title: Atg7 KO rep3

city: Cincinnati

first: FUCHUN

last: YANG

state: OH

address: 3125 Eden Ave.

department: Cancer Biology

institute: University of Cincinnati

description:
Group3
Yang4

data_processing:
Adapter trimmed reads in fastq format was used as our report. Demultiplexing is performed under Illumina BaseSpace default setting. Adapter: AGATCGGAAGAGCACACGTC; AdapterRead2: AGATCGGAAGAGCGTCGTGT
Sequence reads were aligned to the reference genome using the TopHat2 aligner  (Kim, D. et al. Genome Biology 2013), and reads aligning to each known transcript were counted using Bioconductor packages for next-generation sequencing data analysis (Huber, W. et al. Nat Meth 2015).
The differential expression analysis between different sample types was performed using the negative binomial statistical model of read counts as implemented in the edgeR Bioconductor package (Anders, S. et al.  Nat. Protocols 2013).
Supplementary_files_format_and_content: Excel spreadsheet with differential gene expression

source_name: vascular tumor cells

growth_protocol: Vascular tumor cells were grown in endothelial cell culture medium: DMEM (Gibco, 11995-065) containing 10% FBS (Gibco, A31606), , supplemented with 60 USP unites/100 ml porcine heparin (Sigma-Aldrich, 2106), 25mM HEPES, 50 μg/ml endothelial cell growth supplement (Corning, 356006), 1% MEM Non-essential amino acids (Gibco, REF11140-050) and 1% penicillin-streptomycin (Gibco, REF15140-122) in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from cultured tumour cells using GeneJET RNA purification Kit (Thermo Scientific, REF K0731) according to the protocol of product manual. RNA concentration and purity were tested by NanoDrop™ ND-1000 Spectrophotometer (Thermo Fisher Scientific) with a A260/A280 ratio >1.9. 1μg of total RNA for each sample was used for libray preparation.
Library preparation was conducted with NEBNext Ultra II Directional RNA Library Prep kit.

value: lymphatic endothelial cells

value: Atg7 KO


title: Serum Exo-RNA 22-1

status: Public on Jan 12 2023

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

organism: Homo sapiens

source_name: primary lung cancer

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Exosomes were obtained from the serum of NSCLC patients using ExoQuickTM (System Biosciences, LLC, Palo Alto, CA, USA). Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) from  isolated exosomes.

tag: tissue

value: primary lung cancer

tag: response

value: Responder


title: Atg7 KO rep2

type: SRA

country: USA

description:
Group3
Yang3

library_source: transcriptomic

organism: Mus musculus

tag: strain

tag: genotype


title: Subject AA17 T1

type: protein

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.

hyb_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Serum/Plasma

extract_protocol: Blood was collected from patients and healthy controls. The blood was then processed into serum or plasma which was then run on our arrays.

tag: condition

value: Influenza Patients from Athens


title: Serum Exo-RNA 19-1

value: Non-responder


title: Subject AA16 T3

label_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.


title: Subject AA16 T2


title: Subject AA16 T1


title: Subject AA18 T1


title: Atg7 KO rep1

description:
Group3
Yang2


title: Serum Exo-RNA 18-1


title: Atg5 KO rep2

description:
Group4
JG4

value: Atg5 KO


title: Atg5 KO rep1

description:
Group4
JG3


title: Subject AA15 T3


title: Serum Exo-RNA 15-1


title: Subject AA15 T2


title: Serum Exo-RNA 13-1


title: Subject AA19 T1


title: Fip200 KO rep3

description:
Group2
FY6

value: Fip200 KO


title: Fip200 KO rep2

description:
Group2
FY5


title: Subject AA14 T1


title: Serum Exo-RNA 7-1


title: Subject AA12 T2


title: Subject AA13 T1


title: 562 control rep3

description:
Group1a
JG2

value: wildtype


title: Subject AA15 T1


title: Subject AA13 T2


title: Atg5 KO rep3

description:
Group4
Yang1


title: Fip200 KO rep1

description:
Group2
FY4


title: Subject AA11 T1


title: Subject AA11 T2


title: Subject AA14 T2


title: Serum Exo-RNA 16-1


title: Subject AA14 T3


title: Serum Exo-RNA 4-1


title: Subject AA10 T2


title: Subject AA12 T1


title: Serum Exo-RNA 12-1


title: Subject AA13 T3


title: Serum Exo-RNA 6-1


title: Serum Exo-RNA 2-1


title: Subject AA9 T3


title: 562 control rep2

description:
Group1a
JG1


title: CP-A, WGD, experiment 2, rep2

city: Lausanne

first: Luca

last: Nanni

state: Vaud

address: Quartier Sorge

department: Computational Biology

country: Switzerland

institute: Université de Lausanne

library_source: genomic

data_processing:
Reads were mapped to the human hg19 reference genome using bwa mem version 0.7.17 and processed using the Juicer pipeline version 1.6. For each sample, Hi-C maps were generated at resolutions 10 kb, 20 kb, 25 kb, 50 kb, 100 kb, 250 kb, 500 kb, 1 Mb, and 10 Mb. Once assessed the concordance between replicas of the same biological condition, Hi-C maps of the same condition were merged using the mega.sh script provided by the Juicer pipeline. All Hi-C maps were normalized using the Knight-Ruiz method (KR) implemented in the Juicer pipeline.
Assembly: hg19
Supplementary files format and content: .hic files represent binarized Hi-C matrices built using Juicer using reads having MAPQ >= 30
Supplementary files format and content: .hic files named as "mega" represent the aggregation of multiple replicates of the same biological condition

molecule: genomic DNA

source_name: esophageal epithelium

growth_protocol: RPE cells were grown in DMEM/F-12, GlutaMAX™ (catalogue no. 10565018) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, catalogue no. 10270106) and 1% Antibiotic-Antimycotic (Thermo Fisher Scientific, catalogue no. 15240062). CP-A cells were grown in MCDB-153 medium (Sigma-Aldrich, catalogue no. M7403) supplemented with 20mg/L adenine (Sigma-Aldrich, catalogue no. A2786), 400µg/L hydrocortisone (Sigma-Aldrich, catalogue no. H0135), 50mg/L bovine pituitary extract (Thermo Fisher Scientific, catalogue no. 13028014), 1x Insulin-transferrin-sodium selenite media supplement (Sigma-Aldrich, catalogue no. I1884), 8.4 µg/L cholera toxin (Sigma-Aldrich, catalogue no. C8052), 4mM glutamine (Sigma-Aldrich, catalogue no. G7513), 5% foetal bovine serum, and 1% Antibiotic-Antimycotic. K562 (67, XX) was cultured in RPMI medium (Thermo Fisher Scientific, catalogue no. 11875093) supplemented with 10% foetal bovine serum and 1% Penicillin-Streptomycin (Thermo Fisher Scientific, catalogue no. 15140122).

extract_protocol:
1-2 million cells were collected and fixed with 2% formaldehyde (Thermo Fisher Scientific, catalogue no. 11483217). The reaction was quenched with 200mM glycine (VWR, catalogue no. 101194M) final concentration, cells were washed with PBS (Thermo Fisher Scientific, catalogue no. 10010023) and lysed in a solution containing 10mM Tris-HCl pH 8.0 (Thermo Fisher Scientific, catalogue no. 15568025), 10mM NaCl (Sigma-Aldrich, catalogue no. S6546), 0.2% Igepal CA-630 (Sigma-Aldich, catalogue no. I8896), and 1x Proteinase inhibitor cocktail (Roche, catalogue no. 11697498001) at 4°C for 30 minutes. Resulting nuclei were re-suspended in 1X NEB3.1 buffer (New England Biolabs, catalogue no. B7203S). Nuclei suspension was incubated with 0.11% SDS (Carl Roth, catalogue no. CN30) final concentration for 10 minutes at 65°C. Reaction was quenched with 1% Triton-X100 (AppliChem, catalogue no. A1388) and nuclei were digested with 100U MboI restriction enzyme (New England Biolabs, catalogue no. R0147) at 37°C overnight. Restriction enzyme was inactivated according to manufacturer’s specifications and digested nuclei were washed and re-suspended in 1x NEB3.1. Digested ends were then marked with biotin via incubation in 0.03mM biotin-14-dATP (Thermo Fisher Scientific, catalogue no. 19524016), 0.03mM dCTP, 0.03mM dGTP, 0.03mM dTTP (Promega, catalogue no. U1420) and 50U Klenow DNA polymerase I (New England Biolabs, catalogue no. M0210M) for 4 hours at room temperature. Resulting blunt-ends were proximally ligated with 50U T4 DNA Ligase (Thermo Fisher Scientific, catalogue no. EL0011), 1x T4 DNA ligase buffer (Thermo Fisher Scientific, catalogue no. B69), 5% PEG, 1% Triton-X100, 0.1mg/ml BSA (New England Biolabs, catalogue no. B9000S) for 4 hours at room temperature. Crosslink reversal was performed on the proximity-ligated chromatin through the incubation with 300mM NaCl and 1% SDS overnight, at 68°C. The sample was then treated with 50g/ml RNase A (Thermo Fisher Scientific, catalogue no. EN0531) for 30 minutes at 37°C, followed by 400ug/ml Proteinase K (Promega, catalogue no. V3021) at 65°C for one hour. DNA was purified via precipitation with 1.6 volumes of pure ethanol and 0.1 volumes of sodium acetate, pH 5.2 (Thermo Fisher Scientific, catalogue no. R1181) at -80°C. DNA was eluted and then fragmented by sonication at 80V peak incidence power, 10% duty factor, 200 cycles per burst, for 60-80 seconds with an E220 Focused-ultrasonicator (Covaris). Sheared DNA was size selected for library preparation using AMPure XP beads (Beckman Coulter, catalogue no. A63881).
Biotin-marked fragments were isolated with Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher Scientific, catalogue no. 65001) and all subsequent steps were performed on the bead-bound DNA fraction. Hi-C library preparation continued with end polishing reaction, which involved incubation of DNA with 1x T4 ligase buffer (New England Biolabs, catalogue no. B0202S), 2.5mM each dNTP, 50U T4 Polynucleotide Kinase (New England Biolabs, catalogue no. M0201), 12U T4 DNA Polymerase (New England Biolabs, catalogue no. M0203), and 5U Klenow DNA polymerase I, at room temperature for 30 minutes. PolyA tail was added by incubating the DNA sample in 1X NEBuffer™ 2 (New Enlgand Biolabs, catalogue no. B7002S) with 0.5mM dATP and 25U Klenow Fragment (3'→5' exonuclease) (New England Biolabs, catalogue no. M0212) at 37°C for 30 minutes. DNA fragment ends were then ligated to Illumina TruSeq unique dual indexes (Integrated DNA Technologies) in 1X T4 Ligation buffer with 5% PEG and 15U T4 DNA Ligase for 2 hours at room temperature or overnight at 16°C. Lastly, libraries were PCR amplified using Illumina forward (AATGATACGGCGACCACCGAGATCTACAC) and reverse (CAAGCAGAAGACGGCATACGAGAT) primers and KAPA HiFi HotStart ReadyMix (Roche, catalogue no. KK2602) for 6-10 cycles. Resulting fragments were size-selected with AMPure XP beads.

treatment_protocol: For WGD in vitro in RPE TP53-/-, two methods were used to induce cytokinesis failure. Cells were incubated for 24 hours with 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 hours to 4uM dihydrocytochalasin B (Cayman Chemical, catalogue no. 20845) and then were allowed to recover for 48 hours. Alternatively, cells were incubated for 24 hours with 9uM of the CDK1 inhibitor RO-3306 (Sigma-Aldrich, catalogue no. SML0569) for G2 synchronization. Drug was washed and cells were then treated with 4uM dihydrocytochalasin B for 24 hours. Cells were allowed to recover for 48 hours and tetraploid cells were sorted based on cell cycle staining with 1ug/ml Hoechst 33342 (Sigma-Aldrich, catalogue no. H1399). For mitotic slippage induction, 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) was added to the growth medium to CP-A, CP-A TP53-/- and K562 cells, which were then incubated for 72, 72, and 48 hours, respectively. For cells with elongated G1 phase after tetraploidisation, CP-A TP53-/- cells were WGD induced with 0.1ug/ml nocodazole for 72 hours and treated with 0.5uM of the CDK4/6 inhibitor Palbociclib (Sigma-Aldrich, catalogue no. PZ0383) for the last 16 hours of the WGD induction. RPE TP53-/- and CP-A TP53-/- cells were then kept in culture for 20 weeks. RPE TP53-/- control and 20w pWGD cells were injected in NSG mice. After 6 weeks, only 20w pWGD injected mice formed tumours in vivo (T1, T2, T3), which were collected and dissociated into single cells with human Tumour Dissociation Kit (Miltenyi Biotec, catalogue no. 130-095-929) and Mouse Cell Depletion Kit (Miltenyi Biotec, catalogue no. 130-104-694) following manufacturer’s protocols. For CP-A TP53-/- control, 6w pWGD, and 20w pWGD, 100,000 cells were resuspended in complete MDCB-153 media were mixed in a 1:1 ratio with 0.7% sterile noble agar (Thermo Fisher Scientific, catalogue no. J10907), then plated on Costar® ultra-low attachment plates (Corning, catalogue no. 3473) on top of a mixture of 1:1 MCDB-153 media and 1.4% sterile noble agar. Mixture was allowed to solidify in a humidified atmosphere at 37 degrees C overnight, then fresh complete MCDB 153 media was added on top of the layers of agar. Samples were incubated for up to 10 weeks in normal conditions and media was replaced twice a week. Individual colonies were picked from the agar layer and cultured for downstream analysis. For CIN-only induction, RPE TP53-/- cells were synchronised at G1/S border with 5mM thymidine (Sigma-Aldrich, catalogue no. T9250) for 24 hours. Six hours after thymidine block release, the cells were treated with 500nM of the Mps1 inhibitor Reversine (Sigma-Aldrich, catalogue no. R3904) for 12 hours. Before processing for downstream analyses, cells were allowed to recover for six hours. For isolation of high ploidy cells, CP-A TP53-/- cells were stained with 1ug/ml Hoechst 33342 for cell cycle profiling. Dividing cells with high ploidy (high Hoechst 33342 signal, > 4N peak) were bulk sorted. Cells were allowed to recover overnight, and then fixed for downstream analyses.

value: esophageal epithelium

tag: cell line

tag: cell type

value: immortalized non-dysplastic metaplasia (Barrett's oesophagus) epithelial cells

value: WT

value: WGD


title: 562 control rep1

description:
Group1a
FY1


title: Subject AA9 T2


title: PH20211213_FR_10

city: Berkeley

first: Iain

middle: Christopher

last: Clark

address: 374 Stanley Hall

institute: University of California, Berkeley

library_source: transcriptomic single cell

data_processing:
The samples are aligned to a combined human (GRCh38.p13) + mouse (GRCm38.p6) transcriptome index with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13 + GRCm38.p6
Supplementary files format and content: Filterered matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, with 4 files per sample.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: HEK393T / NIH-3T3

growth_protocol: human HEK 293T cells (ATCC # CRL-3216) were grown in DMEM (ThermoFisher #11995073) supplemented with 10% FBS (ThermoFisher #A3840001) and 1% Penicillin-Streptomycin-Glutamine (ThermoFisher #10378016). Murine NIH/3T3 cells (ATCC # CRL-1658) were grown in DMEM (ThermoFisher #11995073) supplemented with 10% bovine calf serum (ATCC # 30-2030) and 1% Penicillin-Streptomycin-Glutamine.

extract_protocol: PIP-seq single cell library prep

treatment_protocol: Cells were grown to a confluence of ~70% and treated with TrypLE Express with Phenol red (ThermoFisher #12605010) for 3 minutes, quenched with an equal volume of growth medium, and centrifuged at 5 min at 200 x g. The supernatant was removed, and the cells resuspended in 1X DPBS without calcium or magnesium. Cells were diluted to their final concentration in 1X DPBS with 0.04% BSA and mixed evenly to create a 50:50 Human:Mouse mixture.

value: HEK393T / NIH-3T3

tag: group

value: Wait 72-hours at 1 degC after lysis


title: Serum Exo-RNA 1-1


title: CP-A, WGD, experiment 2, rep1


title: Subject AA8 T1


title: Subject AA8 T2


title: Subject AA9 T1


title: Subject AA10 T1


title: Subject AA7 T1


title: PH20211213_FR_8


title: MP20211206_FR_4

value: Control


title: MP20211206_FR_3


title: Subject AA7 T2


title: CP-A, control, rep3

value: control


title: Subject AA6 T2


title: CP-A, WGD, experiment 1, rep1


title: Subject AA4 T3


title: CP-A, WGD, experiment 1, rep2


title: CP-A, control, rep4


title: Subject AA6 T1


title: Subject AA4 T1


title: CP-A, control, rep2


title: PH20211213_FR_5


title: Subject AA6 T3


title: CP-A, control, rep1


title: Subject AA5 T1


title: PH20211213_FR_7


title: Subject AA1 T1


title: Subject AA4 T2


title: Subject AA2 T3


title: RPE TP53-/-, 20w pWGD, tumour 3, rep2

source_name: retinal epithelium

value: retinal epithelium

value: hTERT RPE-1

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 20w pWGD T3, in vivo


title: PH20211213_FR_11


title: Subject AA3 T3

value: Influenza Patients from Athens


title: Subject UMR 26

value: Influenza Patients from Marburg


title: PH20211213_FR_9


title: Subject AA3 T2


title: Subject AA3 T1


title: RPE TP53-/-, 20w pWGD, tumour 3, rep1


title: Subject AA2 T1


title: RPE TP53-/-, 20w pWGD, tumour 2, rep2

value: 20w pWGD T2, in vivo


title: Subject UMR 23


title: Subject UMR 20


title: PH20211213_FR_6


title: Subject UMR 25


title: Mixed species - 80K rpcc saturation curve comparison

description:
JI20220520_FR_5
Species mixing experiment

data_processing:
The samples are downsampled using seqtk, aligned to a combined human (GRCh38.p13) + mouse (GRCm38.p6) transcriptome index with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13 + GRCm38.p6
Supplementary files format and content: Filtered matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, with 2 per sample.


title: PH20211213_FR_4


title: Subject UMR 24


title: RPE TP53-/-, 20w pWGD, tumour 2, rep1


title: Subject UMR 22


title: Subject UMR 21


title: Subject UMR 16


title: Subject UMR 15


title: RPE TP53-/-, 20w pWGD, tumour 1, rep2

value: 20w pWGD T1, in vivo


title: Mixed species - 53K rpcc violin plot comparison

description:
JI20220718_FR_2
Species mixing experiment


title: Subject UMR 14


title: Subject UMR 12


title: RPE TP53-/-, WGD, nocodazole+DCB, experiment 1, rep2

value: immortalized retinal epithelial cells

value: WGD (nocodazole +DCB)


title: Subject UMR 19


title: Subject UMR 10


title: Prototype Sample PAP (2)

tag: disease

value: Prototype Autoimmune Disease Sample


title: Prototype Sample AMI


title: RPE TP53-/-, 20w pWGD, tumour 1, rep1


title: Mixed species

description: Species mixing experiment

data_processing:
The sample is aligned to a combined human (GRCh38.p13) + mouse (GRCm38.p6) transcriptome index with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13 + GRCm38.p6
Supplementary files format and content: Filterered matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, with 2 per sample.

source_name: HEK/3T3 cells


title: Subject UMR 9


title: RPE TP53-/-, WGD, nocodazole+DCB, experiment 2, rep2


title: MP20211206_FR_5


title: Subject UMR 17


title: Subject UMR 8


title: RPE TP53-/-, WGD, nocodazole+DCB, experiment 2, rep1


title: Prototype Sample PAP (1)


title: RPE TP53-/-, WGD, nocodazole+DCB , experiment 1, rep1


title: RPE TP53-/-, control, rep2


title: Subject UMR 18


title: Subject UMR 7


title: 24h PMA-treated_replicate 4

city: Boston

first: Srimoyee

last: Mukherjee

state: MA

address: 150 Harrison Ave., Jaharis Bldg., Room #401A

department: Department of Developmental, Molecular & Chemical Biology

institute: Tufts University

data_processing:
Raw data obtained from the sequencing reaction was pre-processed using DPAC which includes a fastp and cutadapt trimming steps to remove sequencing adaptors and poly(A)-tails (Routh, G3, 2017)
Processed Data were aligned to hg19 using HISAT2 (Kim et al, Nature Methods, 2015)
Differential gene expression analysis was performed using DESeq2 (Love et al, Genome Biology 2014)
Alternative polyadenylation analysis was performed using DPAC (Routh, G3, 2019)
Genome_build: hg19

source_name: Blood

growth_protocol: U937 cells were maintained in RPMI 1640 medium supplemented with 2 mM L-glutamine and 10% heat-inactivated fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA extraction was carried out on 5x106 cells treated with PMA for 6 and 24 hours using TRIzol according to manufacturer’s protocol.
Reverse-transcription with oligo-dT primer (unanchored) supplemented with small amounts of 3’-azido-nucleotides (AzVTPs) was done to initiate cDNA synthesis from within the poly(A) tail ensuring stochastic termination upstream of the poly(A) tail. Resulting 3'-azido-blocked cDNA molecules were purified, ‘click-ligated’ and amplified to generate a cDNA sequencing library. These libraries were pooled and sequenced using the manufacturer’s standard operating procedures on a NextSeq 550 obtaining 1×150 bp (130M) single-end reads.
Poly(A)-ClickSeq

treatment_protocol: Differentiation of U937 cell-lines into a macrophage-like phenotype was performed by treatment with 30 nM phorbol-12-myristate-13-acetate (PMA; Sigma-Aldrich, Castle Hill) for 6 and 24 hours.

value: U937 histiocytic lymphoma

tag: treatment

value: 24h PMA

value: Blood

value: Monocyte/macrophage


title: Prototype Sample APS-1 (2)


title: RPE TP53-/-, control, rep1


title: Prototype Sample APS-1 (1)


title: 24h PMA-treated_replicate 3


title: Subject UMR 2


title: Subject UMR 11


title: Subject UMR 3


title: Subject UMR 5


title: Subject UMR 4


title: Subject HC 33

value: Healthy Control


title: 24h PMA-treated_replicate 2


title: 24h PMA-treated_replicate 1


title: Prototype Thyroglobulin


title: Subject HC 31


title: 6h PMA-treated_replicate 3

value: 6h PMA


title: Prototype Scl-70


title: Subject UMR 1


title: Prototype Mitochontria


title: Prototype Ro/SSA


title: 6h PMA-treated_replicate 1


title: Subject HC 30


title: Subject UMR 6


title: Prototype RNP


title: Subject HC 29


title: Prototype Histone


title: Prototype La/SSB


title: Control_replicate 4

value: control


title: Subject HC 28


title: Prototype Centromere


title: Control_replicate 3


title: Subject HC 27


title: Control_replicate 2


title: Subject HC 32


title: Subject SU166

value: ICU Patient from Stanford


title: Subject SU165


title: Subject HC 26


title: Subject SU164


title: Subject SU163


title: Control_replicate 1


title: Subject SU162


title: Subject SU167


title: Subject SU160


title: Subject HC 25


title: Subject SU158


title: Subject SU161


title: Subject SU159


title: Subject HC 24


title: Subject HC 23


title: Subject UMR 45

value: COVID-19 Negative Patient from Marburg


title: P6_867_C862

city: Toulouse

first: Anne

last: Bouloumie

address: 1 avenue du Pr Jean Poulhès

country: France

institute: Inserm

data_processing:
Raw read QC
First and last 10 bases were trimmed and mapped Reference Human.B38 with GeneModel RefGene20170606
Count data generated using GeneModel RefGene20170606
Normalization by DESeq using count data (Gene IDs having at least 10 count or reads in any three samples were kept).
Log2 conversion (0   replaced with 1) using DESeq data (Log2DESeq)
Assembly: Human.B38
Supplementary files format and content: Log2 DESeq

source_name: subcutaneous adipose tissue

growth_protocol: Progenitor cells were immuno-selected from human subcutaneous adipose tissue stromal vascular fraction after collagenase digestion. Cells were seeded at low density (5 000 cells/cm²), then at 80 % confluency, cells were trypsinated and seeded at low density for next passage until passage 6

extract_protocol:
Progenitor cells were lysed in RNAprotect and frozen.
For AmpliSeq transcriptome sequencing library construction,  AmpliSeq™ Library PLUS, AmpliSeq Transcriptome Human Gene Expression Panel and AmpliSeq CD indexes SetA kits were purchased from Illumina and sequencing libraries were constructed as described in AmpliSeq for Illumina Transcriptome Human Gene Expression Panel reference guide (Illumina).

treatment_protocol: P1 progenitor cells were treated by hydrogen peroxide (H2O2) 0.1 µmol/L during 24h

value: subcutaneous adipose tissue

value: primary cells

value: progenitor cells

tag: passage

tag: subject status

value: overweight woman

tag: gender

value: female


title: Subject SU156


title: Subject SU157


title: Subject SU153


title: P1_867 _H2O2_C859


title: Subject SU155


title: P1_813_H2O2_C858


title: P6_813_C861


title: Subject SU152


title: Subject SU150


title: Subject SU151


title: P1_812_H2O2_C857


title: Subject SU149


title: P1_867_C856


title: Subject SU146


title: Subject SU147


title: P1_813_C855


title: P1_812_C854


title: Subject UMR 44


title: Subject SU154


title: Subject SU145


title: Subject UMR 39


title: Subject SU144


title: Subject SU143


title: Subject SU142


title: Subject SU148


title: RPE TP53, control, cell 43

data_processing:
For each cell, paired-end R1 and R2 FASTQ files were separately aligned to the hg19 reference genome using bwa mem version 0.7.17. The scHiCExplorer pipeline was used to generate Hi-C contact maps in Cooler format. Quality control of scHi-C interactions was performed as previously reported. Specifically, since it was previously reported that fend-pairs covered by only one read are likely results of alignment or pairing errors of the sequencing machine, they were removed from the analysis. Cells for which the percentage of singleton interactions was above 75% were also removed from the analysis. Additionally, cells with less than 100000 unfiltered interactions were removed. Finally, for the remaining fend-pairs, which were supported by at least two duplicated reads, duplicates were removed. One cell was removed from the analysis because of the absence of inter-chromosomal interactions involving chromosome 1, indicating technical issues during the library preparation.
Assembly: hg19
Supplementary files format and content: metadata.xlsx contains info for each single-cell
Supplementary files format and content: schic_matrices_binsize_100000.scool contains binned Hi-C matrices for each cell, at 1Mb resolution, in .scool format

growth_protocol: RPE TP53-/- cells were grown in DMEM/F-12, GlutaMAX™ (catalogue no. 10565018) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, catalogue no. 10270106) and 1% Antibiotic-Antimycotic (Thermo Fisher Scientific, catalogue no. 15240062).

extract_protocol:
1-2 million cells were collected and fixed with 2% formaldehyde (Thermo Fisher Scientific, catalogue no. 11483217). The reaction was quenched with 200mM glycine (VWR, catalogue no. 101194M) final concentration, cells were washed with PBS (Thermo Fisher Scientific, catalogue no. 10010023) and lysed in a solution containing 10mM Tris-HCl pH 8.0 (Thermo Fisher Scientific, catalogue no. 15568025), 10mM NaCl (Sigma-Aldrich, catalogue no. S6546), 0.2% Igepal CA-630 (Sigma-Aldich, catalogue no. I8896), and 1x Proteinase inhibitor cocktail (Roche, catalogue no. 11697498001) at 4°C for 30 minutes. Resulting nuclei were re-suspended in 1X NEB3.1 buffer (New England Biolabs, catalogue no. B7203S). Nuclei suspension was incubated with 0.11% SDS (Carl Roth, catalogue no. CN30) final concentration for 10 minutes at 65°C. Reaction was quenched with 1% Triton-X100 (AppliChem, catalogue no. A1388) and nuclei were digested with 100U MboI restriction enzyme (New England Biolabs, catalogue no. R0147) at 37°C overnight. Restriction enzyme was inactivated according to manufacturer’s specifications and digested nuclei were washed and re-suspended in 1x NEB3.1. Digested ends were then marked with biotin via incubation in 0.03mM biotin-14-dATP (Thermo Fisher Scientific, catalogue no. 19524016), 0.03mM dCTP, 0.03mM dGTP, 0.03mM dTTP (Promega, catalogue no. U1420) and 50U Klenow DNA polymerase I (New England Biolabs, catalogue no. M0210M) for 4 hours at room temperature. Next, in-nucleus proximity ligation was done with 50U T4 DNA Ligase, 1x T4 DNA ligase buffer, 5% PEG, 1% Triton-X100, 0.1mg/ml BSA at 16°C overnight, with light mixing. Only pools of nuclei with at least 75% of the population showing integral nuclear membrane were considered for further processing. Nuclei were strained multiple times through a 10µm Nylon Net Filter (Merck-Millipore, catalogue no. NY1009000). Sample preparation was done with DispenKit (SEED Bioscience) and single nuclei were dispensed in skirted Eppendorf twin.tec® PCR Plate 96-wells (Eppendorf, catalogue no. 0030128648) containing 50µl of NEBuffer 3.1 (New England Biolabs, catalogue no. B7203S) using the single cell isolator DispenCell (SEED Biosciences) following manufacturer’s instructions. A nucleus passing through the tip of the DispenCell leaves an electrical impedance change mark, which is proportional to the volume of the nucleus. For RPE TP53-/- cells, a minimum impedance change of 75Ω was detected for the diploid nucleus and 200Ω for the tetraploid nucleus. A lower impedance change was associated with debris or unsuccessful induction of genome doubling in the case of the WGD condition and thus such nuclei were not considered for further processing. To avoid processing of nuclei aggregates, dispensed single nuclei associated with a threshold higher than 400Ω and 800Ω for diploid and tetraploid nuclei, respectively, were also discarded. These ranges were set from quality metrics of a test scHi-C batch. Specifically, an unreasonable number of unique interactions of each fragment end (e.g. > 2 for diploid loci) would indicate a nuclei aggregate rather than a single nucleus. Following dispensing, the single nuclei were de-crosslinked by incubation at 65°C overnight.
Each selected nucleus was mixed with 25µl Dynabeads™ MyOne™ Streptavidin C1 and transferred to a 1.5 ml tube and incubated at room temperature for one hour on a rotating wheel. The bead-bound fragments were digested with 10U of AluI restriction enzyme (New England Biolabs, catalogue no. R0137) in 1x rCutSmart™ Buffer (New England Biolabs, catalogue no. B6004) at 37°C for two hours. PolyA tail was added by incubating the DNA sample in 1X NEBuffer™ 2 (New Enlgand Biolabs, catalogue no. B7002S) with 0.5mM dATP and 25U Klenow Fragment (3'→5' exonuclease) (New England Biolabs, catalogue no. M0212) at 37°C for 30 minutes. DNA fragment ends were then ligated to Illumina TruSeq unique dual indexes (Integrated DNA Technologies) in 1X T4 Ligation buffer with 5% PEG and 15U T4 DNA Ligase overnight at 16°C. Lastly, libraries were PCR amplified using Illumina forward (AATGATACGGCGACCACCGAGATCTACAC) and reverse (CAAGCAGAAGACGGCATACGAGAT) primers and KAPA HiFi HotStart ReadyMix (Roche, catalogue no. KK2602), for 27-30 cycles. Libraries were cleaned with AMPure XP beads, and then ran on a 2% agarose gel at 100V for 50-60 minutes. Successful libraries presented a 300-700bp smear, which was cut from the gel. DNA purification from the agarose was performed using NucleoSpin Gel and PCR Clean‑up (Macherey-Nagel, catalogue no. 740609) following manufacturer’s instructions. An additional AMPure XP bead size selection was generally necessary to remove any primer dimer contamination.

treatment_protocol: For WGD condition, RPE TP53-/- cells were incubated for 24 hours with 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 hours to 4uM dihydrocytochalasin B (Cayman Chemical, catalogue no. 20845). The treatment was removed and cells were allowed to recover for 48 hours.

value: retinal epithelium

value: hTERT RPE-1

value: immortalized retinal epithelial cells


title: RPE TP53, control, cell 42


title: Subject UMR 38


title: Subject UMR 42


title: Subject UMR 37


title: Subject SU140


title: Subject SU138


title: Subject SU141


title: Subject UMR 40


title: Subject UMR 41


title: Subject UMR 36


title: RPE TP53, control, cell 41


title: Subject SU139


title: Subject SU135


title: Subject SU136


title: Subject UMR 43


title: Subject SU137


title: Subject SU134


title: Subject UMR 34


title: RPE TP53, control, cell 40


title: RPE TP53, control, cell 39


title: Subject SU132


title: Subject SU133


title: Subject UMR 33


title: Subject SU130


title: Subject SU131


title: RPE TP53, WGD, cell 29

value: WGD


title: Subject UMR 32


title: Subject UMR 35


title: RPE TP53, WGD, cell 28


title: RPE TP53, WGD, cell 27


title: Subject UMR 31


title: Subject SU128


title: Subject SU127


title: Subject SU125


title: Subject SU129


title: Subject UMR 29


title: RPE TP53, WGD, cell 30


title: Subject SU123


title: Subject SU126


title: RPE TP53, control, cell 38


title: RPE TP53, control, cell 37


title: Subject UMR 28


title: Subject SU122


title: Subject UMR 27


title: RPE TP53, control, cell 36


title: Subject SU119


title: Subject UGMLC 17

value: ARDS Patient from Giessen


title: RPE TP53, control, cell 35


title: Subject UMR 30


title: Subject SU121


title: Subject SU120


title: Subject SU124


title: RPE TP53, control, cell 34


title: Subject SU117


title: Subject SU116


title: Subject SU115


title: Subject SU114


title: Subject SU118


title: RPE TP53, control, cell 33


title: RPE TP53, control, cell 32


title: Subject SU113


title: Subject SU112


title: Subject UGMLC 14


title: Subject UGMLC 15


title: Subject UGMLC 16


title: Subject SU110


title: Subject SU109


title: Subject UGMLC 12


title: Subject SU108


title: Subject SU111


title: Subject SU106


title: RPE TP53, control, cell 29


title: RPE TP53, control, cell 28


title: Subject SU104


title: Subject SU103


title: Subject SU105


title: Subject UGMLC 10


title: RPE TP53, control, cell 27


title: RPE TP53, control, cell 31


title: Subject UGMLC 13


title: Subject SU101


title: Subject SU100


title: Subject UGMLC 9


title: RPE TP53, control, cell 26


title: RPE TP53, control, cell 30


title: RPE TP53, control, cell 25


title: Subject SU099


title: RPE TP53, control, cell 24


title: Subject SU107


title: Subject UGMLC 7


title: Subject SU097


title: Subject SU098


title: Subject UGMLC 6


title: Subject UGMLC 11


title: Subject UGMLC 5


title: Subject SU102


title: Subject SU096


title: Subject SU095


title: RPE TP53, control, cell 23


title: RPE TP53, control, cell 22


title: Subject UGMLC 8


title: Subject UGMLC 4


title: Subject UGMLC 3


title: Subject UGMLC 2


title: Subject UGMLC 1


title: RPE TP53, control, cell 20


title: RPE TP53, control, cell 21


title: RPE TP53, control, cell 19


title: RPE TP53, control, cell 18


title: Subject AA40 T3

value: Influenza Patient from Athens


title: P6_812_C860


title: Subject AA40 T2


title: Subject SU092


title: Subject SU093


title: Subject SU091


title: RPE TP53, control, cell 16


title: RPE TP53, control, cell 17


title: Subject AA40 T1


title: Subject SU086


title: Subject SU088


title: Subject SU087


title: Subject SU085


title: Subject SU084


title: Subject SU082


title: Subject AA39 T3


title: RPE TP53, control, cell 15


title: Subject SU083


title: Subject SU081


title: Subject SU077


title: Subject SU090


title: Subject SU080


title: Subject SU089


title: Subject SU094


title: Subject SU078


title: Subject AA39 T2


title: Subject SU075


title: Subject SU074


title: Subject SU079


title: Subject SU076


title: RPE TP53, WGD, cell 25


title: RPE TP53, WGD, cell 26


title: Subject SU071


title: Subject SU073


title: Subject SU072


title: RPE TP53, control, cell 14


title: Subject SU069


title: Subject SU070


title: Subject SU068


title: Subject AA39 T1


title: RPE TP53, WGD, cell 23


title: Subject SU067


title: RPE TP53, WGD, cell 24


title: Subject SU066


title: Subject AA38 T2


title: RPE TP53, WGD, cell 22


title: Subject SU065


title: RPE TP53, WGD, cell 21


title: Subject AA37 T3


title: Subject SU063


title: Subject SU064


title: Subject AA37 T1


title: Subject AA38 T3


title: Subject SU061


title: Subject SU062


title: RPE TP53, WGD, cell 20


title: Subject AA38 T1


title: Subject AA36 T3


title: Subject AA37 T2


title: Subject AA36 T2


title: RPE TP53, WGD, cell 18


title: Subject SU058


title: RPE TP53, WGD, cell 17


title: Subject SU060


title: Subject SU059


title: RPE TP53, WGD, cell 16


title: Subject SU057


title: RPE TP53, WGD, cell 15


title: Subject SU056


title: Subject SU053


title: Subject SU054


title: RPE TP53, WGD, cell 14


title: Subject SU052


title: Subject SU050


title: Subject AA35 T3


title: Subject AA36 T1


title: Subject SU049


title: RPE TP53, WGD, cell 13


title: RPE TP53, WGD, cell 19


title: Subject SU051


title: Subject AA35 T2


title: Subject AA35 T1


title: Subject SU055


title: Subject SU042


title: Subject SU041


title: Subject AA34 T1


title: Subject SU040


title: Subject SU038


title: Subject SU039


title: Subject SU037


title: Subject SU036


title: Subject SU044


title: RPE TP53, WGD, cell 8


title: Subject SU048


title: Subject SU047


title: Subject SU045


title: RPE TP53, WGD, cell 7


title: RPE TP53, control, cell 12


title: RPE TP53, WGD, cell 12


title: RPE TP53, WGD, cell 9


title: Subject SU046


title: RPE TP53, control, cell 13


title: RPE TP53, WGD, cell 10


title: Subject SU033


title: Subject SU031


title: Subject SU030


title: Subject AA29 T3


title: Subject SU035


title: Subject SU029


title: Subject SU032


title: RPE TP53, WGD, cell 11


title: Subject AA33 T2


title: Subject AA32 T1


title: Subject SU034


title: Subject SU043


title: Subject AA32 T3


title: Subject AA32 T2


title: Subject AA31 T2


title: Subject AA33 T1


title: Subject AA31 T1


title: Subject AA30 T1


title: RPE TP53, WGD, cell 6


title: RPE TP53, WGD, cell 5


title: RPE TP53, WGD, cell 4


title: Subject AA29 T2


title: RPE TP53, WGD, cell 3


title: Subject SU027


title: Subject SU026


title: Subject SU024


title: Subject AA29 T1


title: Subject SU025


title: Subject AA28 T1


title: Subject SU023


title: RPE TP53, WGD, cell 2


title: Subject SU022


title: Subject AA27 T2


title: Subject SU021


title: Subject SU028


title: Subject SU020


title: Subject AA27 T1


title: RPE TP53, WGD, cell 1


title: RPE TP53, control, cell 11


title: RPE TP53, control, cell 10


title: Subject SU018


title: Subject SU019


title: Subject AA26 T2


title: Subject AA26 T1


title: Subject AA25 T1


title: Subject SU017


title: Subject SU016


title: Subject SU015


title: Subject SU014


title: RPE TP53, control, cell 9


title: RPE TP53, control, cell 8


title: Subject SU013


title: Subject AA24 T1


title: RPE TP53, control, cell 6


title: RPE TP53, control, cell 7


title: Subject AA23 T3


title: Subject AA23 T1


title: Subject SU011


title: Subject SU010


title: Subject SU012


title: Subject SU009


title: Subject SU006


title: Subject SU005


title: Subject SU007


title: RPE TP53, control, cell 5


title: Subject AA22 T2


title: Subject SU004


title: RPE TP53, control, cell 4


title: Subject SU003


title: Subject AA21 T3


title: Subject AA22 T1


title: Subject SU001


title: RPE TP53, control, cell 3


title: RPE TP53, control, cell 2


title: Subject SU002


title: Subject SU008


title: Subject HC 22


title: Subject HC 21


title: RPE TP53, control, cell 1


title: Subject HC 20


title: HiC Skate stage 31 pectoral fin posterior region replicate 2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Reads from technical replicates were pooled and aligned using BWA Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events  Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Assembly: custom assembly (uploaded in the same Bioproject)
Supplementary files format and content: contact matrices in hic format

organism: Leucoraja erinaceus

source_name: Pectoral Posterior fin

extract_protocol:
Embryonic skate fin buds were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for fragments between 150-600 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
End-repair, A-tailing and ligation of indexing adapters followed standard procedure for Illumina library preparations for paired-end sequencing. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB).

tag: developmental timing

value: stage 31

value: Control


title: HiC Skate stage 31 pectoral fin posterior region replicate 1


title: CP-A TP53-/- C3, control, H3K9me3

description: LambutaNanni2023_CPA-TP53-Clone3_Ctrl_H3K9me3

data_processing:
Fastq files were processed using the nfcore/chipseq pipeline v1.2.2 (https://nf-co.re/chipseq/) with default parameters, aligning the reads to the hg19 genome. For each sample, the fold-change against the input experiment was then computed using the bamCompare command from the deepTools package version 3.5.1 setting –scaleFactorsMethod readCount, --extendReads,  –-operation ratio, and --binSize 100).
Assembly: hg19
Supplementary files format and content: BigWig files contain input-normalized ChIP-seq signals for each experiment

growth_protocol: RPE TP53-/- cells were grown in DMEM/F-12, GlutaMAX™ (catalogue no. 10565018) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, catalogue no. 10270106) and 1% Antibiotic-Antimycotic (Thermo Fisher Scientific, catalogue no. 15240062). CP-A TP53-/- cells were grown in MCDB-153 medium (Sigma-Aldrich, catalogue no. M7403) supplemented with 20mg/L adenine (Sigma-Aldrich, catalogue no. A2786), 400µg/L hydrocortisone (Sigma-Aldrich, catalogue no. H0135), 50mg/L bovine pituitary extract (Thermo Fisher Scientific, catalogue no. 13028014), 1x Insulin-transferrin-sodium selenite media supplement (Sigma-Aldrich, catalogue no. I1884), 8.4 µg/L cholera toxin (Sigma-Aldrich, catalogue no. C8052), 4mM glutamine (Sigma-Aldrich, catalogue no. G7513), 5% foetal bovine serum, and 1% Antibiotic-Antimycotic.

extract_protocol:
Chromatin immunoprecipitation was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology, catalogue no. 91820S) following the manufacturer’s protocol. Chromatin immunoprecipitation was obtained by incubating chromatin at 4°C overnight with either of the following antibodies, at the recommended dilutions: anti-Acetyl-Histone H3 (Lys27) (Cell Signaling Technology, catalogue no. 8173), anti-Tri-Methyl-Histone H3 (Lys9) (Cell Signaling Technology, catalogue no. 13969), anti-CTCF (Active Motif, catalogue no. 61311), anti-Tri-Methyl-Histone H3 (Lys4) (Cell Signaling Technology, catalogue no. 9751), Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology, catalogue no. 9733).
Library preparation for sequencing from the chromatin immunoprecipitated DNA was performed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs, catalogue no. E7645) following manufacturer’s protocol.

treatment_protocol: For WGD in RPE TP53-/-, cells were incubated for 24 hours with 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 hours to 4uM dihydrocytochalasin B (Cayman Chemical, catalogue no. 20845) and then were allowed to recover for 48 hours. Long-term post-WGD, cells were then kept in culture for 20 weeks. Control and 20w pWGD cells were injected in NSG mice. After 6 weeks, only 20w pWGD injected mice formed tumours in vivo (T1, T2, T3), which were collected and dissociated into single cells with human Tumour Dissociation Kit (Miltenyi Biotec, catalogue no. 130-095-929) and Mouse Cell Depletion Kit (Miltenyi Biotec, catalogue no. 130-104-694) following manufacturer’s protocols. For WGD in CP-A TP53-/-, 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) was added to the growth medium and cells were incubated for 72h.

value: esophageal epithelium

value: immortalized non-dysplastic metaplasia (Barrett's oesophagus) epithelial cells

tag: chip antibody


title: Subject HC 19

value: Healthy Control


title: Subject HC 18


title: Subject AA20 T1


title: Subject HC 17


title: HiC Skate stage 31 pectoral fin anterior region replicate 2

source_name: Pectoral Anterior fin


title: CP-A TP53-/- C3, WGD, CTCF

description: LambutaNanni2023_CPA-TP53-Clone3_WGD_CTCF

value: CTCF


title: Subject AA20 T2


title: Subject HC 16


title: HiC Skate st30 Pectoral fin replicate 2d

data_processing:
Reads from technical replicates were pooled and aligned using BWA Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events  Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Genome_build: custom assembly (uploaded in the same Bioproject)
Supplementary_files_format_and_content: hic format

source_name: Pectoral fin

growth_protocol: Embryos were kept at 15 °C in reconstituted Instant Ocean (Aquarium systems) with 12 h light–dark cycles.

value: stage 30


title: CP-A TP53-/- C3, control, CTCF

description: LambutaNanni2023_CPA-TP53-Clone3_Ctrl_CTCF

value: control


title: Subject AA19 T2


title: Subject AA21 T2


title: Subject HC 7


title: Subject AA21 T1


title: CP-A TP53-/- C3, control, input

description: LambutaNanni2023_CPA-TP53-Clone3_Ctrl_input


title: Subject AA19 T1


title: Subject HC 6


title: HiC Skate st30 Pectoral fin replicate 2b


title: Subject AA18 T1


title: HiC Skate st30 Pectoral fin replicate 2a


title: CP-A TP53-/- C3, WGD, H3K9me3

description: LambutaNanni2023_CPA-TP53-Clone3_WGD_H3K9me3


title: RPE TP53-/-, WGD, CTCF, mouse spike-in


title: HiC Skate stage 31 pectoral fin anterior region replicate 1


title: Subject AA17 T1


title: HiC Skate st30 Pectoral fin replicate 1


title: Subject AA19 T3


title: Subject HC 4


title: Subject HC 5


title: RPE TP53-/-, control, CTCF, mouse spike-in

description: LambutaNanni2023_RPE_TP53_Ctrl_run2_CTCF


title: RPE TP53-/-, WGD, input, mouse spike-in

description: LambutaNanni2023_RPE_TP53_WGD_run2_input


title: Subject AA16 T3


title: HiC Skate st30 Pectoral fin replicate 2c


title: HiChIP H3K4me3 Skate st31 Pectoral Posterior fin replicate 2

data_processing:
Library strategy: HiChIP
Reads from biological replicates were pooled and aligned using GEM  Ligation events were detected using TADbit and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Genome_build: custom assembly (uploaded in the same Bioproject)
Supplementary_files_format_and_content: hic format

source_name: Pectoral posterior fin

extract_protocol:
Either anterior or posterior portions of skate embryonic find buds were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lysed and extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation.
Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

tag: antibody


title: Subject AA16 T2


title: Subject HC 3


title: Subject AA16 T1


title: RPE TP53-/-, control, input, mouse spike-in

description: LambutaNanni2023_RPE_TP53_Ctrl_run2_input


title: CP-A TP53-/- C3, WGD, input

description: LambutaNanni2023_CPA-TP53-Clone3_WGD_input


title: HiChIP H3K4me3 Skate st31 Pectoral Anterior fin replicate 1b

source_name: Pectoral anterior fin


title: RPE TP53-/-, WGD, H3K9me3


title: Subject HC 1


title: HiChIP H3K4me3 Skate st31 Pectoral Anterior fin replicate 1a


title: RPE TP53-/-, WGD, input


title: Subject AA15 T3


title: RNAseq Skate st31 Pelvic fin replicate 2

data_processing:
Alignment with STAR
Filtering of duplicated and not valid reads
Read count per gene with htseq-count
Differential gene expression analysis with DESeq2
Genome_build: custom assembly (uploaded in the same Bioproject)
Supplementary_files_format_and_content: bigWig format for data visualization

source_name: Pelvic fin

extract_protocol:
total RNA was extracted from frozen samples by using the QIAGEN RNeasy Plus Micro Kit
polyA-selected standard Illumina libraries


title: RPE TP53-/-, control, input


title: C9ORF72 ALS iMNs treated with scrambled siRNA replicate 3

city: Los Angeles

first: Justin

last: Ichida

address: 1425 San Pablo Street, BCC 209

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

data_processing:
Reads were aligned to the hg38 transcriptome using aligner STAR (v.2.7.8).
A gene count table was obtained using Partek E/M with Partek® Flow® software, v10.0
Differential expression analysis was performed using DESeq2 (v.1.18.1).
Pathway enirchment analysis was performed using Ingenuity Pathway Analysis (Qiagen)
Computations were performed on the High Performing-Computing Cluster supported by the University of Southern California.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count values for each sample

source_name: neural

growth_protocol: Glia-free induced motor neurons were cultured in N3 medium.

extract_protocol:
RNA was extracted using QIAGEN RNeasy Kits according to the manufacturer's instructions.
3'-Digital Gene Expression RNAseq Library Kit (3’-DGE)
3' RNA-seq libraries were generated using the 3'-Digital Gene Expression RNAseq Library Kit at Novogene Ltd, according to the manufacturers’ directions. Libraries were sequenced at the Novogene on a Illumina NovaSeq 6000 sequencer. A total of 20 million to 30 million 150-bp, paired-end reads were obtained for samples.

treatment_protocol: A lentiviral expression of NGN2, ISL1, LHX3 drives the conversion of induced motor neurons, 3 nM siRNA targetting SYF2 (or a scrambled siRNA) control was added with RNAiMAX.

value: neural

value: induced neurons

value: motor neurons

value: scrambled siRNA


title: C9ORF72 isogenic control iMNs treated with SYF2 siRNA-1 replicate 3

value: C9ORF72 isogenic

value: SYF2 siRNA-1


title: C9ORF72 ALS iMNs treated with SYF2 siRNA-1 replicate 3


title: Subject AA15 T1


title: RPE TP53-/-, control, H3K9me3

value: retinal epithelium

value: hTERT RPE-1

value: immortalized retinal epithelial cells


title: RNAseq Skate st31 Pectoral fin replicate 2

value: stage 31


title: Subject AA14 T3

value: Influenza Patient from Athens


title: Subject HC 2


title: CP-A TP53-/-, clone 3, spontaneous high ploidy, rep2

description: LambutaNanni2023_CPA_TP53_SpontaneousWGD_c3_2

value: esophageal epithelium

value: spontaneous high ploidy


title: HiChIP H3K4me3 Skate st31 Pectoral Posterior fin replicate 1

value: Control


title: RNAseq Skate st31 Pectoral fin replicate 1


title: RPE TP53-/-, control, H3K27me3


title: Subject AA14 T1


title: CP-A TP53-/-, clone 3, spontaneous high ploidy, rep1

description: LambutaNanni2023_CPA_TP53_SpontaneousWGD_c3_1

value: immortalized non-dysplastic metaplasia (Barrett's oesophagus) epithelial cells


title: Subject AA14 T2


title: RPE TP53-/-, control, H3K27ac


title: RPE TP53-/-, WGD, CDK1i+DCB, rep2

value: WGD (CDK1i + DCB)


title: ATACseq Skate st31 Pelvic fin replicate 4

data_processing:
Alignment with Bowtie2
Filtering of duplicated and not valid reads
Differential accessibility analysis, PCA and clustering with DESeq2
Genome_build: custom assembly (uploaded in the same Bioproject)
Supplementary_files_format_and_content: bigWig format for data visualization

extract_protocol:
Embryos were centrifugated at 13000 rpm for 1 min, and then seawater wasa carefully removed. Cells were lysed by gently pipetting in cold lysis buffer
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109


title: RPE TP53-/-, 20w pWGD, tumour 3, input

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 20w pWGD T3, in vivo


title: Subject AA15 T2


title: ATACseq Skate st31 Pelvic fin replicate 3


title: RPE TP53-/-, WGD, CDK1i+DCB, rep1


title: Subject AA13 T2


title: Subject AA13 T3


title: ATACseq Skate st31 Pelvic fin replicate 2


title: RNAseq Skate st31 Pelvic fin replicate 1


title: CP-A TP53-/-, clone 3, 6w pWGD, colony 2, rep2

description: LambutaNanni2023_CPA_TP53_6wColony2_c3_2

value: immortalized non-dysplastic metaplasia (Barrett's oesophagus) epithelial cells grown in soft agar

value: 6w pWGD C2, in vitro


title: Subject AA13 T1


title: RPE TP53-/-, 20w pWGD, tumour 3, H3K9me3

description: LambutaNanni2023_RPE_TP53_20w0T3_H3K9me3


title: CP-A TP53-/-, clone 3, 6w pWGD, colony 2, rep1

description: LambutaNanni2023_CPA_TP53_6wColony2_c3_1


title: RPE TP53-/-, 20w pWGD, tumour 3, H3K4me3

description: LambutaNanni2023_RPE_TP53_20w0T3_H3K4me3


title: RPE TP53-/-, control, H3K4me3

value: control


title: Subject AA12 T2

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.


title: ATACseq Skate st31 Pectoral Posterior fin replicate 2


title: CP-A TP53-/-, clone 3, 6w pWGD, colony 1, rep2

description: LambutaNanni2023_CPA_TP53_6wColony1_c3_2

value: 6w pWGD C1, in vitro


title: ATACseq Skate st31 Pelvic fin replicate 1


title: ATACseq Skate st31 Pectoral Posterior fin replicate 1


title: RPE TP53-/-, 20w pWGD, tumour 3, H3K27me3

description: LambutaNanni2023_RPE_TP53_20w0T3_H3K27me3


title: CP-A TP53-/-, clone 3, 6w pWGD, colony 1, rep1

description: LambutaNanni2023_CPA_TP53_6wColony1_c3_1


title: CP-A TP53-/-, clone 19, 20w pWGD, colony 2, rep2

description: LambutaNanni2023_CPA_TP53_20wColony3_c19_2

value: 20w pWGD C2, in vitro


title: Subject AA11 T2


title: RPE TP53-/-, 20w pWGD, tumour 3, CTCF

value: retinal epithelium

value: CTCF


title: Subject AA11 T1


title: CP-A TP53-/-, clone 19, 20w pWGD, colony 2, rep1

description: LambutaNanni2023_CPA_TP53_20wColony3_c19_1


title: ATACseq Skate st31 Pectoral Anterior fin replicate 2


title: RPE TP53-/-, 20w pWGD, tumour 2, input

value: hTERT RPE-1

value: 20w pWGD T2, in vivo


title: Subject AA10 T2

value: Influenza Patient from Athens


title: LM3_siNC_rep3

city: Guangzhou

first: Li

last: Peng

address: No. 107 Yanjiang West Road

country: China

institute: Sun Yat-Sen Memorial Hospital

data_processing:
The RNA-seq data was filtered with SOAPnuke, and clean reads were obtained.
The clean data were mapped to reference genome using HISAT2, and were aligned to reference coding gene set by Bowtie2.
Then, expression of genes was calculated using by RESM.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: HCC cell lines

extract_protocol:
Total RNA from HCC cells were extracted using Trizol method.
Total RNA was extracted from the cells using Trizol (Invitrogen, USA), qualified and quantified using a Nano Drop and Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, USA). Afterwards, oligo(dT)-attached magnetic beads were purified mRNA. First-strand cDNA and second-strand cDNA were respectively synthesized. The single strand circle DNA was formatted as the final library, and then was subjected to sequencing on BGIseq500 platform. The library preparation and sequencing were conducted by BGI Genomics (Shenzhen, China).

treatment_protocol: HCC cells with the treatment of siFASRL or siNC.

value: HCC cell lines

value: liver

value: siNC


title: RPE TP53-/-, 20w pWGD, tumour 2, H3K9me3

description: LambutaNanni2023_RPE_TP53_20w0T2_H3K9me3


title: RPE TP53-/-, 20w pWGD, tumour 2, H3K4me3

description: LambutaNanni2023_RPE_TP53_20w0T2_H3K4me3


title: Subject AA10 T1


title: LM3_siNC_rep2


title: CP-A TP53-/-, clone 19, 20w pWGD, colony 1, rep1

description: LambutaNanni2023_CPA_TP53_20wColony6_c19_1

value: esophageal epithelium

value: 20w pWGD C1, in vitro


title: CP-A TP53-/-, clone 19, 20w pWGD, colony 1, rep2

description: LambutaNanni2023_CPA_TP53_20wColony6_c19_2


title: Subject AA12 T1


title: CP-A TP53-/-, clone 3, CDK4/6i, rep2

value: immortalized non-dysplastic metaplasia (Barrett's oesophagus) epithelial cells

value: WGD + CDK4/6i


title: LM3_siFASRL_rep3

value: siFASRL


title: RPE TP53-/-, 20w pWGD, tumour 3, H3K27ac

description: LambutaNanni2023_RPE_TP53_20w0T3_H3K27ac

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 20w pWGD T3, in vivo


title: Subject AA9 T2


title: CP-A TP53-/-, clone 3, CDK4/6i, rep1


title: RPE TP53-/-, 20w pWGD, tumour 2, H3K27ac

description: LambutaNanni2023_RPE_TP53_20w0T2_H3K27ac


title: RPE TP53-/-, 20w pWGD, tumour 2, H3K27me3

description: LambutaNanni2023_RPE_TP53_20w0T2_H3K27me3


title: Subject AA9 T3


title: Subject AA9 T1


title: LM3_siFASRL_rep2


title: ATACseq Skate st31 Pectoral Anterior fin replicate 1

value: stage 31

value: Control


title: LM3_siFASRL_rep1


title: RPE TP53-/-, CIN-only, rep2

value: retinal epithelium

value: immortalized retinal epithelial cells

value: CIN-only


title: RPE, control, rep2

value: hTERT RPE-1

value: WT

value: control


title: Subject AA8 T1

value: Influenza Patient from Athens


title: RPE TP53-/-, 20w pWGD, tumour 1, input

value: 20w pWGD T1, in vivo


title: Subject AA8 T2


title: RPE TP53-/-, 20w pWGD, tumour 2, CTCF

value: CTCF

value: 20w pWGD T2, in vivo


title: RPE TP53-/-, CIN-only, rep1


title: RPE TP53-/-, 20w pWGD, tumour 1, H3K9me3

description: LambutaNanni2023_RPE_TP53_20w0T1_H3K9me3


title: Subject AA7 T2


title: LM3_siNC_rep1

value: HCC cell lines

value: liver

value: siNC


title: HepG2_siNC_rep2


title: RPE, control, rep1


title: RPE TP53-/-, 20w pWGD, tumour 1, H3K4me3

description: LambutaNanni2023_RPE_TP53_20w0T1_H3K4me3

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice


title: Subject AA7 T1


title: HepG2_siFASRL_rep3

value: siFASRL


title: K562, WGD, rep4

source_name: bone marrow

value: bone marrow

value: chronic myelogenous leukemia lymphoblasts

value: WGD


title: RPE TP53-/-, 20w pWGD, tumour 1, H3K27ac

description: LambutaNanni2023_RPE_TP53_20w0T1_H3K27ac

value: retinal epithelium


title: HepG2_siNC_rep1


title: RPE TP53-/-, 20w pWGD, tumour 1, H3K27me3

description: LambutaNanni2023_RPE_TP53_20w0T1_H3K27me3


title: K562, WGD, rep3


title: K562, WGD, rep2


title: Subject AA6 T2

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.


title: HepG2_siFASRL_rep2


title: RPE TP53-/-, 20w pWGD, tumour 1, CTCF


title: HepG2_siNC_rep3


title: K562, WGD, rep1


title: HepG2_siFASRL_rep1


title: 22Rv1 cells, drug resistant, immunoprecipitation, rep4

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

institute: Thomas Jefferson University

data_processing:
Base-calling was performed onboard the NextSeq 500 using the integrated instrument computer.
FASTQ generation was performed in the Illumina BaseSpace cloud using bcl2fastq with default parameters.
Read alignment was performed using bwa mem with default parameters
samtools rmdup was used to filter duplicate reads
BigWig files were generated using DeepTools bamCoverage
Assembly: GRCh38
Supplementary files format and content: bigWig genome coverage

source_name: prostate

growth_protocol: Cells were grown in RPMI media supplemented with 10% FBS and antibiotics

extract_protocol:
Cells were crosslinked and DNA sheared and processed for ChIP sequencing acording to standard protocols
Library preparation was done using Swift’s Biosciences Accel-NGS 2S Plus Library Kits for Illumina platforms.  10 ng of DNA was used for library preparation and kit’s protocol was followed for a 200 base pair insert.  An additional two sided bead clean up was done after the PCR step using SPRI beads with the formula .6X, then using the supernatant, 1.2x.   The library was pooled to 1 nM and the sequenced on a NextSeq 500 using the standard loading protocol.

treatment_protocol: No treatments

value: prostate

value: prostate carcinoma epithelial cell

value: Precision AG10008; RRID:AB_2631058


title: 22Rv1 cells, drug resistant, immunoprecipitation, rep1


title: Subject AA5 T1

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.

source_name: Serum/Plasma


title: K562, control, rep2

data_processing:
Reads were mapped to the human hg19 reference genome using bwa mem version 0.7.17 and processed using the Juicer pipeline version 1.6. For each sample, Hi-C maps were generated at resolutions 10 kb, 20 kb, 25 kb, 50 kb, 100 kb, 250 kb, 500 kb, 1 Mb, and 10 Mb. Once assessed the concordance between replicas of the same biological condition, Hi-C maps of the same condition were merged using the mega.sh script provided by the Juicer pipeline. All Hi-C maps were normalized using the Knight-Ruiz method (KR) implemented in the Juicer pipeline.
Assembly: hg19
Supplementary files format and content: .hic files represent binarized Hi-C matrices built using Juicer using reads having MAPQ >= 30
Supplementary files format and content: .hic files named as "mega" represent the aggregation of multiple replicates of the same biological condition

value: control


title: 22Rv1 cells, drug resistant, input chromatin


title: Subject AA4 T3

value: Influenza Patient from Athens


title: Subject AA6 T1


title: Subject AA4 T2


title: K562, control, rep1


title: Subject AA6 T3


title: HeLa_siYTHDF1-3_oeDDX6_rep2

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

description: RiboMinus RNA

data_processing:
Adapter trimming by Cutadapt
Reads mapping by hisat2
Reads alginment by HTSeq
Reads normalization to spike-in RNA
Assembly: hg38
Supplementary files format and content: For [Dataset 1], excel (xlsx) files, with reads mapped to individual genes normalized by ERCC spike-in.

source_name: HeLa

growth_protocol: Wild-type HeLa cells are maintained in DMEM + 10% FBS.

extract_protocol:
For [Dataset 1], total RNA are extracted by TRIzol reagent.
For [Dataset 1], RNA libraries are constructed by SMARTer Stranded Total RNA-Seq Kit v2 (TaKaRa, 634417) stranded protocol after ERCC spike-in (Invitrogen 15596026) added proportional to cell numbers

treatment_protocol: For [Dataset 1], cells are transfected with 30 nM small interfering RNA (siRNA) with standard protocol from the manufacturer, then reseeded and transfected with 1 microgram overexpression plasmid with the standard protocol from the manufacturer

value: HeLa

value: wild-type (ATCC, CCL-2)

value: siYTHDF1-3 oeDDX6

value: siRNA transfection for 48 hrs, plasmid transfection for 24 hrs


title: Subject AA4 T1


title: HSV-319_Day7

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

institute: NIH

description: RNAseq data from PBMC extracted from individual HSV-319

data_processing:
Illumina Casava1.7 software used for basecalling.
The Spliced Transcripts Alignment to a Reference (STAR) software was used for RNA-seq alignment
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for genes and every sample

source_name: PBMC

extract_protocol:
PBMCs were isolated with Ficoll-Hypaque reagent and lysed in QIAzol (Qiagen, Hilden, Germany) and stored at -80°C until use. Their total RNA was extracted and purified with the miRNeasy kit (Qiagen). RNA quality and quantity were estimated using Nanodrop (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s instructions. Briefly 500 ng of total RNA was used for mRNA selection. After the reverse transcription to 1st strand cDNA, strand info was reserved with dUTPs during 2nd strand synthesis. The dsDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library. The library was qualified with Agilent Bioanalyzer and quantified with Qubit 2.0 fluorometer. The cluster generation and pair-end (2x75 bp) sequencing was run on Illumina HiSeq 3000 at NHLBI Sequencing Core. Up to 96 barcoded samples were pooled for one single run, which yielded at least 30M passed filter paired reads per sample.

value: PBMC

tag: age


title: HSV-319_Day30


title: RPE TP53-/-, WGD, rep3

data_processing:
RNA-seq fastq files were analysed using the nfcore/rnaseq pipeline v3.8 (https://nf-co.re/rnaseq) using as aligner star_rsem, mapping the reads to the hg19 genome.
Assembly: hg19
Supplementary files format and content: rnaseq_gene_counts.tsv is the raw count expression matrix at the gene level
Supplementary files format and content: rnaseq_gene_tpm.tsv is the TPM normalized expression matrix at the gene level

source_name: retinal epithelium

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN, catalogue no. 74104) following manufacturer’s protocol.
Total RNA was processed for sequencing with the TruSeq Stranded mRNA kit (Illumina, catalogue no. 20020594) according to the supplier’s recommendations.

tag: tissue

value: hTERT RPE-1

value: immortalized retinal epithelial cells


title: HSV-319_Day1


title: HSV-319_Day37


title: HSV-319_Day0


title: HeLa_siYTHDF1-3_oeControl_rep2

description: RiboMinus RNA

value: siYTHDF1-3 oeControl


title: RPE TP53-/-, WGD, rep2


title: Subject AA3 T3

extract_protocol: Blood was collected from patients and healthy controls. The blood was then processed into serum or plasma which was then run on our arrays.


title: RPE TP53-/-, WGD, rep1


title: Subject AA3 T2


title: K562, control, rep3

extract_protocol:
1-2 million cells were collected and fixed with 2% formaldehyde (Thermo Fisher Scientific, catalogue no. 11483217). The reaction was quenched with 200mM glycine (VWR, catalogue no. 101194M) final concentration, cells were washed with PBS (Thermo Fisher Scientific, catalogue no. 10010023) and lysed in a solution containing 10mM Tris-HCl pH 8.0 (Thermo Fisher Scientific, catalogue no. 15568025), 10mM NaCl (Sigma-Aldrich, catalogue no. S6546), 0.2% Igepal CA-630 (Sigma-Aldich, catalogue no. I8896), and 1x Proteinase inhibitor cocktail (Roche, catalogue no. 11697498001) at 4°C for 30 minutes. Resulting nuclei were re-suspended in 1X NEB3.1 buffer (New England Biolabs, catalogue no. B7203S). Nuclei suspension was incubated with 0.11% SDS (Carl Roth, catalogue no. CN30) final concentration for 10 minutes at 65°C. Reaction was quenched with 1% Triton-X100 (AppliChem, catalogue no. A1388) and nuclei were digested with 100U MboI restriction enzyme (New England Biolabs, catalogue no. R0147) at 37°C overnight. Restriction enzyme was inactivated according to manufacturer’s specifications and digested nuclei were washed and re-suspended in 1x NEB3.1. Digested ends were then marked with biotin via incubation in 0.03mM biotin-14-dATP (Thermo Fisher Scientific, catalogue no. 19524016), 0.03mM dCTP, 0.03mM dGTP, 0.03mM dTTP (Promega, catalogue no. U1420) and 50U Klenow DNA polymerase I (New England Biolabs, catalogue no. M0210M) for 4 hours at room temperature. Resulting blunt-ends were proximally ligated with 50U T4 DNA Ligase (Thermo Fisher Scientific, catalogue no. EL0011), 1x T4 DNA ligase buffer (Thermo Fisher Scientific, catalogue no. B69), 5% PEG, 1% Triton-X100, 0.1mg/ml BSA (New England Biolabs, catalogue no. B9000S) for 4 hours at room temperature. Crosslink reversal was performed on the proximity-ligated chromatin through the incubation with 300mM NaCl and 1% SDS overnight, at 68°C. The sample was then treated with 50g/ml RNase A (Thermo Fisher Scientific, catalogue no. EN0531) for 30 minutes at 37°C, followed by 400ug/ml Proteinase K (Promega, catalogue no. V3021) at 65°C for one hour. DNA was purified via precipitation with 1.6 volumes of pure ethanol and 0.1 volumes of sodium acetate, pH 5.2 (Thermo Fisher Scientific, catalogue no. R1181) at -80°C. DNA was eluted and then fragmented by sonication at 80V peak incidence power, 10% duty factor, 200 cycles per burst, for 60-80 seconds with an E220 Focused-ultrasonicator (Covaris). Sheared DNA was size selected for library preparation using AMPure XP beads (Beckman Coulter, catalogue no. A63881).
Biotin-marked fragments were isolated with Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher Scientific, catalogue no. 65001) and all subsequent steps were performed on the bead-bound DNA fraction. Hi-C library preparation continued with end polishing reaction, which involved incubation of DNA with 1x T4 ligase buffer (New England Biolabs, catalogue no. B0202S), 2.5mM each dNTP, 50U T4 Polynucleotide Kinase (New England Biolabs, catalogue no. M0201), 12U T4 DNA Polymerase (New England Biolabs, catalogue no. M0203), and 5U Klenow DNA polymerase I, at room temperature for 30 minutes. PolyA tail was added by incubating the DNA sample in 1X NEBuffer™ 2 (New Enlgand Biolabs, catalogue no. B7002S) with 0.5mM dATP and 25U Klenow Fragment (3'→5' exonuclease) (New England Biolabs, catalogue no. M0212) at 37°C for 30 minutes. DNA fragment ends were then ligated to Illumina TruSeq unique dual indexes (Integrated DNA Technologies) in 1X T4 Ligation buffer with 5% PEG and 15U T4 DNA Ligase for 2 hours at room temperature or overnight at 16°C. Lastly, libraries were PCR amplified using Illumina forward (AATGATACGGCGACCACCGAGATCTACAC) and reverse (CAAGCAGAAGACGGCATACGAGAT) primers and KAPA HiFi HotStart ReadyMix (Roche, catalogue no. KK2602) for 6-10 cycles. Resulting fragments were size-selected with AMPure XP beads.

value: bone marrow


title: RPE TP53-/-, control, rep3


title: HeLa_siYTHDF1-3_oeControl_rep1

description: RiboMinus RNA


title: HSV-315_Day180

description: RNAseq data from PBMC extracted from individual HSV-315


title: HSV-315_Day187


title: Subject AA2 T3


title: HeLa_siControl_oeDDX6_rep2

description: RiboMinus RNA

value: siControl oeDDX6


title: RPE TP53-/-, control, rep2


title: HeLa_siControl_oeDDX6_rep1

description: RiboMinus RNA


title: Subject AA2 T1


title: RPE TP53-/-, control, rep1


title: HeLa_siYTHDF1-3_oeDDX6_rep1

description: RiboMinus RNA


title: Subject AA3 T1


title: HSV-315_Day37


title: Subject AA1 T1


title: HeLa_siControl_oeControl_rep2

description: RiboMinus RNA

value: siControl oeControl


title: RPE TP53-/-, 6w pWGD, experiment 4, tumour 3

data_processing:
Paired-end FASTQ files for each sample were aligned jointly to the human_g1k_hs37d5 from the 1000 Genomes Phase 3 using bwa mem version 0.7.17, sorted with samtools version 1.101 using the sort command. Mismatches in read pairing were fixed using the fixmate command. Duplicate reads were identified with the Genome Analysis Toolkit (GATK) using the MarkDuplicatesSpark command. Base quality scores were corrected with BaseRecalibrator and ApplyBQSR from the GATK suite.
CNVs were identified using the Control-FREEC software version 11.6.
Single-nucleotide variants were called using the Mutect algorithm from the GATK. VCF files were then converted to MAF using vcf2maf and assembled into a single file. Only SNP variants were considered in the analysis.
Assembly: human_g1k_hs37d5
Supplementary files format and content: RPE_somatic_all.maf contains annotated mutations in MAF format detected in RPE samples
Supplementary files format and content: ControlFREEC_log2_coverage_ratio_10Kb.seg is a segmentation file (to be loaded in IGV) showing the coverage ratio at 10Kb resolution between each RPE sample and RPE WT, as computed by Control-FREEC
Supplementary files format and content: RPE_cnvs_20wTumors_merged.bed are CNVs detected by Control-FREEC and shared between 20 week post-WGD tumors in RPE cells
Supplementary files format and content: RPE_filtered_cnvs.seg is a segmentation file (to be loaded in IGV) containing, for each sample, the significant CNVs detected by Control-FREEC
Library strategy: whole genome sequencing

extract_protocol:
DNA was extracted from cells using DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69504) following manufacturer’s protocol.
Library preparation was performed with TruSeq DNA PCR-Free (Illumina, catalogue no. 2001596) or TruSeq DNA Nano (Illumina, catalogue no. 2001596) kits.

treatment_protocol: For WGD, RPE TP53-/- cells were incubated for 24 hours with 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 hours to 4uM dihydrocytochalasin B (Cayman Chemical, catalogue no. 20845) and then were allowed to recover for 48 hours. Cells were then kept for 6 weeks (6w pWGD) and 20 weeks (20w pWGD) in vitro. Control and 20w pWGD cells were injected in NSG mice. After 6 weeks, only 20w pWGD injected mice formed tumours (in vivo T1, T2, T3), which were collected and dissociated into single cells with human Tumour Dissociation Kit (Miltenyi Biotec, catalogue no. 130-095-929) and Mouse Cell Depletion Kit (Miltenyi Biotec, catalogue no. 130-104-694) following manufacturer’s protocols.

value: retinal epithelium

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 6w pWGD T3, in vivo


title: HSV-315_Day30


title: RPE TP53-/-, 6w pWGD, experiment 4, tumour 2

value: 6w pWGD T2, in vivo


title: HSV-315_Day1


title: HeLa_siControl_oeControl_rep1

description: RiboMinus RNA


title: Huh7_rep2

first: Meng

last: Li

address: 2003 Zonal Avenue

data_processing:
RNA-Seq data were analyzed with Partek Flow version 10.0.21 (Partek Inc, Chesterfield, MO)
Raw sequencing reads were trimmed from both ends with the Quality Score method (bases with a quality score of <20 were trimmed from both ends and trimmed reads shorter than 25 nucleotides were excluded from downstream analyses)
Trimmed reads were mapped to human genome hg38 using Star version 2.7.8a with default parameter settings and using Gencode v38 annotation as guidance
Aligned reads were quantified to Gencode v38 annotation using the Partek E/M method
Genes with fewer than 10 raw reads in all samples were excluded from downstream analysis. Raw read counts were normalized using upper quartile normalization with an offset of 1.  Normalized counts were analyzed for differential expression using the Partek gene-specific analysis method.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

extract_protocol:
Total cellular RNA were extracted with Quick-RNA miniprep kit according to the manufacture's protocol followed by RNA quality assessment using Agilent 2100 bioanalyzer.
cDNA library were synthesized using NEB Next Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacture's protocol.

value: hepatocellular carcinoma


title: HSV-315_Day0


title: Huh7_rep1


title: HSV-315_Day7


title: Subject UMR 26

value: Influenza Patient from Marburg


title: Subject UMR 24


title: Subject UMR 25


title: Subject UMR 23


title: HepG_rep2

value: hepatoblastoma


title: HSV-310_Day187

description: RNAseq data from PBMC extracted from individual HSV-310


title: RPE TP53-/-, 6w pWGD, experiment 3, tumour 1

value: 6w pWGD T1, in vivo


title: HepG_rep1


title: RPE TP53-/-, 6w pWGD, experiment 2, tumour 3


title: HSV-310_Day30


title: Subject UMR 21


title: RPE TP53-/-, 6w pWGD, experiment 4, tumour 1


title: DMSO2_rep1

source_name: Human Hepatocytes

value: Human Hepatocytes

value: DMSO2 (140mM)


title: Subject UMR 20


title: HSV-310_Day37

value: PBMC


title: DMSO_rep2


title: DMSO_rep1


title: HSV-310_Day7


title: RPE TP53-/-, 6w pWGD, experiment 2, tumour 2

value: hTERT RPE-1


title: RPE TP53-/-, 6w pWGD, experiment 3, tumour 3


title: HSV-310_Day1


title: Subject UMR 19


title: RPE TP53-/-, 6w pWGD, experiment 4

value: immortalized retinal epithelial cells

value: 6w pWGD


title: NT_rep2

value: Non treatment (Control)


title: Subject UMR 17


title: HSV-310_Day180


title: RPE TP53-/-, 6w pWGD, experiment 3, tumour 2


title: Subject UMR 18


title: RPE TP53-/-, 6w pWGD, experiment 3


title: Subject UMR 22


title: HSV-310_Day0


title: DMSO2_rep2


title: Subject UMR 16


title: HSV-306_Day187

description: RNAseq data from PBMC extracted from individual HSV-306


title: RPE TP53-/-, 6w pWGD, experiment 2


title: RPE TP53-/-, 6w pWGD, experiment 2, tumour 1


title: HSV-306_Day180


title: RPE TP53-/-, 20w pWGD, experiment 1, tumour 3

value: 20w pWGD T3, in vivo


title: Fresh 1000 cell PC9:H1975 9:1 with drug treatment

description: Combination of the above for H1975 and PC9 cell lines

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0.
Assembly: GRCh38.p13
Supplementary files format and content: Matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, most of which have four files per sample: 2 lanes from 2 reads. Two samples were sequenced on a single lane NovaSeq run, and therefore only have the two reads from a single lane.

source_name: Mixture of PC9 and H1975 cells (9:1)

growth_protocol: Cells were cultured in RPMI-1640 (Gibco #11875093) with 10% fetal bovine serum (FBS), penicillin, and streptomycin in an incubator at 37C with 5% CO2.

extract_protocol:
Cells were processed according to the PIP-seq scRNA-seq workflow
PIP-seq single cell library prep

treatment_protocol: 1 uM Gefitinib (Frontier Scientific, 501411677) or DMSO was added to culture flasks 24 hours before cells were harvested for processing. PC9 and H1975 were both treated with Gefitinib and DMSO.

value: Mixture of PC9 and H1975 cells (9:1)

tag: Sex

value: pooled male and female


title: RPE TP53-/-, 20w pWGD, experiment 1, tumour 2

value: retinal epithelium

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 20w pWGD T2, in vivo


title: Fresh 2000 cell PC9 with control DMSO treatment

description: lung adenocarcinoma cell line; harbor a driver mutation in the EGFR gene

source_name: PC9 cells

tag: strain

value: PC9 cells

value: male


title: HSV-306_Day37


title: Fresh 2000 cell PC9 with drug treatment


title: HSV-306_Day30


title: Fresh 2000 cell H1975 with control DMSO treatment

description: non-small cell lung cancer cells; L858R and EGFR mutations at T790M, resulting in complete resistance to gefitinib

source_name: H1975 cells

value: H1975 cells

value: female

value: unknown


title: Subject UMR 15

value: Influenza Patient from Marburg


title: HSV-306_Day7

value: PBMC


title: RPE TP53-/-, 20w pWGD, experiment 1, tumour 1

value: hTERT RPE-1

tag: genotype

value: 20w pWGD T1, in vivo


title: Fresh 2000 cell H1975 with drug treatment


title: Subject UMR 14


title: RPE TP53-/-, 6w pWGD, experiment 1, tumour 3

tag: condition

value: 6w pWGD T3, in vivo


title: RPE TP53-/-, 20w pWGD, experiment 1

tag: cell line

value: immortalized retinal epithelial cells

value: 20w pWGD


title: Subject UMR 12


title: Subject UMR 11


title: HeLa_EDC4_rep2

data_processing:
Adapter trimming by Trimmomatic
Reads mapping by hisat2
Reads alginment by HTSeq
Assembly: hg38
Supplementary files format and content: For [Dataset 1] and [Dataset 2], comma-separated values (csv) files, with reads mapped to individual genes normalized by ERCC spike-in. For [Dataset 3], P-body enrichment values obtained by DESeq2 in R

source_name: HeLa cells

extract_protocol:
For [Dataset 1] and [Dataset 2], total RNA are extracted by TRIzol reagent. For [Dataset 3], RNA from the immunoprecipitated P-body cores are extracted by TRIzol reagent followed by isopropanol precipitation.
For [Dataset 1] and [Dataset 2], RNA libraries are constructed by SMARTer Stranded Total RNA-Seq Kit v2 (TaKaRa, 634417) stranded protocol after ERCC spike-in (Invitrogen 15596026) added proportional to cell numbers   For [Dataset 3], RNA libraries are constructed by SMARTer Stranded Total RNA-Seq Kit v2 (TaKaRa, 634417) stranded protocol

treatment_protocol: For [Dataset 1], cells are transfected with 20 nM small interfering RNA (siRNA) with standard protocol from the manufacturer. For [Dataset 2], cells are transfected with 30 nM small interfering RNA (siRNA) with standard protocol from the manufacturer.

tag: cell type

value: wild-type (ATCC, CCL-2)

tag: ip antibody

value: Abcam ab72408


title: NT_rep1

value: Human Hepatocytes

value: Non treatment (Control)


title: HeLa_EDC3_rep2

value: Abcam ab168851


title: Subject UMR 9

tag: disease


title: Subject UMR 10


title: HSV-306_Day1


title: HSV-306_Day0


title: HSV-303_Day187

description: RNAseq data from PBMC extracted from individual HSV-303


title: RPE TP53-/-, 6w pWGD, experiment 1, tumour 1

value: retinal epithelium

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 6w pWGD T1, in vivo


title: HSV-303_Day180


title: HeLa_input_rep2


title: Subject UMR 8


title: HSV-303_Day37


title: RPE TP53-/-, 6w pWGD, experiment 1, rep2

value: 6w pWGD


title: HeLa_EDC4_rep1


title: RPE TP53-/-, 6w pWGD, experiment 1, rep1


title: HSV-303_Day30


title: Subject UMR 7


title: Subject UMR 6


title: RPE TP53-/-, WGD, rep2

value: WGD


title: RPE TP53-/-, 6w pWGD, experiment 1, tumour 2

value: 6w pWGD T2, in vivo


title: HSV-303_Day7

value: PBMC


title: Subject UMR 4

value: Influenza Patient from Marburg


title: HeLa_EDC3_rep1


title: RPE TP53-/-, WGD, rep1

value: hTERT RPE-1


title: Subject UMR 5


title: HeLa_input_rep1


title: HSV-219_Day37

description: RNAseq data from PBMC extracted from individual HSV-219


title: HSV-303_Day1


title: HeLa_siDDX6_siDF123_rep2

tag: treatment

value: siDDX6_siDF123 transfection for 48hrs


title: Subject UMR 3


title: HeLa_siDDX6_rep2

value: siDDX6 transfection for 48hrs


title: Subject UMR 2


title: RPE, control

value: immortalized retinal epithelial cells

value: WT

value: control


title: HSV-303_Day0


title: HSV-219_Day30


title: Subject SU167

value: ICU Patient from Stanford


title: HeLa_siControl2_rep2

value: wild-type (ATCC, CCL-2)

value: siControl2 transfection for 48hrs


title: donor 4, RPE, peripheral, atac

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

description:
donor_4_per_atac
ATAC portion of a 10X Multiome sample

library_source: genomic single cell

data_processing:
FASTQ files were generated from base calls with the bcl2fastq software (Illumina). Sequencing reads were mapped to the GRCh38 reference genome (GRCh38 Reference - 2020-A-2.0.0 prepared by 10X Genomics). Mapping and quantification were carried out by Cell Ranger ARC (v2.0.0, 10X Genomics) using the ‘count’ function with all parameters at default values. Nuclei passing default Cell Ranger quality control cutoffs were used for subsequent filtering and analysis.
For gene expression libraries, nuclei were first filtered with the Seurat (v3.1) subset() function prior to integration (5). Nuclei with nUMI less than 100 (to remove nuclei with poor read quality) or greater than 4000 (to remove nuclei likely to be doublets) were removed. Nuclei with greater than 10% of reads originating from mitochondrial genes or greater than 2.5% of reads originating from ribosomal RNA genes were also removed, as these metrics indicate incomplete lysis. A “neural_retina_genes” score was then assigned to each nucleus in order to identify and remove contamination of the desired RPE sample. Nuclei with greater than 50% of their counts originating from known neural retina cell-specific genes (i.e. CNGB1, PDE6A, CA10, CADPS, and NRXN3) were removed.
For each of the gene expression libraries, reads were normalized with the Seurat (v3.1) NormalizeData() function, and variable features were identified with the FindVariableFeatures() function. Integration anchors between datasets were identified using the FindIntegrationAnchors() function with the following parameters: dims=1:25, k.filter=100, k.score=20. Nuclei were integrated using the IntegrateData() function with the following parameters: dims=1:25, k.weight=30. Uniform manifold approximation and projection (UMAP) was performed using the first 15 principal components. Seurat clusters were identified using the FindClusters() function with the following parameters: resolution=0.5, algorithm=3 (indicating use of the smart local moving (SLM) algorithm. Data scaling, principal component analysis, and clustering of the gene expression data were all performed using Seurat (v3.1).
For ATAC libraries, nuclei were filtered with the Signac (v1.4.0) subset function. Nuclei with fewer than 1000 or greater than 30000 peak region fragments were removed. Term frequency inverse document frequency (TF-IDF) normalization and partial singular value decomposition were performed on each ATAC library using RunTFIDF() and RunSVD() (Signac) with default settings. Gene activities were computed using GeneActivity().
Integration anchors between ATAC datasets were identified using reciprocal LSI projection using FindIntegrationAnchors() in Signac. Dimensions 2-30 were used. LSI embeddings were integrated using IntegrateEmbeddings based on these anchors and using dimensions 1-30.
Gene expression and ATAC portions of the experiment were combined using Weighted Nearest Neighbor (WNN) analysis (Seurat). Integrated ATAC and gene expression objects were subset to include only common cells (i.e., cells that passed both ATAC and gene expression quality control thresholds). UMAP and cluster identification were performed on the resulting object. Cluster identification used the SLM algorithm with a resolution of 0.5 (5).
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data matrix files are provided in comma-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).
Supplementary files format and content: Processed gene activity data matrix files are provided in comma-delimited format for count (*_count.csv) and processed/normalized (*_normalized.csv) activity values. For processed/normalized files, log-normalized activity values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene activity values. For count files, raw gene activity level were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: retinal pigment epithelium

extract_protocol:
Donor eyes were obtained from the Iowa Lions Eye Bank following full consent of the next of kin and in full compliance with the Declaration of Helsinki. Anterior segments were removed at the limbus and posterior poles were dissected with 4 cuts at 90 degree intervals. Following removal of the vitreous and neural retina, the RPE was gently scraped away from the underlying Bruch’s membrane and choroid using a Beaver-Visitec #6900 surgical blade (TestEquity). RPE cells were collected from either the submacular region (corresponding to the central ~8mm) or from the temporal quadrant. Cryopreserved RPE samples were thawed rapidly at 37˚C and washed once in PBS-/-. Cells were then pelleted and nuclei were isolated using the Chromium Nuclei Isolation Kit (10X Genomics) following manufacturer’s suggested protocol for Single Cell Multiome ATAC and Gene Expression libraries. Briefly, cells were resuspended in Lysis Buffer on ice and dissociated with a pestle. Dissociated material was filtered with the supplied column and nuclei were subsequently washed once with Wash Buffer. Nuclei were resuspended in diluted Nuclei Buffer supplemented with RNase Inhibitor (10X Genomics).
Nuclei were counted using trypan blue exclusion on a Luna automated counter. Nuclei were then processed following the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (Rev. E). For each sample, 6,000 nuclei were targeted. Eight cycles were used for ATAC library index PCR. Nine cycles were used for cDNA amplification. Sixteen cycles were used for Gene Expression Library sample index PCR. Library quality was checked using the Bioanalyzer system prior to sequencing. Gene expression and ATAC libraries were sequenced separately on the Novaseq 6000 platform (Illumina). Sequencing was carried out by the Genomics Division of the Iowa Institute of Human Genetics.

value: retinal pigment epithelium

tag: region

value: peripheral

tag: donor

tag: disease status

value: healthy


title: donor 4, RPE, macula, atac

description:
donor_4_mac_atac
ATAC portion of a 10X Multiome sample

value: macula


title: HSV-219_Day7


title: HeLa_siDDX6_rep1


title: HeLa_siDDX6_siDF123_rep1


title: HeLa_siControl2_rep1


title: Subject SU166


title: HSV-219_Day1


title: Subject SU165


title: HSV-214_Day187

description: RNAseq data from PBMC extracted from individual HSV-214


title: RPE TP53-/-, control

value: retinal epithelium


title: HeLa_siYTHDF3_rep2

value: siYTHDF3 transfection for 48hrs


title: Subject UMR 1


title: donor 3, RPE, macula, atac

description:
donor_3_mac_atac
ATAC portion of a 10X Multiome sample


title: Subject SU164


title: donor 2, RPE, peripheral, atac

description:
donor_2_per_atac
ATAC portion of a 10X Multiome sample


title: Subject SU163


title: donor 2, RPE, macula, atac

description:
donor_2_mac_atac
ATAC portion of a 10X Multiome sample


title: HSV-214_Day180

value: PBMC


title: HeLa_siYTHDF2_rep2

value: siYTHDF2 transfection for 48hrs


title: donor 1, RPE, peripheral, atac

description:
donor_1_per_atac
ATAC portion of a 10X Multiome sample


title: HeLa_siYTHDF123_rep2

value: siYTHDF123 transfection for 48hrs


title: HeLa_siYTHDF1_rep2

value: siYTHDF1 transfection for 48hrs


title: HSV-214_Day37


title: HSV-214_Day30


title: Subject SU162

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.


title: Subject SU161


title: donor 3, RPE, peripheral, atac

description:
donor_3_per_atac
ATAC portion of a 10X Multiome sample


title: HSV-214_Day7


title: Subject SU160


title: donor 4, RPE, peripheral, gex

description:
donor_4_per_gex
Gene expression portion of a 10X Multiome sample


title: Subject SU159


title: HSV-214_Day1


title: donor 4, RPE, macula, gex

description:
donor_4_mac_gex
Gene expression portion of a 10X Multiome sample


title: HSV-219_Day0


title: Subject SU158


title: HeLa_siYTHDF3_rep1


title: donor 3, RPE, peripheral, gex

description:
donor_3_per_gex
Gene expression portion of a 10X Multiome sample


title: HSV-214_Day0


title: HeLa_siControl_rep2

value: siControl transfection for 48hrs


title: donor 3, RPE, macula, gex

description:
donor_3_mac_gex
Gene expression portion of a 10X Multiome sample


title: HeLa_siYTHDF2_rep1


title: Subject SU156


title: HeLa_siControl_rep1


title: HSV-211_Day180

description: RNAseq data from PBMC extracted from individual HSV-211


title: donor 2, RPE, peripheral, gex

description:
donor_2_per_gex
Gene expression portion of a 10X Multiome sample


title: Subject SU154


title: HeLa_siYTHDF123_rep1


title: HSV-211_Day37


title: donor 1, RPE, peripheral, gex

description:
donor_1_per_gex
Gene expression portion of a 10X Multiome sample


title: HSV-211_Day30


title: Subject SU153


title: NC_cell_4

city: Amsterdam

first: Jitendra

last: Badhai

address: Plesmanlaan 121

department: Division Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

description:
JB86
read counts_mouse.txt

data_processing:
Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. The sequence reads were mapped to the mouse genome (mm10) or hg 38, using TopHat (2.0.12). TopHat was run with default. Reads with mapping quality less than 10 and non-primary alignments were discarded. Remaining reads were counted using HTSeq-count. Statistical analysis of the differential expression of genes was performed using DESeq2
Assembly: mm10, Grcm38
Supplementary files format and content: read counts table
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: pleura

extract_protocol:
for RNA seq: RNA was isolated from tumor cell lines and mouse tumors with the Qiagen All Prep DNA/RNA kit. Quantification and quality assessment for RNA were performed with a Bioanalyzer (RIN >6.5) (Agilent, Santa Clara, CA, USA).
for RNAseq: Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads.

value: pleura

value: mouse mesothelioma cells


title: NC_cell_5

description:
JB94
read counts_mouse.txt


title: HSV-211_Day7


title: BNC_cell_6

description:
JB99
read counts_mouse.txt


title: MDM non-stimulated P2

city: Paris

first: Jeremie

last: Rosain

address: 24 boulevard du Montparnasse

institute: Institut Imagine

data_processing:
The RNA-seq FASTQ files were first inspected with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure that the raw data were of high quality
We retained only genes with at least 1 count-per-million (CPM) in at least two samples
Assembly: For each subject, the two FASTQ files generated were then mapped onto the human reference genome (Ensembl GRCh37 release 75) with STAR v.2.7.3a, in the two-pass mode
Supplementary files format and content: Reads were quantified to generate gene-level feature counts from the read mapping, with HTSeq-count v.0.11.2
Supplementary files format and content: We normalized the datasets with the functions DGEList and calcNormFactors from the edgeR version 3.26.8 package201 implemented in R v.3.6.3

source_name: Monocyte-derived macrophages

extract_protocol:
Total RNA was extracted from cells with the Quick-RNA MicroPrep kit (#R1051, Zymo Research), and treated with DNAse (Zymo) to remove residual genomic DNA. Ribosomal RNA (rRNA) and mitochondrial RNA (mRNA) were depleted.
RNA-seq libraries were prepared with the Illumina RiboZero TruSeq Stranded Total RNA Library Prep Kit (Illumina)
Libraries were  sequenced using NovaSeq in the 100 or 150-nt, paired-end configuration

value: Monocyte-derived macrophages

value: Non-stimulated


title: Subject SU152

value: ICU Patient from Stanford


title: donor 1, RPE, macula, gex

description:
donor_1_mac_gex
Gene expression portion of a 10X Multiome sample


title: HSV-211_Day1


title: Subject SU157


title: HSV-211_Day187


title: BNC_cell_5

description:
JB92
read counts_mouse.txt


title: HeLa_siYTHDF1_rep1

value: wild-type (ATCC, CCL-2)


title: donor 2, RPE, macula, gex

description:
donor_2_mac_gex
Gene expression portion of a 10X Multiome sample

value: retinal pigment epithelium


title: Subject SU155


title: HSV-211_Day0


title: MDM IFNg 8h P2

value: IFN-g 1000 IU/mL 8 hours


title: BNC_cell_4

description:
JB82
read counts_mouse.txt


title: HSV-206_Day180

description: RNAseq data from PBMC extracted from individual HSV-206


title: MDM non-stimulated HC3

value: WT/WT


title: HSV-206_Day187


title: MDM IFNg 2h P2

value: IFN-g 1000 IU/mL 2 hours


title: MDM IFNg 8h HC3


title: Subject SU150


title: MDM non-stimulated HC2


title: MDM IFNg 2h HC3


title: Subject SU151


title: HSV-206_Day37


title: HSV-206_Day30


title: MDM IFNg 2h HC2


title: MDM non-stimulated HC1


title: MDM IFNg 8h HC2


title: HSV-206_Day7


title: Subject SU147


title: Subject SU148