title: Daudi, Phase 2, Replicate 3

city: RTP

first: Logan

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: TC00000853_H03

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

source_name: Daudi

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).

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.

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

value: Daudi

tag: batch

value: Phase 2

tag: assay plate

tag: assay well

tag: growth mode

value: Suspension


title: donor1, unstimulated, 50000 cells, replicate 1

status: Public on Feb 11 2025

type: SRA

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: Library name: d1_Un_u50_rep1

library_source: genomic

data_processing:
Raw sequences were processed with HICUP 0.8.3 for QC, alignment to the Hg38 genome with Bowtie2, and filtering of invalid ligation products. The resulting BAM alignment files were converted to the multiresolution ".hic" format using built-in tools in HICUP, and normalised using 'Juicer pre' with the default settings.
Assembly: Hg38
Supplementary files format and content: ".hic" format is a highly compressed binary format that contains genomic contact matrices from multiple resolutions (5k, 10k, 25k, 50k, 100k, 250k, 500k, 1M and 2.5M) and using a range of normalisations (VC, VC_SQRT, SCALE and KR), as well as raw observed and expected values, and Pearson correlation matrices. These files can be visualised directly using the java software Juicebox.

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

growth_protocol: Healthy human donor blood cones were ordered from NHS Blood and Transplant Services, UK under UCL Research Ethics Committee Approval reference 3138/001. This agreement ensures donor anonymity and so donations do not come with any demographic information. The contents of each cone were diluted in 8ml 1xPBS and layered onto 15ml Ficoll in x4 50ml tubes. Tubes were subjected to centrifugation at 2000rpm for 20 min at RT. Peripheral blood mononuclear cells (PBMCs) were aspirated using a transfer pipette and washed 2x in 10ml 2mM EDTA 1xPBS in 15ml conical tubes 350xg 5 min at room temperature, RT). A third wash was done at 200xg 5 mins at RT to maximise platelet removal. PBMCs were spun at 350xg and resuspended in x1 Mojosort buffer (1xPBS, 2mM EDTA, 0.5% BSA) and diluted to 1x108 PMBCs/ml. All cell counts were done using a OLS CASY cell counter. mCD4+ T cells were isolated by magnetic separation Biolegend (480064) following manufactures protocol. Purity was assessed by flow cytometry.

extract_protocol:
Cells were counted and spun into pellets of the required numbers (50000, 250000, or 1000000) at 5000xg for 5 mins. Supernatant was removed until <20ul of liquid + cell pellet remained. The pellets were snap frozen on dry ice and then stored in at -70oC until processing. All pellets were committed to the mammalian cell low input Arima Genomics Inc workflow (https://arimagenomics.com/wp-content/files/User-Guide-Arima-HiC-for-Mammalian-Cell-Lines.pdf, September, 2024) with the following modifications; conditioning incubation time 20 mins, restriction enzyme cutting time 1hr. Proximally ligated DNA samples were QC for biotin nucleotide incorporation if enough material was available. Sonication was done using a S220 Covaris machine (Imperial College London) with the manufacturer’s recommended settings to achieve ~400bp fragment peaks. Fragment distribution was assessed using an Agilent TapeStation 4150 using a dsDNA D1000 or D5000 cartridge.
Final libraries were QC before shipment by Qubit dsDNA assay and TapeStation as above. Libraries were submitted for sequencing to Novogene(UK)

treatment_protocol:
Isolated T cells were activated at 2.5x106/ml in RPMI 10% FBS 0.5% Penicillin/Streptomycin solution (Gibco, 15070063). The base of 24-well culture dishes was treated 45 mins with 1ml 1xPBS containing anti-CD3 antibody Biolegend (317326) clone OKT at 476ng/ml Plates were washes x1 with 1xPBS. Added on day-0 only was anti-CD28 antibody Biolegend (302902) clone CD28.2 at 1000ng/ml. T cells were allowed to expand in wells for x3 days with 1000U/ml IL-2 (Prepotech, 200-02) added daily. For days 4 and 5 T cells were transferred to T25 untreated culture flasks with additional RPMI added to prevent medium exhaustion (assessed by colour change pink to yellow). 1000U/ml IL-2 was added on each of these days.
Fluorescent antibody panel (Live/Dead(blue), L23105), CD3 Biolegend(317336), CD4 Biolegend(317414), CD45RO Biolegend(304204), CD69 Biolegend(310910), CD25 Biolegend(302606) was validated for specificity using fluorescence minus one. 3x105 cells were pelleted 4oC 350xg 5 min and suspended in 100μl 1xPBS 0.001% Live/Dead(blue) dye. 1μl of each fluorescent antibody was added and briefly vortexed before incubation at 4oC for 30 mins. Stained cells were spun and washed x1 with 0.5ml ice-cold 1xPBS 1% FBS 2mM EDTA 0.01% sodium azide, with final suspensions in 300μl. Samples were run on a BD LSR Fortessa with baseline voltage setting (except CD25, in which the voltage was reduced by 50 units) with gating and analysis done in FlowJo v_10.8.1.

tag: tissue

value: blood

tag: cell type

value: primary CD4+ memory T-cells

tag: donor

tag: treatment


title: Daudi, Phase 2, Replicate 1

middle: J

country: USA

description: Library name: TC00000853_H01

library_source: transcriptomic

molecule: total RNA

tag: cell line


title: liver.WT.1292290

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292290

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

organism: Mus musculus

source_name: liver

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: liver

tag: genotype


title: PSMB10G209R_ctrl_24hr_rep1

type: RNA

city: Borstel

first: Yuqin

last: Wang

address: Parkallee 26

country: Germany

institute: FZB

description: Gene expression after 24hr in control treated PSMB10G209R skin fibroblast

hyb_protocol: 1650 ng of Cy3-labelled cRNA was fragmented according to Low Input Quick Amp Labelling Kit Protocol (Agilent) with 2xHI-RPM Hybridization Buffer for 30 min at 60°C. Hybridization on Agilent Human Whole Genome 4x44k V2 arrays was performed at 65°C for 17h under constant rotation in a hybidization oven. Washing was performed using the GE Wash buffer 1 (Agilent) at RT and Ge Wash Buffer 2 (Agilent) at 37°C for each 1 min. Washed slides were air-dried and immediately scanned.

scan_protocol: Slides were immediately scannend on an Agilent SureScan Scanner with Dye Channel =Green, 5 µm Resolution and scanning area=61 x 21.6 mm.

data_processing: Agilent Feature Extraction Software V 11.5 was used with default options (GE 1-color protocol) to extract raw data. Txt files were imported into GeneSpring software Version 13 under omission of compromised flags. Flags were accepted if at least 100 percent of samples in any 1 out of 7 conditions were detected.

source_name: PSMB10G209R skin fibroblast, ctrl, 24hr

label_protocol: Cy3-labelling of total RNA was conducted with the Low Input Quick Amp Labelling Kit (Agilent) according to manufacturer´s instructions. Dye incorporation rate and specific yield was calculated using an NanoDrop spectrophotometer.

growth_protocol: Skin fibroblasts of patient(PSMB10G209R) and neonatal individual of comparative age(PSMB10wt) were cultured in 50ug/mL PureCol(Advanced BioMatrix) coated cell culture plates. The medium for cultivation comprised of DMEM high glucose (4.5 g/L)  GlutaMAX™ (Thermo Fisher Scientific) supplemented with 10 % (v/v) fetal bovine serum (FBS) (Capricorn Scientific), 100 U/mL penicillin/streptomycin (Gibco, Thermo Fisher Scientific). phSF were grown in a humidified environment with 5% CO2 at 37 °C and passaged into new cell culture plate twice a week when reach confluency of 80-90%.

extract_protocol: Total RNA from PSMB10WT and PSMB10G209R skin fibroblast were extracted using TriZol and quality controlled by Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Kit according to manufacturer´s instructions.

treatment_protocol: Recombinant Human IFN-γ were dissolved in PBS, aliquoted and stored in -80°C. 200,000 skin fibroblasts were seeded in 6-well plate the day before the treatment. Change new medium of pre-planted cell after it reaches 70% confluency. Add 75U/ml Recombinant Human IFN-γ into new medium. Cells  treated with IFN-γ were then cultured for 24 hours.

value: skin

tag: age

value: neonatal


title: donor1,unstimulated, 250000 cells, replicate 2

description: Library name: d1_Un_u250_rep2


title: liver.WT.1292289

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.WT.1292289


title: ZT20_1 WT

city: HUDDINGE

first: Ivan

middle: Martinov

last: Vlassakev

address: HÄLSOVÄGEN 7C

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

description: Library name: Sample E2

data_processing:
Raw non-demultiplexed fastq files were processed using zUMIs (version 2.4.1 or newer) with STAR (v2.5.4b) to generate expression profiles for both the 5′ ends containing UMIs as well as combined full-length and UMI data.
Mouse cDNA was mapped against mm10 genome with CAST SNPs masked with N to avoid mapping bias. Data were quantified with gene annotations from Ensembl GRCm38.91.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: eWAT

extract_protocol:
RNA from all samples was extracted via the Qiagen kit according to manufacturer's instructions.
High-sensitivity DNA chip (Agilent Bioanalyzer) were used to check library size distribution. All cDNA concentrations were quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Scientific). Tagmentation was carried out in 2 µl, consisting of 1× tagmentation buffer (10 mM Tris, pH 7.5, 5 mM MgCl2, 5% DMF), 0.08–0.1 µl ATM (Illumina XT DNA sample preparation kit), 1 µl cDNA and water. Library amplification of the tagmented samples was performed using 1.5 µl custom designed Nextera index primers. After tagmentation, samples were pooled, and the pool was purified with Ampure XP beads. Libraries were sequenced at the 75-bp single end, 50-bp single end or 150-bp paired end on a high-output flow cell using an Illumina NextSeq500 instrument, an Illumina HiSeq3000 instrument or a NovaSeq S4 flow cell 150-bp paired end.

value: eWAT

value: WT


title: ZT20_2 WT

description: Library name: Sample F2


title: Zt16_4 WT

description: Library name: Sample D2


title: liver.Het.1292288

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292288


title: donor1, unstimulated, 250000 cells, replicate 1

description: Library name: d1_Un_u250_rep1


title: CCD-18Co, Phase 2, Replicate 2

description: Library name: TC00000853_G11


title: donor1, unstimulated, 1000000 cells, replicate 2

description: Library name: d1_Un_u1000_rep2


title: Zt16_3 WT

description: Library name: Sample C2


title: donor1, unstimulated, 1000000 cells, replicate 1

description: Library name: d1_Un_u1000_rep1


title: Zt16_2 WT

description: Library name: Sample B2


title: Daudi, Phase 2, Replicate 2

description: Library name: TC00000853_H02


title: liver.Het.1292287

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292287


title: HepG2, Phase 2, Replicate 2

description: Library name: TC00000853_G08


title: liver.Het.1292286

description:
Dchs1_counts.txt
Dchs1_TPM.txt
liver.Het.1292286


title: CCD-18Co, Phase 2, Replicate 1

description: Library name: TC00000853_G10


title: HepG2, Phase 2, Replicate 3

description: Library name: TC00000853_G09


title: Zt12_4 WT

description: Library name: Sample P1


title: donor1, IL2, 50000 cells, replicate 2

description: Library name: d1_il2_u50_rep2

value: IL2 activation


title: donor1, IL2, 250000 cells, replicate 2

description: Library name: d1_il2_u250_rep2


title: Zt16_1 WT

description: Library name: Sample A2


title: donor1, IL2, 50000 cells, replicate 1

description: Library name: d1_il2_u50_rep1


title: liver.WT.1291451

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291451


title: donor1, IL2, 250000 cells, replicate 1

description: Library name: d1_il2_u250_rep1


title: liver.Het.1291450

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291450


title: liver.WT.1291453

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291453


title: MCF7, Phase 2, Replicate 1

description: Library name: TC00000853_G04


title: donor1, IL2, 1000000 cells, replicate 2

description: Library name: d1_il2_u1000_rep2


title: Zt12_1 WT

description: Library name: Sample M1


title: liver.WT.1291452

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291452


title: Zt12_2 WT

description: Library name: Sample N1


title: HepG2, Phase 2, Replicate 1

description: Library name: TC00000853_G07


title: Zt12_3 WT

description: Library name: Sample O1


title: U-2 OS, Phase 2, Replicate 3

description: Library name: TC00000853_G03

source_name: U-2 OS

value: U-2 OS


title: liver.Het.1291449

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291449


title: MCF7, Phase 2, Replicate 3

description: Library name: TC00000853_G06


title: donor1, IL2, 1000000 cells, replicate 1

description: Library name: d1_il2_u1000_rep1


title: ZT8_3 WT

description: Library name: Sample K1


title: U-2 OS, Phase 2, Replicate 2

description: Library name: TC00000853_G02


title: ZT8_4 WT

description: Library name: Sample L1


title: liver.Het.1291448

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291448


title: MCF7, Phase 2, Replicate 2

description: Library name: TC00000853_G05


title: donor1, IL2+TCR, 50000 cells, replicate 2

description: Library name: d1_ab_u50_rep2

value: IL2+TCR activation


title: liver.WT.1291447

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291447


title: CCD-18Co, Phase 2, Replicate 3

description: Library name: TC00000853_G12


title: liver.WT.1291446

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291446


title: U-2 OS, Phase 2, Replicate 1

description: Library name: TC00000853_G01


title: donor1, IL2+TCR, 50000 cells, replicate 1

description: Library name: d1_ab_u50_rep1


title: kidney.Het.1291445

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291445

source_name: kidney

value: kidney


title: ZT4_4 WT

description: Library name: Sample H1


title: ZT4_3 WT

description: Library name: Sample G1


title: ZT8_2 WT

description: Library name: Sample J1


title: ZT4_2 WT

description: Library name: Sample F1


title: BT-483, Phase 2, Replicate 3

description: Library name: TC00000853_F12

value: Adherent


title: CAL-78, Phase 2, Replicate 2

description: Library name: TC00000853_F08


title: ZT4_1 WT

description: Library name: Sample E1


title: liver.Het.1291441

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291441


title: liver.WT.1291440

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291440


title: liver.Het.1291444

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291444


title: donor1, IL2+TCR, 1000000 cells, replicate 2

description: Library name: d1_ab_u1000_rep2


title: BT-483, Phase 2, Replicate 1

description: Library name: TC00000853_F10


title: donor1, IL2+TCR, 250000 cells, replicate 1

description: Library name: d1_ab_u250_rep1


title: donor3, IL2, replicate 2

description: Library name: d3_il2_rep2

data_processing:
Read counts were obtained with DESeq2 1.38.3 after quantitation with Salmon v.1.4.0 against the Ensembl hg38 v.106 transcriptome
Assembly: Hg38
Supplementary files format and content: raw_counts.txt: tab-delimited text file containing raw gene counts for each individual sample

extract_protocol:
Cells were pelleted and frozen in freezing buffer (fetal bovine serum 10% DMSO) at –70◦C. Total RNA was extracted from each sample and a high molecular weight fraction (>200nt) isolated using the Qiagen RNeasy (74134) kit with on-column DNase treatment (79254), according to the manufacturer’s instructions. Final elution’s were done at 50µl NFW and were snap frozen on dry ice. RNA quality was assessed by Novogene (UK) with a Bioanalyzer (Agilent Technologies), and samples with a RIN score > 6.5 and mass >500ng were forwarded to Novogene’s lncRNA-seq protocol for library prep and sequencing
Libraries were prepared by Novogene, using their lncRNA protocol with rRNA depletion.


title: liver.Het.1291439

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291439


title: donor1, IL2+TCR, 250000 cells, replicate 2

description: Library name: d1_ab_u250_rep2


title: liver.Het.1291438

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291438


title: donor3, unstimulated, replicate 2

description: Library name: d3_un_rep2


title: donor1, IL2+TCR, 1000000 cells, replicate 1

description: Library name: d1_ab_u1000_rep1


title: EFM-19, Phase 2, Replicate 1

description: Library name: TC00000853_F04


title: CAL-78, Phase 2, Replicate 3

description: Library name: TC00000853_F09


title: liver.Het.1291442

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291442


title: donor3, IL2+TCR, replicate 1

description: Library name: d3_ab_rep1


title: donor3, IL2+TCR, replicate 2

description: Library name: d3_ab_rep2


title: ZT8_1 WT

description: Library name: Sample I1


title: BT-483, Phase 2, Replicate 2

description: Library name: TC00000853_F11


title: donor2, IL2+TCR, replicate 2

description: Library name: d2_ab_rep2


title: ZT0_4 WT

description: Library name: Sample D1


title: Huh-7, Phase 2, Replicate 2

description: Library name: TC00000853_F02


title: ZT0_3 WT

description: Library name: Sample C1


title: EFM-19, Phase 2, Replicate 3

description: Library name: TC00000853_F06


title: Huh-7, Phase 2, Replicate 1

description: Library name: TC00000853_F01


title: donor2, IL2+TCR, replicate 1

description: Library name: d2_ab_rep1


title: KO ZT20_3

description: Library name: B9

extract_protocol:
RNA from all samples was extracted via the Qiagen kit according to manufacturer's instructions.
High-sensitivity DNA chip (Agilent Bioanalyzer) were used to check library size distribution. All cDNA concentrations were quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Scientific). Tagmentation was carried out in 2 µl, consisting of 1× tagmentation buffer (10 mM Tris, pH 7.5, 5 mM MgCl2, 5% DMF), 0.08–0.1 µl ATM (Illumina XT DNA sample preparation kit), 1 µl cDNA and water. Library amplification of the tagmented samples was performed using 1.5 µl custom designed Nextera index primers. After tagmentation, samples were pooled, and the pool was purified with Ampure XP beads. Libraries were sequenced at the 75-bp single end, 50-bp single end or 150-bp paired end on a high-output flow cell using an Illumina NextSeq500 instrument, an Illumina HiSeq3000 instrument or a NovaSeq S4 flow cell 150-bp paired end.
SmartSeq3 RNA-seq


title: liver.WT.1291434

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291434


title: donor2, IL2, replicate 2

description: Library name: d2_il2_rep2


title: EFM-19, Phase 2, Replicate 2

description: Library name: TC00000853_F05


title: CAL-78, Phase 2, Replicate 1

description: Library name: TC00000853_F07


title: donor3, IL2, replicate 1

description: Library name: d3_il2_rep1


title: ZT0_2 WT

description: Library name: Sample B1


title: donor3, unstimulated, replicate 1

description: Library name: d3_un_rep1


title: ZT0_1 WT

description: Library name: Sample A1


title: liver.Het.1291437

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291437


title: KO ZT20_5

description: Library name: D9


title: Huh-7, Phase 2, Replicate 3

description: Library name: TC00000853_F03


title: donor2, unstimulated, replicate 2

description: Library name: d2_un_rep2


title: liver.Het.1291436

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291436


title: liver.Het.1291443

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291443


title: SaOS-2, Phase 2, Replicate 1

description: Library name: TC00000853_E10


title: KO ZT20_4

description: Library name: C9


title: donor2, unstimulated, replicate 1

description: Library name: d2_un_rep1


title: SaOS-2, Phase 2, Replicate 3

description: Library name: TC00000853_E12


title: MHH-CALL-4, Phase 2, Replicate 3

description: Library name: TC00000853_E09


title: donor1, IL2+TCR, replicate 3

description: Library name: d1_ab_rep3


title: liver.WT.1291435

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291435


title: liver.WT.1291430

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291430


title: liver.WT.1291432

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291432


title: KO ZT16_3

description: Library name: M8


title: liver.Het.1291433

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291433


title: KO ZT20_2

description: Library name: A9


title: donor1, IL2+TCR, replicate 2

description: Library name: d1_ab_rep2


title: KO ZT16_5

description: Library name: O8


title: MHH-CALL-4, Phase 2, Replicate 1

description: Library name: TC00000853_E07


title: KO ZT20_1

description: Library name: P8


title: SaOS-2, Phase 2, Replicate 2

description: Library name: TC00000853_E11


title: donor1, IL2+TCR, replicate 1

description: Library name: d1_ab_rep1


title: KO ZT16_2

description: Library name: L8


title: liver.WT.1291431

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291431


title: KO ZT16_4

description: Library name: N8


title: liver.WT.1291429

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291429


title: T-47D, Phase 2, Replicate 3

description: Library name: TC00000853_E06


title: liver.Het.1291427

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291427


title: donor2, IL2, replicate 1

description: Library name: d2_il2_rep1


title: MHH-CALL-4, Phase 2, Replicate 2

description: Library name: TC00000853_E08


title: liver.WT.1291428

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291428


title: donor1, IL2, replicate 3

description: Library name: d1_il2_rep3


title: KO ZT16_1

description: Library name: K8


title: T-47D, Phase 2, Replicate 2

description: Library name: TC00000853_E05


title: donor1, IL2, replicate 2

description: Library name: d1_il2_rep2


title: liver.Het.1291426

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291426


title: T-47D, Phase 2, Replicate 1

description: Library name: TC00000853_E04


title: KO ZT12_4

description: Library name: I8


title: liver.Het.1291425

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291425


title: donor1, IL2, replicate 1

description: Library name: d1_il2_rep1


title: donor1, unstimulated, replicate 3

description: Library name: d1_un_rep3


title: KO ZT12_3

description: Library name: H8


title: KO ZT12_2

description: Library name: G8


title: hNP1, Phase 2, Replicate 3

description: Library name: TC00000853_E03


title: KO ZT12_1

description: Library name: F8


title: donor1, unstimulated, replicate 1

description: Library name: d1_un_rep1


title: liver.Het.1291422

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291422


title: donor1, unstimulated, replicate 2

description: Library name: d1_un_rep2


title: liver.Het.1291423

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291423


title: liver.Het.1291421

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291421


title: KO ZT8_5

description: Library name: E8


title: hNP1, Phase 2, Replicate 1

description: Library name: TC00000853_E01


title: liver.WT.1291420

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291420


title: KO ZT8_4

description: Library name: D8


title: SU-DHL-6, Phase 2, Replicate 2

description: Library name: TC00000853_D11


title: Pt2_untreated_3

city: Bethesda

first: Matthew

middle: CS

last: Denley

state: MD

address: 35 Convent Dr

institute: NIH

description: Library name: KK17-2_con_MT

data_processing:
Raw sequencing reads were preprocessed using the SUSHI framework. Adapter sequences and low-quality reads were trimmed off using fastp v0.02. Filtered reads were pseudo-aligned against the reference human genome assembly GRCh38.p13 and quantified using Kallisto v0.46.1.
Assembly: Reference human genome assembly GRCh38.p13
Supplementary files format and content: SUSHI framework, fastp, Kallisto, edgeR, clusterProfiler.

source_name: fibroblast

growth_protocol: Neural cultures were fed daily with NMM until day 45, after which 48-hour cycles were implemented whereby every second day 2/3 of the medium was removed and 2 mL NMM plus maturation supplements GDNF and BDNF (both at 20 ng/mL, StemCellTechnologies, Cat. 78058 and 78005) were supplied to neuronal cultures. In this way, neuronal cultures were maintained up to a maximum of day 120. Neural maintenance medium (NMM: 48.4 mL KnockOut DMEM/F12, Gibco, Cat. 12660-102; 48.5 mL Neurobasal, Gibco, Cat. 12348-017; 1 mL B-27 Supplement, Gibco, Cat. 17504-044; 500 µL N-2 Supplement, Gibco, Cat. 17502-048; 500 µL Non-essential amino acids, Gibco, Cat. 11140-050; 500 µL GlutaMAX, Gibco, Cat. 35050-061; 500 µL Penicillin-Streptomycin, Gibco, Cat. 15140-122; 90 µL 2-Mercaptoethanol, Gibco, Cat. 31350010; 25 µL Insulin solution, Sigma, Cat. I9278-5ML)

extract_protocol:
RNA extracted from liquid-nitrogen snap frozen cell pellets (DIV range: 65 – 78, mean: 75) that were lysed using QIAshredder (Qiagen, 79656) with RNA extracted using the RNeasy® Mini Kit (Qiagen, Cat. 74106). Prior to sequencing, RNA quality was assessed using an ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) to ensure sample purity was between A260/280 = 1.8-2.2 and A260/230 ≥ 1.8.
Peak illustration was conducted using an Agilent 5400 and the low marker was used to calibrate the size of peaks.
Libraries were pooled and sequenced in paired-end mode on an Illumina NovaSeq 6000 at Novogene. Between 960 to 8800 ng of total RNA was provided and ≥ 20 million read pairs per sample were acquired.

treatment_protocol: For treatment studies, 0.1 mM mM dimethyl 2-oxoglutarate (Sigma, Cat. 349631) (DM-2OG) was added for 24 hours before cell collection.

value: fibroblast

value: hiPSC

value: Neuronal


title: KO ZT8_3

description: Library name: C8


title: SU-DHL-6, Phase 2, Replicate 1

description: Library name: TC00000853_D10

value: Phase 2


title: liver.WT.1291418

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291418


title: Ct1_untreated_3

description: Library name: BJ32_con_WT

value: wt


title: DOHH-2, Phase 2, Replicate 3

description: Library name: TC00000853_D09

value: Suspension


title: liver.Het.1291424

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291424


title: KO ZT8_2

description: Library name: B8


title: KO ZT12_5

description: Library name: J8


title: KO ZT8_1

description: Library name: A8


title: liver.WT.1291417

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291417


title: hNP1, Phase 2, Replicate 2

description: Library name: TC00000853_E02


title: DOHH-2, Phase 2, Replicate 1

description: Library name: TC00000853_D07


title: Pt2_DM2OG_1

description: Library name: KK17-2_tr_MT_1


title: SU-DHL-6, Phase 2, Replicate 3

description: Library name: TC00000853_D12


title: liver.Het.1291416

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291416


title: KO ZT4_5

description: Library name: P7


title: Pt2_untreated_2

description: Library name: KK17-2_con_MT_2


title: liver.Het.1291415

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291415


title: Pt2_untreated_1

description: Library name: KK17-2_con_MT_1


title: KO ZT4_4

description: Library name: O7


title: Pt1_untreated_3

description: Library name: AV4_con_MT


title: liver.WT.1291414

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291414


title: liver.Het.1291419

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291419


title: KO ZT4_2

description: Library name: M7


title: Huh-1, Phase 2, Replicate 2

description: Library name: TC00000853_D05


title: Pt1_DM2OG_2

description: Library name: AV14_tr_MT_1


title: Huh-1, Phase 2, Replicate 1

description: Library name: TC00000853_D04


title: Pt1_untreated_2

description: Library name: AV4_con_MT_2


title: Pt2_DM2OG_2

description: Library name: KK17-2_tr_MT_2


title: liver.WT.1291412

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291412


title: CAL-148, Phase 2, Replicate 2

description: Library name: TC00000853_D02


title: liver.Het.1291413

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291413


title: liver.WT.1291411

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291411


title: KO ZT0_4

description: Library name: J7


title: DOHH-2, Phase 2, Replicate 2

description: Library name: TC00000853_D08


title: Pt1_DM2OG_1

description: Library name: AV4_tr_MT_1


title: Huh-1, Phase 2, Replicate 3

description: Library name: TC00000853_D06


title: Hs-5, Phase 2, Replicate 3

description: Library name: TC00000853_C12


title: CAL-148, Phase 2, Replicate 3

description: Library name: TC00000853_D03


title: KO ZT4_1

description: Library name: L7


title: KO ZT4_3

description: Library name: N7


title: KO ZT0_5

description: Library name: K7


title: Pt1_untreated_1

description: Library name: AV4_con_MT_1


title: Ct2_DM2OG_1

description: Library name: CI-ND2_tr_WT_1


title: KO ZT0_2

description: Library name: H7


title: liver.WT.1291410

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291410


title: liver.Het.1291408

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291408


title: Ct2_DM2OG_2

description: Library name: CI-ND2_tr_WT_2


title: liver.WT.1291409

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291409


title: WT ZT20_5

description: Library name: F7


title: KO ZT0_3

description: Library name: I7


title: liver.Het.1291407

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291407


title: Ct2_untreated_2

description: Library name: CI-ND2_con_WT_2


title: Hs-5, Phase 2, Replicate 1

description: Library name: TC00000853_C10


title: KO ZT0_1

description: Library name: G7


title: WT ZT20_4

description: Library name: E7


title: liver.Het.1291405

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291405


title: Hs 839.T, Phase 2, Replicate 2

description: Library name: TC00000853_C08


title: Hs 839.T, Phase 2, Replicate 3

description: Library name: TC00000853_C09


title: WT ZT20_3

description: Library name: D7


title: Ct2_untreated_1

description: Library name: CI-ND2_con_WT_1


title: CAL-148, Phase 2, Replicate 1

description: Library name: TC00000853_D01


title: Ct1_DM2OG_1

description: Library name: BJ32_tr_WT_1


title: Hs-5, Phase 2, Replicate 2

description: Library name: TC00000853_C11


title: Ct1_DM2OG_2

description: Library name: BJ32_tr_WT_2


title: liver.Het.1291406

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291406


title: Ct1_untreated_2

description: Library name: BJ32_con_WT_2


title: Hs 839.T, Phase 2, Replicate 1

description: Library name: TC00000853_C07


title: WT ZT20_2

description: Library name: C7


title: Ct1_untreated_1

description: Library name: BJ32_con_WT_1


title: liver.Het.1291404

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291404


title: NCI-H2171, Phase 2, Replicate 2

description: Library name: TC00000853_C05


title: NCI-H2171, Phase 2, Replicate 3

description: Library name: TC00000853_C06


title: WT ZT20_1

description: Library name: B7


title: liver.WT.1291403

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291403


title: liver.WT.1291402

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291402


title: NCI-H2171, Phase 2, Replicate 1

description: Library name: TC00000853_C04


title: WT ZT16_5

description: Library name: A7


title: liver.WT.1291401

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291401


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

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description:
Library name: experiment_R1
isolation after 11 days of culture

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: Mesenchymal stromal cell

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 flowcytometric sorting for double positive cells (BD FACSAriaTM fusion) and further cultured for 11 days.

value: Mesenchymal stromal cell

value: guides HyperCpGs + dCAS9-DNMT3A/3L


title: NCI-H2106, Phase 2, Replicate 3

description: Library name: TC00000853_C03


title: NCI-H2106, Phase 2, Replicate 2

description: Library name: TC00000853_C02


title: liver.Het.1291399

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291399

value: liver


title: liver.Het.1291400

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.Het.1291400


title: WT ZT16_4

description: Library name: P6


title: DU145 EMD KD Sample 3

city: Los Angeles

first: Edwin

last: Posadas

state: CA

address: 8700 Beverly Blvd, Davis Building, Room 5094C

department: urology

institute: Cedars-Sinai Medical Center

description:
Library name: Sample 18
DU145shEMD-3

data_processing:
According to Novogene's sample QC standards, low quality and adaptor reads were removed, and all samples passed internal QC standards.
raw reads were aligned to h38 via STAR and expression was quantified via RSEM (version 1.3.1, rsem-calculate-expression).
Assembly: GRCh38
Supplementary files format and content: csv, RNA-seq counts

growth_protocol: C4-2B and 22Rv1 were maintained in RPMI-1640 medium with 10% FBS and 1% penicillin/streptomycin. DU145 were cultured in DMEM (Thermo Fisher Scientific) with 10% FBS and 1% penicillin/streptomycin. All cultures were grown in a humidified 5% CO2 environment at 37°C. The cell lines were periodically tested with Mycoplasma Detection Kit (Lonza) and were clear of contamination.

extract_protocol:
Total RNA was extracted with the RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
RNA library and transcriptome sequencing were performed by Novogene (Sacramento, CA, USA).

treatment_protocol: C4-2B, 22Rv1 and DU145 cells were transfected with EMD siRNA (sc-35296, Santa Cruz) and control scramble siRNA (sc-37007, Santa Cruz) using Lipofectamine 3000 (Fisher Scientific), as described by the manufacturer. Then, 24 h after the addition of the transfection mix, liposomes were removed, and fresh medium was added.

value: EMD knockdown


title: WT ZT16_3

description: Library name: O6

value: eWAT


title: NCI-H2106, Phase 2, Replicate 1

description: Library name: TC00000853_C01


title: liver.WT.1291398

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291398


title: DU145 EMD KD Sample 1

description:
Library name: Sample 16
DU145shEMD-1


title: NCI-H1105, Phase 2, Replicate 2

description: Library name: TC00000853_B11


title: DU145 Control Sample 3

description:
Library name: Sample 15
DU145CO-3

value: control


title: liver.WT.1291397

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291397


title: DU145 Control Sample 2

description:
Library name: Sample 14
DU145CO-2


title: NCI-H1105, Phase 2, Replicate 3

description: Library name: TC00000853_B12


title: liver.WT.1291396

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291396


title: WT ZT16_2

description: Library name: N6

value: WT


title: WT ZT12_5

description: Library name: L6


title: NCI-H1105, Phase 2, Replicate 1

description: Library name: TC00000853_B10


title: NCI-H1436, Phase 2, Replicate 3

description: Library name: TC00000853_B09


title: heart.WT.1291395

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291395

source_name: heart

value: heart


title: heart.Het.1291394

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291394


title: WT ZT12_4

description: Library name: K6


title: 22RV1 EMD KD Sample 3

description:
Library name: Sample 12
EMD3_RV1


title: NCI-H1436, Phase 2, Replicate 2

description: Library name: TC00000853_B08


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

description:
Library name: control_R1
isolation after 11 days of culture

value: scramble guide + dCAS9-DNMT3A/3L


title: DU145 EMD KD Sample 2

description:
Library name: Sample 17
DU145shEMD-2


title: 22RV1 EMD KD Sample 2

description:
Library name: Sample 11
EMD2_RV1


title: heart.WT.1291393

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291393


title: WT ZT12_1

description: Library name: H6


title: 22RV1 EMD KD Sample 1

description:
Library name: Sample 10
EMD1_RV1


title: NCI-H1436, Phase 2, Replicate 1

description: Library name: TC00000853_B07


title: WT ZT16_1

description: Library name: M6


title: heart.WT.1291392

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291392


title: heart.Het.1291391

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291391


title: WT ZT8_5

description: Library name: G6


title: WT ZT8_3

description: Library name: E6


title: C3A, Phase 2, Replicate 3

description: Library name: TC00000853_B06


title: C3A, Phase 2, Replicate 2

description: Library name: TC00000853_B05


title: heart.WT.1291389

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291389


title: C3A, Phase 2, Replicate 1

description: Library name: TC00000853_B04


title: WT ZT8_4

description: Library name: F6


title: heart.Het.1291390

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291390


title: 22RV1 Control Sample 2

description:
Library name: Sample 8
ctrl2_RV1


title: DU145 Control Sample 1

description:
Library name: Sample 13
DU145CO-1


title: WT ZT8_2

description: Library name: D6


title: WT ZT12_3

description: Library name: J6


title: PLC/PRF/5, Phase 2, Replicate 3

description: Library name: TC00000853_B03


title: WT ZT12_2

description: Library name: I6


title: heart.Het.1291388

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291388


title: C42B EMD KD Sample 3

description:
Library name: Sample 6
EMD3


title: PLC/PRF/5, Phase 2, Replicate 2

description: Library name: TC00000853_B02


title: heart.WT.1291387

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291387


title: WT ZT8_1

description: Library name: C6


title: C42B EMD KD Sample 2

description:
Library name: Sample 5
EMD2


title: 22RV1 Control Sample 3

description:
Library name: Sample 9
ctrl3_RV1


title: WT ZT4_5

description: Library name: B6


title: PLC/PRF/5, Phase 2, Replicate 1

description: Library name: TC00000853_B01


title: C42B Control Sample 3

description:
Library name: Sample 3
Con3


title: MG-63, Phase 2, Replicate 2

description: Library name: TC00000853_A11


title: liver.WT.1291386

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291386


title: 22RV1 Control Sample 1

description:
Library name: Sample 7
ctrl1_RV1


title: liver.WT.1291384

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291384


title: C42B EMD KD Sample 1

description:
Library name: Sample 4
EMD1


title: WT ZT4_3

description: Library name: P5


title: liver.WT.1291385

description:
Fat4_counts.txt
Fat4_TPM.txt
liver.WT.1291385


title: C42B Control Sample 1

description:
Library name: Sample 1
Con1


title: MG-63, Phase 2, Replicate 1

description: Library name: TC00000853_A10


title: WT ZT4_2

description: Library name: O5


title: WT ZT4_1

description: Library name: N5


title: heart.WT.1291382

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291382


title: HOS, Phase 2, Replicate 3

description: Library name: TC00000853_A09

source_name: HOS

value: HOS


title: C42B Control Sample 2

description:
Library name: Sample 2
Con2


title: WT ZT4_4

description: Library name: A6


title: heart.Het.1291383

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291383


title: Patient-derived organoid 10

city: Rotterdam

first: Marco

last: Huberts

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Viroscience

country: Netherlands

institute: Erasmus Medical Centre

description:
Library name: 001.ORG48
Column name in salmon.merged.gene_counts.tsv: x001.ORG48

data_processing:
Long non-coding RNAs, irrelevant genes, including uncharacterized genes (LOCXXX), and genes with expression counts lower than four were removed from all sample sets.
Assembly: Sequences from the obtained FastQ files were trimmed to remove low-quality bases and adapter sequences, aligned to the GRCh38 reference genome (NCBI GRCh38, genome.fa) to map the reads to their corresponding genomic locations using the associated gene annotation file (genes.gtf), and then counted and normalized using the nf-core pipeline, resulting in the number of transcripts per million reads (TPM).
Supplementary files format and content: raw counts for each sample in a tsv file
Supplementary files format and content: transcript per million-normalized values for each sample in a tsv file

source_name: PDAC

extract_protocol:
RNA from PDOs were isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN) and concentrations were determined using Nanodrop One C (ThermoFisher Scientific, #ND-ONEC-W).
A library of the RNA extracted from PDOs was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L). Total RNA was depleted from ribosomal RNA (rRNA) using the Qiagen fast select kit (#334387).

value: PDAC

value: Untreated


title: heart.WT.1291380

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291380


title: WT ZT0_5

description: Library name: M5


title: HOS, Phase 2, Replicate 2

description: Library name: TC00000853_A08

value: Adherent


title: heart.Het.1291381

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291381


title: HOS, Phase 2, Replicate 1

description: Library name: TC00000853_A07


title: WT ZT0_4

description: Library name: L5


title: Patient-derived organoid 7

description:
Library name: 015.ORG64
Column name in salmon.merged.gene_counts.tsv: x015.ORG64


title: Detroit 551, Phase 2, Replicate 2

description: Library name: TC00000853_A05

source_name: Detroit 551

value: Detroit 551


title: WT ZT0_3

description: Library name: K5


title: heart.Het.1291379

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291379


title: Detroit 551, Phase 2, Replicate 3

description: Library name: TC00000853_A06

value: Phase 2


title: heart.Het.1291378

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291378


title: WT ZT0_2

description: Library name: J5


title: NCI-H1092, Phase 2, Replicate 3

description: Library name: TC00000853_A03


title: Patient-derived organoid 5

description:
Library name: 008.ORG45
Column name in salmon.merged.gene_counts.tsv: x008.ORG45


title: heart.Het.1291377

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291377


title: MG-63, Phase 2, Replicate 3

description: Library name: TC00000853_A12


title: Patient-derived organoid 9

description:
Library name: 004.ORG35
Column name in salmon.merged.gene_counts.tsv: x004.ORG35


title: Patient-derived organoid 6

description:
Library name: 011.ORG66
Column name in salmon.merged.gene_counts.tsv: x011.ORG66


title: heart.WT.1291376

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291376


title: Patient-derived organoid 3

description:
Library name: 012.ORG136
Column name in salmon.merged.gene_counts.tsv: x012.ORG136


title: mPDAC1, RPMI, - lipids 2

city: Chicago

first: Patrick

middle: Bryan

last: Jonker

state: IL

address: 929 E 57th St

institute: University of Chicago

description: Library name: Sample 17

data_processing:
Data processing and analysis were done using the R-based Galaxy platform (https://usegalaxy.org/; Afgan et al., 2018). Quality control was performed prior and after concatenation of the raw data with the tools MultiQC and FastQC, respectively. All samples passed the quality check with most showing ~20% sequence duplication, sequence alignment greater or equal to 80%, below and below 50% GC coverage, all of which is acceptable and/or indicative of good quality for RNASeq samples
Samples were aligned and counts were generated using the tools HISAT2 (Galaxy Version 2.2.1+galaxy0, NCBI genome build GRCm38/mm10) and featureCounts (Galaxy Version 2.0.1+galaxy1), respectively
Assembly: GRCm38/mm10
Supplementary files format and content: Normalized count (limma) txt file.

growth_protocol: Cell culture was performed in static culture conditions. Because TIFM contains fewer nutrients than standard culture, media was changed on TIFM-cultured cell lines every 24 hours. Glucose was routinely measured using a GlucCell glucometer 109 to ensure TIFM-cultured cells never experienced more than a 30% drop in glucose availability. Lastly, passaging TIFM maintained cells using standard trypsin (0.025%)/EDTA solution to detach cells leads to loss of viability upon replating of cells. Therefore, cells were detached with a 1:1 mixture of 0.5% trypsin–EDTA (Thermo Fisher) and serum- free RPMI- 1640  media (Thermo Fisher). This allowed routine passaging and plating of cells with less loss of viability.  These modifications were followed for both TIFM and RPMI cultured cells.

extract_protocol:
RNA was harvested using the Qiagen RNeasy kit.
Strand-specific RNA-SEQ libraries were prepared using an TruSEQ mRNA RNA-SEQ library protocol (Illumina). Library quality and quantity were assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000.

treatment_protocol: Lipid deprivation was done using medium +/- lipid stripped dialyzed FBS that was made using previously published protocols to chemically strip lipids from FBS (see following protocol: https://bio-protocol.org/en/bpdetail?id=2876&type=0). Cells were grown 6 cm dishes, washed once and treated with TIFM, RPMI, or TIFM with 1.19 mM arginine plus or minus exogenous lipids. After 24 hours, cells were washed 3x with PBS and RNA was harvested using the Qiagen RNeasy kit.

value: Pancreatic cancer epithelial cells

value: Lipid deprived (24 hours)


title: Detroit 551, Phase 2, Replicate 1

description: Library name: TC00000853_A04


title: mPDAC1, RPMI, - lipids 3

description: Library name: Sample 18


title: mPDAC1, RPMI, - lipids 1

description: Library name: Sample 16


title: Patient-derived organoid 8

description:
Library name: 016.ORG101
Column name in salmon.merged.gene_counts.tsv: x016.ORG101


title: Patient-derived organoid 2

description:
Library name: 014.ORG121
Column name in salmon.merged.gene_counts.tsv: x014.ORG121


title: NCI-H1092, Phase 2, Replicate 2

description: Library name: TC00000853_A02

value: Suspension


title: heart.Het.1291375

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291375


title: Patient-derived organoid 4

description:
Library name: 013.ORG138
Column name in salmon.merged.gene_counts.tsv: x013.ORG138


title: SET-2, Phase 1, Replicate 3

description: Library name: TC00000367_H11

value: Phase 1


title: NCI-H1092, Phase 2, Replicate 1

description: Library name: TC00000853_A01


title: heart.Het.1291374

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291374


title: SET-2, Phase 1, Replicate 2

description: Library name: TC00000367_H10


title: heart.Het.1291373

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291373


title: Patient-derived organoid 1

description:
Library name: 009.ORG19
Column name in salmon.merged.gene_counts.tsv: x009.ORG19


title: mPDAC1, RPMI, + lipids 3

description: Library name: Sample 15

value: Lipid replete


title: SET-2, Phase 1, Replicate 1

description: Library name: TC00000367_H09


title: WT ZT0_1

description: Library name: I5


title: mPDAC1, RPMI, + lipids 2

description: Library name: Sample 14


title: mPDAC1, TIFM, - lipids 3

description: Library name: Sample 12


title: heart.Het.1291370

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291370


title: heart.WT.1291372

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291372


title: NCI-H1092, Phase 1, Replicate 3

description: Library name: TC00000367_H08


title: heart.Het.1291371

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291371


title: Patient-derived tumor organoid PO10A-3

city: Atlanta

first: Youssef

middle: M

last: Zohdy

state: GA

address: 1365 Clifton Road NE

department: Neurosurgery

institute: Emory University

description: Library name: Sample 62

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

source_name: Patient-derived tumor organoid

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-derived tumor organoid


title: Patient-derived tumor organoid PO10B-3

description: Library name: Sample 65


title: mPDAC1, RPMI, + lipids 1

description: Library name: Sample 13


title: NCI-H1092, Phase 1, Replicate 1

description: Library name: TC00000367_H06


title: mPDAC1, TIFM, - lipids 2

description: Library name: Sample 11


title: NCI-H1092, Phase 1, Replicate 2

description: Library name: TC00000367_H07


title: Patient-derived tumor organoid PO10B-2

description: Library name: Sample 64


title: heart.WT.1291368

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291368


title: mPDAC1, TIFM, - lipids 1

description: Library name: Sample 10


title: mPDAC1, TIFM, + lipids 3

description: Library name: Sample 9


title: heart.Het.1291367

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291367


title: DV-90, Phase 1, Replicate 3

description: Library name: TC00000367_H05


title: Patient-derived tumor organoid PO10A-1

description: Library name: Sample 60


title: Patient-derived tumor organoid PO10B-1

description: Library name: Sample 63


title: mPDAC1, TIFM, + lipids 2

description: Library name: Sample 8


title: heart.WT.1291366

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291366


title: Patient-derived tumor organoid PO10A-2

description: Library name: Sample 61


title: Patient-derived tumor organoid PO9-3

description: Library name: Sample 59


title: DV-90, Phase 1, Replicate 2

description: Library name: TC00000367_H04


title: mPDAC1, TIFM, + lipids 1

description: Library name: Sample 7


title: heart.WT.1291365

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291365


title: DV-90, Phase 1, Replicate 1

description: Library name: TC00000367_H03


title: Patient-derived tumor organoid PO9-2

description: Library name: Sample 58


title: heart.Het.1291369

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291369


title: mPDAC1, TIFM + arg, - lipids 3

description: Library name: Sample 6


title: heart.Het.1291364

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291364


title: mPDAC1, TIFM + arg, - lipids 2

description: Library name: Sample 5


title: KP-N-RT-BM-1, Phase 1, Replicate 2

description: Library name: TC00000367_G12


title: heart.Het.1291362

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291362


title: Patient-derived tumor organoid PO8-2

description: Library name: Sample 55


title: KP-N-RT-BM-1, Phase 1, Replicate 1

description: Library name: TC00000367_G11


title: mPDAC1, TIFM + arg, - lipids 1

description: Library name: Sample 4


title: Patient-derived tumor organoid PO8-3

description: Library name: Sample 56


title: heart.WT.1291361

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291361


title: DMS 454, Phase 1, Replicate 3

description: Library name: TC00000367_G10

source_name: DMS 454

value: DMS 454


title: DMS 454, Phase 1, Replicate 2

description: Library name: TC00000367_G09


title: mPDAC1, TIFM + arg, + lipids 2

description: Library name: Sample 2


title: Patient-derived tumor organoid PO7-3

description: Library name: Sample 53


title: mPDAC1, TIFM + arg, + lipids 3

description: Library name: Sample 3


title: Patient-derived tumor organoid PO8-1

description: Library name: Sample 54


title: mPDAC1, TIFM + arg, + lipids 1

description: Library name: Sample 1


title: DMS 454, Phase 1, Replicate 1

description: Library name: TC00000367_G08


title: Patient-derived tumor organoid PO7-2

description: Library name: Sample 52


title: CHON-001, Phase 1, Replicate 3

description: Library name: TC00000367_G07


title: heart.WT.1291359

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291359


title: GLORI_3_hippocampus_synapse_rep4

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 47

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).

source_name: brain

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.

value: brain


title: heart.Het.1291358

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291358


title: Patient-derived tumor organoid PO7-1

description: Library name: Sample 51


title: CHON-001, Phase 1, Replicate 2

description: Library name: TC00000367_G06


title: GLORI_3_hippocampus_cytoplasm_rep4

description: Library name: Sample 46


title: Patient-derived tumor organoid PO9-1

description: Library name: Sample 57


title: heart.WT.1291363

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291363


title: KP-N-RT-BM-1, Phase 1, Replicate 3

description: Library name: TC00000367_H02


title: Patient-derived tumor organoid PO6-3

description: Library name: Sample 50


title: CHON-001, Phase 1, Replicate 1

description: Library name: TC00000367_G05


title: heart.WT.1291357

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291357


title: RNA_seq_hippocampus_synapse_rep2

description: Library name: Sample 44


title: heart.WT.1291360

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291360


title: A-704, Phase 1, Replicate 3

description: Library name: TC00000367_G04


title: heart.Het.1291355

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291355


title: heart.Het.1291356

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291356


title: RNA_seq_hippocampus_synapse_rep1

description: Library name: Sample 43


title: Patient-derived tumor organoid PO6-2

description: Library name: Sample 49


title: Patient-derived tumor organoid PO5B-2

description: Library name: Sample 47


title: heart.WT.1291354

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291354


title: RNA_seq_hippocampus_cytoplasm_rep3

description: Library name: Sample 42


title: A-704, Phase 1, Replicate 1

description: Library name: TC00000367_G02


title: heart.Het.1291353

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291353


title: Patient-derived tumor organoid PO5B-1

description: Library name: Sample 46


title: RNA_seq_hippocampus_cytoplasm_rep2

description: Library name: Sample 41


title: BHY, Phase 1, Replicate 3

description: Library name: TC00000367_F12

source_name: BHY

value: BHY


title: Patient-derived tumor organoid PO5A-3

description: Library name: Sample 45


title: RNA_seq_hippocampus_cytoplasm_rep1

description: Library name: Sample 40


title: BHY, Phase 1, Replicate 2

description: Library name: TC00000367_F11


title: heart.Het.1291352

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291352

value: heart


title: Patient-derived tumor organoid PO5A-2

description: Library name: Sample 44


title: heart.Het.1291351

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291351


title: GLORI_3_hippocampus_synapse_rep3

description: Library name: Sample 39

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


title: BHY, Phase 1, Replicate 1

description: Library name: TC00000367_F10


title: RNA_seq_hippocampus_synapse_rep3

description: Library name: Sample 45


title: heart.WT.1291350

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291350


title: Daudi, Phase 1, Replicate 3

description: Library name: TC00000367_F09

source_name: Daudi

value: Daudi


title: GLORI_3_hippocampus_synapse_rep2

description: Library name: Sample 38


title: Patient-derived tumor organoid PO4-3

description: Library name: Sample 42


title: Daudi, Phase 1, Replicate 2

description: Library name: TC00000367_F08


title: Patient-derived tumor organoid PO4-2

description: Library name: Sample 41


title: heart.WT.1291348

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291348


title: Patient-derived tumor organoid PO6-1

description: Library name: Sample 48


title: A-704, Phase 1, Replicate 2

description: Library name: TC00000367_G03


title: Patient-derived tumor organoid PO5A-1

description: Library name: Sample 43


title: Patient-derived tumor organoid PO4-1

description: Library name: Sample 40


title: GLORI_3_hippocampus_cytoplasm_rep3

description: Library name: Sample 36


title: GLORI_3_hippocampus_synapse_rep1

description: Library name: Sample 37


title: heart.WT.1291347

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291347


title: Daudi, Phase 1, Replicate 1

description: Library name: TC00000367_F07


title: heart.WT.1291349

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291349


title: GLORI_3_hippocampus_cytoplasm_rep2

description: Library name: Sample 35


title: HUVEC/TERT2, Phase 1, Replicate 3

description: Library name: TC00000367_F06


title: Patient-derived tumor organoid PO3-3

description: Library name: Sample 39


title: heart.WT.1291345

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291345


title: GLORI_3_hippocampus_cytoplasm_rep1

description: Library name: Sample 34


title: Patient-derived tumor organoid PO3-2

description: Library name: Sample 38


title: heart.Het.1291346

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291346


title: GLORI_3_10ng_totalRNA_rep3

description: Library name: Sample 33


title: HUVEC/TERT2, Phase 1, Replicate 2

description: Library name: TC00000367_F05


title: heart.WT.1291344

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291344


title: HUVEC/TERT2, Phase 1, Replicate 1

description: Library name: TC00000367_F04


title: GLORI_3_10ng_totalRNA_rep2

description: Library name: Sample 32


title: SK-MEL-28, Phase 1, Replicate 3

description: Library name: TC00000367_F03


title: heart.Het.1291343

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291343


title: GLORI_3_10ng_totalRNA_rep1

description: Library name: Sample 31


title: SK-MEL-28, Phase 1, Replicate 2

description: Library name: TC00000367_F02


title: Patient-derived tumor organoid PO2-3

description: Library name: Sample 36


title: Patient-derived tumor organoid PO3-1

description: Library name: Sample 37


title: GLORI_3_20ng_totalRNA_rep3

description: Library name: Sample 30


title: heart.WT.1291342

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291342


title: heart.WT.1291341

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291341


title: Patient-derived tumor organoid PO2-1

description: Library name: Sample 34


title: HBEC3-KT, Phase 1, Replicate 3

description: Library name: TC00000367_E11


title: heart.WT.1291340

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291340


title: GLORI_3_20ng_totalRNA_rep2

description: Library name: Sample 29


title: Patient resected tumor P10B-3

description: Library name: Sample 33

source_name: Patient resected tumor

value: Patient resected tumor


title: HBEC3-KT, Phase 1, Replicate 2

description: Library name: TC00000367_E10


title: heart.WT.1291339

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291339


title: Patient resected tumor P10B-2

description: Library name: Sample 32


title: HBEC3-KT, Phase 1, Replicate 1

description: Library name: TC00000367_E09


title: Patient resected tumor P10B-1

description: Library name: Sample 31


title: Patient resected tumor P10A-3

description: Library name: Sample 30


title: CCD-18Co, Phase 1, Replicate 3

description: Library name: TC00000367_E08


title: YC, replicate 2, scRNAseq

city: Daejeon

first: Kwon Yong

last: Tak

address: Gu Sung Street

country: South Korea

institute: KAIST

description: 10x Genomics

library_source: transcriptomic single cell

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)
Preprocessing done on Scanpy (v19.0) platform
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: liver cells

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.

treatment_protocol: Mice at the age of 4months were fed a control diet or a DCC-supplemented diet (0.1%) for 6weeks to induce advanced biliary fibrosis.

value: liver cells

tag: strain

value: 6 months old


title: heart.Het.1291337

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291337


title: YC, replicate 1, scRNAseq

description: 10x Genomics


title: Patient resected tumor P10A-2

description: Library name: Sample 29


title: Patient-derived tumor organoid PO2-2

description: Library name: Sample 35


title: SK-MEL-28, Phase 1, Replicate 1

description: Library name: TC00000367_E12

value: Adherent


title: CCD-18Co, Phase 1, Replicate 1

description: Library name: TC00000367_E06


title: Vhl/Rassf1a Cre rep3

city: Freiburg

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

institute: University Hospital Freiburg

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using trimmomatic (v 0.38) (parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:3 TRAILING:10 MINLEN:25)
Sequences were aligned using the STAR aligner (v 2.5.2b) (parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --quantMode GeneCounts)
Raw counts were generated using STAR --quantMode GeneCounts
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file of raw counts for each sample

source_name: E13.5 embryos

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey Nagel).
RNA libraries were prepared using the Illumina TruSeq Stranded RNA library preparation kit.

treatment_protocol: Mouse embryonic fibroblasts were isolated from mice.

value: E13.5 embryos

value: mouse embryonic fibroblast

value: KO


title: Patient resected tumor P10A-1

description: Library name: Sample 28


title: heart.WT.1291336

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291336


title: kidney.WT.1291334

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291334

value: kidney


title: Patient resected tumor P9-3

description: Library name: Sample 27


title: YF, replicate 1, scRNAseq

description: 10x Genomics


title: HepG2, Phase 1, Replicate 3

description: Library name: TC00000367_E05


title: Patient resected tumor P9-2

description: Library name: Sample 26


title: HepG2, Phase 1, Replicate 2

description: Library name: TC00000367_E04


title: Vhl/Rassf1a Cre rep1


title: kidney.WT.1291332

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291332


title: HepG2, Phase 1, Replicate 1

description: Library name: TC00000367_E03


title: YC, replicate 3, scRNAseq

description: 10x Genomics


title: heart.WT.1291338

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.WT.1291338


title: CCD-18Co, Phase 1, Replicate 2

description: Library name: TC00000367_E07


title: Patient resected tumor P9-1

description: Library name: Sample 25


title: hTERT-HPNE, Phase 1, Replicate 3

description: Library name: TC00000367_E02

source_name: hTERT-HPNE

value: hTERT-HPNE


title: kidney.WT.1291331

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291331


title: Vhl/Rassf1a GFP rep2

value: control


title: hTERT-HPNE, Phase 1, Replicate 2

description: Library name: TC00000367_D12

value: Phase 1


title: Patient resected tumor P8-3

description: Library name: Sample 24


title: Vhl/Rassf1a GFP rep1


title: kidney.Het.1291335

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291335


title: Patient resected tumor P8-2

description: Library name: Sample 23


title: kidney.Het.1291330

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291330


title: Vhl/Rassf1a Cre rep2


title: hTERT-HPNE, Phase 1, Replicate 1

description: Library name: TC00000367_D11


title: Rassf1a Cre rep3


title: kidney.Het.1291329

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291329


title: Patient resected tumor P8-1

description: Library name: Sample 22


title: HTB-9, Phase 1, Replicate 3

description: Library name: TC00000367_D10


title: kidney.Het.1291333

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291333


title: Rassf1a Cre rep2


title: Vhl/Rassf1a GFP rep3


title: Patient resected tumor P7-3

description: Library name: Sample 21


title: kidney.WT.1291327

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.WT.1291327


title: Patient resected tumor P7-2

description: Library name: Sample 20


title: kidney.Het.1291328

description:
Fat4_counts.txt
Fat4_TPM.txt
kidney.Het.1291328


title: Rassf1a GFP rep3


title: HTB-9, Phase 1, Replicate 1

description: Library name: TC00000367_D08


title: HTB-9, Phase 1, Replicate 2

description: Library name: TC00000367_D09


title: Patient resected tumor P7-1

description: Library name: Sample 19


title: MCF7, Phase 1, Replicate 3

description: Library name: TC00000367_D07


title: Rassf1a GFP rep2


title: heart.Het.1291326

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291326


title: heart.Het.1291325

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291325


title: Patient resected tumor P6-3

description: Library name: Sample 18


title: Rassf1a GFP rep1


title: MCF7, Phase 1, Replicate 2

description: Library name: TC00000367_D06


title: heart.Het.1291324

description:
Fat4_counts.txt
Fat4_TPM.txt
heart.Het.1291324


title: Patient resected tumor P6-2

description: Library name: Sample 17


title: MCF7, Phase 1, Replicate 1

description: Library name: TC00000367_D05


title: lung.Het.1291323

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291323

source_name: lung

value: lung


title: Vhl Cre rep3


title: Patient resected tumor P6-1

description: Library name: Sample 16


title: Vhl Cre rep2


title: lung.WT.1291322

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291322


title: Patient resected tumor P5B-3

description: Library name: Sample 15


title: U-2 OS, Phase 1, Replicate 3

description: Library name: TC00000367_D04

source_name: U-2 OS

value: U-2 OS


title: U-2 OS, Phase 1, Replicate 2

description: Library name: TC00000367_D03


title: Rassf1a Cre rep1


title: Vhl Cre rep1


title: U-2 OS, Phase 1, Replicate 1

description: Library name: TC00000367_D02


title: Patient resected tumor P5B-2

description: Library name: Sample 14


title: Vhl GFP rep3


title: lung.WT.1291320

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291320


title: Vhl GFP rep2


title: Patient resected tumor P5A-3

description: Library name: Sample 12


title: Patient resected tumor P5B-1

description: Library name: Sample 13


title: ARPE-19, Phase 1, Replicate 3

description: Library name: TC00000367_C12


title: lung.WT.1291319

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291319


title: ARPE-19, Phase 1, Replicate 2

description: Library name: TC00000367_C11


title: lung.Het.1291321

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291321


title: lung.Het.1291318

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291318


title: Patient resected tumor P5A-2

description: Library name: Sample 11


title: ARPE-19, Phase 1, Replicate 1

description: Library name: TC00000367_C10


title: Patient resected tumor P5A-1

description: Library name: Sample 10


title: lung.WT.1291317

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291317


title: A549, Phase 1, Replicate 3

description: Library name: TC00000367_C09


title: lung.WT.1291316

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291316


title: Vhl GFP rep1


title: WT Cre rep2


title: Patient resected tumor P4-3

description: Library name: Sample 9


title: A549, Phase 1, Replicate 2

description: Library name: TC00000367_C08


title: lung.WT.1291315

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291315


title: WT Cre rep1


title: Patient resected tumor P4-2

description: Library name: Sample 8


title: WT GFP rep3


title: lung.WT.1291314

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291314


title: A549, Phase 1, Replicate 1

description: Library name: TC00000367_C07


title: Patient resected tumor P4-1

description: Library name: Sample 7


title: BJ-5ta, Phase 1, Replicate 3

description: Library name: TC00000367_C06


title: WT GFP rep2


title: Patient resected tumor P3-3

description: Library name: Sample 6


title: WT GFP rep1


title: lung.WT.1291312

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291312


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

description: Library name: TC00000367_C04


title: Vhl/Rassf1a rep4

description: Vhl_Rassf1a_filtered_feature_bc_matrix.h5

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

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.

value: proximal tubule epithelial cell

value: Vhl/Rassf1a KO


title: WT Cre rep3


title: lung.WT.1291311

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.WT.1291311


title: Patient resected tumor P3-1

description: Library name: Sample 4


title: lung.Het.1291310

description:
Fat4_counts.txt
Fat4_TPM.txt
lung.Het.1291310


title: Patient resected tumor P2-3

description: Library name: Sample 3