title: hTERT-RPE1, Phase 1, Replicate 2

description: Library name: TC00000367_C02

data_processing:
Read alignment: Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Probe counts: Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples
Supplementary files format and content: All probe sequences and gene annotations for the hWTv2 TempO-seq probe set are provided as a single table

extract_protocol:
For adherent cell lines cultured in multiwell plate format (6-well, 12-well, 24-well), growth media was removed and cells were gently rinsed once with a volume of 1X phosphate-buffered saline (PBS). The 1X PBS was removed and 1 mL of 1X BioSpyder lysis buffer was added to each well. Cultures were immediately inspected under a microscope to evaluate the extent of cell lysis.  Cells were then incubated for 20 minutes at room temperature protected from light. After 20 minutes, cell cultures were again inspected under a microscope to confirm efficient cell lysis. Using a P1000 pipette, the lysate contained in each well was titurated four times and used rinse the growth surface of the mutliwell plate. Lysates were then transferred to RNase-free microcentrifugre tubes and stored at -80C prior to shipment to BioSpyder for TempO-Seq whole transcriptome profiling. For cell lines cultured in suspension, the number of live cells in suspension were quantified in a small aliquote of cells using trypan blue dye exclusion. A volume of cell suspension corresponding to the desired number of cells for TempO-Seq analysis were then transfered to a sterile 1.5 mL microcentrifuge tube. Cells were pelleted at maximum speed for 2 minutes using an Eppendorf 5340R centrifuge equipped with a microtube rotor (FA-45-48-11). Residual media was removed and 1 mL of 1X BioSpyder lysis buffer was added. The cell lysates were titurated several times with a manual P1000 pipette to dissolve the cell pellet and ensure effective lysis. Lysates were stored at -80C prior to shipment to BioSpyder for TempO-Seq whole transcriptome profiling.  The TempO-Seq assay was performed on cell lysates as described (Harrill et al. 2021) without RNA extraction.
Plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. Cell lysates were then analyzed by BioSpyder using the unattenuated TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The TempO-seq libraries for Phase 1 were sequenced to a target read depth of 6.0x106 mapped reads per sample. The TempO-seq libraries for Phase 2 were generated and sequenced to a target read depth of 4.5x106 mapped reads per sample.


title: Vhl/Rassf1a rep2

status: Public on Feb 11 2025

type: SRA

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

description: Vhl_Rassf1a_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
cellranger count (version 7.0.0) was used for the alignment of sequence reads to the reference genome, filtering, barcode counting, and UMI counting.
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format (H5) of filtered feature-count matrix per genotype

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
RNA was isolated following the 10x Genomics® Single Cell Protocols (Cell Preparation Guide).
RNA libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.

treatment_protocol: Mouse kidneys were dissected and dissociated. Proximal tubule epithelial cells were isolated via FACS based on the surface marker LTL.

tag: tissue

value: kidney

tag: cell type

value: proximal tubule epithelial cell

tag: genotype

value: Vhl/Rassf1a KO


title: Patient resected tumor P2-1

city: Atlanta

first: Youssef

middle: M

last: Zohdy

state: GA

address: 1365 Clifton Road NE

department: Neurosurgery

country: USA

institute: Emory University

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
Raw RNA reads processing was conducted following the validated nf-core bulk RNA-seq bioinformatics pipeline. Adapter sequences and low-quality sequences were analyzed using FastQC and trimmed from the reading using TrimGalore. The RNA-seq reads were aligned to the human reference genome hg38 using STAR v2.7.11 and quantified using Salmon. Differential expression values were calculated with DESeq2 in R (R Core Team, 2022).
Assembly: hg38
Supplementary files format and content: FPKM

organism: Homo sapiens

source_name: Patient resected tumor

extract_protocol:
The frozen tumor and organoid samples stored were thawed, and immediate steps were taken for RNA extraction. To ensure consistency, all samples were processed simultaneously to avoid any potential batch effects. RNA was extracted and purified from the patient specimens using the Direct-zol RNA Microprep Kit (Cat. #R2063), following the manufacturer’s protocol. Nuclease-free commercially available water was used during the RNA isolation process. The quality and quantity of the extracted RNA were immediately assessed using Nanodrop UV measurements. Following the measurements, all isolated RNA samples were stored at -80° C until sequencing.
An RNA-seq library was generated utilizing the Illumina mRNA sample prep kit (Cat. #RS-100-0801) according to the manufacturer's protocol in 3 technical replicates for each sample. The library constructs' size and concentration were verified with a bioanalyzer before sequencing on the Illumina NovaSeq6000. The raw reads' quality was evaluated to confirm the success of the library preparation and sequencing processes.

value: Patient resected tumor


title: lung.WT.1291308

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291308

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina bcl2fastq v2.17.
Reads were decoded based on their barcodes and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (NCBI GRCm38) using ArrayStudio software (OmicSoft Corp. (Cary, NC) allowing two mismatches
Reads mapped to the exons of a gene were summed at the gene level.
Assembly: NCBI GRCm38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains TPM values for each sample

source_name: lung

extract_protocol:
Total RNA was purified from tissues using MagMAX™-96 for Microarrays Total RNA Isolation kit (Life Technologies (Carlsbad, CA)), according to manufacturer’s specifications. Genomic DNA was removed using MagMAX Turbo DNase buffer and TURBO DNase from the MagMAX kit listed above. Messenger RNA was purified from total RNA using Dynabeads mRNA purification kit (Invitrogen (Waltham, MA)).
Strand-specific RNA sequencing (RNA-seq) libraries were prepared using KAPA mRNA-Seq Library Preparation kit (Kapa Biosystems (Wilmington, MA)). After mRNA quality control analysis, RNA-seq libraries were prepared and long read sequencing (75bp, single end, 15M reads) was used for all samples. Sequencing was performed on Illumina HiSeq®2500 by a multiplexed single-read run with 33 cycles.

value: lung


title: Rassf1a rep4

value: Rassf1a KO


title: Patient resected tumor P2-2

description: Library name: Sample 2


title: Vhl/Rassf1a rep1


title: hTERT-RPE1, Phase 1, Replicate 1

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Library name: TC00000367_B12

growth_protocol:
MCF7 cells (ATCC, HTB-22TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
U-2 OS cells (ATCC, HTB-96TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
HepG2 cells (ATCC, HB-8065TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
Daudi cells (ATCC, CCL-213TM) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
NCI-H1092 cells (ATCC, CRL-5855TM) were cultured in DMEM:F12 medium (ATCC, 30-2006) containing 5% heat-inactivated fetal bovine serum (Millipore Sigma, F4135), 0.005 mg/mL Insulin (ThermoFisher, 12585014), 0.01 mg/mL transferrin (Millipore Sigma, T5391), 30 nM sodium selenite (Millipore Sigma, T5391), 10 nM hydrocortisone (Millipore Sigma, H0135), 10 nM beta-estradiol (Millipore Sigma, E2557), 2 mM L-glutamine (ThermoFisher, 25030081) and 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
CCD-18Co cells (ATCC, CRL-1459TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
BHY cells (DSMZ, ACC 404) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
SK-MEL-28 cells (ATCC, HTB-72TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
KP-N-RT-BM-1 cells (JCRB/Xenotech, IFO50432) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
A-704 cells (ATCC, HTB-45TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
DMS 454 cells (ECAAC / Millipore Sigma, 95062832) cells were cultured in Waymouth's MB 752/1 medium (ThermoFisher, 11220035) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016) + 2 mM L-glutamine (ThermoFisher, 25030081) + GM-CSF (Millipore Sigma, H5666).
DV-90 cells (DSMZ, ACC 307) cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016) + 2 mM L-Glutamine (ThermoFisher, 25030081) + 1X Non-Essential Amino Acids (NEAA, ThermoFisher, 11140050).
SET-2 cells (DSMZ, ACC 608) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 20% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
T-47D cells (ATCC, HTB-133) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016) + 0.2 U/mL Insulin (Millipore Sigma, I1882).
EFM-19 cells (DSMZ, ACC 231) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
CAL-148 cells (DSMZ, ACC 460) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016) + 0.01 µg/mL epidermal growth factor (EGF, R & D Systems, 236-EG-200).
BT-483 cells (ATCC, HTB-121TM) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 20% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016) + 0.01 mg/mL insulin (ThermoFisher, 25030081).
SaOS-2 cells (ATCC, HTB-85TM) were cultured in McCoy's 5A medium (ATCC, 30-2007) + 20% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
HOS cells (ATCC, CRL-1543TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
CAL-78 cells (DSMZ, ACC 449) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 20% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
MG-63 cells (ATCC, CRL-1427TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
C3A cells (ATCC, CRL-10741TM) cells were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
Huh-7 cells (CLS, 300156) cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
Huh-1 cells (JCRB, JCRB0199) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
PLC/PRF/5 cells (ATCC, CRL-8024TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
DOHH-2 cells (DSMZ, ACC 47) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
SU-DHL-6 cells (ATCC, CRL-2959TM) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 10% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
MHH-CALL-4 cells (DSMZ, ACC 337) were cultured in Roswell Park Memorial Institute 1640 medium (RPMI-1640, ATCC, 30-2001) + 20% heat inactivated fetal bovine serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
Hs-5 cells (ATCC, CRL-11882TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
Detroit 551 cells (ATCC, CCL-110TM) were cultured in Eagle's Minimal Essential Medium (ATCC, 30-2003) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
BJ-5ta cells (ATCC, CRL-4001TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV) and Medium-199 (ThermoFisher, 11150059) in a 1:4 ratio + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 0.01 mg/mL Hygromycin B (ThermoFisher, 10687010).
Hs 839.T cells (ATCC, CRL-7572) were cultured in  Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
NCI-H1436 cells (ATCC, CRL-5871TM) were cultured in DMEM:F12 medium (ATCC, 30-2006) containing 5% heat-inactivated fetal bovine serum (Millipore Sigma, F4135), 0.005 mg/mL Insulin (ThermoFisher, 12585014), 0.01 mg/mL transferrin (Millipore Sigma, T5391), 30 nM sodium selenite (Millipore Sigma, T5391), 10 nM hydrocortisone (Millipore Sigma, H0135), 10 nM beta-estradiol (Millipore Sigma, E2557), 2 mM L-glutamine (ThermoFisher, 25030081) and 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
NCI-H1105 cells (ATCC, CRL-5856TM) were cultured in DMEM:F12 medium (ATCC, 30-2006) containing 5% heat-inactivated fetal bovine serum (Millipore Sigma, F4135), 0.005 mg/mL Insulin (ThermoFisher, 12585014), 0.01 mg/mL transferrin (Millipore Sigma, T5391), 30 nM sodium selenite (Millipore Sigma, T5391), 10 nM hydrocortisone (Millipore Sigma, H0135), 10 nM beta-estradiol (Millipore Sigma, E2557), 2 mM L-glutamine (ThermoFisher, 25030081) and 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
NCI-H2171 cells (ATCC, CRL-5929TM) were cultured in DMEM:F12 medium (ATCC, 30-2006) containing 5% heat-inactivated fetal bovine serum (Millipore Sigma, F4135), 0.005 mg/mL Insulin (ThermoFisher, 12585014), 0.01 mg/mL transferrin (Millipore Sigma, T5391), 30 nM sodium selenite (Millipore Sigma, T5391), 10 nM hydrocortisone (Millipore Sigma, H0135), 10 nM beta-estradiol (Millipore Sigma, E2557), 2 mM L-glutamine (ThermoFisher, 25030081) and 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
NCI-H2106 cells (ATCC, CRL-5923TM) cells were cultured in DMEM:F12 medium (ATCC, 30-2006) containing 5% heat-inactivated fetal bovine serum (Millipore Sigma, F4135), 0.005 mg/mL Insulin (ThermoFisher, 12585014), 0.01 mg/mL transferrin (Millipore Sigma, T5391), 30 nM sodium selenite (Millipore Sigma, T5391), 10 nM hydrocortisone (Millipore Sigma, H0135), 10 nM beta-estradiol (Millipore Sigma, E2557), 2 mM L-glutamine (ThermoFisher, 25030081) and 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
ASC52Telo cells (ATCC, SCRC-4000TM) were cultured in Mesenchymal Stem Cell Basal Medium (ATCC, PCS-500-030) + Mesenchymal Stem Cell Growth Kit (ATCC, PCS-500-040) + 0.2 mg/mL Geneticin (G418, InvivoGen, ant-gn-1).
CHON-001 cells (ATCC, CRL-2846TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, ATCC, 30-2002) + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 0.1 mg/mL Geneticin (G418, InvivoGen, ant-gn-1)
HBEC3-KT cells (ATCC, CRL-4051TM) were cultured in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) + Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040).
HSAEC1-KT cells (ATCC, CRL-4050TM) were cultured in SABMTM Small Airway Basal Medium (Lonza, CC-3119) + Small Airway Cell Growth Medium SingleQuotsTM Supplements and Growth Factors (Lonza, CC-4124).
hTERT-RPE1 cells (ATCC, CRL-4000TM) were cultured in DMEM:F12 medium (ATCC, 30-2006) + 0.01 mg/mL Hygromycin B (ThermoFisher, 10687010).
hTERT-HME1 cells (ATCC, CRL-4010TM) were cultured in MEBMTM Mammary Epithelial Cell Growth Basal Medium (Lonza, CC-3151) + MEGMTM Mammary Epithelial Cell Growth Medium SingleQuotsTM Kit (Lonza, CC-4136).
hTERT-HPNE cells (ATCC, CRL-4023TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Millipore Sigma, D-5030) with 2 mM L-glutamine (xxx) and 1.5 g/L sodium biocarbonate (xxx) and Medium M3 base (Incell Corp, M300F-500) in a 3:1 ratio + 5% heat-inactivated fetal bovine serum (Millipore Sigma, F4135) + 10 ng/mL human recombinant EGF (R & D Systems, 236-EG-200) + 5.5 mM D-glucose (Millipore Sigma, G7021) + 750 ng/mL Puromycin (InvivoGen, ant-pr-1).
HUVEC/TERT2 cells (ATCC, CRL-4053TM) were cultured in Vascular Cell Basal Medium (ATCC, PCS-100-030) + Endothelial Cell Growth Kit-VEGF (PSC-100-041, PSC-100-041).
Ker-CT cells (ATCC, CRL-4048TM) were cultured in KBM-GoldTM Keratinocyte Basal Medium (Lonza, 192151) + Keratinocyte Cell Growth Medium SingleQuotsTM Supplements and Growth Factors (Lonza, 192152).
RPTEC/TERT1 cells (ATCC, CRL-4031TM) were cultured in DMEM:F12 medium (ATCC, 30-2006) + hTERT Immortalized RPTEC Growth Kit (ATCC, ACS-4007) + 0.1 mg/mL Geneticin (G418, InvivoGen, ant-gn-1).
TeloHAEC cells (ATCC, CRL-4052TM) were cultured in Vascular Cell Basal Medium (ATCC, PCS-100-030) + Endothelial Cell Growth Kit-VEGF (ATCC, PSC-100-041) + 0.3 µg/mL Puromycin (InvivoGen, ant-pr-1).
TIME cells (ATCC, CRL-4025TM) were cultured in Vascular Cell Basal Medium (PCS-100-030) + Microvascular Endothelial Cell Growth Kit-VEGF (PSC-110-041) + 12.5 µg/mL Blasticidine S hydrochloride (Millipore Sigma, 15205).
ARPE-19 cells (ATCC, CRL-2302TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
HTB-9 cells (ATCC, 5637) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
A549 cells (ATCC, CRL-185TM) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning, 10-013-CV)  + 10% heat inactivated fetal bovie serum (Millipore Sigma, F4135) + 1X penicillin streptomycin glutamine (ThermoFisher, 10378016).
hNP1 cells (ArunA Biomedical) were cultured in Knockout DMEM/F-12 medium (ThermoFisher, 12660012) + 1X StemPro neural supplement (ThermoFisher, A1050801) + 1X GlutaMAX (ThermoFisher, 35050061) + 20 ng/mL human recombinant epidermal growth factor (EGF, ThermoFisher, PHG0311) and 20 ng/mL human recombinant basic fibroblast growth factor (FGF-basic, ThermoFisher, PHG0021).
HepaRG_2D: HepaRG cells (Lonza, NSHPRG) were cultured in a two-dimensional differentiated configuration as described in Ramaighari et al. (2019).
HepaRG_3D: HepaRG cells (Lonza, NSHPRG) were cultured in a three-dimensional differentiated configuration as described in Ramaighari and Ferguson (2019).

treatment_protocol: No treatments were applied to cultured cells other than those described in growth and extract protocols.

tag: cell line

tag: batch

value: Phase 1

tag: assay plate

tag: assay well

tag: growth mode

value: Adherent


title: lung.Het.1291307

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291307


title: hTERT-HME1, Phase 1, Replicate 2

description: Library name: TC00000367_B10


title: BJ-5ta, Phase 1, Replicate 2

description: Library name: TC00000367_C05


title: lung.WT.1291313

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291313


title: Rassf1a rep3


title: lung.WT.1291306

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291306


title: Rassf1a rep2


title: hTERT-HME1, Phase 1, Replicate 3

description: Library name: TC00000367_B11


title: Patient resected tumor P3-2

description: Library name: Sample 5


title: hTERT-RPE1, Phase 1, Replicate 3

description: Library name: TC00000367_C03


title: lung.Het.1291305

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291305


title: Rassf1a rep1


title: hTERT-HME1, Phase 1, Replicate 1

description: Library name: TC00000367_B09


title: HSAEC1-KT, Phase 1, Replicate 3

description: Library name: TC00000367_B08


title: Vhl/Rassf1a rep3


title: HSAEC1-KT, Phase 1, Replicate 2

description: Library name: TC00000367_B07


title: lung.Het.1291304

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291304


title: lung.WT.1291309

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291309


title: Sample4_explanted

city: Vancouver

first: Ying

last: Wang

state: British Columbia

address: 166-1081 Burrard St

department: Pathology and Laboratory Medicine, UBC

country: Canada

institute: Centre for Heart Lung Innovation - St. Paul's Hospital

description: Library name: Sample4

data_processing:
FASTQ files were created with the 10X Space Ranger Pipeline by Princess Margaret Genomic Centre (ON, Canada), with settings according to the manufacturer's protocol
Sequences were aligned to the GRCH38 human reference  by Princess Margaret Genomic Centre (ON, Canada) to generate gene counts, with settings according to the manufacturer's protocol
Assembly: GRCH38 Human Genome (version 2020-A)
Supplementary files format and content:
metrics_summary.csv: Run summary metrics in CSV format
filtered_feature_bc_matrix.h5: Contains only tissue-associated barcodes in HDF5 format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
molecule_info.h5: Contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or protein barcode.
raw_feature_bc_matrix.h5: Contains all detected barcodes in HDF5 format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
raw_probe_bc_matrix.h5: Contains UMI counts of each probe for all detected barcodes in HDF5 format.
probe_set.csv: Copy of the input probe set reference CSV file.
aligned_fiducials.jpg: Aligned fiducials of tissue image
aligned_tissue_image.jpg: Result of merging CytAssist and Microscope images
cytassist_image.tiff: Copy of the original CytAssist image input
detected_tissue_image.jpg: Shows aligned fiducial slows, bounding box to show capture spots within region of interest
scalefactors_json.json: Provides relative scale of user-supplied image, spatial output images, and Visium Array
spatial_enrichment.csv: Displays Moran's I value for each feature
tissue_hires_image.png: Hi-resolution image of sample
tissue_lowres_image.png: Low-resolution image of sample
tissue_positions.csv: contains spatial location on full resolution image for each capture spot
raw_matrix.mtx.gz: Combines raw_barcodes and raw_features into a sparse matrix, with capture spots as rows and features as columns
matrix.mtx.gz: Same as raw_matrix, but with only tissue-detected barcodes
raw_barcodes.tsv.gz: Contains all detected  barcodes
barcodes.tsv.gz: Contains all tissue-detected barcodes
raw_features.tsv.gz: Contains all detected features
features.tsv.gz: Contains only tissue-detected features
Library strategy: Spatial Transcriptomics

source_name: DIT Coronary Artery

extract_protocol:
FFPE tissue were mounted on Visium SD slides and stained by H&E
Library preparation and sequencing was performed by Princess Margaret Genomic Centre (ON, Canada) according to the manufacturer's protocol

value: DIT Coronary Artery

tag: tissue source

value: from freshly explanted hearts


title: Sample4d1_explanted

description: Library name: Sample4d1


title: Vhl rep4

value: Vhl KO


title: lung.WT.1291303

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291303


title: lung.WT.1291302

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291302


title: Vhl rep3


title: Vhl rep2


title: Sample3a1_explanted

description: Library name: Sample3a1


title: RPTEC/TERT1, Phase 1, Replicate 3

description: Library name: TC00000367_B05


title: MSCs scramble guide dCAS9-DNMT3A Day 11 Replica 2

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: Library name: control_R2

data_processing:
Trimming using TrimGalore.
Alignment (STAR).
Processing to count matrices (salmon).
Assembly: hg38
Supplementary files format and content: quant.sf files with counts.

source_name: bone marrow

growth_protocol: Primary human mesenchymal stromal cells were isolated from bone-marrow samples of patients undergoing orthopedic surgery after written and informed consent. Cells of three donors were cultured in DMEM low-glucose (Sigma-Aldrich) supplemented with pooled human platelet lysate (10%), L-Glutamine (2mM, GibcoTM), penicillin-streptomycin (100U/ml, GibcoTM) and heparin (5 IU/ml, B. Braun) at 37°C / 5% CO2.

extract_protocol:
RNA was isolated using the RNA plus kit (Macherey Nagel).
QuantSeq 3´-mRNA Library Prep / Lexogen.

treatment_protocol: For transfection of MSCs 1 million cells, 2.5μg of plasmids for CRISPR-constructs, and 2.5μg of gRNA plasmids were combined inside of a NEON 100ul pipet tip with 1 pulse (20ms) at 1700V. Cells were cultured in the above mentioned MSC culture medium, but without antibiotics for the first 24 hours. After 48 hours, cells were resuspended in MACS buffer for flow cytometric sorting for double positive cells (BD FACSAriaTM fusion) and further cultured for 11 days.

value: bone marrow

value: Mesenchymal stromal cell

tag: treatment

value: scramble guide + dCAS9-DNMT3A/3L

tag: time point

value: isolation after 11 days after transfection


title: Sample2_autopsy

description: Library name: Sample2

value: from autopsies


title: lung.WT.1291301

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291301


title: Vhl rep1


title: lung.Het.1291300

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291300


title: MSCs HyperCpGs targeted dCAS9-DNMT3A Day 11 Replica 2

description: Library name: experiment_R2

value: guides HyperCpGs + dCAS9-DNMT3A/3L


title: RPTEC/TERT1, Phase 1, Replicate 2

description: Library name: TC00000367_B04


title: RPTEC/TERT1, Phase 1, Replicate 1

description: Library name: TC00000367_B03


title: WT rep4

value: kidney

value: WT


title: lung.Het.1291299

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291299


title: WT rep3

value: proximal tubule epithelial cell


title: GLORI_3_100ng_totalRNA_rep3

city: Beijing

first: Bo

last: Lu

address: Yiheyuan Road No.5

department: School of Life Sciences

country: China

institute: Peking University

description: Library name: Sample 27

data_processing:
Raw reads were treated by Trim Galore (v0.6.6) for adaptor trimming and quality control with the following parameters: "--nextseq 20 --phred33 --clip_R1 3 --stringency 1 -e 0.3 --length 25". Then trimmed reads were deduplicated by Seqkit (v0.13.2) using the following parameters: "seqkit rmdup -j 20 -s".
Clean reads were mapped to A-to-G converted versions of the genome with STAR (v2.7.5c) and then transcriptome with bowtie (v1.3.0).
high-confidence m6A sites were identified and quantified by GLORI-tools (https://github.com/liucongcas/GLORI-tools).
Assembly: GRCh38/GRCm38
Supplementary files format and content: The files ending with "totalm6A.FDR.txt" contain information of high-confidence m6A sites. "Chr": chromosome; "Sites": genomic loci; "Strand": DNA strand; "Gene": annotated gene; "CR": conversion rate for genes; "AGcov": the number of reads that cover the site with A and G; "Acov": the number of readsthat cover the site with A. "Genecov": mean coverage for the whole gene; "Ratio": methylation level for the site; "Pvalue": P value of the test for A rate based on the background; P_adjust: FDR adjusted P value.
Supplementary files format and content: The files ending with "genes.fpkm.txt" contain gene names and gene expression values (FPKM).
Library strategy: GLORI

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C; Male C57BL/6J mice (6-week-old) were housed in a specific-pathogen-free barrier. The barrier maintained 12-hour light-dark cycle and 22 ± 1°C room temperature with ~50% humidity.

extract_protocol:
mRNA was purified by oligo (dT) beads. Mice hippocampus samples were performed Ribo-off treatment.
RNA libraries were prepared using  SMARTer Stranded Total RNA-Seq kits (v2) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.


title: lung.WT.1291298

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291298


title: Sample2d1_autopsy

description: Library name: Sample2d1


title: WT rep2


title: ASC52Telo, Phase 1, Replicate 3

description: Library name: TC00000367_B02


title: GLORI_3_20ng_totalRNA_rep1

description: Library name: Sample 28


title: GLORI_3_100ng_totalRNA_rep2

description: Library name: Sample 26


title: WT rep1


title: HSAEC1-KT, Phase 1, Replicate 1

description: Library name: TC00000367_B06


title: lung.WT.1291296

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291296


title: GLORI_3_100ng_totalRNA_rep1

description: Library name: Sample 25


title: ASC52Telo, Phase 1, Replicate 1

description: Library name: TC00000367_A11


title: Ker-CT, Phase 1, Replicate 3

description: Library name: TC00000367_A10

source_name: Ker-CT

value: Ker-CT


title: GLORI_2_20ng_totalRNA_rep2

description: Library name: Sample 24


title: lung.WT.1291295

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291295

value: lung


title: scRNA_TET2_KO_PINO_DAY21_REP1

city: Toronto

first: Yitong

last: Yang

address: 101 College st

institute: University of Toronto

data_processing:
The FATSQ files were processed using Cellranger v7.0.0 pipeline to generate count matrices. Cells were filtered using the following cutoffs: 200 < nFeature < 9000; percent of mitochondrial reads < 12.5. The filtered reads were then normalized accounting for cell cycle difference using the SCTransform function from the Seurat package (v5.0.1).
Assembly: mm10
Supplementary files format and content: matrix files

extract_protocol:
Mice were then euthanized after 3 weeks of treatment and Lin-Kit+ (LK) bone marrow cells were enriched from the bone marrow using selection kits (STEMCELL, #19856 and #18757). The purified cells were resuspended in IMDM medium (Wisent, #319-105-CL) for subsequent procedures.
The purified cells were subjected to library preparation using 10x Genomics Chromium Single Cell 3′ v3.1 kit and 3’ sequencing on illumina Novaseq 6000 sequencing system.

value: bone marrow cells

value: HSPC

value: TET2 knockout

value: Pinometostat 60mg/kg BID


title: Ker-CT, Phase 1, Replicate 2

description: Library name: TC00000367_A09

value: Phase 1

value: Adherent


title: scRNA_TET2_KO_PINO_DAY21_REP2

value: bone marrow


title: lung.Het.1291294

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291294


title: Ker-CT, Phase 1, Replicate 1

description: Library name: TC00000367_A08


title: GLORI_2_20ng_totalRNA_rep1

description: Library name: Sample 23


title: GLORI_2_100ng_totalRNA_rep2

description: Library name: Sample 22


title: scRNA_TET2_KO_VEH_DAY21_REP1

value: VEHICLE


title: Sample1a1_autopsy

description: Library name: Sample1a1

value: DIT Coronary Artery


title: lung.Het.1291292

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291292


title: TIME, Phase 1, Replicate 2

description: Library name: TC00000367_A06

source_name: TIME

value: TIME


title: ASC52Telo, Phase 1, Replicate 2

description: Library name: TC00000367_A12


title: TIME, Phase 1, Replicate 3

description: Library name: TC00000367_A07


title: scRNA_WT_PINO_DAY21_REP2

value: wildtype


title: GLORI_2_100ng_totalRNA_rep1

description: Library name: Sample 21


title: TIME, Phase 1, Replicate 1

description: Library name: TC00000367_A05


title: lung.Het.1291293

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291293


title: lung.Het.1291290

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291290


title: GLORI_2_STM2457+_rep1

description: Library name: Sample 19

molecule: polyA RNA


title: GLORI_2_STM2457+_rep2

description: Library name: Sample 20


title: lung.Het.1291291

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291291


title: scRNA_WT_PINO_DAY21_REP1


title: TeloHAEC, Phase 1, Replicate 3

description: Library name: TC00000367_A04

source_name: TeloHAEC

value: TeloHAEC


title: scRNA_WT_VEH_DAY21_REP2


title: GLORI_2_IVT_rep3

description: Library name: Sample 18


title: GLORI_2_IVT_rep2

description: Library name: Sample 17


title: TeloHAEC, Phase 1, Replicate 2

description: Library name: TC00000367_A03


title: scRNA_WT_VEH_DAY21_REP1


title: TeloHAEC, Phase 1, Replicate 1

description: Library name: TC00000367_A02


title: KO_SGC0946_1uM_DAY7_ChIP-seq_REP2

description: 8_0CDO_01RMPMCC_KO-SGC2_H3K79me2_mm-dm_i67

library_source: genomic

data_processing:
Illumina base-call data were processed and demultiplexed using bcl2fastq2 v2.20 and low-quality bases with Phred scores less than 33 were trimmed. 75 bp single-end sequence reads were subsequently mapped to the genome through BWA v0.7.12 algorithm with default settings. Low quality reads were filtered out and PCR duplicates were removed. Aligned sequencing reads, or tags, were extended to 200bp from the 3’ end, followed by dividing the genome into 32bp bins and counting the number of fragments in each bin. Determination of enriched regions was done using SICER 1.1 peak calling tool, with FDR < 1e-10 and gap parameter of 600bp used as cutoffs. False ChIP-seq peaks as defined within the ENCODE blacklist were removed. Differential methylation analysis was conducted using DiffBind R package version 3.10.0 and signals from each sample were normalized to library size. Hypermethylated regions in pairwise comparisons were defined using log2(FC in normalized reads) > 1.5 and padj <0.01 as cutoffs. Hypomethylated regions were defined using log2(FC in normalized reads) < -1.5 and padj <0.01 as cutoffs. Average peak signals from two replicates of each sample were obtained through randomly sampling 50 percent of reads from the corresponding BAM file of each replicate, and then merged using Samtools version 1.14.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

growth_protocol: Cells were cultured in HPCHOXB4 growth media containing DMSO (0.01%) or SGC0946 (1uM) for seven days prior to harvest.

extract_protocol:
Cells were fixed with 1% formaldehyde (Thermo Scientic, #410730050) according to the Active MotifChIP cell extraction protocol. Fixed cell pellets were submitted to Active Motif for ChIP-seq analysis. Birefly, 15ug of chromatin and 10uL of H3K79me2 antibody (Active Motif, #39143) were used for each IP reaction.
Library preparation and sequencing were conducted by Active Motif.

value: SGC0946 1uM

tag: antibody


title: GLORI_2_IVT_rep1

description: Library name: Sample 16


title: lung.Het.1291288

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291288


title: lung.WT.1291287

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291287


title: HepaRG (3D), Phase 1, Replicate 3

description: Library name: TC00000366_A07

source_name: HepaRG

value: HepaRG

value: Spheroid


title: GLORI_2_2ng_mRNA_rep3

description: Library name: Sample 15


title: KO_SGC0946_1uM_DAY7_ChIP-seq_REP1

description: 7_0CDN_01RMPMCC_KO-SGC1_H3K79me2_mm-dm_i64

value: H3K79me2 antibody (Active Motif, #39143)


title: lung.WT.1291297

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291297

value: lung


title: GLORI_2_2ng_mRNA_rep2

description: Library name: Sample 14


title: HepaRG (3D), Phase 1, Replicate 2

description: Library name: TC00000366_A06


title: HepaRG (3D), Phase 1, Replicate 1

description: Library name: TC00000366_A05


title: lung.WT.1291285

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291285


title: GLORI_2_2ng_mRNA_rep1

description: Library name: Sample 13


title: lung.Het.1291289

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291289


title: KO_DMSO_DAY7_ChIP-seq_REP2


title: HepaRG (2D), Phase 1, Replicate 3

description: Library name: TC00000366_A04


title: WT_SGC0946_1uM_DAY7_ChIP-seq_REP2

description: 6_0CM0_01RMPMCC_WT-SGC2_H3K79me2_mm-dm_i43


title: GLORI_2_10ng_mRNA_rep3

description: Library name: Sample 12


title: WT_SGC0946_1uM_DAY7_ChIP-seq_REP1

description: 5_0CLZ_01RMPMCC_WT-SGC1_H3K79me2_mm-dm_i39


title: lung.Het.1291286

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291286


title: lung.WT.1291283

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291283


title: KO_DMSO_DAY7_ChIP-seq_REP1


title: lung.WT.1291284

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291284


title: GLORI_2_10ng_mRNA_rep2

description: Library name: Sample 11


title: GLORI_2_10ng_mRNA_rep1

description: Library name: Sample 10


title: HepaRG (2D), Phase 1, Replicate 1

description: Library name: TC00000366_A02


title: lung.Het.1291281

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291281


title: WT_DMSO_DAY7_ChIP-seq_REP1


title: lung.Het.1291280

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291280


title: RNA-seq_GDF10 Replicate 4

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RNA-seq_GDF10-4

data_processing:
RNA-seq reads were mapped using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon). The reads were mapped to the rn6 genome (Rnor_6.0).
Transcription abundance estimates generated by Salmon
Assembly: rn6
Supplementary files format and content: quant.sf file generated by Salmon: tab-delimited txt file containing TPM results for reads aligned to the standard rn6 genome. Quantification is done on the transcript level.

organism: Rattus norvegicus

source_name: cardiomyocytes

growth_protocol: Isolated primary cardiomyocytes were grown in DMEM medium supplemented with 2% FBS, 1X PenStrep antibiotic . Cells were incubated in a 6-well plate at 37C with 5% carbon dioxide in an upright position with vented.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Isolation Kit (Macherey-Nagel, Germany) according to the manufacturer's instructions.; quality and quantity determined by nanodrop and RNA TapeStation
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation protocol.

treatment_protocol: Following ~40 hours of growth in vitro, neonatal rat cardiomyocytes in independent culture wells were incubated in 1X DMEM with GDF10 (10 or 50 ng/uL), BMP2 (50 ng/uL) or ACTVA (50 ng/uL) for 48 hours at 37ºC. At 48 hours post-treatment, cells were washed in warm Dulbecco’s sterile PBS, scraped with lysis buffer from NucleoSpin RNA Isolation Kit (Macherey-Nagel, Germany) and then flash-frozen in liquid nitrogen for mRNA isolation.

value: cardiomyocytes


title: RNA-seq_GDF10 Replicate 3

description: Library name: RNA-seq_GDF10-3


title: GLORI_2_50ng_mRNA_rep2

description: Library name: Sample 8


title: lung.WT.1291279

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291279


title: YF, replicate 2, scATACseq

city: Daejeon

first: Kwon Yong

last: Tak

address: Gu Sung Street

country: South Korea

institute: KAIST

description: 10x Genomics

data_processing:
The barcoded processing, sequence mapping and gene counting were done using cellranger-atac-2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tsv files, matrix files, and bed files

molecule: nuclear RNA

source_name: liver

extract_protocol:
Liver was extracted from transcardiac perfused mouse and enzyme dissociated to cell level.
Library was performed according to the manufacter’s instructions (Chromium Next GEM single cell ATAC v2, 10x Genomics). Cells were lysed using cold lysis buffer. The nuclei concentration was determined using Countess II Automated Cell Counter and the nuclei morphology was examined using microscopy.

value: liver cells

value: liver

tag: strain

tag: age

value: 6 months old


title: RNA-seq_GDF10 Replicate 2

description: Library name: RNA-seq_GDF10-2


title: YF, replicate 1, scATACseq

description: 10x Genomics


title: lung.Het.1291278

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291278


title: GLORI_1_10ng_mRNA_rep3

description: Library name: Sample 6


title: scRNA_TET2_KO_VEH_DAY21_REP2

value: bone marrow cells

value: HSPC

value: TET2 knockout


title: HepaRG (2D), Phase 1, Replicate 2

description: Library name: TC00000366_A03

value: Phase 1

value: Adherent


title: lung.Het.1291277

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291277


title: RNA-seq_Control Replicate 4

description: Library name: RNA-seq_Control-4


title: OF, replicate 2, scATACseq

description: 10x Genomics

value: 24 months old


title: RNA-seq_GDF10 Replicate 1

description: Library name: RNA-seq_GDF10-1


title: lung.Het.1291276

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291276


title: GLORI_1_10ng_mRNA_rep2

description: Library name: Sample 5


title: OF, replicate 1, scATACseq

description: 10x Genomics


title: GLORI_1_10ng_mRNA_rep1

description: Library name: Sample 4


title: WT_DMSO_DAY7_ChIP-seq_REP2

value: bone marrow

value: wildtype


title: lung.Het.1291282

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291282


title: RNA-seq_Control Replicate 3

description: Library name: RNA-seq_Control-3


title: RNA-seq_Control Replicate 2

description: Library name: RNA-seq_Control-2


title: GLORI_2_50ng_mRNA_rep3

description: Library name: Sample 9


title: RNA-seq_Control Replicate 1

description: Library name: RNA-seq_Control-1


title: GLORI_1_50ng_mRNA_rep3

description: Library name: Sample 3


title: lung.WT.1291275

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291275


title: YF, replicate 3

description: 10x Genomics

data_processing:
The barcoded processing, sequence mapping and gene counting were done using the Cell Ranger software v 4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

extract_protocol:
Liver was extracted from transcardiac perfused mouse and enzyme dissociated to cell level.
Library was performed according to the manufacter’s instructions (Chromium Single Cell 3′ Reagent Kit v3.1, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: YF, replicate 2

description: 10x Genomics


title: lung.Het.1291274

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291274


title: lung.WT.1291273

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291273


title: YF, replicate 1

description: 10x Genomics


title: GLORI_1_50ng_mRNA_rep2

description: Library name: Sample 2


title: GLORI_1_50ng_mRNA_rep1

description: Library name: Sample 1


title: OF, replicate 5

description: 10x Genomics

value: 22~24 months old


title: lung.Het.1291272

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291272


title: GLORI_2_50ng_mRNA_rep1

description: Library name: Sample 7


title: Donor 4, Clone 02, Bad Killer, 2 months cultured

city: London

first: Daniel

last: Davis

address: Exhibition Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: Sample 27
LongTermCultured_STARcounts.Rinput
CR11

data_processing:
Unmapped paired-reads of 76bp from an Illumina HiSeq4000 sequencer were examined using a quality control pipeline consisting of FastQC v0.11.3 and FastQ Screen v0.13.0. The reads were trimmed to remove any adapter or poor quality sequence using Trimmomatic v0.39 (Bolger, Lohse, and Usadel 2014); reads were truncated at a sliding 4bp window, starting 5’, with a mean quality <Q20, and removed if the final length was less than 35bp.  Additional flags included: 'ILLUMINACLIP:./Truseq3-PE-2_Nextera-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35'. Normalisation and differential expression analysis was performed using DESeq2 v1.22.2 on R v3.5.0 (Love, Huber, and Anders 2014).  Factors for donor and killing-status were included in the model, or status alone.  Log fold change shrinkage was applied using the lfcShrink function along with the "apeglm" algorithm.
Assembly: The filtered reads were mapped to the human reference sequence analysis set (hg38/Dec. 2013/GRCh38) from the UCSC browser, using STAR v2.7.2b (Dobin et al. 2013).  The genome index was created using the comprehensive Gencode v35 gene annotation (Harrow et al. 2012) applying a flag suitable for the read length (--sjdbOverhang 75). During mapping the flags ‘--quantMode GeneCounts’ was used to generate read counts into genes.
Supplementary files format and content: Rinput files with gene counts for each sample

source_name: Peripheral Blood

extract_protocol:
RNA was extracted using the RNeasy® Mini Kit (Qiagen). For each clone, 1ug of RNA was used for next-generation sequencing.
RNA libraries were prepared using Illumina stranded mRNA prep kit, labelled using dual unique barcodes and pooled prior to loading onto the Illumina HiSeq 4000 system.

value: Peripheral Blood

value: Natural Killer Cell Clone

value: Long-term cultured


title: OF, replicate 4

description: 10x Genomics


title: lung.Het.1291271

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291271

value: lung


title: Donor 4, Clone 17, Good Killer, 2 months cultured

description:
Library name: Sample 25
LongTermCultured_STARcounts.Rinput
CR8


title: Donor 4, Clone 16, Good Killer, 2 months cultured

description:
Library name: Sample 26
LongTermCultured_STARcounts.Rinput
CR7


title: HEK293T scramble guide dCAS9-DNMT3A Day 7 Replica 3

data_processing:
Trimming using TrimGalore
alignment (STAR)
processing to count matrices (salmon)
Assembly: hg38
Supplementary files format and content: quant.sf files with counts

growth_protocol: HEK293T cells were cultured in Dulbecco's Modified Eagle Medium (GibcoTM) with 10% fetal calf serum (FCS; Bio&Sell) and Penicillin-Streptomycin (Life Technologies) at 37°C / 5% CO2, and passaged manually at 80 - 90% confluency.

extract_protocol:
RNA was isolated using the RNA plus kit (Macherey Nagel).
QuantSeq 3´-mRNA Library Prep / Lexogen

treatment_protocol: HEK293T cells were transfected with the TransIT®-LT1 transfection reagent (Mirus Bio) in 6-well plates with 1.25μg of plasmids for the CRISPR-construct and 1.25μg of plasmids for single gRNA. We either pooled two gRNAs targeting PDE4C or up to nine gRNAs for multiplexed editing. After 24 hours we selected the transfected cells either by puromycin treatment (2 ug/ml for 2 days) or flowcytometric sorting for double positive cells (BD FACSAriaTM fusion).

value: scramble guide + dCAS9-DNMT3A/3L

value: isolation after 7 days of culture


title: lung.Het.1291270

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291270


title: Donor 3, Clone 29, Good Killer, 5 months cultured

description:
Library name: Sample 24
LongTermCultured_STARcounts.Rinput
CR10


title: HEK293T scramble guide dCAS9-DNMT3A Day 7 Replica 2


title: lung.Het.1291269

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291269


title: OF, replicate 1

description: 10x Genomics

value: liver cells

value: liver


title: HEK293T HyperCpGs targeted dCAS9-DNMT3A Day 7 Replica 3

value: guides HyperCpGs + dCAS9-DNMT3A/3L


title: lung.Het.1291268

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291268


title: Donor 3, Clone 25, Bad Killer, 5 months cultured

description:
Library name: Sample 23
LongTermCultured_STARcounts.Rinput
CR9


title: HEK293T scramble guide dCAS9-DNMT3A Day 7 Replica 1


title: Donor 3, Clone 23, Bad Killer, 2 months cultured

description:
Library name: Sample 22
LongTermCultured_STARcounts.Rinput
CR5


title: lung.Het.1291267

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291267


title: HEK293T HyperCpGs targeted dCAS9-DNMT3A Day 7 Replica 2


title: Donor 3, Clone 50, Bad Killer, 2 months cultured

description:
Library name: Sample 21
LongTermCultured_STARcounts.Rinput
CR2


title: Donor 3, Clone 17, Good Killer, 2 months cultured

description:
Library name: Sample 20
LongTermCultured_STARcounts.Rinput
CR4


title: lung.WT.1291266

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291266


title: OC, replicate 6

description: 10x Genomics


title: OC, replicate 4

description: 10x Genomics


title: Donor 3, Clone 54, Good Killer, 2 months cultured

description:
Library name: Sample 19
LongTermCultured_STARcounts.Rinput
CR3


title: HEK293T HyperCpGs targeted dCAS9-DNMT3A Day 7 Replica 1


title: OC, replicate 5

description: 10x Genomics


title: OC, replicate 3

description: 10x Genomics


title: lung.WT.1291265

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291265


title: lung.WT.1291264

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291264


title: Donor 3, Clone 43, Good Killer, 2 months cultured

description:
Library name: Sample 18
LongTermCultured_STARcounts.Rinput
CR1


title: Ionizing radiation-induced senescence, rep 6

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
Raw reads were trimmed using Lianti analysis toolkit
Trimmed reads were aligned to reference genome using bwa
Aligned reads were sorted and filtered by samtools
Copy number variation were called by ginkgo
Assembly: hg38
Supplementary files format and content: deletions detected in each sample in a bed format.
Library strategy: single nucleus WGS

growth_protocol: IMR90 primary human fibroblasts were grown at 37°C, 3.5% O2, 5% CO2, in Dulbecco’s modified Eagle’s medium (Gibco 10313-121) with 10% FBS (Corning 35-0-11-CV), 1% penicillin/streptomycin (Gibco 15140-122) and 2 mM glutamine (Gibco 25030-081). Cells were checked routinely for mycoplasma contamination.

extract_protocol:
Cells were trypsinized, washed in PBS, and resuspended at 20x cell pellet volume in cold nuclear isolation buffer A with digitonin (50 nM HEPES pH 7.3, 150 mM NaCl, 1x dual protease and phosphatase inhibitor, 25 g/mL digitonin) by pipetting. The suspensions were rotated at 4°C for 30 minutes, then centrifuged at 500g for 5 minutes at 4°C. Nuclear pellets were washed twice with cold NIB-250 buffer (250 mM sucrose, 15mM Tris-Cl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2) and resuspended in sorting buffer (DPBS with 2% FBS, 0.5 mM spermidine, 500 ng/mL DAPI). Nuclei were sorted by FACSAriaII with a 100um nozzle (see also Fig.S7) into individual strip tubes containing LIANTI lysis buffer.
LIANTI

treatment_protocol: IR senescence was induced by 20 Gray x-ray irradiation of 20-30% confluent cells. Cells were split after returning to confluence in 3 days and collected 10 days after IR.

value: fibroblast

value: wild type

value: 20 Gy irradiation


title: OF, replicate 2

description: 10x Genomics


title: Ionizing radiation-induced senescence, rep 5


title: OC, replicate 2

description: 10x Genomics


title: OC, replicate 1

description: 10x Genomics


title: kidney.WT.1291263

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291263

value: kidney


title: Donor 2, Clone 235, Bad Killer

description:
Library name: Sample 17
ShortTermCultured_STARcounts.Rinput
CR10

value: Short-term cultured


title: kidney.Het.1291262

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291262


title: Ionizing radiation-induced senescence, rep 4


title: Ionizing radiation-induced senescence, rep 3


title: Donor 2, Clone 59, Bad Killer

description:
Library name: Sample 16
ShortTermCultured_STARcounts.Rinput
CR1


title: kidney.Het.1291260

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291260


title: Ionizing radiation-induced senescence, rep 2


title: kidney.WT.1291261

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291261


title: OF, replicate 3

description: 10x Genomics


title: KO_SGC0946_1uM_DAY7_REP2

description: the reverse read file for this sample was corrupted so it has fewer reads than the forward read file

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 system. Reads containing adaptors and low-quality reads with Phred scores less than 33 were filtered. Clean reads were then mapped to the reference genome using the STAR software v2.6.1d. Quantification of mapped reads was conducted on FeatureCounts (v1.5.0-p3) program and default parameters were applied.
Assembly: mm10
Supplementary files format and content: The processed data file contains FPKM values of all sequenced genes grouped by gene name
Supplementary files format and content: excel sheet

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy plus kit (Qiagen, #74134) and quantified using a Nanodrop spectrophotometer. All samples had a RIN value greater than 9.
Samples were submitted to Novogene Corporation for sequencing analysis. Library construction, sequencing, and processing of sequencing data were done by Novogene following their standard pipeline.

treatment_protocol: Cells were cultured in HPCHOXB4 growth medium supplemented with DMSO or SGC0946 at 1uM for seven days prior to harvest.

value: bone marrow

value: HSPC

value: TET2 knockout

value: SGC0946 1uM


title: Ionizing radiation-induced senescence, rep 1


title: Donor 2, Clone 100, Bad Killer

description:
Library name: Sample 14
ShortTermCultured_STARcounts.Rinput
CR4

value: Peripheral Blood

value: Natural Killer Cell Clone


title: KO_SGC0946_1uM_DAY7_REP1


title: WT_SGC0946_1uM_DAY7_REP1

description: raw data files for this sample were corrupted and are not included in the submission

value: wildtype


title: irradiation-induced senescent, RG7388, rep 6

data_processing:
The first 14 nt of both R1 and R2 reads were trimmed using CutAdapt
Trimmed reads were aligned to reference genome using bwa
Aligned reads were sorted and filtered by samtools
Copy number variation were called by ginkgo
Assembly: hg38
Supplementary files format and content: deletions detected in each sample in a bed format.
Library strategy: single nucleus WGS

extract_protocol:
Cells were trypsinized, washed in PBS, and resuspended at 20x cell pellet volume in cold nuclear isolation buffer A with digitonin (50 nM HEPES pH 7.3, 150 mM NaCl, 1x dual protease and phosphatase inhibitor, 25 g/mL digitonin) by pipetting. The suspensions were rotated at 4°C for 30 minutes, then centrifuged at 500g for 5 minutes at 4°C. Nuclear pellets were washed twice with cold NIB-250 buffer (250 mM sucrose, 15mM Tris-Cl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2) and resuspended in sorting buffer (DPBS with 2% FBS, 0.5 mM spermidine, 500 ng/mL DAPI). Nuclei were sorted by FACSAriaII with a 100um nozzle (see also Fig.S7) into individual strip tubes containing LIANTI lysis buffer.
PicoPLEX Gold

treatment_protocol: Cells were split after returning to confluence in 3 days, then treated with MDM2 inhibitors, RG7388 (Selleckchem), 5 minutes after IR. Drugs were replaced by media change every 3 days after irradiation and collected 11 days after IR


title: Donor 2, Clone 63, Bad Killer

description:
Library name: Sample 12
ShortTermCultured_STARcounts.Rinput
CR2


title: Proliferating, rep 2


title: kidney.Het.1291256

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291256


title: irradiation-induced senescent, RG7388, rep 5


title: kidney.WT.1291259

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291259


title: Proliferating, rep 1


title: kidney.WT.1291258

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291258


title: Donor 2, Clone 65, Bad Killer

description:
Library name: Sample 13
ShortTermCultured_STARcounts.Rinput
CR3


title: KO_SGC0946_1uM_DAY7_REP3


title: Donor 2, Clone 197, Good Killer

description:
Library name: Sample 10
ShortTermCultured_STARcounts.Rinput
CR8


title: Donor 2, Clone 182, Good Killer

description:
Library name: Sample 11
ShortTermCultured_STARcounts.Rinput
CR6


title: irradiation-induced senescent, RG7388, rep 4


title: kidney.WT.1291254

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291254


title: irradiation-induced senescent, RG7388, rep 3


title: KO_DMSO_DAY7_REP1


title: Donor 2, Clone 204, Bad Killer

description:
Library name: Sample 15
ShortTermCultured_STARcounts.Rinput
CR9


title: KO_DMSO_DAY7_REP2


title: Donor 2, Clone 193, Good Killer

description:
Library name: Sample 8
ShortTermCultured_STARcounts.Rinput
CR7


title: kidney.Het.1291257

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291257


title: WT_SGC0946_1uM_DAY7_REP2

description: the reverse read file for this sample was corrupted so the forward read file was submitted as a single-end run


title: irradiation-induced senescent, RG7388, rep 2


title: kidney.WT.1291253

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291253


title: WT_SGC0946_1uM_DAY7_REP3


title: Donor 2, Clone 160, Good Killer

description:
Library name: Sample 7
ShortTermCultured_STARcounts.Rinput
CR5


title: irradiation-induced senescent, RG7388, rep 1


title: WT_DMSO_DAY7_REP3


title: KO_DMSO_DAY7_REP3


title: kidney.WT.1291255

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291255


title: WT_DMSO_DAY7_REP2


title: kidney.WT.1291251

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291251


title: irradiation-induced senescent, DMSO, rep 4

value: DMSO, 20 Gy IR


title: WT_DMSO_DAY7_REP1


title: kidney.WT.1291252

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291252


title: Donor 1, Clone 24, Bad Killer

description:
Library name: Sample 6
ShortTermCultured_STARcounts.Rinput
KS3


title: vehicle, 5 months, female, rep 5

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: mm10
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

growth_protocol: This study was approved by the Institutional Animal Care and Use Committee at Sanford Burnham Prebys MDI. C57BL6 mice were purchased from Jackson Labs and Charles River and group housed under specific pathogen free conditions with ad libitum access to water and food (Teklad 2018).

extract_protocol:
Fresh liver was lysed in Trizol (Ambion 15596026), and RNA was isolated with chloroform according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 10 mg/kg HDM201 (Novartis) suspended in phosphate-buffered methylcellulose according to the manufacturer’s instructions (0.5% methylcellulose in phosphate buffer, pH6.8, 50mM) by daily oral gavage in the morning. Mice were monitored daily and weighed every 2-3 days during treatment. After 14 days of treatment, mice were euthanized by CO2 asphyxiation in the morning

value: 5 months

tag: gender

value: female

value: Vehicle


title: Donor 1, Clone 33, Good Killer

description:
Library name: Sample 4
ShortTermCultured_STARcounts.Rinput
KS5


title: kidney.Het.1291248

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291248


title: kidney.WT.1291249

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291249


title: irradiation-induced senescent, DMSO, rep 3


title: Donor 2, Clone 277, Good Killer

description:
Library name: Sample 9
ShortTermCultured_STARcounts.Rinput
CR11


title: kidney.Het.1291247

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291247


title: irradiation-induced senescent, DMSO, rep 2


title: Donor 1, Clone 39, Good Killer

description:
Library name: Sample 3
ShortTermCultured_STARcounts.Rinput
KS6


title: irradiation-induced senescent, DMSO, rep 1


title: vehicle, 5 months, female, rep 4

value: liver


title: proliferating, DMSO, rep 4

value: fibroblast

value: DMSO


title: vehicle, 5 months, female, rep 2


title: Donor 1, Clone 29, Good Killer

description:
Library name: Sample 2
ShortTermCultured_STARcounts.Rinput
KS4


title: kidney.WT.1291246

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291246


title: vehicle, 5 months, female, rep 1


title: proliferating, DMSO, rep 2

value: wild type


title: vehicle, 5 months, female, rep 3


title: Homo sapiens, Ishikawa Cells, experiment ETV6 overexpress, biol rep2

city: Shanghai

first: Siqi

last: Fei

address: No. 2005, Songhu Road

institute: Fudan University

description:
Library name: PE-2
Column name gene_count.txt: PE-2

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters. The expression count matrix was obtained by FeatureCounts.
Assembly: hg38
Supplementary files format and content: Tab separated table count values of genes for each sample

source_name: Ishikawa

growth_protocol: Ishikawa cells (Shanghai iCell Cellverse, Cat#iCell-h113) were cultured in DMEM/F12 medium (Gibco, Cat#11320033) supplemented with 10% fetal bovine serum (FBS; Gibco,Cat#10099) and Penicillin-Streptomycin (100U/mL, Invitrogen, Cat#15070063). Cells were maintained at 37°C with 21% O2 and 5% CO2. Ishikawa cells were infected with lentiviruses expressing EV or pCDH-ETV6.

extract_protocol:
RNA was harvested using TRIzol Reagent (Thermo Fisher, Cat#15596018CN). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA extracted according to the manufacturer’s instructions. RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: Ishikawa

value: experiment


title: proliferating, DMSO, rep 3


title: Donor 1, Clone 03, Bad Killer

description:
Library name: Sample 5
ShortTermCultured_STARcounts.Rinput
KS1

value: Short-term cultured


title: kidney.Het.1291244

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291244

value: kidney


title: Homo sapiens, Ishikawa Cells, experiment ETV6 overexpress, biol rep3

description:
Library name: PE-3
Column name gene_count.txt: PE-3


title: kidney.Het.1291245

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291245


title: Donor 1, Clone 45, Good Killer

description:
Library name: Sample 1
ShortTermCultured_STARcounts.Rinput
KS7


title: proliferating, DMSO, rep 1


title: kidney.Het.1291243

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291243


title: kidney.WT.1291250

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291250


title: vehicle, 5 months, male, rep 3

value: male


title: vehicle, 5 months, male, rep 5


title: Homo sapiens, Ishikawa Cells, control blank, biol rep2

description:
Library name: NC-2
Column name gene_count.txt: NC-2

value: Control blank


title: IMR90 cells, IR, HDM201, rep 1

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: hg38
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

extract_protocol:
Cells were lysed in Trizol (Ambion 15596026) and RNA was isolated using  a commercial kit (Zymo Directzol)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were split after returning to confluence in 3 days, then treated with MDM2 inhibitors, RG7388 (Selleckchem) and HDM201 (Novartis), starting day 4. Drugs were replaced by media change every 3 days after irradiation (day 4, 7, and 10 after IR) and collected 11 days after IR.

tag: condition

value: IR


title: IMR90 cells, IR, HDM201, rep 3


title: vehicle, 5 months, male, rep 4


title: Homo sapiens, Ishikawa Cells, experiment ETV6 overexpress, biol rep1

description:
Library name: PE-1
Column name gene_count.txt: PE-1


title: Homo sapiens, Ishikawa Cells, control blank, biol rep1

description:
Library name: NC-1
Column name gene_count.txt: NC-1


title: kidney.WT.1291242

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291242

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina bcl2fastq v2.17.
Reads were decoded based on their barcodes and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (NCBI GRCm38) using ArrayStudio software (OmicSoft Corp. (Cary, NC) allowing two mismatches
Reads mapped to the exons of a gene were summed at the gene level.
Assembly: NCBI GRCm38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains TPM values for each sample

extract_protocol:
Total RNA was purified from tissues using MagMAX™-96 for Microarrays Total RNA Isolation kit (Life Technologies (Carlsbad, CA)), according to manufacturer’s specifications. Genomic DNA was removed using MagMAX Turbo DNase buffer and TURBO DNase from the MagMAX kit listed above. Messenger RNA was purified from total RNA using Dynabeads mRNA purification kit (Invitrogen (Waltham, MA)).
Strand-specific RNA sequencing (RNA-seq) libraries were prepared using KAPA mRNA-Seq Library Preparation kit (Kapa Biosystems (Wilmington, MA)). After mRNA quality control analysis, RNA-seq libraries were prepared and long read sequencing (75bp, single end, 15M reads) was used for all samples. Sequencing was performed on Illumina HiSeq®2500 by a multiplexed single-read run with 33 cycles.


title: IMR90 cells, IR, HDM201, rep 2


title: vehicle, 5 months, male, rep 2


title: IMR90 cells, IR, RG7388, rep 3


title: Homo sapiens, Ishikawa Cells, control blank, biol rep3

description:
Library name: NC-3
Column name gene_count.txt: NC-3


title: IMR90 cells, IR, RG7388, rep 2


title: kidney.WT.1291241

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291241


title: kidney.WT.1291239

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291239


title: kidney.Het.1291240

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291240


title: vehicle, 5 months, male, rep 1


title: HDM201, 24 months, male, rep 5

value: 24 months


title: HDM201, 24 months, male, rep 3


title: NT

first: Phoolwanti

last: Rani

address: 5401 TATA hall, 9600 Gilman Dr

department: Molecular Biology

institute: University of California, San Diego

description:
Library name: NT
This sample represents biological replicates.

data_processing:
The quality of reads were determined using FastQC.
The reads with greater than Q30 values were selected for further analysis.
The reads were aligned to the Goslar genome (NC_048170.1) using bowtie2/2.5.0.
The duplicated reads were removed using Samtools.
then sam files were converted to bam files and sorted.
featureCounts was used to obtain a count matrix from the bam files.
Read counts were normalized using the DESeq2 median of ratio method.
The correlation coefficient for RNA-seq biological replicates was calculated using R's
cor function with the "pearson" method.
A heatmap was generated using the pheatmap function to visualize these correlations.
For the Venn diagram,  overlapping and unique genes were plotted using the VennDiagram
R package.
Assembly: (NC_048170.1)
Supplementary files format and content: bedgraph files are included.

organism: Escherichia phage vB_EcoM_Goslar

source_name: E. coli

growth_protocol: Strains were grown on Luria-Bertani (LB) plates with 1% agarose.

extract_protocol:
Total RNA was isolated using Monarch Total RNA isolation miniprep kit- T2010S
The  libraries were prepared (NEB E7770S, NEB E7600S).
libraries were sequenced using novaseq 6000.

treatment_protocol: MC1000 was infected with Goslar for indicated time points.

value: MC1000 E. coli (host cell)


title: ChmAKD

description:
Library name: ChmAKD
This sample represents biological replicates.
AG1


title: IMR90 cells, IR, DMSO, rep 3


title: kidney.WT.1291238

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291238


title: HDM201, 24 months, male, rep 4


title: IMR90 cells, IR, RG7388, rep 1


title: kidney.Het.1291237

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291237


title: WT60mpi

description:
Library name: WT60mpi
This sample represents biological replicates.


title: WT20Mpi

description:
Library name: WT20Mpi
This sample represents biological replicates.


title: WT30mpi

description:
Library name: WT30mpi
This sample represents biological replicates.


title: kidney.WT.1291236

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291236


title: HDM201, 24 months, male, rep 2


title: HDM201, 24 months, male, rep 1


title: IMR90 cells, IR, DMSO, rep 2


title: WT15mpi

description:
Library name: WT15mpi
This sample represents biological replicates.


title: kidney.Het.1291234

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291234


title: vehicle, 24 months, male, rep 4


title: kidney.Het.1291235

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291235


title: WT5mpi

description:
Library name: WT5mpi
This sample represents biological replicates.


title: kidney.WT.1291233

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291233


title: vehicle, 24 months, male, rep 5


title: vehicle, 24 months, male, rep 3


title: IMR90 cells, proliferating, HDM201, rep 2

value: proliferating


title: IMR90 cells, proliferating, HDM201, rep 3


title: kidney.Het.1291232

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291232


title: vehicle, 24 months, male, rep 2


title: kidney.WT.1291231

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291231


title: IMR90 cells, IR, DMSO, rep 1


title: Lemna aequinoctialis, control, 3

city: Dongjak-gu

first: Ye-Been

last: Lee

state: Seoul

address: 84, Heukseok-ro

institute: Chung-ang university

description: Library name: sample-con-3

data_processing:
Data processing was performed using a suite of bioinformatics tools, including FastQC and Trimmomatic for quality control, Trinity for de novo transcriptome assembly, SeqKit for filtering sequences shorter than 200 bp, CD-HIT for clustering redundant sequences, TransDecoder for ORF prediction, BWA and featureCounts for read alignment and counting, edgeR for differential expression analysis, DAVID for functional enrichment, DIAMOND for aligning DEG sequences to SwissProt, and Metaboanalyst for pathway enrichment analysis.
Assembly: GUFAH
Supplementary files format and content: text files raw read conts for each samples

organism: Lemna aequinoctialis

source_name: Lemna aequinoctilis plant cell

extract_protocol:
The plant RNA extraction was performed using the NucleoSpin RNA Plant Mini Kit. A powdered plant sample (100 mg) was mixed with 500 μL of Lysis buffer and 5 μL of β-mercaptoethanol, vortexed for 15 seconds, and incubated at room temperature for 3 minutes. After centrifugation at 13,000 rpm for 1 minute, 300 μL of the supernatant was transferred to a new tube, mixed with 300 μL of Membrane Lysis buffer, and filtered using an EzPure filter, followed by centrifugation at 13,000 rpm for 1 minute. Absolute ethanol (250 μL) was added to the filtrate, vortexed, and loaded onto a mini-column, which was centrifuged at 13,000 rpm for 1 minute. The column was washed with 500 μL of Wash buffer, and DNase I (70 μL) was applied for 10 minutes at room temperature for gDNA digestion. After centrifugation at maximum speed, the RNA was eluted with 50 μL of nuclease-free water and stored at –70°C.
RNA sequencing libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit for 150-bp paired-end sequencing on the Illumina platform.

value: Lemna aequinoctilis plant cell

value: control


title: IMR90 cells, proliferating, RG7388, rep 1


title: HDM201, 20 months, female, rep 4

value: 20 months

value: female


title: Lemna aequinoctialis, IPA treat, 3

description: Library name: sample-IPA-3

value: indole-3-propionic acid


title: vehicle, 24 months, male, rep 1

value: liver

value: Vehicle


title: Lemna aequinoctialis, control, 2

description: Library name: sample-con-2


title: kidney.Het.1291230

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291230


title: Lemna aequinoctialis, control, 1

description: Library name: sample-con-1


title: IMR90 cells, proliferating, DMSO, rep 3

value: fibroblast

value: wild type

value: DMSO


title: HDM201, 20 months, female, rep 3


title: IMR90 cells, proliferating, RG7388, rep 2


title: IMR90 cells, proliferating, DMSO, rep 2


title: IMR90 cells, proliferating, HDM201, rep 1


title: kidney.Het.1291227

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291227

value: kidney


title: Lemna aequinoctialis, IPA treat, 2

description: Library name: sample-IPA-2


title: HDM201, 20 months, female, rep 1


title: IMR90 cells, proliferating, RG7388, rep 3


title: kidney.Het.1291229

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291229


title: spn1 141-305 Rep1

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
Library name: Mini_1
spn1 141-305 RNA-seq

data_processing:
A concatenated fasta file was created using i) cDNA sequences of S. cerevisiae (release 113 from Ensembl), ii) cDNA sequences of S. pombe (from PomBase), iii) whole genome sequence of S. cerevisiae, and iv) whole genome sequence of S. pombe. A Salmon index was created using the concatenated fasta, setting the whole genome sequences as decoys. Transcript quantification was performed using Salmon v1.9 with libType set as automatic (Patro et al. 2017). Differential gene expression analysis was performed using DeSeq2 (Love et al. 2014) (v1.30.1) in R (v4.0.3). For spike-in normalization, size factors were estimated by setting S. pombe genes as control genes, resulting in the distribution of log2FC for S. pombe genes centered at 0. The expression matrix across genotypes was transformed using the “rlog” function in DESeq2 to yield normalized counts file: rld_all.tsv.gz.
Assembly: S. cerevisiae: R64;  S. pombe: cDNA: PomBase; Genome: Wood et al. Nature 2002
Supplementary files format and content: The expression matrix across genotypes was transformed using the “rlog” function in DESeq2 to yield normalized counts file: rld_all.tsv.gz.
Supplementary files format and content: Results tables were generated using the function results in DeSeq2, which extracted a results table with log2 fold changes, p values and adjusted p values: K192N_vs_WT.tsv.gz, Mini_vs_K192N.tsv.gz, Mini_vs_WT.tsv.gz

organism: Saccharomyces cerevisiae

growth_protocol: All Saccharomyces cerevisiae strains were grown in yeast extract, peptone, and dextrose (YPD; 2% dextrose) media at 30°C. The strains used in this study were previously created as described (Li et al., 2018 PMID:  29300974; Thurston et al., 2018 PMID:  30301740; Zhang et al., 2008 PMID:  18086892). Strains were transformed with a covering plasmid expressing wild-type SPN1 flanked by the TOA1 promoter and terminator. Endogenous SPN1 was replaced by a LEU2 fragment flanked by the SPN1 promoter and terminator through homologous recombination. Plasmids containing wild-type SPN1, spn1K192N, or spn1141-305 under the control of their native promoter and terminator were introduced into strains by plasmid shuffling.

extract_protocol:
RNA was isolated from yeast expressing either wild-type Spn1, spn1K192N, or spn1141-305 in triplicate 10-ml cultures by hot-acid phenol extraction as previously described (Iyer and Struhl 1996). Cells were grown in YPD at 30°C to mid-exponential phase (OD600 ~ 1.0), harvested, and each sample was spiked to obtain a final concentration of 1 S. pombe to 10 S. cerevisae cells.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms.

value: BY4741 spn1delta::LEU2 + pAA344


title: Lemna aequinoctialis, IPA treat, 1

description: Library name: sample-IPA-1


title: spn1 K192N Rep3

description:
Library name: K192N_3
spn1 K192N RNA-seq

value: BY4741 spn1delta::LEU2 + pCR312


title: vehicle, 20 months, female, rep 2


title: kidney.WT.1291226

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291226


title: HDM201, 20 months, female, rep 2


title: HDM201, 20 months, female, rep 5


title: kidney.Het.1291224

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291224


title: spn1 141-305 Rep3

description:
Library name: Mini_3
spn1 141-305 RNA-seq


title: kidney.WT.1291222

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291222


title: IMR90 cells, proliferating, DMSO, rep 1


title: spn1 141-305 Rep2

description:
Library name: Mini_2
spn1 141-305 RNA-seq


title: kidney.Het.1291225

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291225


title: MSCs HyperCpGs targeted dCAS9-DNMT3A Day 11 Replica 3

type: genomic

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina) according to the standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan).

data_processing:
Dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file.
Processed data: MSC_Hyperlibrary_beta_detp.csv includes nomalized beta-values.

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated using the Macherey Nagel Tissue kit.

treatment_protocol: For transfection of MSCs 1 million cells, 2.5μg of plasmids for CRISPR-constructs, and 2.5μg of gRNA plasmids were combined inside of a NEON 100ul pipet tip with 1 pulse (20ms) at 1700V. Cells were cultured in the above mentioned MSC culture medium, but without antibiotics for the first 24 hours. After 48 hours, cells were resuspended in MACS buffer for flowcytometric sorting for double positive cells (BD FACSAriaTM fusion) and further cultured for 11 days.

value: bone marrow

value: Mesenchymal stromal cells

tag: epigenetic modification

value: Hyperlibrary (targets:PDE4C, FHL2, KLF14, ELOVL2, TEAD1) + dCAS9-DNMT3A

value: isolation after 11 days of culture


title: TOF-ND1_Day8

city: Hong Kong

first: Chun Ho

last: Chan

address: 5 Sassoon Road Pokfulam

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Raw sequencing reads were filtered, aligned against GRCh38 genome with bam files generated with Rsubread
Genome_build: GRCh38
Supplementary_files_format_and_content: csv (raw counts)

source_name: hiPSC

extract_protocol:
Total RNA was isolated with TRIzol LS Reagent according to manufacturer's protocol
Constructed with Illumina Stranded mRNA Prep according to manufacturer's protocol

treatment_protocol: Day0: Embryoid body formation; Day1-4: Mesendoderm Induction via WNT activation; Day4-5: Cardiac Mesoderm Induction via WNT inhibition; Day5: Cardiac progenitor isolation through cell sorting

value: hiPSC

tag: heart condition

value: TOF

tag: clinically verifed with digeorge syndrome

value: Yes


title: vehicle, 20 months, female, rep 4

tag: tissue

value: 20 months

value: female

tag: genotype


title: TOF-DG1_Day7

tag: cell type


title: spn1 K192N Rep2

description:
Library name: K192N_2
spn1 K192N RNA-seq

tag: cell line


title: kidney.Het.1291223

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291223


title: TOF-ND1_Day6


title: TOF-ND1_Day5


title: spn1 K192N Rep1

description:
Library name: K192N_1
spn1 K192N RNA-seq


title: TOF-ND1_Day7


title: vehicle, 20 months, female, rep 3

value: liver


title: MSCs scramble guide dCAS9-DNMT3A Day 11 Replica 3

value: scramble guide + dCAS9-DNMT3A


title: vehicle, 20 months, female, rep 1

value: Vehicle


title: TOF-DG1_Day6


title: WT Rep1

description:
Library name: WT_1
WT RNAseq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: kidney.Het.1291221

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291221


title: TOF-DG1_Day5


title: kidney.Het.1291217

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291217


title: kidney.Het.1291220

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291220


title: WT Rep2

description:
Library name: WT_2
WT RNAseq


title: TOF-DG1_Day8


title: comp-mut-dN-4

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
In our sequencing strategy, 21nt read  R1 of pooled libraries contains two parts of UMI splitted by barcode. We move UMI sequences to be next to each other and remove additional nucleotide. For this we use awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for 55nt read R2 of pooled libraries was demultiplexed into separate fastq files for each replica using BRBseqTools (v 1.6) and R1. Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

organism: Arabidopsis thaliana

source_name: 21 day old seedlings

growth_protocol: Seeds were stratified for 2 days at 4ºC and grown on soil under a 16 h light/8 h dark (long-day) conditions.

extract_protocol:
Total plant RNA was isolated from 3-week-old plants grown using Trizol reagent (Sigma) according to manufacturer’s instructions.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 ul of water. 15 ul of recovered cDNA pools were mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA samples were used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCRs were performed using 10 ul tagmented DNA in 50 ul reaction with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain two reads: R1 (contain barcode and UMI) and R2 (contain mRNA sequence).
OTHER: 3'RNA-seq

value: 21 day old seedlings


title: WT Rep3

description:
Library name: WT_3
WT RNAseq


title: Control2_Day8

value: healthy


title: comp-mut-dN-3


title: kidney.WT.1291219

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291219

source_name: kidney

value: kidney


title: Control2_Day7


title: comp-mut-dN-2


title: kidney.Het.1291216

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291216


title: kidney.WT.1291218

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291218


title: comp-mut-dN-1


title: MSCs HyperCpGs targeted dCAS9-DNMT3A Day 11 Replica 1


title: HEK293T FHL2 targeted dCAS9-DNMT3A Replica 1

description:
HEK_FHL2_DNMT3A_R1
DNMT3A_FLH2_D14_R1

data_processing:
Dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file.
Processed data: HEK_FLH2_beta_detp.csv includes normalized beta-values.

value: guides FHL2 + dCAS9-DNMT3A

value: isolation after 14 days of culture


title: MSCs HyperCpGs targeted dCAS9-DNMT3A Day 11 Replica 2

value: bone marrow

value: Mesenchymal stromal cells


title: kidney.WT.1291205

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291205


title: Control2_Day6


title: kidney.WT.1291206

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291206


title: MSCs scramble guide dCAS9-DNMT3A Day 11 Replica 2

value: isolation after 11 days of culture


title: HEK293T control (FHL2 guides only) Replica R2

description:
HEK_CTRL_R2
control_FHL2_D14_R2

value: guides FHL2 only


title: comp-wt-dN-3


title: Control2_Day5

value: hiPSC


title: comp-wt-dN-4


title: Control1_Day7

value: Yes


title: Control1_Day8


title: S4-8

city: Zhangjiakou

first: Xiaojuan

last: Hou

state: Heibei

address: No.11, South Zuanshi Road, Zhangjiakou, China

institute: Hebei North University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq2.Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
After reads ressembled by StringTie2[i], gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
Asprofile was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OBiO Technology (Shanghai) Corp., Ltd. (Shanghai, China).

treatment_protocol: When applied, Hypidone hydrochloride  (5 mg/kg) was treated continuously for 7 days.

value: brain

value: treated with hypidone hydrochloride after MCAO surgery


title: T-cells HyperCpGs targeted dCAS9-DNMT3A Day 21 Replica 3

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina) according to the standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan)

data_processing:
dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file
Processed data: T_cell_R3_Hyperlibrary_beta_detp.csv includes normalized beta-values.

source_name: blood

growth_protocol: Human primary T-cells were then cultured in TexMacs medium (Miltenyi Biotec) with 10% FCS (Bio&Sell), IL-2 (50 IU/mL, GibcoTM) and Penicillin Streptomycin 100U/ml (GibcoTM) at 37°C / 5% CO2.

treatment_protocol: Transfection of T cells was performed using the NEON transfection system (Invitrogen). 5 million T cells were transfected with 5μg of plasmids for CRISPR-constructs and 5μg of gRNA plasmids inside of a NEON 100ul pipet tip with 1 pulse (20ms) at 2100V. After 24 hours, cells were resuspended in MACS buffer for flowcytometric sorting for double positive cells (BD FACSAriaTM fusion) and further cultured in TexMACS medium as indicated above for up to 21 days.

value: blood

value: primary T-cells

value: guides HyperCpGs (PDE4C, FHL2, ELOVL2, KLF14, and TEAD1) + dCAS9-DNMT3A/3

value: isolation after 21 days of culture


title: S4-7


title: comp-wt-dN-2

value: 21 day old seedlings


title: HEK293T control (FHL2 guides only) Replica R1

description:
HEK_CTRL_R1
control_FHL2_D14_R1


title: S4-2


title: Control1_Day6

value: healthy


title: comp-wt-dN-1


title: comp-mut-4


title: T-cells scramble guide dCAS9-DNMT3A Day 21 Replica 3

value: scramble guide + dCAS9-DNMT3A/3L


title: S2-5

value: treated with MCAO surgery


title: T-cells scramble guide dCAS9-DNMT3A Day 3 Replica 3

description:
scrambleCTRL_D10_R3
isolation after 10 days of culture

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina)  according to the standard Illumina protocol

data_processing:
dye bias correction, pOOBAH, ssnoob normalization, remove of non-CpG probes, remove of probes with SNP and remove of flagged probes in manifest b5 file
*processed value definition: normalized beta-value

label: Cy5 and Cy3

source_name: primary T-cells


title: comp-mut-3


title: MSCs scramble guide dCAS9-DNMT3A Day 11 Replica 1

source_name: bone marrow

value: scramble guide + dCAS9-DNMT3A


title: S2-6


title: HEK293T FHL2 targeted dCAS9-DNMT3A Replica 2

description:
HEK_FHL2_DNMT3A_R2
DNMT3A_FLH2_D14_R2

value: guides FHL2 + dCAS9-DNMT3A

value: isolation after 14 days of culture


title: S2-4


title: T-cells scramble guide dCAS9-DNMT3A Day 3 Replica 2

description:
scrambleCTRL_D10_R2
isolation after 10 days of culture


title: Control1_Day5


title: ACLY_KO_survival_5

city: New Brunswick

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
T17survival

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.46.0, with the Gencode GRCm39 (version M34) transcriptome as the reference
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes the DESeq normalized counts

source_name: Leukemic spleen

growth_protocol: Acly conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40μm filter, and subsequently subjected to red blood cell lysis. RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1μg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For acute experiments, mice were allowed to become overtly leukemic and then treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and leukemic spleens were collected 72h later. For surival experiments, 48h upon transplantation with Acly conditional knockout leukemic cells, mice were treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and their surivival was monitored afterwards. Samples were collected at the time of humane endpoint.

value: Leukemic spleen

value: Acly deleted

tag: group

value: survival


title: T-cells scramble guide dCAS9-DNMT3A Day 3 Replica 1

description:
scrambleCTRL_D10_R1
isolation after 10 days of culture


title: S1-5

value: control


title: kidney.WT.1291228

city: Tarrytown

first: Gabor

last: Halasz

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291228

value: kidney


title: comp-mut-2


title: S1-6

value: brain


title: ACLY_KO_survival_4

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
T15survival


title: S1-4


title: comp-wt-3


title: ACLY_KO_survival_3

description:
Acly_KO_survival_vs_WT_survival_DESeqNormalizedCounts.csv
T14survival


title: comp-wt-2