATP and 1 μl extra T4 PNK were added to the reaction and the mixture was kept for 30 min at 37 ℃. The RNA was purified by ethanol precipitation.
The libraries were constructed after depletion of rRNA using NEBNext small RNA library prep set for Illumina (NEB)
Sequencing was performed using an Illumina®HiSeq 2500 system, utilizing a 51 bp paired-end configuration

treatment_protocol: Tet-shNS or Tet-shALKBH1 transduced MOLM13 cells were treated with doxycycline (1 ug/ml) for 4 days to induce ALKBH1 KD. Then cells were treated with 100 μg/ml cycloheximide for 7 min at 37 ℃ to prevent translation before standard ribosome profiling protocol.

value: acute myeloid leukemia

value: shNS


title: PDAC-CA-Tumor-24

description: Library name: 51_B3_S3


title: MOLM13_shNS_Ribo_rep1

description: Ribosome-profiling


title: end_4

value: PBMCs

value: RT


title: kidney biopsy N2

value: pABMR


title: MOLM13_shNS_mRNA_rep2

description: RNA-seq

data_processing:
The raw reads (R1 only) were adapter trimmed by Cutadapt with parameters: -m 25 -M 40 -a AGATCGGAAGAGCACACGTCT. The human tRNA, rRNA and snoRNA sequences were removed from trimmed reads by using Bowtie software. Then the clean reads were mapped to human transcriptome (hg38 version + GENCODE v37) by utilizing STAR software. The reads counts and TPM on gene level were estimated by RSEM.
Assembly: hg38
Supplementary files format and content: tab-seperated results from RSEM, containing gene expression information


title: start_4


title: baseline_4


title: PDAC-CA-Tumor-22

description: Library name: 46_B13_S2


title: PDAC-CA-Tumor-21

description: Library name: 45_C6_S12


title: vancomycin_end_3

value: end


title: kidney biopsy N274


title: kidney biopsy N10


title: PDAC-CA-Tumor-20

description: Library name: 43_C10_S10


title: kidney biopsy N255


title: MOLM13_shALKBH1_Ribo_rep1

description: Ribosome-profiling


title: kidney biopsy N127


title: PDAC-CA-Tumor-19

description: Library name: 36_E5_S2


title: kidney biopsy N254


title: kidney biopsy N190


title: PDAC-CA-Tumor-23

description: Library name: 48_A3_S1


title: vancomycin_baseline_3


title: kidney biopsy N184


title: PDAC-CA-Tumor-18

description: Library name: 31_A8_S6


title: end_2


title: MOLM13_shALKBH1_mRNA_rep1

description: RNA-seq


title: MOLM13_shNS_mRNA_rep1

description: RNA-seq


title: kidney biopsy N207

value: TCMR


title: start_2


title: baseline_2


title: kidney biopsy N82

value: Mixed