title: S18_Input_d3_KO4

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

country: Canada

institute: McGill University

data_processing:
The quality of the sequencing reads was confirmed using the FastQC tool (Babraham Bioinformatics), and low-quality bases were trimmed from the read extremities using Trimmomatic v.0.33. The reads were mapped to the UCSC mouse mm9 reference genome with Bowtie 1.0.0, and BAP1 binding sites identified using peak detection algorithm MACS1.4, with comparisons for read enrichment against control input DNA from the same cells. Normalized sequence read density profiles (bigwig) were generated with Homer tool and visualized with IGV.
Gene ontology (GO) and disease ontology enrichment analyses on genes associated with BAP1 ChIP-Seq binding clusters were performed on GREAT 4.0.4 with Basal plus extension option, searching for genes within 2kb upstream, 2kb downstream, and 200kb in distal.
Assembly: mm9
Supplementary files format and content: bigwig files

extract_protocol:
CH12F3 cells were either unstimulated or stimulated with a cocktail consisting of recombinant human TGFβ1 (R&D systems, 240-B, 1 ng/mL), recombinant mouse IL4 (Preprotech, 214-14, 10 ng/mL), and functional grade purified α-mouse CD40 (eBiosciences, 16-0401, 1 ug/mL) for 72 hours to induce IgA class-switching.
Cells were fixed with 1% formaldehyde in the culture media for 10 minutes at room temperature, followed by addition of 0.125M of glycine to stop fixation. Nuclei were extracted with 5 minutes lysis in 0.25% Triton buffer, followed by 30 minutes in 200mM NaCl buffer. Nuclei were resuspended in sonication buffer and sonicated for twelve cycles of 30 seconds with a digital sonifier (Branson Ultrasonics) at 80%, with 30 seconds rest in cooled circulating water. Beads immunocomplexes were prepared overnight by conjugating 40μL of Dynabeads Protein G (Invitrogen, Life Technologies) with antibodies: anti-BAP1 (Cell Signaling Technology, D1W9B, 52.8 μg), anti-FLAG M2 (Sigma, F1804, 5 μg) or anti-H2AK119Ub (Cell Signaling Technology, D27C4, 5 μg). Immunoprecipitation was performed by overnight incubation of antibody-bead matrices with sheared chromatin from the equivalent of 5x106 cells. For BAP1-FLAG ChIP, 6 washes were performed with medium-stringency buffers, while 4 low-stringency washes were used for histone ChIP . Samples were de-crosslinked by overnight incubation at 65̊C in 1% SDS buffer. Following RNaseA and Proteinase K enzymatic treatments, ChIP DNA was purified using Qiaquick PCR Cleanup kit (Qiagen).
DNA yields and quality were assessed using Bioanalyzer (Agilent). Library preparation were performed using the KAPA HyperPrep Kit. Sequencing was assessed using Novaseq 6000.

tag: cell line

tag: cell type

value: B lymphocytes

tag: chip antibody

tag: treatment

value: 72hrs TGFβ1+IL4+CD40 stimulation


title: Sample 89_Reverse polarity

status: Public on Feb 15 2024

type: genomic

city: Bethesda

first: Kenneth

last: Aldape

state: Maryland

address: Building 10, Room 2S235

department: NCI, LABORATORY OF PATHOLOGY (HNC7Z18)

country: USA

institute: National Institute of Health

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC array Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software
matrix processed value definition: Beta values were caluclated using single sample Noob method
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from kidney tissue samples using illumina EPIC array kit according to standard instructions

tag: institue

value: NYU

tag: tissue

value: Kidney tissue

tag: disease state

value: Tumor

tag: diagnosis

value: Reverse polarity


title: Sample 86_PRCC

value: UCSF

tag: gender

value: Male

value: PRCC


title: Sample 87_PRCC


title: Sample 88_Reverse polarity


title: S17_H2AK119ub_d3_KO4

type: SRA

library_source: genomic

organism: Mus musculus

value: anti-H2AK119Ub (Cell Signaling Technology, D27C4)


title: Sample 96_AML

value: AML


title: S20_Input_d3_KO5


title: Sample 85_ccRCC

value: NIH

value: Female

value: ccRCC


title: Sample 84_Hybrid

value: Hybrid


title: S16_Input_d3_KO3


title: S14_H2AK119ub_d3_WT


title: S13_Input_d3_WT


title: S15_H2AK119ub_d3_KO3


title: Sample 80_HLRCC

value: HLRCC


title: Sample 79_HLRCC


title: Sample 82_HLRCC


title: S10_H2AK119ub_UN_KO5

value: unstimulated


title: Sample 78_RCC_unclassifiable


title: Sample 81_HLRCC


title: S19_H2AK119ub_d3_KO5

value: B lymphocytes


title: S8_H2AK119ub_UN_KO4


title: S9_Input_UN_KO4


title: Sample 77_ChRCC

value: ChRCC


title: S7_Input_UN_KO3


title: Sample 76_ChRCC


title: S6_H2AK119ub_UN_KO3


title: Sample 75_ccRCC


title: S5_H2AK119ub_UN_WT


title: Sample 83_HLRCC


title: S4_Input_UN_FLAGx3BAP1


title: Sample 74_ccRCC


title: Sample 73_ccRCC


title: Sample 72_ccRCC


title: S3_Flag_UN_FLAGx3BAP1

value: anti-FLAG M2 (Sigma, F1804)


title: S2_Input_UN_WT


title: S12_BAP1_d3_WT

value: anti-BAP1 (Cell Signaling Technology, D1W9B)

value: 72hrs TGFβ1+IL4+CD40 stimulation


title: Sample 71_ccRCC

value: Kidney tissue

value: Tumor


title: S11_Input_UN_KO5


title: S1_BAP1_UN_WT


title: IPS, _SKM INDUCED, REP5

city: East Lansing

first: michael

last: halbisen

state: MI

address: 603 Wilson Rd

department: Biochemistry

institute: Michigan State University

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IX_SKM10

library_source: transcriptomic

data_processing:
Post sequencing processing began with Trimmomatic/0.39-Java-11
FastQC/0.11.7-Java-1.8.0_162 was used for assessing post-trimming quality control.
Resultant reads were mapped using hisat2/2.1.0
sorted by name using SAMtools/1.9
HTSeq/0.11.2-Python-3.6.6 (Putri et al. 2021, https://www.python.org/) was then used to count reads for each annotated transcript.
Assembly: mm10
Supplementary files format and content: .csv, samples names are in the first row, gene identifiers (Ensembl ID) in the first column, raw counts in cells

molecule: polyA RNA

source_name: INDUCED PLURIPOTENT

growth_protocol: CELL CULTURE

extract_protocol:
TRIZOL/QuantiTect Reverse Transcription Kit (Qiagen)
llumina Stranded mRNA Library Preparation kit

treatment_protocol: REPROGRAMMING METHOD

value: INDUCED PLURIPOTENT

tag: genotype

value: REPROGRAMMING OF MEFS TO A PLURIPOTENT STATE USING 3 FACTORS (_SKM)


title: Sample 70_ccRCC

value: UCSF

value: Male


title: Sample 69_ccRCC

value: NIH


title: IPS, _SKM INDUCED, REP4

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IX_SKM09


title: Sample 67_ccRCC

value: Female


title: IPS, _SKM INDUCED, REP3

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IX_SKM08


title: Sample 68_ccRCC

value: ccRCC


title: Sample 66_ccRCC


title: IPS, _SKM INDUCED, REP1

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IX_SKM06


title: IPS, _SKM INDUCED, REP2

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IX_SKM07


title: IPS, OSKM INDUCED, REP5

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IXOSKM05

value: REPROGRAMMING OF MEFS TO A PLURIPOTENT STATE USING 4 FACTORS (OSKM)


title: Sample 64_ccRCC


title: Sample 65_ccRCC


title: IPS, OSKM INDUCED, REP4

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IXOSKM04


title: Sample 62_ccRCC


title: Sample 63_ccRCC


title: IPS, OSKM INDUCED, REP3

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IXOSKM03


title: IPS, OSKM INDUCED, REP2

description:
filtered-3-counts-Alex032522-OSKM-SKM.xlsx
RA02_IXOSKM02


title: Sample 61_ccRCC


title: Sample 60_ccRCC


title: IPS, OSKM INDUCED, REP1

description:
filtered-3-counts-Alex020722-IXEN.xlsx
RA02_IXOSKM01

source_name: INDUCED EXTRAEMBRYONIC

value: INDUCED EXTRAEMBRYONIC

value: DIFFERENTIATION OF ESC TO INDUCED XEN CELL STATE


title: Sample 57_ccRCC


title: IXEN, REP4

description:
filtered-3-counts-Alex020722-IXEN.xlsx
RA01_IXEN82


title: IXEN, REP2

description:
filtered-3-counts-Alex020722-IXEN.xlsx
RA01_IXEN81


title: Sample 55_ccRCC


title: IXEN, REP5

description:
filtered-3-counts-Alex020722-IXEN.xlsx
RA01_IXEN83


title: Sample 58_ccRCC


title: IXEN, REP3

description:
filtered-3-counts-Alex020722-IXEN.xlsx
RA01_IXEN80


title: IXEN, REP1

description:
filtered-3-counts-Alex020722-IXEN.xlsx
RA01_IXEN79


title: Sample 56_ccRCC


title: Sample 52_ccRCC


title: Sample 51_ccRCC


title: Sample 54_ccRCC


title: Sample 53_ccRCC


title: fl/fl_cre Rep1

description: Total B cells were isolated from mouse spleens via magnetic enrichment using with the EasySep Mouse CD19 Positive Selection Kit II (Stem Cell Technologies). For the FACS-sorting of B cell subsets, mouse spleens were mechanically dissociated in PBS with 0.1% BSA and 2mM EDTA, passed through 40 μm cell-strainers, and subjected to red blood cell lysis in ACK buffer (0.15M NH4Cl, 10mM KHCO3, 0.1mM EDTA). Cells were stained with the following antibodies: APC anti-CD267/TACI (ebio8F10-3, eBioscience); Alexa Fluor 488 anti-GL7 (GL7, Biolegend); Brilliant Violet 421 anti-CD95/Fas (Jo2, BD Biosciences) and anti-CD138 (281-2, Biolegend);  Brilliant Violet 650 anti-CD45R/B220 (RA3-6B2, BioLegend); Biotin anti-IgG1 (polyclonal, 1070-08, Southern Biotech); PE-Cy7 anti-CD19 (6D5, BioLegend); PerCP-Cy5.5 antiCD4 (RM4-4, Biolegend), anti-CD8a (53-6.7, Biolegend), anti-CD11b (M1/70, eBioscience), anti-NK1.1 (PK136, Biolegend), and anti-TER119 (Ly-76, Biolegend). Brilliant Violet 785 Streptavidin (Biolegend) was used to detect biotin-conjugated antibodies. Viability Dye 7-AAD (Biolegend) or eFluor® 506 (eBioscience) was used to discriminate dead GC B cells or dead plasma cells, respectively. Sorting was performed on the FACSAria (BD Biosciences).

data_processing:
The quality of the sequencing reads was confirmed using the FastQC tool (Babraham Bioinformatics), and low-quality bases were trimmed from the read extremities using Trimmomatic v.0.33.The reads were then mapped to the mouse UCSC mm9 reference genome assembly using Hisat2 v2.2.1. Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of at least 5 counts per 106 reads (CPM) in 4 samples for GC cells and 1 sample for plasma cells, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package. Dimension reduction analysis was performed using the Principal Component and Partial Least Squares regression method.
Pairwise comparisons were performed between the genotypes or between the treatments, and genes with changes in expression ≥ |2.0| fold and Benjamini-Hochberg adjusted p values ≤ 0.05 were considered significant.
For data visualization in Integrative Genomics Viewer (IGV) bigwig files were generated using a succession of genomeCoverageBed and wigToBigWig tools and scaled per 10x106 exon-mapped reads. Gene ontology (GO) enrichment analyses on differentially expressed gene clusters were performed with DAVID Bioinformatics Resources 6.8, and Gene Set Enrichment Analysis (GSEA) was performed with GSEA tool v4.3.2 using MSigDB v2022.1 with default configuration and permutation within gene sets.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include feature counts for each sample, where rRNA have been excluded.

molecule: total RNA

source_name: Spleen cells

extract_protocol:
RNA was extracted using the EZ-10 DNAaway RNA kit (Bio Basic), according to the manufacturer’s protocol, and quantified with NanoDrop (ThermoFisher Scientific). cDNA was prepared using the Moloney murine leukemia virus (MMLV) reverse-transcription kit and quantitative PCRs run on a StepOnePlus instrument with PowerSYBR master mix (all from ThermoFisher Scientific). Primers were purchased from Integrated DNA Technologies.
RNA yields and quality were assessed using Bioanalyzer (Agilent). rRNA depletion and library preparation were performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: Spleen cells

value: Germinal center B cells

value: FACS sorted


title: Sample 49_ccRCC


title: Sample 50_ccRCC


title: fl/fl_cre Rep2


title: Sample 59_ccRCC


title: fl/fl_cre Rep4


title: +/+_cre Rep4

value: +/+ cre


title: +/+_cre Rep3


title: +/+_cre Rep2


title: +/+_cre Rep5

value: Plasma cells


title: Sample 48_ccRCC

value: Kidney tissue


title: fl/fl_cre Rep5


title: Sample 45_ccRCC

value: Tumor


title: +/+_cre Rep1


title: Sample 44_ccRCC


title: RGC_3_AC

city: Houston

first: Jin

last: Li

state: Texas

address: 1 Baylor Plaza

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

description:
10x Genomics
MouseRetinaAtlas_countmatrix.h5ad

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads are processed by Cell Ranger pipeline version 7.0.1
Assembly: mm10 (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz)
Supplementary files format and content: A .h5ad file of count matrix

source_name: retina

extract_protocol:
We have generated 16 scRNA-seq samples of the mouse C57BL6/J retina. After dissection, retinas were dissociated into single cells using papain-based enzyme following the published protocol 10. With activated 45U of papain (Worthington, Cat. #LS003126) solution (1mg L-Cystine, Sigma; 8 KU of DNase I, Affymetrix; in 5 ml DPBS), retina was incubated at 37C for ~20min. Which was followed by the replacement of incubation buffer with 2ml ovomucoid solution (15 mg ovomucoid, Worthington Biochemical; 15 mg BSA Thermo Fisher Scientific; in 10 ml DPBS) and 500ul deactivated FBS. The retina tissue was carefully triturated and filtered by 20 um plastic mesh. Repeat the step with additional 1ml ovomucoid solution until no tissue is visible. Spin the cells down at 300g, 4C for 10 min, and cells were used in the next step.
To deplete the photoreceptors, cells were resuspended in 0.5% BSA and stained with CD73-PE antibody for 10min at 4C (for each million cells, add 98ul 0.5% BSA with 2ul CD73-PE antibody), and washed with 35 ml 0.5% BSA at 4C for 10min. After being stained with Anti-PE microbeads (for each million cells, add 80ul 0.5% BSA and 20ul microbeads), for 15 min at 4C, cells were washed and resuspended in 0.5% BSA. CD73 negative neuronal cells were enriched by autoMACS Pro Separator (Miltenyi Biotec) DEPLETES mode and ready for the next step. Similarly, CD90.2 positive neuronal cells were enriched with CD90.2 microbeads (for each 10million cells, 90ul 0.5% BSA and 10ul CD90.2 microbeads were used) and autoMACS POSSEL-S mode. Cells viability was 85%-87% when checked with DAPI staining under microscope.
Guided by 10X manufacturer’s protocols (https://www.10xgenomics.com), single cell cDNA library was prepared and sequenced. Briefly, single cell suspension was loaded on a Chromium controller to obtain single cell GEMS (Gel Beads-In-Emulsions) for the reaction. The library was prepared with Chromium Next GEM single cell 3’ kit V2 (10X Genomics) and sequenced on Illumina Novaseq 6000 (https://www.illumina.com). Our in-house generated single cell data was sequenced at the Single Cell Genomics Core at Baylor College of Medicine.

value: retina

tag: age

value: Postnatal month 4

value: wild-type

value: CD90.2 enrichment


title: 10x_retina_WT_4M reaction 2

value: Male

value: No enrichment


title: RGC_live_AC


title: 10x_retina_WT_4M reaction 1


title: Sample 46_ccRCC

value: NIH

value: Female

value: ccRCC


title: Sample 42_ccRCC


title: Sample 40_Hybrid

value: Hybrid


title: fl/fl_cre Rep3

value: Spleen cells


title: 10x_retina0401CD73Nv3

value: Postnatal week 8

value: CD73 enrichment


title: Sample 39_Hybrid


title: Sample 38_Hybrid


title: Sample 43_ccRCC


title: 10x_retina0315CD73Nv2


title: Sample 37_Hybrid


title: 10x_retina0315CD73NDRv2 reaction 5


title: 10x_retina0315CD73NDRv2 reaction 4


title: Sample 36_Hybrid


title: 10x_retina0315CD73NDRv2 reaction 3


title: Sample 35_Hybrid


title: 10x_retina0315CD73NDRv2 reaction 1


title: 10x_retina0315CD73NDRv2 reaction 2


title: Sample 33_Hybrid


title: Sample 32_Hybrid


title: 10x_mouse_CD90


title: Sample 31_Hybrid


title: Sample 41_PRCC T1

value: PRCC T1


title: 10x_Retina0426Cd73N


title: 10x_Retina0423Cd73N


title: Sample 30_Hybrid


title: Sample 29_Hybrid


title: 10x_retina0315CD73Nv3


title: 10x3_Ms_WT_PBS_2L

value: Postnatal day 17


title: Sample 28_Hybrid

value: Kidney tissue


title: 10x_Retina0313v2


title: Sample 27_Hybrid

value: Tumor


title: 10x3_Ms_WT_P90

value: retina

value: Postnatal day 90


title: Sample 25_Hybrid


title: 10x3_Ms_WT_P40

value: Postnatal day 40

value: wild-type


title: 10x3_Ms_WT_P180 reaction 2

value: Male

value: Postnatal day 180


title: 10x3_Ms_WT_P180 reaction 1

value: No enrichment


title: 10x3_Ms_WT_P14

value: Postnatal day 14


title: Sample 23_HLRCC

value: NIH

value: Female

value: HLRCC


title: Sample 26_Hybrid

value: Hybrid


title: Sample 22_HLRCC


title: Sample 34_Hybrid


title: CGG-Cit

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

country: China

institute: Sichuan University

data_processing:
The raw data was analyzed by Cell Ranger v3.0 using default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: calvarial bone defect areas

extract_protocol:
We created 2-mm calvarial bone defects on the parietal bones and implanted CGG hydrogels or CGG-Cit hydrogels. At 2 weeks post-surgery, the defect regions were carefully trimmed, and tissues were digested in 0.3% collagenase in α-MEM. Cell suspensions were filtered through 70 μm strainers, and single cells were subjected to RNA sequencing.
The 10x libraries were constructed using Chromium Controller and Chromium Single Cell 3’Reagent Kits. In brief, single-cell suspensions in each channel of the chip were loaded on a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in emulsion).  Then the 10x libraries of each channel were prepared using the Chromium Single Cell 3’Gel Bead and Library Kit v2 (PN-120236, 120267, 120262;  10x Genomics)或者 v3 (PN-1000153， 1000075, 120262; 10x Genomics). Libraries were sequenced by the Illumina NovaSeq sequencer with 150-bp  paired-end reads in Novogene Bioinformatics Technology Co., Ltd (Tianjing, China)

value: calvarial bone defect areas

value: C57BL/6 mice, wild type

value: CGG-Cit hydrogel implantation


title: CGG

value: CGG hydrogel implantation


title: YID-G3_S157

city: Nedlands

first: Scott

last: Fisher

state: Western Australia

address: 35 Stirling Highway, Nedlands

department: Institute for Respiratory Health

country: Australia

institute: The University of Western Australia

data_processing:
Raw sequencing files were aligned against the murine reference genome (GRCm38) using Kallisto (v0.46.1).
Transcript abundance was converted into gene-level estimate using Tximport package (v1.22) in Rstudio.
Gene counts data was normalized by DEseq2 package and filtered for low-expressed genes in Rstudio.
Assembly: GRCm38
Supplementary files format and content: DESeq normalized gene count data

source_name: Asbesos induced tumor

growth_protocol: Male mice from different CC strains were mated with female MexTAg mice to generate CC-MexTAg mouse model.

extract_protocol:
Whole tumors were harvested and stored in RNAlater (Thermo fisher) at -80C. Tumours were homogenized with tissue ruptor (Qiagen) and total RNA was extracted using Rneasy mini kit (Qiagen) and 500 ng of total RNA was used to construct sequenting libraries.
Sureselect strand specific mRNA library prep kit (Agilent technology australia) was used for RNA library prepration at Genomics WA (Perth, Australia).

treatment_protocol: The resultant CC‑MexTAg progeny were given two intraperitoneal injections of 3 mg Wittenoom crocidolite (blue) asbestos delivered one month apart.

tag: survival

value: Below median survival

value: Asbesos induced tumor

tag: strain

value: YIDxMexTAg

tag: disease

value: Asbestos related disease (mesothelioma)

value: No treatment


title: Sample 21_HLRCC

value: Kidney tissue

value: Tumor


title: Sample 19_HLRCC

value: Male


title: Sample 20_HLRCC


title: YID-E1-Tu2_S67

value: Above median survival


title: YID-D1-Tu2_S66


title: Sample 18_HLRCC

value: NIH


title: Sample 15_HLRCC


title: Sample 14_Reverse polarity

value: NYU

value: Reverse polarity


title: WOB2-H3_S2


title: Sample 13_PRCC T1

value: PRCC T1


title: WOB2-N3_S1


title: WAB2-H2_S26


title: Sample 24_HLRCC

value: HLRCC


title: Sample 11_PRCC

value: UCSF

value: PRCC


title: VUX2-G1_S158

value: VUXxMexTAg


title: VUX-E2_S35


title: Sample 9_PRCC


title: Sample 12_PRCC


title: VUX-D1_S9


title: VIT-K2_S28

value: Below median survival

value: VITxMexTAg


title: Sample 10_PRCC T1


title: VIT-A2_S27

value: Asbesos induced tumor


title: Sample 8_Oncocytoma

value: Oncocytoma


title: TOFU-K2_S153

value: TOFUxMexTAg

value: Asbestos related disease (mesothelioma)

value: No treatment


title: Sample 16_HLRCC

value: Female

value: Kidney tissue

value: Tumor


title: Sample 17_HLRCC

value: NIH

value: Male


title: Sample 5_RCC_unclassifiable


title: YID-D1-Tu1_S65

value: Above median survival

value: YIDxMexTAg


title: TOFU-C3_S25


title: VUX2-B1_S151


title: Sample 6_Oncocytoma


title: Sample 4_ccPRCC

value: ccPRCC


title: TAS-J2_S8

value: TASxMexTAg


title: Sample 1_HLRCC

value: HLRCC


title: Sample 2_ChRCC

value: ChRCC


title: TAS-H2_S24

value: Below median survival


title: TAS-E3_S34

value: Asbesos induced tumor


title: Sample 3_Oncocytic neoplasm

value: UCSF

value: Oncocytic neoplasm


title: TAS-D3_S6

value: Asbestos related disease (mesothelioma)


title: Sample 7_Oncocytoma

value: Oncocytoma


title: YID-C1_S149

value: No treatment


title: Rogan-E5_S2

value: RoganxMexTAg


title: Rogan-C3-Tu2_S1


title: Rogan-C3-Tu1-_S37


title: H1N1_Mannose_3

city: HongKong

first: Shuofeng

last: Yuan

address: 102 Pok Fu Lam Road

country: Hong Kong

institute: The University of Hong Kong

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 48bp.

data_processing:
The DEGs in treated samples were submitted to DAVID server for pathway enrichment and cluster analysis. Gene Ontology (GO) enrichment analysis of DEGs was implemented using the GOseq R package. KOBAS
Human Genome GRCh38 (downloaded from GENCODE) was used as reference genome. Note that the annotation contains a total of 60,725 genes and the total number of transcripts is 199,348.
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp
Subsequently, sequencing reads were filtered for rRNA sequence and remaining reads were used for downstream analysis
Reads were mapped to the reference genome using STAR (default parameters) with the following exception: twopassMode: Basic
Assembly: Differentially expression analysis was done using EBSeq
Supplementary files format and content: Results of differentially expressed gene analysis
Supplementary files format and content: Results of differentially expressed transcript analysis

source_name: lung

growth_protocol: 10%FBS DMEM for A549 culturing; 0.1ug/ml TPCK-0.3%BSA-DMEM for H1N1 infection

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit(Qiagen, Cat. No. / ID: 74104).
Sequencing libraries were constructed and sequenced in the Proteomics and Metabolomics Core (LKS Faculty of Medicine, The University of Hong Kong). After filtering the low-quality reads, clean reads were mapped to reference sequences using HISAT/Bowtie2.

treatment_protocol: The lung epithelial A549 cells were pre-treated with 25mM mannose or PBS control overnight. The cells were then infected with H1N1 (2MOI) and incubated in DMEM medium with 25mM mannose or PBS control. At 24hpi, total cellular RNAs of the virus-infected-PBS, virus-infected-mannose, or non-infected groups (n =3) were collected.

value: lung

value: adenocarcinomicepithelial cells

value: WT

value: 25mM mannose treatment

tag: infection status

value: infected with H1N1


title: H1N1_PBS_3

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 45bp.

value: PBS treatment


title: Piping-J1_S62

value: PipingxMexTAg


title: H1N1_Mannose_1

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 46bp.


title: H1N1_Mannose_2

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 47bp.


title: Piping-I3_S63

value: Above median survival


title: TAS-I1_S7

value: TASxMexTAg


title: ROGAN-E3_S145


title: TAS-H5_S159

value: Below median survival


title: Rogan-J2-Tu2_S39

value: Asbesos induced tumor


title: Rogan-J2-Tu1_S38


title: H1N1_PBS_2

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 44bp.


title: PEF2-G2-Tu2_S71


title: WT_SeV_6hr_3

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

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

source_name: Bonemarrow derived dendritic cell

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Bone marrow was harvested from the femurs of wt and Lba1 KO mice and cultured in RPMI1640 with 10% FCS and 10 ng/ml of GM-CSF for 6 days.　The medium was changed every 2 days.

extract_protocol: RNA samples were extracted from cells using TRIzol reagent (ThermoFisher).

treatment_protocol: BMDCs were infected with Sendai virus (moi=5).　Total RNA was collected 6 hours after infection.  Total RNA was collected 6 hours after infection

value: wt

value: BMDC


title: H1N1_PBS_1

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 43bp.


title: PEF2-A2-Tu1_S72

value: Asbestos related disease (mesothelioma)


title: KO_SeV_6hr_1

value: Lba1 KO


title: KO_SeV_6hr_3


title: KO_SeV_6hr_2


title: Mock_Infection_3

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 42bp.

value: mock infected


title: WT_SeV_6hr_1


title: WT_SeV_6hr_2


title: Mock_Infection_2

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 41bp.


title: MEE-I2_S156

value: MEExMexTAg

value: No treatment


title: Piping-N1_S64


title: MEE-E2-Tu2_S64


title: HT1080 wild-type 1 µM tubastatin long 2

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39 with default settings
Trimmed sequence reads were mapped to GrCh38.83 using bowtie2 v2.4.5 as implemented by RSEM v1.3.3, with default settings
Mapped sequences were annotated and counted using RSEM v1.3.3 with default settings
Read count extraction was performed using tximport v1.26.1
Read count statistical analysis was performed using DESeq2 v1.38.2
Assembly: Human NCBI genome build GrCH38 build 83
Supplementary files format and content: Expected counts from RSEM output for all conditions and ENSEMBL entries, cross-referenced to gene names and UNIPROT entries

source_name: Connective tissue

growth_protocol: HT1080 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
3x10^6 cells were pelleted, resuspended in MEM with 5% glycerol, and frozen at -80 °C. Cells were shipped on dry ice, and total RNA extracted by Creative Genomics using a commercially available kit. Quality of RNA was verified using RNA Screen Tape (Agilent). RNA was rRNA-depleted using the Ribo-Zero plus kit (Illumina).
Libraries were prepared using the PE150 platform (Illumina) following the manufacturer's instructions.

value: Connective tissue

value: fibrosarcoma

value: 1 uM tubastatin A, 14 days


title: MEE-E2-Tu1_S63


title: HT1080 wild-type 1 µM tubastatin long 1

value: WT


title: MEE-B1-Tu2_S50


title: HT1080 wild-type 5 µM PCI-34051 long 3


title: HT1080 wild-type 1 µM tubastatin long 3


title: HT1080 wild-type 5 µM PCI-34051 long 2


title: MEE-B1-Tu1_S49


title: MEE-A3-Tu2_S21


title: HT1080 wild-type 5 µM PCI-34051 long 1


title: PUB-I1_S152

value: PUBxMexTAg


title: HT1080 KDAC8H143A PCI34051 3

value: 5 uM PCI-34051, 2 days


title: PEF2-G2-Tu1_S70

value: Above median survival


title: HT1080 KDAC8H143A PCI34051 2


title: LOX-F4_S5

value: LOXxMexTAg


title: Sample 47_ccRCC

value: NIH

value: Male

value: Kidney tissue

value: Tumor

value: ccRCC


title: MEE-A3-Tu1_S20

value: Asbesos induced tumor

value: Asbestos related disease (mesothelioma)


title: LOX-F2_S55


title: LOX-D1-Tu2_S56


title: Mock_Infection_1

description: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp.

value: lung

value: adenocarcinomicepithelial cells

value: PBS treatment

value: mock infected


title: HT1080 KDAC6H611A TubastatinA 3

value: Connective tissue

value: fibrosarcoma

value: 1 uM tubastatin A, 2 days


title: Lox-D1-Tu1_S40

value: No treatment


title: HT1080 KDAC6H611A TubastatinA 1


title: HT1080 KDAC8H143A PCI34051 1

value: 5 uM PCI-34051, 2 days


title: LOX-E4_S147

value: Above median survival

value: LOXxMexTAg


title: HT1080 KDAC6H611A TubastatinA 2


title: LOX-B4-Tu3_S4


title: LOX-C1_S54


title: HT1080 KDAC6H216A TubastatinA 3


title: HT1080 KDAC6H216A TubastatinA 1


title: HT1080 KDAC6H216A TubastatinA 2


title: LOX-A3_S146


title: C4-2 cells, siMTHFD1L 3

city: Taichung

first: Wei-Chung

last: Cheng

address: No. 91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

data_processing:
1. trim adapter: trimmomatic
2. Alignment: Hisat2
3. Expression profiling: stringtie
Assembly: Homo_sapiens.GRCh38

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini Kit. 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SureSelect XT HS2 mRNA Library Preparation Kit following manufacturer's protocols.

treatment_protocol: PC-3 and C4-2 cell lines were treated with specific MTHFD1L siRNAs (Sigma-Aldrich) using the T-Pro NTR II transfection reagent (T-Pro Biotechnology) for three days.

value: prostate cancer cells

value: MTHFD1L knockdown


title: LAX-K2_S37

value: LAXxMexTAg


title: LOX-B4-Tu1_S3


title: C4-2 cells, siMTHFD1L 1


title: LAX-H1_S41


title: LAX-G3_S42


title: C4-2 cells, siMTHFD1L 2


title: C4-2 cells, siControl 3

value: WT


title: C4-2 cells, siControl 2


title: LAX-E2_S38

value: Asbesos induced tumor


title: LAX-F2_S39

value: Below median survival

value: Asbestos related disease (mesothelioma)


title: PC-3 cells, siMTHFD1L 3


title: LAT-F5-Tu2_S9

value: LATxMexTAg


title: PC-3 cells, siMTHFD1L 1


title: LAX-C2_S40


title: PC-3 cells, siControl 3


title: LAT-E2_S41


title: SLK23, ARDS, PBMC, Time_1

city: Seattle

first: Carmen

last: Mikacenic

state: Washington

address: 1201 Ninth Avenue

institute: Benaroyra Research Institute

description:
11_SLK23-V1
11_SLK23-V1_PBMC

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination

source_name: Blood

extract_protocol:
Blood taken from patients immediately and 72 hours after intubation on ventilators, whole cells sorted for live CD45+ CD15+ Leukocytes
NextSeq 10x chemistry; Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.

value: Blood

value: Leukocytes


title: PC-3 cells, siMTHFD1L 2


title: LAT-D3-Tu4_S60


title: SLK21, Non-ARDS, PBMC, Time_2

description:
10_SLK21-V2
10_SLK21-V2_PBMC


title: C4-2 cells, siControl 1


title: SLK23, ARDS, PBMC, Time_2

description:
12_SLK23-V2
12_SLK23-V2_PBMC


title: LAT-F5-Tu1_S8


title: PC-3 cells, siControl 2


title: LAT-D3-Tu3_S7


title: PC-3 cells, siControl 1


title: SLK21, Non-ARDS, PBMC, Time_1

description:
9_SLK21-V1
9_SLK21-V1_PBMC


title: LAT-D3-Tu2_S58


title: SLK7, ARDS, PBMC, Time_2

description:
6_SLK7-V2
6_SLK7-V2_PBMC


title: SLK12, Non-ARDS, PBMC, Time_2

description:
8_SLK12-V2
8_SLK12-V2_PBMC


title: H1048_AU15330_24h_2

city: Ann Arbor

first: Arul

last: Chinnaiyan

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

data_processing:
Files were first processed using FastQC for quality check then run through kallisto quant.
Individual samples were combined into one TPM table using tidyverse in R and the hg38 transcript to gene key. R package edgeR was then used to generate the cpm table.
Additional downstream analysis was performed in R using packages limma, edgeR, gsea.
Assembly: hg38
Supplementary files format and content: A single combined CPM table in csv format has been generated for all samples.

growth_protocol: Cells were cultured in ATCC-formulated RPMI with 10% FBS and penicillin.streptomycin except NCI-H929, which using ATCC-formulated RPMI with 0.05mM 2-mercaptoethanol, 10% FBS and penicillin

extract_protocol: Riboerase was selected for MM1.S samples and all the other samples were selected PolyA +RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina X, (2×100 nucleotide read length) with sequence coverage to 15-20M paired reads.

treatment_protocol: Cell were plated at 70-80% confluence in a 6-well plate and treated with AU-15330 dissolved in DMSO at 1uM for 12-24h.


title: SLK7, ARDS, PBMC, Time_1

description:
5_SLK7-V1
5_SLK7-V1_PBMC


title: LAT-D3-Tu1_S57


title: H1048_AU15330_24h_1


title: SLK22, ARDS, PBMC, Time_1

description:
4_SLK22
4_SLK22_PBMC


title: SLK14, Non-ARDS, PBMC, Time_1

description:
3_SLK14
3_SLK14_PBMC


title: LAT-D2_S6


title: SLK8, Non-ARDS, PBMC, Time_1

description:
2_SLK8
2_SLK8_PBMC


title: SLK3, ARDS, PBMC, Time_1

description:
1_SLK3
1_SLK3_PBMC


title: H1048_DMSO_24h_2

value: DMSO


title: LAT-A2_S155


title: H1048_DMSO_24h_1


title: De-input

city: Nanjing

first: Xing

last: Ma

address: No.1 Weigang, Nanjing, Jiangsu 210095, P. R. China

institute: Nanjing Agricultural University

description:
deme_pH55_merged_input_peaks.narrowPeak
deme_pH7_merged_input_peaks.narrowPeak

data_processing:
All clean reads in three biological replicates were aligned to the MSU v7.0 reference genome using BWA
SAMtools was used to exclude reads with mapping quality below 10
PCR duplicates were removed by using Picard
All aligned reads with at least length 50 were used for calling peaks by using callpeak function of MACS2 (version 2.1.1) (Zhang et al. 2008) with parameters as below: --extsize 200 -q 0.05 -nomodel -f BAMPE. Input and IgG data were used as controls.
Supplementary files format and content: narrowPeak files of MACS2 outputs

organism: Oryza sativa Japonica Group

source_name: seedling

growth_protocol: After pre-germination at room temperature (RT) for three days, uniformly germinated Nipponbare (Oryza sativa L., Japonica) rice seeds were put on the nutrient soil and grew in a greenhouse at 28-30℃ and a 14h/10h light-dark cycle. Two-week old seedlings were harvested and stored at -80℃ until used.

extract_protocol:
The fine powder was used for nuclei preparation and genomic DNA extraction following the procedures as described previously
The genomic DNA was fragmented into sizes, ranging from 100-500 bp, using the water-based Biorupter (Diagnode), followed by DNA extraction and purification. Total 5μg fragmented genomic DNA was diluted in iM stabilization buffer (50mM Tris-AcOH, pH=5.5) for denaturing and re-association treatment using a PCR program as below: 95°C for 8 min，95°C for 30s (-0.5 °C /cycles, 129 cycles)，35°C hold on. The re-associated DNA was diluted with iM-IP incubation buffer (50mM Tris-AcOH, 1mM MgCl2, 130nM CaCl2, 1%BSA and Complete mini, pH=5.5), then incubated with 3μg iMab antibody (Ab01462-23.0, Kappa) for 4 h at 4℃. The antibody incubation reaction was incubated with 30 μl of washed protein G Dynalbeads (10004D, Invitrogen) for another 4 h at 4°C. The iMab-bound DNA was finally eluted with 200 μl elution buffer (0.1M NaHCO3 and 1% SDS) at 65°C for two times with 15 min each. Three biologically replicated iM-IPed DNA or Input/IgG-IPed control DNA was used for library preparation. All libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S). Libraries were finally quality controlled and sequenced using paired-end mode on Illumina NovaSeq platform.

treatment_protocol: For zebularine treatment, an inhibitor of DNA methyltransferase leading to a global reduction of DNA methylation, 100 of 5-d-old rice seedlings were treated with 80 µM zebularine (Sigma-Aldrich Z4775) dissolved in DMSO or DMSO only (as control) for another five days. The zebularine-treated or untreated seedlings were collected and kept at -80℃ until used. For genomic DNA with M.CviP I (M0227S, NEB) treatment, a type of CpG Methyltransferase resulting in a global increase CG methylation in the eukaryotic genomes. 4 μg of purified rice genomic DNA was incubated with 8 units of M.CviP I with an addition of 640 μM SAM (S-adenosyl-methionine) at 37℃ for 1 h in a total of 20 μl reaction system. After inactivation of the enzyme activity with incubation at 65℃ for 20 min, M.CviP I treated DNA was recovered by using phenol/chloroform extraction followed by pre-cold alcohol precipitation.

value: demethylation


title: KAV-G2_S20

value: KAVxMexTAg


title: De-55-IP-Rep2

description:
deme_pH55_merged_igg_peaks.narrowPeak
deme_pH55_merged_input_peaks.narrowPeak

value: iMab


title: KAV-D4_S19

value: No treatment


title: SLK12, Non-ARDS, PBMC, Time_1

description:
7_SLK12-V1
7_SLK12-V1_PBMC


title: De-55-IP-Rep1


title: H526_AU15330_24h_2


title: H526_AU15330_24h_1


title: pc131_normal, snMultiome_ATAC

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

description: pc131_normal.filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
The snMultiome datasets was processed by cellranger-arc version 2.0.2. The reference genome was GRCh38. cellranger-arc count was used to generated the gene and peaks feature for the libraries.
Assembly: GRCh38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

source_name: Pancreas

extract_protocol:
Isolation procedure was adapted from Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000375). Nuclei were isolated from a 50mg piece of frozen tissue. The tissue was cut into 5 small sections with a razor blade. The tissue pieces were homogenized for 1.5 minutes with a tissue homogenizer and pestle in 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, and 1U/L RNase Inhibitor (Sigma-Aldrich, 03335402001) in nuclease free water. The tissue was allowed to dissociate in the lysis buffer for 5 minutes before passing through a 70m cell strainer. The solution was then centrifuged for 5 minutes at 500 x g at 4C. The supernatant was removed and replaced with 1 mL 1% BSA and 1U/L RNase Inhibitor in DPBS and allowed to incubate for 5 minutes before resuspension. The nuclei were centrifuged again at 500 x g, 4C for 5 minutes. The pellet was resuspended in 1mL 1% BSA and 1U/L RNase Inhibitor in DPBS and passed through a 30m cell strainer. All steps were performed on ice. Nuclei were stained with 7-Aminoactinomycin D (7-AAD) Ready Made Solution 1:100 (Sigma, SML-1633) and sorted with a FACSAria III Cell Sorter.  Nuclei were collected into 10% BSA and 1U/L RNase Inhibitor.
Prepared per manufacturer's instructions (10X Genomics, 1000283; CG000338 Rev E)

value: Pancreas

tag: condition

value: Normal Adjacent


title: pc131_normal, snMultiome_GEX


title: H526_DMSO_24h_2


title: De-55-IgG

value: IgG


title: KAV-A3-tu2_S22

value: Above median survival


title: H526_DMSO_24h_24h_1


title: tumor_4, snATAC-seq

data_processing:
The snATAC-seq datasets was processed by cellranger-atac version 2.1.0. The reference genome was GRCh38. cellranger-atac count was used to generated accessibility counts for the libraries.
Assembly: GRCh38
Supplementary files format and content: *.filtered_peak_bc_matrix.h5 : Filtered peak barcode matrix in hdf5 format.

extract_protocol:
Isolation procedure was adapted from Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000375). Nuclei were isolated from a 50mg piece of frozen tissue. The tissue was cut into 5 small sections with a razor blade. The tissue pieces were homogenized for 1.5 minutes with a tissue homogenizer and pestle in 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Nonidet P40 Substitute, and 1mM DTT in nuclease free water. The tissue was allowed to dissociate in the lysis buffer for 5 minutes before passing through a 70mm cell strainer. The solution was then centrifuged for 5 minutes at 500 x g at 4°C. The supernatant was removed and replaced with 1 mL 1% BSA in DPBS and allowed to incubate for 5 minutes before resuspension. The nuclei were centrifuged again at 500 x g, 4°C for 5 minutes. The pellet was resuspended in 1mL 1% BSA in DPBS and passed through a 30mm cell strainer. All steps were performed on ice. Nuclei were stained with 7-Aminoactinomycin D (7-AAD) Ready Made Solution 1:100 (Sigma, SML-1633) and sorted with a FACSAria III Cell Sorter.  Nuclei were collected into 10% BSA.
Prepared per manufacturer's instructions (10X Genomics, 1000176; CG000209 Rev F)

value: PDAC Tumor


title: KAV-A3-tu1_S21


title: De-7-IP-Rep1

description:
deme_pH7_merged_igg_peaks.narrowPeak
civ_pH7_merged_input_peaks.narrowPeak


title: GIT-K2_S66

value: GITxMexTAg


title: MM1S_AU15330_24h_2


title: tumor_3, snATAC-seq


title: pc131_tumor, snMultiome_ATAC

description: pc131_tumor.filtered_feature_bc_matrix.h5


title: GIT-K1_S65

value: Asbesos induced tumor


title: De-7-IgG


title: MM1S_AU15330_24h_1


title: pc131_tumor, snMultiome_GEX


title: Cvip-input

description:
civ_pH55_merged_input_peaks.narrowPeak
civ_pH7_merged_input_peaks.narrowPeak

value: hypermethylation


title: GIT-K1-pm-tu_S69

value: Asbestos related disease (mesothelioma)


title: De-7-IP-Rep2


title: MM1S_DMSO_24h_2


title: tumor_1, snATAC-seq


title: MM1S_DMSO_24h_1


title: benign_4, snATAC-seq

value: Benign


title: GIT-G2_S71

value: Below median survival


title: Cvip-55-IP-Rep2

description:
civ_pH55_merged_igg_peaks.narrowPeak
civ_pH55_merged_input_peaks.narrowPeak


title: Cvip-55-IP-Rep1


title: FUF-H2-2_S161

value: FUFxMexTAg


title: Cvip-7-IP-Rep2

description:
civ_pH7_merged_igg_peaks.narrowPeak
civ_pH7_merged_input_peaks.narrowPeak


title: Cvip-55-IgG


title: benign_2, snATAC-seq


title: H929_AU15330_24h_1


title: benign_3, snATAC-seq


title: H929_AU15330_24h_2


title: FUF-H2-1_S160


title: Cvip-7-IP-Rep1


title: H929_DMSO_24h_2

value: DMSO


title: CIS-G4_S30

value: CISxMexTAg


title: H929_DMSO_24h_1


title: tumor_2, snATAC-seq


title: CIS-G3-Tu2_S10


title: Cvip-7-IgG


title: GIT-H3_S68


title: CK-7-IP-Rep2

description:
ck_pH7_merged_igg_peaks.narrowPeak
ck_pH7_merged_input_peaks.narrowPeak

value: untreated


title: Run 1 WT RFP replicate 3

first: Pedro

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Read quality analysis was performed with FastQC.Barcode splitting, read collapse, and trimming of adaptor sequences was performed using scripts from the icSHAPE pipeline. Trimmed reads were first mapped to a costume genome that includes rRNA and repeated genomic sequences. Reads that did not map to the costume genome were then aligned to the human genome (hg38) using STAR (v.2.7.6a). Mapped reads were counted by htseq-count program and differential analysis was performed using DEseq2.
Assembly: hg38
Supplementary files format and content: count matrix
Library strategy: Ribo-seq

extract_protocol:
Cells were flash frozen by submerging the bottoms of dishes in liquid nitrogen. Cells were collected and lysed by scraping in lysis buffer containing cycloheximide. Cell lysates were triturated and clarified by centrifugation. Input samples were extracted from aliquot of lysate using trizol reagent according to the manufacturer's protocol. Following phase separation, the aqueous phase was applied to a Qiagen RNAeasy column and purified according to kit instructions. For ribosome prototected fragments, lyates were treated with RNase I and loaded onto 15%–45% sucrose gradients. Samples were fractionated and fractions containing 80S monosomes were precipitated with ethanol. After precipitation, monosome containing fractions were resuspended in trizol reagent. Sample workup was performed with a Zymo direct-zol kit following the manufacturer's protocol.
Samples were ribodepleted using Ribopoo ribosome RNA Homo sapiens depletion kit supplemented with custom-made oligos. RPF and input fractions were fragmented and size-selected on denaturing Urea PAGE gels. 3' adaptors sequencing adaptors were added with RNA ligase and reactions were reverse-transcribed with SuperScript IV. Sample cDNA was circularized with circLigase and libraries were PCR amplified to add Illumina sequencing primers. Libraries were sequenced on a NextSeq 2000 P2 instrument.

value: renal cell carcinoma

value: WT

value: ribosome protected


title: CIS-G3-Tu1_S29

value: No treatment


title: H526_dTAG_POU2AF2_AU15330_HAtag

data_processing:
Trimmomatic version 0.39 (settings TruSeq3-PE-2.fa:2:30:10, minlen 50)
Reads were aligned to hg38 (GRCh38) using bwa (“bwa mem” command with options -5SP -T0, version 0.7.17-r1198-dirty).
Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates).
Peak calling was performed using MACS2
Removed blacklisted regions of the genome from the peaks list (From encode's file ENCFF356LFX.bed)
Assembly: hg38
Supplementary files format and content: bigwigs, peak beds

extract_protocol: Chromatin immunoprecipitation experiments were carried out using the ideal ChIP-seq kit for transcription Factors (Diagenode) as per the manufacturer’s protocol. Chromatin from 2×106 cells was used for each ChIP reaction with 4μg of the target protein antibody. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 10 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the standard protocol.

treatment_protocol: Cell were plated at 70-80% confluence in a 150mm culture plate and treated with AU-15330 dissolved in DMSO at indicated concentrations (1uM) and for labeled durations (4-6h) .

tag: antibody


title: Run 1 WT RFP replicate 2

tag: cell line


title: H526_dTAG_POU2AF2_DMSO_HAtag


title: Run 1 WT RFP replicate 1

tag: cell type


title: benign_1, snATAC-seq

value: Pancreas


title: CIS-E2-Tu2_S12


title: Run 1 WT input replicate 3

value: input


title: CIS-E2-Tu1_S11


title: MM1S_AU15330_POU2AF1


title: CK-7-IgG

tag: chip antibody

value: IgG


title: MM1S_AU15330_IRF4

tag: treatment


title: Run 1 WT input replicate 2


title: BS-de-ck

data_processing:
BS-seq data were trimmed by using Fastp to remove the adapter sequences, then mapped to the rice reference genome (MSU7.0) by using Bismark
The methylated cytosines were counted from total uniquely mapped reads using the Bismark methylation extractor script.
Differential methylation regions (DMRs), including hyper and hypo DMRs, were identified by using intersect and dmr function of CGmapTools with the cutoffs: P-value < 0.01 and ΔmC ≥ 0.1.
Supplementary files format and content: txt files containing information of  hyper and hypo DMRs respectively

extract_protocol:
The fine powder was used for nuclei preparation and genomic DNA extraction following the procedures as described previously
5 µg of M. Cvip I-/zebularine-treated genomic DNA and CK were used for bisulfite treatment followed by library preparation and sequencing, which was conducted by Berry Genomics company (Beijing)


title: CC081-C5_S48

value: Above median survival


title: BS-de

value: demethylation


title: CC081-C4_S49

value: Asbesos induced tumor


title: MM1S_DMSO_POU2AF1


title: MM1S_DMSO_IRF4


title: Run 1 mutant RPF replicate 3

value: Mutant


title: BS-cvip-ck


title: CC081-A1_S50

value: Asbestos related disease (mesothelioma)


title: H526_dTAG_POU2F3_AU15330_HAtag


title: CC074-G1_S23


title: Run 1 mutant RPF replicate 2


title: CC074-B3-tu9_S29


title: sgIcam1_Act_2

city: Amsterdam

first: Chun-Pu

last: Lin

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: NKI-AvL

data_processing:
Read mapping was performed using STAR (2.6.0c)
Read counts per gene were quantified using HTSeq (0.11.4)
Read counts were normalised using DEseq2 (1.24.0)
Assembly: mouse GRCm38
Supplementary files format and content: Raw counts

source_name: splenic

growth_protocol: CD8+ T cells were maintained in CD8 T cell medium (RPMI, 10% FBS, 100U/ml penicillin, 100μg/ml streptomycin, 10ng/ml IL-2 (ImmunoTools), and 50μM 2-mercaptoethanol (Merck)) at a concentration of 1x10^6 cells/ml

extract_protocol:
Cells were washed with PBS and resuspended in the RLT buffer (Qiagen). The total RNA was isolated using the RNeasy Mini Kit (Qiagen), including an on-column DNase digestion (Qiagen).
Librararies were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated with anti-CD3 (1.25ug per/ 2x10^6 cells) on 24-well stimulation plates for 24h. Cells were then removed from the plates and harvested for sequencing.

value: splenic

value: Primary OT-I cell

value: CD8 T cell


title: Run 1 mutant RPF replicate 1


title: H526_dTAG_POU2F3_DMSO_HAtag

value: DMSO


title: BS-cvip

value: hypermethylation


title: H1048_dTAG_POU2F3_AU15330_6h_HAtag


title: Run 1 mutant input replicate 3

value: renal cell carcinoma


title: CK-7-IP-Rep1

value: iMab

value: untreated


title: sgIcam1_Act_1


title: Run 1 mutant input replicate 2


title: CC074-B3-tu8_S28

value: No treatment


title: CC074-B3-tu6_S27


title: Run 1 WT input replicate 1

value: WT


title: sgCtrl_Act_2

value: wt


title: CC074-B3-tu3_S26


title: H1048_dTAG_POU2F3_DMSO_HAtag


title: sgIcam1_Rest_2

value: rest


title: sgCtrl_Act_1


title: Run 1 mutant input replicate 1

value: input


title: CC074-B3-tu2_S25

value: Above median survival


title: Canine adipose-derived mesenchymal stem cells - biological replicate 8 - condition P6

city: Zagreb

first: Marina

last: Prišlin

address: Savska cesta 148

department: Virology Department

country: Croatia

institute: Croatian Veterinary Institute

description:
Test group
6-22 6p

data_processing:
Following data acquisition, normalization, and in-depth analysis were conducted using the specialized RT2 Profiler PCR Array Data Analysis software, accessible online at https://dataanalysis2.qiagen.com/pcr (accessed November 10th, 2023). For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, PGK1, ACTB. The statistical significance was calculated based on a Student’s t-test of the replicate 2^ (- Delta CT) values for each gene in the control and treatment groups. The software automatically appointed a fold change cutoff of 2.0, equal to log2Fold Change ± 1.0.
Fold Change worksheet reports test/control ( P6/P3) ratios.

label: SYBR Green

organism: Canis lupus familiaris

source_name: Isolated and in vitro cultured adipose tissue cells

label_protocol: Genomic DNA elimination and complementary DNA synthesis from 800 ng of RNA was accomplished using the RT2 First Strand kit (Qiagen, Cat. 330401) as instructed by the manufacturer. Subsequently, a commercially available RT² Profiler™ PCR Array for Dog Mesenchymal Stem Cells (PAFD-082ZR, Qiagen) with SYBR Green-optimized primer assays (Qiagen, Cat. 330603) was applied, following the manufacturer's instructions for Rotor-Gene Q (Qiagen). The array featured primers targeting 84 genes, categorized as stemness markers, MSC-specific, MSC-associated, and MSC-differentiation genes associated with osteogenesis, adipogenesis, chondrogenesis, myogenesis, and tenogenesis.

growth_protocol: The extraction of cAD-MSCs was carried out within a two-hour window from sample collection. This process involved rinsing and cutting the adipose tissue with a scalpel, followed by enzymatic digestion using 0.5% collagenase type 1 (Gibco, Cat. 17100017). The obtained stromal vascular fraction was subsequently placed into T25 cell culture flasks (Nunc, Thermo Fisher Scientific) and cultured in basal media comprising 79% Dulbecco's Modified Eagle Medium with Low Glucose (DMEM Low Glucose) (Gibco, Cat. 31885049), 20% Fetal Bovine Serum (FBS) (Gibco; Cat. 1027010), and 1% Penicillin/Streptomycin (Sigma-Aldrich, Cat. P4333-100ML) at 37°C. Media was replaced after 24 hours, and when adherent cells reached 90% confluence, subculturing was performed using a solution of 0.05% Trypsin and 0.02% EDTA (Sigma-Aldrich, Cat. 59417C-500ML) until proliferation arrest was observed.

extract_protocol: Gene expression analysis using an RT-qPCR array was conducted following total RNA extraction at two-time points during in vitro culture, P3 and P6. The cAD-MSCs reached approximately 90% confluence in T75 cell culture flasks (Nunc, Thermo Fisher Scientific). Subsequently, the cells were detached using a cell scraper (Nunc, Thermo Fisher Scientific) and centrifuged at 235× g for 10 minutes. Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Cat. 74106) with 2M dithiothreitol (Sigma-Aldrich, Cat. 43815-1G), following the manufacturer's instructions for approximately 107 cells. The extracted RNA was stored at -80°C until gene expression analysis.

tag: Sex

value: female

value: cAD-MSCs

tag: passage


title: CC074-B3-tu1_S24

tag: tissue

value: Asbesos induced tumor

value: Asbestos related disease (mesothelioma)


title: sgIcam1_Rest_1

value: splenic

value: Primary OT-I cell


title: H1048_DMSO_HAtag

value: DMSO


title: CC060-H2-tu2_S33


title: Canine adipose-derived mesenchymal stem cells - biological replicate 6 - condition P6

description:
Test group
2-22 6p


title: H929_AU15330_POU2AF1


title: CC060-G2_S32


title: sgCtrl_Rest_2

value: CD8 T cell


title: H929_DMSO_IRF4


title: Canine adipose-derived mesenchymal stem cells - biological replicate 5 - condition P6

description:
Test group
1-22 6p


title: sgCtrl_Rest_1


title: CC060-B1_S31


title: H929_DMSO_POU2AF1


title: Canine adipose-derived mesenchymal stem cells - biological replicate 9 - condition P6

description:
Test group
7-22 6p


title: H1048_AU15330


title: Canine adipose-derived mesenchymal stem cells - biological replicate 4 - condition P6

description:
Test group
14-21 6p


title: BAT_SC_4

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

description: RRBS

data_processing:
Raw read sequencing quality and adapter contamination were assessed using FastQC
Raw reads were aligned to the bisulfite genome using Bismark
Methylation calls in CpG, CHG, and CHH contexts were made using bismark_methylation_extractor.
Assembly: GRCm38 release V23
Supplementary files format and content: zipped text files with methylation calls

source_name: brown adipose tissue

growth_protocol: Upon weaning, all mice were housed in groups of 2-3 per cage, with a 12h light/12h dark cycle, and were provided adequate bedding and nesting material and unrestricted access to water and a standard chow diet (PicoLab 5V5R) throughout the study.

extract_protocol:
10-week-old ad lib-fed mice were euthanized between zeitgeber time ZT3-ZT6, and interscapular BAT was dissected and weighed after cardiac perfusion with 20 mL PBS. Tissues were snap-frozen in liquid nitrogen and stored at -80°C immediately after dissection. Genomic DNA was extracted from 0.020-0.025g BAT samples obtained from four mice each from TN, RT, and SC groups using a PureLink Genomic DNA Mini Kit (ThermoFisher Scientific) according to manufacturer protocol.
Sample libraries were generated from 150 ng genomic DNA and bisulfite conversion was performed using the Ovation RRBS Methyl-Seq System 1-16 with TrueMethyl oxBS kit (Tecan) per manufacturer protocol.  After cleanup, library concentration was measured using a Qubit Fluorometer, and fragment distribution was checked using a 2100 Bioanalyzer high sensitivity chip.
Sequencing at a depth of 50-65 million reads per sample was carried out on an Illumina Nextseq 550 System using a NextSeq 500/550 High Output Kit v2.5 (150 Cycles) (Illumina), per manufacturer protocol for 75 bp paired-end sequencing. Libraries were run on an Illumina Nextseq 550 instrument using the MetSeq Primer 1 (NuGEN) mixed with the Read 1 primer (Illumina) according to the Ovation RRBS Methyl-Seq System 1-16 protocol for the first read and the Read 2 primer (Illumina) for the second read, along with standard Illumina indexing primers.  Multiplexed samples were spiked with 10% PhiX Control v3 Library calibration control for run quality monitoring.  After the run, FASTQ files were generated using Basespace software (Illumina).

treatment_protocol: Male C57BL/6J mice were housed at thermoneutral (TN, 28oC) or standard room temperatures (RT, 22oC) beginning immediately after at weaning (3 weeks of age). At 8 weeks of age, a cohort of RT-housed mice were housed under severe cold (SC, 8oC) for two weeks

value: brown adipose tissue

value: male

value: wildtype

value: severe cold, 2 weeks (SC, 8C)


title: H1048_AU15330_6h_HAtag


title: H929_AU15330_IRF4_4964


title: CC059-F2-Tu2_S11

value: No treatment


title: BAT_SC_3

description: RRBS


title: CC059-F2-Tu1_S10


title: Canine adipose-derived mesenchymal stem cells - biological replicate 7 - condition P6

description:
Test group
3-22 6p


title: H1048_DMSO


title: Canine adipose-derived mesenchymal stem cells - biological replicate 2 - condition P6

description:
Test group
9-21 6p


title: BAT_SC_2

description: RRBS


title: Canine adipose-derived mesenchymal stem cells - biological replicate 1 - condition P6

description:
Test group
6-21 6p


title: BAT_SC_1

description: RRBS


title: H526_AU15330_POU2F3


title: CC059-E2-Tu2_S31

value: Below median survival


title: CC059-E2-Tu3_S44


title: H526_DMSO_POU2F3


title: siPLEKHA1_3

city: New Haven

first: Haikuo

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: GRCh38.101
Supplementary files format and content: Gene count matrix (tsv)
Supplementary files format and content: Gene CPM matrix (tsv)

source_name: RPTEC

extract_protocol:
Column-based RNA extraction
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems).
mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: RPTEC


title: BAT_RT_4

description: RRBS

value: room temperature housing (RT, 22C)


title: BAT_RT_3

description: RRBS


title: Canine adipose-derived mesenchymal stem cells - biological replicate 9 - condition P3

description:
Control Group
7-22 3p


title: siPLEKHA1_2


title: siPLEKHA1_1


title: CC059-B5_S12

data_processing:
Raw sequencing files were aligned against the murine reference genome (GRCm38) using Kallisto (v0.46.1).
Transcript abundance was converted into gene-level estimate using Tximport package (v1.22) in Rstudio.
Gene counts data was normalized by DEseq2 package and filtered for low-expressed genes in Rstudio.
Assembly: GRCm38
Supplementary files format and content: DESeq normalized gene count data

extract_protocol:
Whole tumors were harvested and stored in RNAlater (Thermo fisher) at -80C. Tumours were homogenized with tissue ruptor (Qiagen) and total RNA was extracted using Rneasy mini kit (Qiagen) and 500 ng of total RNA was used to construct sequenting libraries.
Sureselect strand specific mRNA library prep kit (Agilent technology australia) was used for RNA library prepration at Genomics WA (Perth, Australia).

value: Above median survival


title: CC059-E2-Tu1_S43


title: Canine adipose-derived mesenchymal stem cells - biological replicate 8 - condition P3

description:
Control Group
6-22 3p

value: female


title: BAT_RT_2

description: RRBS


title: Canine adipose-derived mesenchymal stem cells - biological replicate 3 - condition P6

description:
Test group
13-21 6p

value: cAD-MSCs


title: CC059-B1-Tu2_S62

value: Asbesos induced tumor


title: Canine adipose-derived mesenchymal stem cells - biological replicate 7 - condition P3

description:
Control Group
3-22 3p


title: siPPFIBP1_3


title: Canine adipose-derived mesenchymal stem cells - biological replicate 6 - condition P3

description:
Control Group
2-22 3p


title: siPPFIBP1_2


title: CC059-B1-Tu1_S61

value: Asbestos related disease (mesothelioma)


title: Canine adipose-derived mesenchymal stem cells - biological replicate 5 - condition P3

description:
Control Group
1-22 3p


title: BAT_TN_4

description: RRBS

value: thermoneutral housing (TN, 28C)


title: Canine adipose-derived mesenchymal stem cells - biological replicate 4 - condition P3

description:
Control Group
14-21 3p


title: CC059-A2-Tu1_S42


title: BAT_TN_3

description: RRBS


title: CC058-I4_Tu1_G1_S43


title: BAT_TN_2

description: RRBS


title: CC058-I4-Tu2_H1_S44


title: BAT_TN_1

description: RRBS


title: siPPFIBP1_1


title: Canine adipose-derived mesenchymal stem cells - biological replicate 1 - condition P3

description:
Control Group
6-21 3P


title: NT_siRNA_3

value: NTsiRNA


title: CC058-H4_S46


title: NT_siRNA_2


title: ENDSEQ-AGS-NC3

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
END-seq reads were aligned to the human (hg19) genome using Bowtie (version 1.1.2) with the options–best–all –strata –l 50. 3 mismatches were allowed while keepinng the best strata for tags with multiple alignments (-n 3 –k 1).
MACS 1.4.3 was used for peak calling of H.pylori-infected data, with default parameters (p value cutoff for peak detection = 1x10E-5;–keep-dup = auto). Uninfected cells were used as control, keeping > 10-fold-enriched peaks.
For genome browser tracks visualization, aligned bed files were converted into bedgraph using bedtools genomecov, following by bedGraphToBigWig to make a bigwig file. Values were normalized to reads per million. Visualization of genomic profiles was done by the Integrative Genomic Viewer (IGV) browser.
Assembly: hg19
Supplementary files format and content: bigwig file
Library strategy: END-seq

source_name: stomach

growth_protocol: Wild-type Adenocarcinoma Gastric cells (AGS) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco), penicillin streptomycin, L-Glutamine and Sodium Pyruvate (Gibco) at 37 °C.  Infection with H. pylori CagA-positive (ATCC43054) strain was performed for 24h.  with MOI of 100-140 (for AGS cells).

extract_protocol:
single-cell suspensions of AGS (8 million), were washed with PBS, and resuspended in cell suspension buffer (Bio-Rad), embedded in agarose, and transferred into plug molds (Bio-Rad). Plugs were allowed to solidify at 4°C and were then incubated with Proteinase K solution (Puregene, QIAGEN) for 1 hr at 50°C and then for ON at 37°C, followed by consecutive washes in a wash buffer containing 10 mM Tris-HCl (pH 8.0) and 50 mM EDTA (Wash Buffer) and then in a TE Buffer containing (10 mM Tris (pH 8.0) and 1 mM EDTA). Washed plugs were subsequently treated with RNaseA (Puregene, QIAGEN), washed again in Wash Buffer, and stored at 4°C (up to 2-4 days).
Blunting, A-tailing, and ligation to END-seq hairpin adaptor 1 were done at 37°C, 4°C respectively. DNA recovered from melted plugs was sheared to a length between 150 and 200 bp by sonication (Covaris), and biotinylated DNA fragments were purified using streptavidin beads (MyOne C1, Invitrogen). Following streptavidin capture, the newly generated ends were end repaired using T4 DNA polymerase (15 U), Klenow fragment (5 U), and T4 polynucleotide kinase (15 U); A-tailed with Klenow exo-fragment (15 U); and finally ligated to END-seq hairpin adaptor 2 using the NEB Quick ligation kit. After the second adaptor ligation, libraries were prepared by first digesting the hairpins on both adapters with USER enzyme (NEB) and PCR amplified for 16 cycles using TruSeq index adapters. PCR reactions were run on a 2% agarose gel and a smear of 200-400bp was cut and gel purified using MACHEREY-NAGEL extraction Kit (740609.50S).  Quantification of the library was performed by KAPA Library Quantification Kit for Illumina Platforms (Roche) and using dsDNA HS Assay Kit and QUBIT (Molecular Probes, Life Technologies) and qualification was done using the Agilent HS DNA Kit and Bioanalyzer 2100.  10nM of each library was pooled together and was diluted to 4nM according to NextSeq manufacturer’s instructions. 1.7pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced by Illumina NextSeq 500 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

value: stomach

value: AGS cell line

value: Gastric adenocarcinoma

value: WT

value: uninfected


title: Neoplts_2

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data Formatting bcltofastq-2.19.0
Data Cleaning fastp 0.20.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.6a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1n subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification3 salmon-1.3.0, --seqBias --gcBias --posBias
Assembly: m38 + Gencode-M25 Annotation
Supplementary files format and content: raw gene counts

source_name: mouse monocytes

extract_protocol:
Trizol RNA extraction
To remove contaminating DNA and DNases, 600 ng of RNA from each sample was processed with the TURBO DNA-free kit (Invitrogen) according to manufacturers instructions. Cleaned RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NextSeq 550 sequencer (Illumina, San Diego, CA). Single end reads of 75nt were generated for each sample.

value: mouse monocytes

value: P7 platelet coincubation


title: Canine adipose-derived mesenchymal stem cells - biological replicate 3 - condition P3

description:
Control Group
13-21 3p


title: Canine adipose-derived mesenchymal stem cells - biological replicate 2 - condition P3

description:
Control Group
9-21 3P


title: BAT_RT_1

institute: Baylor College of Medicine

description: RRBS

value: brown adipose tissue

value: male

value: wildtype


title: CC058-B2_S45

value: Above median survival

value: No treatment


title: NT_siRNA_1

last: Li

value: RPTEC


title: 12_VDN_T98G_Hypoxia_1microM_onamento_Exp3_Treated_S12

city: Tartu

first: Vijayachitra

last: Modhukur

address: L. Puusepa 8

country: Estonia

institute: University of Tartu

data_processing:
The reads underwent trimming using the Fastp program.
Reads were aligned to the GRCh37 human genome with the STAR aligner (v2.7.10a)
Read count estimation was  performed using featureCounts tool with default parameters.
Assembly: GRCh37 human genome
Supplementary files format and content: "edgeR_filtered_normalized_counts.xlsx" .This file contains the raw read count matrix. This file is in excel format..

source_name: onametostat in hypoxia

growth_protocol: Growth medium: ATCC EMEM + 10% FBS + antibiotic/antimycotic; 37 deg; normoxia (20% oxygen, 5% carbon dioxide, 75% nitrogen); passaging twice per week at 1/6 or similar ratio

extract_protocol:
The RNA extraction was performed using the RNeasy Mini Kit, together with DNase I treatment (Qiagen, Hilden, Germany), following the manufacturer’s instructions
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation protocol (Illumina, USA), following the manufacturer’s instructions, and using 10 ng of RNA as input.

treatment_protocol: 48-h treatment with 1 microM onametostat or 0.1% (vol/vol) DMSO in growth medium under different oxygenation conditions - normoxia (20% oxygen, 5% carbon dioxide, 75% nitrogen) or hypoxia (1% oxygen, 5% carbon dioxide, 95% nitrogen)

value: T98-G cell line

tag: study group

value: glioblastoma

tag: compound

value: PRMT5 inhibitor onametostat

tag: oxygenation


title: ENDSEQ-AGS-NC2

tag: genotype


title: CC053-G3-tu2_S67

first: Scott

last: Fisher

address: 35 Stirling Highway, Nedlands

institute: The University of Western Australia

tag: survival

value: Asbesos induced tumor

value: Asbestos related disease (mesothelioma)


title: Control_3

value: Control monocytes


title: CC053-H1_S4

tag: strain


title: 10_VDN_T98G_Hypoxia_1microM_onamento_Exp1_Treated_S10


title: 11_VDN_T98G_Hypoxia_1microM_onamento_Exp2_Treated_S11


title: CC053-G3-tu1_S36

tag: disease


title: ENDSEQ-AGS-NC1

value: stomach

value: AGS cell line

value: Gastric adenocarcinoma


title: 9_VDN_T98G_Normoxia_1microM_onamento_Exp3_Treated_S9

source_name: onametostat in normoxia


title: Neoplts_3

value: mouse monocytes


title: CC053-F1-Tu4_S8

value: Below median survival


title: ENDSEQ-AGS-HP3

value: WT

value: H.pylori infection


title: ENDSEQ-AGS-HP2


title: CC053-F1-Tu2_S7


title: Adultplts_3

value: adult platelet coincubation


title: 7_VDN_T98G_Normoxia_1microM_onamento_Exp1_Treated_S7


title: CC053-F1-Tu1_S6


title: ENDSEQ-AGS-HP1


title: 6_VDN_T98G_Hypoxia_0_1percentDMSO_Exp3_Control_S6

source_name: DMSO in hypoxia

value: negative control (DMSO)


title: Neoplts_1

value: P7 platelet coincubation


title: Adultplts_1


title: CC053-B1_S3

value: No treatment


title: Adultplts_2


title: control_2


title: Hemanoid_d16_IL3+M-CSF (CD34+)

city: Hannover

first: Nico

last: Lachmann

address: Carl-Neuberg-Str. 1

department: Pediatric Pneumology, Allergology and Neonatology

country: Germany

institute: Medizinische Hochschule Hannover

description: MCFC day 16, IL-3+M-CSF, CD34 enriched

data_processing:
Equal molar proportions of generated libraries were pooled accordingly, denatured with NaOH, and were finally diluted to 2pM according to the ‘Denature and Dilute Libraries Guide’ (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool was sequenced on an Illumina NextSeq 550 sequencer using one High Output Flowcell for 75 cycles and 400 Million clusters (#20024906; Illumina). Sequencing was performed according to the following settings: 28bp as sequence read 1; 56bp as sequence read 2; 8bp as index read 1; no index read 2.
The 10x Genomics CellRanger analysis pipeline set was used with default parameters. Briefly, BCL files were demultiplexed into FASTQ files by cellranger mkfastq (v4.0.0) using the respective sample sheet with utilized 10X barcodes. The cellranger count pipeline (v7.0.0) was used to align read data to the reference genome provided by 10X Genomics (Human reference dataset refdata-gex-GRCh38-2020-A), counting aligned reads per gene, and calculating clustering and summary statistics.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: filtered feature barcode matrices

growth_protocol: We used a modified version of the previously described EB-based hematopoietic differentiation protocol (Lachmann et al., 2013; van Wilgenburg et al., 2013) to differentiate human induced pluripotent stem cells (hiPSCs) into macrophages.  To initiate the differentiation process, we generated embryoid bodies (EBs) from detached iPSC colonies (strain #MHHi015-A, hPSCreg) using 2 mg/ml collagenase IV (#17104019, Invitrogen). These EBs were cultivated on an orbital shaker in iPSC-medium without basic fibroblast growth factor (bFGF), but with the addition of 10 μM Rock inhibitor (Y-27632; Tocris).  Following 2-3 days of cultivation, we changed the medium. After 5 days, mature EBs were manually selected and transferred to adherent plates containing differentiation medium I. This medium was supplemented with either 50 ng/ml interleukin-3 (IL-3, Peprotech) or a combination of 25 ng/ml IL-3 and 50 ng/ml macrophage colony-stimulating factor (M-CSF, Peprotech).  Samples for single-cell RNA transcriptome analysis were collected at the mature EB stage and again at d8 or d16 after the initiation of hematopoietic differentiation in differentiation medium I, for both cytokine conditions.

extract_protocol:
EB and adherent myeloid-cell-forming-complexes were dissociated with TrypLE Express (#12605028, Thermo Fischer Scientific) for 10-30 minutes at 37°C and filtered through a 70 µm mesh. Subsequently, the single-cell suspension was stained for CD34 expression (#11-0349, 1:50, eBioscience) and DAPI (Sigma) and further enriched by sorting (FACS Aria, BD) for live and CD34+ cells.
Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics). A twofold excess of cells was loaded to the 10x controller in the specified volume in order to reach a target number of 5000 cells per sample. Fragment length distribution of generated cDNAs and libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).

value: iPS cell line

value: healthy donor

value: feeder-based small scale macrophage differentiation

tag: cytokine condition

tag: time point

value: day 16


title: 4_VDN_T98G_Hypoxia_0_1percentDMSO_Exp1_Control_S4

value: T98-G cell line

value: glioblastoma


title: Ad-H

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
Read Quantification3 salmon-1.5.2, --seqBias --gcBias --posBias
Assembly: mg39 + Gencode-M27 Annotation
Supplementary files format and content: raw gene counts

source_name: platelet

extract_protocol:
Trizol RNA isolation
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NextSeq 550 sequencer (Illumina, San Diego, CA). Single end reads of 75nt were generated for each sample.

value: platelet


title: Ad-G


title: 5_VDN_T98G_Hypoxia_0_1percentDMSO_Exp2_Control_S5


title: CC053-A1-tu2_S35

city: Nedlands

source_name: Asbesos induced tumor

value: Above median survival

value: Asbesos induced tumor

value: Asbestos related disease (mesothelioma)


title: 3_VDN_T98G_Normoxia_0_1percentDMSO_Exp3_Control_S3

source_name: DMSO in normoxia


title: Ad-C


title: CC053-A4_S5


title: 2_VDN_T98G_Normoxia_0_1percentDMSO_Exp2_Control_S2


title: Hemanoid_d16_IL3 (CD34+)

description: MCFC day 16, IL-3 only, CD34 enriched


title: Control_1

value: mouse monocytes

value: Control monocytes


title: 8_VDN_T98G_Normoxia_1microM_onamento_Exp2_Treated_S8

value: PRMT5 inhibitor onametostat


title: CC053-A1-tu1_S34


title: 1_VDN_T98G_Normoxia_0_1percentDMSO_Exp1_Control_S1


title: EB_d0 (CD34+)

description: EB day 0, CD34 enriched

value: control

value: day 0


title: CC046-L3-Tu1_S16


title: TMA2, Visium

city: Rome

first: Antonio

last: Agostini

address: Largo Francesco Vito, 1

country: Italy

institute: Università Cattolica del Sacro Cuore

description: Visium

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the  Space Ranger software v1.3.1 following standard workflow
Assembly: GRCh38
Supplementary files format and content: matrix files, json files, csv

source_name: Pancreatic Tissue

extract_protocol:
5μm section for each TMA were positioned in each  indivdual capture area, and processed following manufacturer reccomendations.
Libraries were obtained according to the manufacter's instructions: For Visium the tissue were processed following the Visim Spatial Gene Expression for FFPE.

value: Pancreatic Tissue


title: Ad-A


title: CC046-J5-Tu2_S14

value: No treatment


title: TMA1, Visium

description: Visium


title: P7-E


title: P7-I


title: CC046-H2_S13


title: Mutant Run 1 IP replicate 3

city: Bethesda

data_processing:
Following sequencing, read quality was assessed with FastQC. Barcode split, read collapse, and adaptor trimming was performed using scripts from the icSHAPE pipeline. Trimmed reads were first mapped to a costume geneme that includes rRNA and repeat genome sequences. Reads that did not map to the costume genome were then aligned to hg38 using STAR (v/2.7.6.a). Peak analysis was performed using MACS2. Peaks were required to appear in at least 2 replicates for further analysis. Peak intersection with the hg38 longest transcript isoforms was performed using bedtools (v/2.30.0). Peak changes were identified in DESeq2 or edgeR.
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
Total RNA was collected using Trizol reagent according to the manufacturer’s protocol. Following separation of the aqueous and organic phases, the aqueous phase was removed and purified with a Qiagen RNA kit according to the manufacturer’s protocol.
mRNA was polyA selected through two rounds of selection with oligo dT magnetic beads. Following polyA selection, mRNA was fragmented using ZnCl2 before selection with m6A-specific antibody. 3' adaptors sequencing adaptors were added with RNA ligase and reactions were reverse-transcribed with SuperScript IV. cDNA was circularized with circLigase and libraries were PCR amplified to add Illumina sequencing primers. Libraries were sequenced on a NextSeq 550 instrument.

value: renal cell carcinoma

value: Mutant

value: IP


title: CC044-K1-Tu3_S19

value: Below median survival


title: Hemanoid_d8_IL3 (CD34+)

description: MCFC day 8, IL-3 only, CD34 enriched

value: iPS cell line

value: healthy donor

value: feeder-based small scale macrophage differentiation

value: day 8


title: Mutant Run 1 IP replicate 2


title: Hemanoid_d8_IL3+M-CSF (CD34+)

description: MCFC day 8, IL-3+M-CSF, CD34 enriched


title: CC044-K1-Tu2_S18

value: Asbesos induced tumor


title: CC046-L3-Tu2_S47

value: Above median survival

value: Asbestos related disease (mesothelioma)


title: P7-C

value: platelet


title: CC044-K1-Tu1_S17


title: AD3_D90B

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

data_processing:
Spaceranger version 1.0 was used to demulitplex the data, generate gene expression matrices by aligning the FASTQs to GRCH38.
The pipeline was also used to calculate spot co-ordinates using fiducial detection and to identify the spots covered by the tissue. The results from Spaceranger were imported into R using Spaniel (version 1.12). The data from each sample, which was derived from 4 consecutive sections within the tissue, was normalised and clustered, with a resolution of 0.5, using Seurat as described in the scRNA analysis section.
Supplementary files format and content: csvFile containing filtered count matrix for each cell
Supplementary files format and content: csv with metadata for each cell, contains clusters
Supplementary files format and content: Scaling factors from spaceranger
Supplementary files format and content: Image file processed by space ranger - 4,000 pixels in its largest dimension
Library strategy: Spatial Transcriptomics

source_name: organoid

extract_protocol:
Fresh frozen sections of four fetal retina samples of 8, 10, 11 and 13PCW were used for the spatial transcriptome analyses performed with the Visium Spatial Gene Expression kit from 10XGenomics. First the tissue optimisation was performed defining 30 minutes as the most optimal permeabilization time window. The spatial transcriptomic procedure was performed according to manufacturer’s instructions. Four tissue sections from each sample were carefully placed into the four capture areas, fixed, haematoxylin and eosin stained and images in order to preserve histological information. This makes it possible to overlay the cell tissue image and the gene expression data in a later step. After permeabilization, reverse transcription reagents were added on top of the tissues. The tissues were subsequently removed, leaving the cDNA coupled to the arrayed oligonucleotides on the slide.
The cDNA-RNA hybrids were cleaved off the chip and the sequencing libraries were prepared. The sequencing depth varied between 25,000,000 and 150,000,000 million reads.

value: organoid

tag: developmental stage

tag: section

value: B


title: AD3_D90A

value: A


title: Mutant Run 1 IP replicate 1

tag: cell line

tag: cell type


title: Ad-B


title: WT Run 1 IP replicate 3

value: WT

tag: treatment


title: P7-B


title: AD3_D60D

value: D


title: AD3_D60C

value: C


title: AD3_D90D


title: CC044-J3-Tu3_S4

value: No treatment


title: WT Run 1 IP replicate 1

value: renal cell carcinoma

value: IP


title: CC044-J3-Tu2_S3

value: Below median survival


title: P7-A


title: WT Run 1 IP replicate 2


title: AD3_D60B


title: AD3_D90C


title: XBPTG2

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (Homo_sapiens.GRCh38.94.gtf) and read counts obtained for each gene/transcript/feature
For the detection of diﬀerentially expressed genes, three different methods have been applied:  a) DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281]: a shrinkage estimation has been applied for dispersions and calculation of expression fold changes, to improve stability and interpretability of estimates  b) edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]: An overdispersed Poisson model is used to account for both biological and technical variability, and Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts.  c) Limma & Voom: a linear model was ﬁtted to the data that has been prepared with Voom [https://www.ncbi.nlm.nih.gov/pubmed/24485249], and empirical Bayes moderated t-statistics were calculated using the limma package [https://www.ncbi.nlm.nih.gov/pubmed/16646809] from Bioconductor.  Adjustment of p-values was done by the determination of false discovery rates (FDR) using Benjamini- Hochberg procedure.
Assembly: GRCh38.94
Supplementary files format and content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: human epithelial renal cell line (HK2) deficient in XBP1 gene and under thapsigargin treatment

growth_protocol: human epithelial renal cell line (HK2) (CRL-2190; ATCC) were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/ streptomycin, 1% insulin transferrin selenite  and 5ng/ml hydrocortisone.

extract_protocol:
PureLink TM RNA Mini kit (Invitrogen), with Dnase treatment. Total RNA was eluted in RNase-free water
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide(Part#15031047Rev.E)" with the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA Single Indexes (Illumina Inc. Cat. # 20020492 and 20020493)
mRNA stranded library sequencing

treatment_protocol: Cell were stimulated with thapsigargin (4 μM) in absence or presence  of JQ1 (500nM) for 24h

value: human epithelial renal cell line


title: Mutant Run 1 input replicate 3

value: Mutant

value: input


title: CC044-J3-Tu1_S2

value: Asbesos induced tumor


title: Mutant Run 1 input replicate 2


title: CC044-I2_S10

value: Above median survival


title: AD3_D35D


title: XBPTG1


title: Mutant Run 1 input replicate 1


title: JQ2

source_name: human epithelial renal cell line (HK2)  under thapsigargin treatment in presence of JQ1 drug


title: CC044-F4-Tu2_S32

value: Asbestos related disease (mesothelioma)


title: WT Run 1 input replicate 2


title: CC044-H2_S9


title: JQ1

source_name: human epithelial renal cell line (HK2) under thapsigargin treatment in presence of JQ1 drug


title: CC044-F4-Tu3_S46


title: AD3_D35B


title: AD3_D35C


title: WT Run 1 input replicate 3


title: AD3_D35A


title: ATF1

source_name: human epithelial renal cell line (HK2) udeficient in ATF4 gene and under thapsigargin treatment


title: ATF2

source_name: human epithelial renal cell line (HK2) deficient in ATF4 gene and under thapsigargin treatment


title: TG1

source_name: human epithelial renal cell line (HK2) under thapsigargin treatment


title: AD3_D20D