title: V_8_1_5, p604, day8, DonorII, Input

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Samples were sequenced on an Illumina HiSeq2500.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 36 bp
ChIP-seq reads were mapped to UCSC hg19, using the BWA tool (Li & Durbin, 2009).
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peak calling was conducted with diffReps (Shen et al., 2013).
bigWig files were generated using the tool makeUCSCfile of HOMER.
Assembly: hg19
Supplementary files format and content: bigWig, peaks

source_name: NHDF

growth_protocol: Neonatal human dermal fibroblasts (nHDFs) from two different human donors were purchased from Lonza (#CC-2509). HEK293 cells (ATCC), LentiX-293T cells (ATCC), H1299 cells (ATCC) and neonatal human dermal fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin-streptomycin (Gibco) under standard culture conditions. Patient-derived MCC cell line WaGa was cultured in Roswell Park Memorial Institute (RPMI; Gibco) medium. H1299 cells were transfected with polyethyleneimine (PEI). 10 µg DNA were mixed with DMEM w/o supplements and PEI at a ratio of 1:10 and added to a 10 cm dish of monolayered cells. For luciferase-based promoter assays, H1299 or HEK293 cells were transfected using Fugene HD (Promega), according to the manufacturer’s protocol, at a 3:1 ratio of DNA and FuGene HD. Production of lentiviral particles was conducted in Lenti-X 293T cells as described (Siebels et al., 2020). NHDFs were infected as previously described (Liu et al., 2016).

extract_protocol:
Native chromatin immunoprecipitation (nChIP) was conducted as described (Brind’Amour et al., 2015), using a starting material of 200,000 nHDFs per IP. The following antibodies were used for the nChIP reactions: rabbit mAbs α-H3K4me3 (1:200; Merck Millipore), α-H3K27me3 (1:300; Cell Signaling), α-H3K9me3 (1:200; Active Motif), α-H3K27ac (1:200; abcam) and IgG (1:200; Merck Millipore).
For sequencing of extracted DNA, libraries were prepared using the NEXTFlexTM ChIP-Seq Library Prep Kit (Bioo Scientific) according to the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq2500.

treatment_protocol: Use of a lentiviral transduction system to overexpress MCPyV T antigens (large Tumor (LT), small Tumor (sT), and truncated LT (LTtr)) in primary human dermal fibroblasts. Transcriptional profiling to investigate the interaction of T antigens with host cellular gene regulatory processes, focusing on inflammatory cytokines and interferon-stimulated genes (ISGs). Analysis of transcriptional changes induced by T antigens, such as the induction of inflammatory cytokines by both sT and LT, the short-term induction of ISGs by LT, and the stable repression of ISG transcription by sT. Investigation of the balancing effect of sT on immune recognition during the initial phase of infection and its potential role in maintaining a persistent infection. Evaluation of the transcriptional changes when sT is co-overexpressed with LTtr, reflecting the immunogenic feature of MCCs and their ability to attract innate and adaptive immune cells.

value: NHDF

value: sT

tag: chip antibody


title: V_8_1_6, p604, day8, DonorI, Input

status: Public on Apr 04 2024

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: V_8_1_5, p601, day8, DonorII, Input

value: mCherry control


title: V_8_1_6, p601, day8, DonorI, Input


title: V_8_1_8, p604, day8, DonorI, H3K27ac


title: V_8_1_8, p604, day8, DonorII, H3K27ac


title: V_8_1_8, p601, day8, DonorII,H3K27ac


title: V_8_1_8, p601, day8, DonorI, H3K27ac


title: V_8_1_7, p601, day8, DonorII, H3K9me3


title: V_8_1_7, p601, day8, DonorI, H3K9me3


title: V_8_1_5, p604, day8, DonorII, H3K27me3


title: V_8_1_5, p601, day8, DonorII, H3K27me3


title: V_8_1_6, p604, day8, DonorI, H3K27me3


title: V_8_1_6, p601, day8, DonorI, H3K27me3


title: V_8_1_5, p604, day8, DonorII, H3K4me3


title: V_8_1_6, p604, day8, DonorI, H3K4me3


title: V_8_1_6, p601, day8, DonorI, H3K4me3


title: p602and604_d3_DonorII

description: 210504_NB501882_0269_AHLNG7BGXH/nf648/V_8_5_2_NHDF_Donor_2_sTplusLT_d3_S12_R1_001

library_source: transcriptomic

data_processing:
Sequencing was conducted on an Illumina HiSeq 2500 platform (SR50). Reads were mapped to the human genome (hg19) using the STAR 2.6.0c tool (Dobin et al., 2013).
Differential gene expression (DEG) analysis was performed using DESeq2, as described by Love et al. (2014).
Gene Onotology (GO) analysis was performed with the DAVID tool, using DEGs with padj. <0.05 and log2FC >1/<-1. GO terms associated with biological processes were selected with an FDR or p-value <0.05, and a minimum of five genes within a GO term.
All unfiltered tables from the GO term analysis are shown in supplementary table S3. Volcano plots, heat maps and bubble plots were generated with R Studio. PCA plots were created using Python
Assembly: hg19
Supplementary files format and content: wig files were generated using bedGraphToBigWig

molecule: total RNA

source_name: nHDFs

extract_protocol:
Isolated RNA was examined on a Bioanalyzer with the RNA Nano kit (Agilent). RNA-Seq library preparation was carried out for with 1 µg of RNA from all samples that passed an RNA Integrity Number (RIN) of 0.7. mRNA enrichment was performed using the NEBNext Poly(A) Magentic Isolation Module (NEB).
RNA library preparation was conducted using the NEXTFlex Rapid Directional qRNA-Seq Kit (Bioo Scientific), according to the manufacturer’s protocol.

treatment_protocol: Use of a lentiviral transduction system to overexpress MCPyV T antigens (large Tumor (LT), small Tumor (sT), and truncated LT (LTtr)) in primary human dermal fibroblasts.

value: nHDFs

value: dermal fibroblasts

tag: genotype

value: NHDFs+WaGa

tag: treatment

value: sT+LT

tag: time

value: Day 3


title: p602and604_d3_DonorI

description: 210504_NB501882_0269_AHLNG7BGXH/nf647/V_8_5_1_NHDF_Donor_1_sTplusLT_d3_S11_R1_001


title: p602_d3_DonorI

description: 210302_NB501882_0250_AHLM2YBGXH/nf613/V842_NHDF_Donor_1_LT_d3_S19_R1_001

value: LT


title: RNAseq_K562_wt_r1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
5287_1_K562_17_r1_ATCACGA_S38
RNA-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype
rna_seq_count_table.tsv

data_processing:
1. DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Assembly: hg38
Supplementary files format and content: 1. DamID: BigWig files of log2-normalized pADamID scores for 25 kb genomic bins; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios (linked to the corresponding *early sample records).

growth_protocol: K562 cells (from ATCC) were cultured according to their ATCC guidelines.

extract_protocol:
1. DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested by centrifugation and immediately fixed in ice-cold ethanol.
1. DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018.
1. OTHER: DamID; 2. RNA-seq; 3. OTHER: Repli-seq

treatment_protocol: 1. DamID: cells were transduced with lentivirus containing Dam constructs. Three days after transduction, genomic DNA was isolated.; 2. Repli-seq: BrdU was added to a final concentration of 100 uM and cells were incubated at 37 °C for another 2 h.

value: WT


title: p600and601_d9_DonorII

description: 200817_NB501882_0221_AHFMVLBGXG/nf299/V_8_3_2_p600_601_Donor_II_d9_S13_R1_001

value: GFP+mCherry control

value: Day 9


title: p604and605_d9_DonorII

description: 200817_NB501882_0221_AHFMVLBGXG/nf300/V_8_3_2_p604_605_Donor_II_d9_S14_R1_001

value: sT+LTtr


title: p604and605_d12_DonorI

description: 200420_NB501882_0195_AHJCNWBGXF/nf210/8_2_3_p604and605_d12_S14_R1_001

value: Day 12


title: p602_d8_DonorII

description: 200817_NB501882_0221_AHFMVLBGXG/nf298/V_8_4_1_p602_Donor_II_d8_S12_R1_001

value: Day 8


title: p602_d8_DonorI

description: 200817_NB501882_0221_AHFMVLBGXG/nf297/V_8_4_2_p602_Donor_I_d8_S11_R1_001


title: V_8_1_7, p604, day8, DonorII, H3K9me3


title: V_8_1_7, p604, day8, DonorI, H3K9me3


title: p605_d8_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf36/8_2_1_p605_d8_S8_R1_001

value: Lttr


title: p600_d3_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf33/8_2_1_p600_d3_S5_R1_001

value: GFP control


title: p605_d8_DonorII

description: 191008_NB501882_0151_AHC235BGXC/nf142/8_2_3_p605_d8_S23_R1_001

value: LTtr


title: p600_d8_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf34/8_2_1_p600_d8_S6_R1_001


title: p600_d8_DonorII

description: 191008_NB501882_0151_AHC235BGXC/nf141/8_2_3_p600_d8_S22_R1_001


title: p605_d3_DonorII

description: 191008_NB501882_0151_AHC235BGXC/nf140/8_2_3_p605_d3_S21_R1_001


title: p605_d3_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf35/8_2_1_p605_d3_S7_R1_001


title: p601_d8_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf30/8_1_3_p601_d8_S2_R1_001


title: V_8_1_5, p601, day8, DonorII, H3K4me3

value: NHDF


title: p604_d3_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf31/_8_1_3_p604_d3_S3_R1_001

value: sT


title: p604_d8_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf32/8_1_3_p604_d8_S4_R1_001

value: nHDFs


title: p601_d3_DonorI

description: 190228_NB501882_0102_AHYJJ2BGX9/nf29/8_1_3_p601_d3_S1_R1_001

value: dermal fibroblasts

value: mCherry control


title: p600_d3_DonorII

description: 191008_NB501882_0151_AHC235BGXC/nf139/8_2_3_p600_d3_S20_R1_001

value: NHDFs+WaGa


title: p604_d8_DonorII

description: 190927_NB501882_0150_AHC2MHBGXC_single/nf138/8_1_5_p604_d8_S4_R1_001


title: p604_d3_DonorII

description: 190927_NB501882_0150_AHC2MHBGXC_single/nf136/8_1_5_p604_d3_S2_R1_001

value: Day 3


title: p601_d3_DonorII

description: 190927_NB501882_0150_AHC2MHBGXC_single/nf135/8_1_5_p601_d3_S1_R1_001


title: untreated_DonorII

description: 200420_NB501882_0195_AHJCNWBGXF/nf208/8_0_mock_NHDF_Donor_II_P9_S12_R1_001

value: untreated

value: Day 0


title: p600and601_d12_DonorI

description: 200420_NB501882_0195_AHJCNWBGXF/nf209/8_3_1_p600and601_d12_S13_R1_001

value: GFP+mCherry control


title: p602_d3_DonorII

description: 210302_NB501882_0250_AHLM2YBGXH/nf614/V842_NHDF_Donor_2_LT_d3_S20_R1_001

value: LT


title: untreated_DonorI

description: 200420_NB501882_0195_AHJCNWBGXF/nf207/8_0_mock_NHDF_Donor_I_P9_S11_R1_001


title: b0-HUDEP2 (Day 8) Rep 3

city: Melbourne

first: JIM

last: Vadolas

state: Choose State/Province

address: Wright St, Clayton

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Raw data then went through read quality assessment by FastQC (version 0.11.5), mapping to the human genome (GRch38) by the STAR aligner and gene-level reads quantification using the Rsubread package.
Assembly: mapping to the human genome (GRch38)

source_name: Erythroid

growth_protocol: HUDEP-2 cells cells were maintained in StemSpan SFEM (STEMCELL technologies) supplemented with 50 ng/mL human stem cell factor (hSCF, PeproTech), 3 IU/mL erythropoietin (Janssen), 1 μM dexamethasone (Sigma-Aldrich), 1 μg/mL, doxycycline (Sigma-Aldrich) and 1X Penicillin-Streptomycin-Glutamine (PSG, Gibco). Differentiation medium consists of Iscove’s modified Dulbecco’s media (IMDM, Thermo Fisher Scientific) supplemented with 10 IU/mL EPO, 1μM mifepristone (Sigma-Aldrich), 5% human AB serum (Sigma-Aldrich), 500 μg/mL human holo-transferrin (Sigma-Aldrich), 3 IU/ml heparin (Sigma-Aldrich), 10 μg/mL insulin (Sigma-Aldrich) and 1X PSG.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol and 500ng were used for library preparation.
HUDEP-2 (n=3) and β0 HUDEP-2 (n=3) RNA samples were submitted for sequencing at Azenta Life Sciences (Suzhou China).
100bp paired-end polyA-enriched RNA sequencing were performed with a depth of minimum of 20 million read counts per sample. The sequencing library was sequenced on the Illumina HiSeq2500 at Azenta.

tag: tissue

value: erythroid

tag: age


title: b0-HUDEP2 (Day 8) Rep 2


title: b0-HUDEP2 (Day 8) Rep 1


title: HUDEP2 (Day 8) Rep 3


title: HUDEP2 (Day 8) Rep 2


title: b0-HUDEP2 (Day 0) Rep 3


title: HUDEP2 (Day 8) Rep 1


title: b0-HUDEP2 (Day 0) Rep 2


title: b0-HUDEP2 (Day 0) Rep 1


title: HUDEP2 (Day 0) Rep 2


title: HUDEP2 (Day 0) Rep 1


title: HUDEP2 (Day 0) Rep 3


title: Multiome - ATAC - Sample 1

city: Boston

first: Mehmet

middle: K.

last: Samur

state: MA

address: 440 Brookline Avenue

department: Department of Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: MM1S + HS5 co-culture (72 hours)

data_processing:
Sequenced reads were processed using 10x Genomics Cell Ranger ARC v2.0.0. The reads were aligned to the pre-built human reference genome GRCh38 - v2020-A-2.0.0 (May 3, 2021) provided by 10X Genomics.
Assembly: hg38
Supplementary files format and content: Tab-separated data and matrix files
Library strategy: Multiome (10X Genomics) - scRNA-Seq & scATAC-Seq

source_name: MM1S + HS5 cells

extract_protocol:
Co-cultured MM1S and HS5 cells were processed for single-cell Multiome ATAC + Gene Expression (10X Genomics) with a targeted nuclei recovery of approximately 10,000. Nuclei were isolated according to the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression (10X Genomics, CG000365 Rev A). Approximately one million cells were added to a 5.0 mL low binding tube and centrifuged (300×g for 5 min at 4°C) using a swinging bucket rotor. Cells were washed twice with PBS +0 .04% BSA and were passed through 40uM Flowmi cell strainer to remove any clumps. After pelleting the strained cells, the cell pellet was resuspended in 100 µL of chilled 10X Genomics Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1 % NP-40 Substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, 1 U/μL RNase inhibitor 40 U/mL) by pipette-mixing 10 times. Cells were incubated on ice for 3 min, followed by dilution with 1 mL of chilled Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/mL RNase inhibitor 40 U/mL). Nuclei were then centrifuged (500×g for 3 min at 4°C), and the supernatant was slowly removed. The nuclei were washed one additional time with 1 mL Wash Buffer. Nuclei were resuspended in chilled diluted nuclei buffer (1X Nuclei Buffer, 1 mM DTT, 1 U/mL RNase inhibitor 40 U/mL).
The single-cell ATAC library construction and gene expressionlibrary construction was carried out as described in the Chromium NextGEMSingle CellMultiomeATAC +Gene Expression User Guide (CG000338 Rev A). ATAC and GEX libraries weresequenced separately on anHiSeq4000(Illumina) before demultiplexing,alignment to the reference genome, andpost-alignment quality control.

value: MM1S + HS5 cells

tag: disease state

value: Multiple Myeloma


title: Finnish_healthy_3576

type: RNA

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

country: Finland

institute: University of Helsinki

description: Study subject, 3576_F cell sample

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing:
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 50%. Replicate control probes were combined by their median values.
Log2 transformation and quantile normalization.

source_name: PBMC

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Cells were incubated at +37 °C incubator at 5% CO2 for 24 hours in complete RPMI.

extract_protocol: Total RNA was isolated from 1x106 PBMCs by AllPrep DNA/RNA Universal Kit (Qiagen). Quantity of the samples were determined by NanoDrop spectrophotometer and Qubit fluorometere, and quality by Agilent Bioanalyzer 2100. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: PBMCs were extracted from the blood by CPT tubes.

tag: gender

value: Male

tag: nationality

value: Finnish

tag: diagnosis

value: healthy


title: p601_d8_DonorII

description: 190927_NB501882_0150_AHC2MHBGXC_single/nf137/8_1_5_p601_d8_S3_R1_001

value: Day 8


title: Finnish_healthy_3574

description: Study subject, 3574_F cell sample


title: Finnish_asthmatic_3573

description: Study subject, 3573_F cell sample

value: asthmatic


title: Multiome - GEX - Sample 1

description: MM1S + HS5 co-culture (72 hours)

molecule: nuclear RNA


title: Finnish_healthy_3572

description: Study subject, 3572_F cell sample


title: Finnish_healthy_3570

description: Study subject, 3570_F cell sample


title: Finnish_healthy_3567

description: Study subject, 3567_F cell sample

value: Female


title: Finnish_asthmatic_3571

description: Study subject, 3571_F cell sample


title: Finnish_asthmatic_3566

description: Study subject, 3566_F cell sample


title: Finnish_healthy_3569

description: Study subject, 3569_F cell sample


title: Finnish_healthy_3568

description: Study subject, 3568_F cell sample


title: Finnish_healthy_3565

description: Study subject, 3565_F cell sample


title: Finnish_healthy_3563

description: Study subject, 3563_F cell sample


title: Finnish_healthy_3564

description: Study subject, 3564_F cell sample


title: Finnish_healthy_3562

description: Study subject, 3562_F cell sample


title: Finnish_healthy_3561

description: Study subject, 3561_F cell sample


title: Finnish_healthy_3559

description: Study subject, 3559_F cell sample


title: Finnish_healthy_3560

description: Study subject, 3560_F cell sample


title: Finnish_asthmatic_3557

description: Study subject, 3557_F cell sample


title: Finnish_healthy_3556

description: Study subject, 3556_F cell sample


title: Finnish_healthy_3555

description: Study subject, 3555_F cell sample


title: Finnish_asthmatic_3552

description: Study subject, 3552_F cell sample


title: Finnish_healthy_3551

description: Study subject, 3551_F cell sample


title: Finnish_healthy_3575

description: Study subject, 3575_F cell sample


title: Finnish_healthy_3546

description: Study subject, 3546_F cell sample


title: Finnish_asthmatic_3547

description: Study subject, 3547_F cell sample


title: Finnish_asthmatic_3545

description: Study subject, 3545_F cell sample


title: Finnish_asthmatic_3549

description: Study subject, 3549_F cell sample


title: Finnish_healthy_3548

description: Study subject, 3548_F cell sample


title: Finnish_asthmatic_3544

description: Study subject, 3544_F cell sample


title: Finnish_asthmatic_3542

description: Study subject, 3542_F cell sample


title: Finnish_asthmatic_3543

description: Study subject, 3543_F cell sample


title: Finnish_asthmatic_3537

description: Study subject, 3537_F cell sample


title: Finnish_healthy_3539

description: Study subject, 3539_F cell sample


title: Finnish_healthy_3538

description: Study subject, 3538_F cell sample


title: Finnish_healthy_3540

description: Study subject, 3540_F cell sample


title: Finnish_healthy_3541

description: Study subject, 3541_F cell sample


title: Finnish_asthmatic_3533

description: Study subject, 3533_F cell sample


title: Finnish_asthmatic_3534

description: Study subject, 3534_F cell sample


title: Finnish_asthmatic_3536

description: Study subject, 3536_F cell sample


title: Finnish_healthy_3531

description: Study subject, 3531_F cell sample


title: Finnish_healthy_3530

description: Study subject, 3530_F cell sample


title: Finnish_healthy_3529

description: Study subject, 3529_F cell sample


title: Finnish_healthy_3558

description: Study subject, 3558_F cell sample


title: Finnish_asthmatic_3528

description: Study subject, 3528_F cell sample


title: Finnish_healthy_3527

description: Study subject, 3527_F cell sample


title: Finnish_healthy_3526

description: Study subject, 3526_F cell sample


title: Finnish_asthmatic_3525

description: Study subject, 3525_F cell sample


title: Finnish_healthy_3520

description: Study subject, 3520_F cell sample


title: Finnish_asthmatic_3522

description: Study subject, 3522_F cell sample


title: Finnish_healthy_3523

description: Study subject, 3523_F cell sample


title: GD3- Bgal- 4

city: Nice

first: Julien

last: Cherfils-Vicini

address: 28 Avenue de Valombrose

country: France

institute: IRCAN - CNRS - INSERM

data_processing:
The primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool.
Sequence alignment was done on the mouse genome (GRCm38) with STAR1 (v2.7.3a).
Gene expression was quantified using Salmon2 (V1.4) and the annotation of known genes from genecode vM25.
We normalized gene expression using Transcripts Per Million (TPM) by normalizing each gene length by the total read counts. RNA-seq quality control was evaluated by considering total number of reads, alignment and duplication rate.
Assembly: GRCm38
Supplementary files format and content: Counts and TPM

organism: Mus musculus

source_name: Lungs

extract_protocol:
Total RNA extraction was performed using the Single Cell RNA Purification Kit (Norgen, ref#48200) following manufacturer’s instructions.
The library was prepared from 3 000pg of total RNA with SMART-Seq Stranded Mammalian Single Cell kit (Takara/Clontech, 634470) according to manufacturer’s instructions.

treatment_protocol: Four 9-week-old pathogen-free male C57BL/6 mice (Charles River) were treated with intratracheal instillation of 50 µl of phosphate-buffered saline (PBS) or bleomycin (2.5 U.kg−1, Sigma-Aldrich). After 28 days the lungs were recovered and dissociated by Dispase (Corning), collagenase A, and DNase I (Roche) digestion for 30 min at 37°C. The cells were filtrated, recovered in DMEM 10% FBS and incubated with Bafilomycin A1 100nM (Sigma-Aldrich, ref#196000) for 1 hour at 37°, 5% CO2. Then they were stained for SA-β-Galactosidase with a Senescence Assay Kit (abcam, ref#ab228562) following the manufacturer’s protocol. The cells were then stained with directly AF647 coupled antibody directed against GD3 for 30 min at 4°C after saturation with Fc-Block anti-CD16/CD32 antibodies (clone 2.4G2) for 15 min on ice. They were incubated with DAPI as a viability marker for 10min.

value: Lungs

tag: strain

tag: Sex

value: Bleomycin

tag: markers

value: GD3- Bgal-


title: Finnish_asthmatic_3524

description: Study subject, 3524_F cell sample


title: Finnish_healthy_3519

description: Study subject, 3519_F cell sample


title: Finnish_healthy_3517

description: Study subject, 3517_F cell sample


title: Finnish_healthy_3516

description: Study subject, 3516_F cell sample


title: GD3+ Bgal- 4

value: GD3+ Bgal-


title: GD3- Bgal+ 4

value: GD3- Bgal+


title: GD3- Bgal- 3


title: Finnish_healthy_3515

description: Study subject, 3515_F cell sample


title: Finnish_asthmatic_3518

description: Study subject, 3518_F cell sample


title: Finnish_healthy_3514

description: Study subject, 3514_F cell sample


title: GD3+ Bgal+ 3

value: GD3+ Bgal+


title: Finnish_healthy_3512

description: Study subject, 3512_F cell sample


title: GD3+ Bgal- 3


title: GD3- Bgal+ 3


title: Finnish_asthmatic_3511

description: Study subject, 3511_F cell sample


title: GD3- Bgal- 2


title: Finnish_healthy_3513

description: Study subject, 3513_F cell sample


title: Finnish_asthmatic_3510

description: Study subject, 3510_F cell sample


title: GD3- Bgal+ 2


title: Finnish_healthy_3509

description: Study subject, 3509_F cell sample


title: GD3+ Bgal- 2


title: GD3+ Bgal+ 2


title: Finnish_healthy_3508

description: Study subject, 3508_F cell sample


title: Finnish_healthy_3507

description: Study subject, 3507_F cell sample


title: GD3- Bgal+ 1


title: GD3- Bgal- 1


title: GD3+ Bgal- 1


title: Finnish_healthy_3506

description: Study subject, 3506_F cell sample


title: St_VDC_0126.01

type: genomic

city: Bellaterra

first: Cristina

last: Marín García

state: Barcelona

address: Plaça Cívica

country: Spain

institute: Universitat Autònoma de Barcelona

description: VDC 20220126.01 (11)

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: GenomeStudio v2.0

label: Cy3, Cy5

organism: Mus musculus domesticus

source_name: Mouse tail

label_protocol: standard protocol

extract_protocol: Extraction of genomic DNA from frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: population

value: VDC

value: tail


title: GD3+ Bgal+ 1


title: St_VDC_1022.02

description: VDC 20211022.02 (10)


title: St_VDC_1022.01

description: VDC 20211022.01 (9)


title: Finnish_asthmatic_3505

description: Study subject, 3505_F cell sample


title: Finnish_asthmatic_3504

description: Study subject, 3504_F cell sample


title: snmC-seq2 of mus musculus: adult male amygdala WSB 1 [WSB_amy_1_methyl]

city: Los Angeles

first: Patrick

last: Chen

state: CA

address: 635 Charles E Young Dr S

department: Psychiatry

institute: UCLA

data_processing:
Reads were mapped using Bismark V0.22.3, followed by cell filtering based on mCCC levels, global mCG levels, global mCH levels, total mapped reads, Bismark mapping rate, and percent genome covered
Methylation features were calculated as fractions of methylcytosine over total cytosine across gene bodies ± 2kb flanking regions and 100kb bins spanning the entire genome. Methylation features were further split into CG and CH methylation types. Principal component analysis was run using Scanpy followed by knn using only the top 16 principal components by amount of variance explained and k=15. Harmony was used to correct batch between strains and unbias clusters arising from strain differences. After Harmony was applied, iterative clustering was performed with a combination of leiden unsupervised clustering and UMAP dimensionality reduction, identifying clusters as cell types by marker gene hypomethylation
genome build/assembly: mm10
processed data files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type

source_name: amydala

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2032
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2032

value: Brain

value: male

value: amydala

value: WSB

tag: method


title: snmC-seq2 of mus musculus: adult male amygdala PWK 1 [PWK_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2030
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2030

value: PWK


title: snmC-seq2 of mus musculus: adult male amygdala PWK 2 [PWK_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2031
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2031


title: Finnish_healthy_3503

description: Study subject, 3503_F cell sample

value: Finnish

value: healthy


title: St_VDC_1014.01

description: VDC 20211014.01 (7)

value: Male


title: snmC-seq2 of mus musculus: adult male amygdala CAST 1 [CAST_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2028
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2028

value: CAST


title: snmC-seq2 of mus musculus: adult male amygdala BALBC 2 [BALBC_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2027
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2027

value: BALBC


title: snmC-seq2 of mus musculus: adult male amygdala WSB 2 [WSB_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2033
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2033


title: snmC-seq2 of mus musculus: adult male amygdala CAST 2 [CAST_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2029
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2029


title: snmC-seq2 of mus musculus: adult male amygdala FVB 1 [FVB_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2024
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2024

value: FVB


title: Russian_healthy_3240

description: Study subject, 3240_R cell sample

value: Russian


title: St_VDC_1007.01

description: VDC 2021107.01 (5)


title: St_VDC_1007.02

description: VDC 2021107.02 (6)


title: Finnish_healthy_3502

description: Study subject, 3502_F cell sample


title: snmC-seq2 of mus musculus: adult male amygdala FVB 2 [FVB_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2025
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2025


title: snmC-seq2 of mus musculus: adult male amygdala AJ 2 [AJ_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2023
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2023

value: AJ


title: Russian_healthy_3237

description: Study subject, 3237_R cell sample


title: St_VDC_0513.02

description: VDC 20210513.02 (4)


title: snmC-seq2 of mus musculus: adult male amygdala BL6 2 [B6_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2021
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2021


title: St_VDC_0513.01

description: VDC 20210513.01 (3)


title: snmC-seq2 of mus musculus: adult male amygdala BL6 1 [B6_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2020
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2020


title: snmC-seq2 of mus musculus: adult male amygdala DBA 2 [DBA_amy_2_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2019
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2019

value: DBA


title: St_VDC_1014.02

description: VDC 20211014.02 (8)


title: Russian_healthy_3203

description: Study subject, 3203_R cell sample

value: Female


title: snmC-seq2 of mus musculus: adult male amygdala DBA 1 [DBA_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2018
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2018


title: snATAC-seq of mus musculus: adult male amygdala BL6 2 [B6_amy_2_ATAC]

library_source: genomic single cell

data_processing:
Reads were mapped, assigned cell barcodes, and the UMIs were collapsed using Cell Ranger ATAC V2.0.0 to generate a fragments file
We first used Model-based Analysis for ChIP-Seq (MACS) to call sample specifc de-novo peaks from its fragments file, then merged this between samples to generate a unified peaks set while filtering for peak length. Cells were filtered out based on useable read-pairs, number of fragments overlapping peaks, ratio of fragments overlapping peaks, nucleosome signal, and TSS enrichment score
We built a gene-by-cell transcriptional activity matrix that counts per cell, at the gene body and 2000bp upstream to capture the promoter region, the total number of ATAC-seq counts. We transferred the single-nucleus RNA annotation onto the single-nucleus ATAC cells by linking the RNAs expression profiles with ATAC transcriptional activity profiles through canonical correlation analysis (CCA) described in Seurat.
genome build/assembly: mm10
processed data files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type
processed data files format and content: tab-separated file including number of cells for each sample and cell type

extract_protocol:
DNA was prepared from isolated/sorted nuclei using 10X Genomics protocol (CG000209)
Libraries were prepared using 10X Genomics protocol (CG000209)

value: snATAC-seq


title: snmC-seq2 of mus musculus: adult male amygdala BALBC 1 [BALBC_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2026
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2026


title: Russian_healthy_3202

description: Study subject, 3202_R cell sample

extract_protocol: Total RNA was isolated from 1x106 PBMCs by AllPrep DNA/RNA Universal Kit (Qiagen). Quantity of the samples were determined by NanoDrop spectrophotometer and Qubit fluorometere, and quality by Agilent Bioanalyzer 2100. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.


title: snATAC-seq of mus musculus: adult male amygdala BL6 1 [B6_amy_1_ATAC]


title: St_VDC_1113.01

description: VDC 20201113.01 (1)

extract_protocol: Extraction of genomic DNA from frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: VDC

value: tail


title: snATAC-seq of mus musculus: adult male amygdala DBA 2 [DBA_amy_2_ATAC]

value: Brain

value: male


title: snRNA-seq of mus musculus: adult male amydala BL6 2 [B6_amy_2_RNA]

library_source: transcriptomic single cell

data_processing:
Reads were mapped, assigned cell barcodes, and the UMIs were collapsed using Cell Ranger V6.0.2 to generate a count matrix
Cells were filtered based on total UMI count, unique genes expressed, and mitochondrial fraction
Gene counts were normalized using SCTransform, cells were integrated using recirpocal principal components analysis in Seurat 4.0.5, and cell types were called by performing PCA on all integrated genes and running a de-novo Louvain clustering algorithm in the top 15 principal components space with resolution set to 0.1
genome build/assembly: mm10
processed data files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type
processed data files format and content: tab-separated file including number of cells for each sample and cell type

extract_protocol:
RNA was prepared from isolated/sorted nuclei using 10X Genomics protocol (CG000286)
Libraries were prepared using the 10X Genomics protocol (CG000286)

value: amydala

value: snRNA-Seq


title: Russian_healthy_3200

description: Study subject, 3200_R cell sample


title: St_CTR_0128.04

description: CTR 20220128.04 (6)

value: CTR


title: snATAC-seq of mus musculus: adult male amygdala DBA 1 [DBA_amy_1_ATAC]


title: snRNA-seq of mus musculus: adult male amydala DBA 2 [DBA_amy_2_RNA]


title: snmC-seq2 of mus musculus: adult male amygdala AJ 1 [AJ_amy_1_methyl]

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2022
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2022


title: Russian_healthy_3236

description: Study subject, 3236_R cell sample

value: healthy


title: Russian_healthy_3199

description: Study subject, 3199_R cell sample

value: Male


title: St_CTR_0930.12

description: CTR 20210930.12 (4)


title: snRNA-seq of mus musculus: adult male amydala BL6 1 [B6_amy_1_RNA]


title: Russian_healthy_3198

description: Study subject, 3198_R cell sample


title: snRNA-seq of mus musculus: adult male amydala DBA 1 [DBA_amy_1_RNA]


title: St_CTR_0930.10

description: CTR 20210930.10 (3)


title: Mouse, kidney, E1KO, Female, rep4

city: Bethesda

first: Jakub

last: Jankowski

state: MD

address: 8 Center DR.

department: NIDDK

institute: NIH

data_processing:
For samples where two technical replicates were performed, reads were concatenated first
Then, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
Subsequently, samples were aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013).
Finally, HTSeq (Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Assembly: mm10
Supplementary files format and content: .tabular files with raw read counts

source_name: Kidney

extract_protocol:
Total RNA was isolated from whole mouse kidneys using PureLink™ RNA Mini Kit (Invitrogen).
Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301).Libraries were sequenced using Illumina HiSeq 3000 using standard protocols.

value: Kidney

value: Klotho E1 KO

value: female


title: Mouse, kidney, E1KO, Female, rep3


title: Mouse, kidney, E1KO, Female, rep1


title: St_CTR_0128.01

description: CTR 20220128.01 (5)


title: Russian_healthy_3197

description: Study subject, 3197_R cell sample

value: Russian


title: Mouse, kidney, E1KO, Female, rep2


title: Russian_healthy_3196

description: Study subject, 3196_R cell sample


title: St_VDC_0331.01

description: VDC 20210331.01 (2)


title: Mouse, kidney, E1KO, Male, rep4


title: Russian_healthy_3201

description: Study subject, 3201_R cell sample


title: St_CTR_0922.03

description: CTR 20210922.03 (1)


title: St_CTR_0922.04

description: CTR 20210922.04 (2)


title: Mouse, kidney, E1KO, Male, rep3


title: Mouse, kidney, E1KO, Male, rep1


title: Russian_healthy_3195

description: Study subject, 3195_R cell sample


title: St_CFB_0622.04

description: CFB 20210622.04 (7)

value: CFB


title: Mouse, kidney, E1KO, Male, rep2


title: Mouse, kidney, WT, Female, rep4

value: Klotho E1 WT


title: Russian_asthmatic_3194

description: Study subject, 3194_R cell sample

value: Female

value: asthmatic


title: Mouse, kidney, WT, Female, rep3


title: St_CFB_0324.01

description: CFB 20210324.01 (6)


title: Russian_healthy_3193

description: Study subject, 3193_R cell sample


title: St_CFB_1027.03

description: CFB 20201027.03 (5)


title: Russian_healthy_3192

description: Study subject, 3192_R cell sample


title: Mouse, kidney, WT, Female, rep1


title: Mouse, kidney, WT, Female, rep2


title: St_CFB_1026.08

description: CFB 20201026.08 (4)


title: Russian_healthy_3191

description: Study subject, 3191_R cell sample


title: Mouse, kidney, WT, Male, rep1


title: Mouse, kidney, WT, Male, rep2


title: St_CFB_1026.05

description: CFB 20201026.05 (3)


title: Russian_healthy_3190

description: Study subject, 3190_R cell sample


title: Mouse, kidney, WT, Male, rep3


title: WXS of Vk32245 growing in vitro 1

city: Scottsdale

first: Peter

middle: Leif

last: Bergsagel

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

description:
Vk32245_MM_V_V_F_MYC_mc32295_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

data_processing:
Sequenced reads were trimmed for adaptor sequences with fastp version 0.22 and mapped to genome using bwa. Copy number was determined using GATK4 ModelSegments with penalty of 0 and 5. Structural variants were called using Lumpy as implemented in Smoove release 19. Identical SV in unrelated tumors were assumed to be germline and removed. SNV were called using Mutect 2. Identical SNV in unrelated tumor samples were assumed to be germline and removed.
processed data files format and content: Tab deliminated text file with segmented copy number data and binary vcf.gz summarizing single nucleotide variants
Assembly: GRCm38 with addition of DNA sequences for VkMYC transgene, CRE, FGFR3_IRES_GFP, and human CRBN BAC containing IL5Ra, TRNT, CRBN

source_name: in vitro

extract_protocol:
Cells were used to extract DNA using PureGene
DNA libraries were constructed using NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs)

value: in vitro

tag: tumor type

value: in vitro tumor

value: plasma cell

tag: disease

value: multiple myeloma

value: MYC

tag: myc transgene_stop_codon_reversion


title: St_CFB_1026.02

description: CFB 20201026.02 (2)

value: tail


title: Russian_healthy_3187

description: Study subject, 3187_R cell sample


title: St_CFB_1026.01

description: CFB 20201026.01 (1)


title: WXS of Vk32245 growing in vitro 2

description:
Vk32245_MM_V_V_F_MYC_mc32579_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

tag: cell line

tag: cell type

tag: genotype


title: WXS of Vk32052 passaged in vivo harvested from spleen

description:
Vk32052_MM_R_EM_F_MYC.CrbnNull.CRBN_mc32358_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

source_name: spleen

extract_protocol:
CD138-selected cells were used to extract DNA using PureGene
DNA libraries were constructed using NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs)

tag: tissue

value: spleen

value: Transplant recipient


title: WXS of Vk31422 passaged in vivo harvested from spleen

description:
Vk31422_MM_R_EM_F_MYC.CRE_mc31734_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk29400 passaged in vivo harvested from bone marrow

description:
Vk29400_MM_R_BM_F_MYC.CRE_mc29977_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

source_name: bone marrow

value: bone marrow


title: WXS of Vk31507 passaged in vivo harvested from spleen

description:
Vk31507_MM_R_EM_M_MYC.CrbnNull.CRBN_mc32510_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: male


title: Russian_healthy_3186

description: Study subject, 3186_R cell sample

value: healthy


title: WXS of Vk29087 passaged in vivo harvested from spleen

description:
Vk29087_MM_R_EM_M_MYC.CRE_29847b_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk29790 passaged in vivo harvested from spleen

description:
Vk29790_MM_R_EM_F_MYC.CrbnHet.CRBN_mc32184_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: female


title: SC5314_WT_37_Rep3_RPF

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

data_processing:
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13
Processed reads were uniquely mapped to non-dubious ORF (Allele A, C_albicans_SC5314_version_A22) extended by 18 nt into the UTRs
Assembly: C_albicans_SC5314_version_A22
Supplementary files format and content: tab-delimited text file include raw counts for each sample

organism: Candida albicans

source_name: Yeast

growth_protocol: C. albicans cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4) at 30°C and 37°C , 200 revolutions per minute in yeast extract peptone dextrose (YPD).

extract_protocol:
The cells were lysed using a Freezer-Mill (SPEX SamplePrep) with the settings: 2 cycles of 2 min precooling, 2 min at 5 CPS and 1 min intermittent cooling. Samples were cleared by two rounds of centrifugation (5 min; 4 °C; 10,000 g). 10 A260 units of cleared lysates were digested with 600U Ambion RNase I for 1 h at 22 °C and the reaction was inhibited by the addition of 15 μl SuperaseIn.
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

treatment_protocol: Cells were harvested by vacuum filtration using a 0.45 µm nitrocellulose filter and immediately flash frozen in liquid nitrogen.

value: SC5314 - wild type

tag: growth temperature


title: Mouse, kidney, WT, Male, rep4

value: Kidney


title: Russian_healthy_3185

description: Study subject, 3185_R cell sample

value: Russian


title: SC5314_WT_37_Rep2_RPF


title: Russian_healthy_3183

description: Study subject, 3183_R cell sample

value: Male


title: WXS of Vk25214 de novo tumor harvested from spleen

description:
Vk25214_MM_O_EM_F_MYC.MIRnull_mc31255_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: original de novo tumor


title: Russian_healthy_3184

description: Study subject, 3184_R cell sample


title: SC5314_WT_37_Rep1_RPF


title: WXS of Vk27181 passaged in vivo harvested from spleen

description:
Vk27181_MM_R_EM_M_MYC_27401_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: SC5314_WT_30_Rep3_RPF


title: Russian_healthy_3182

description: Study subject, 3182_R cell sample


title: WXS of Vk25283 de novo tumor harvested from spleen

description:
Vk25283_MM_O_EM_M_MYC.MDRhet_mc31256_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk25183 de novo tumor harvested from spleen

description:
Vk25183_MM_O_EM_M_MYC.MIRnull_mc28335_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: SC5314_WT_30_Rep2_RPF


title: Russian_healthy_3181

description: Study subject, 3181_R cell sample

value: Female


title: WXS of Vk25039 de novo tumor harvested from spleen

description:
Vk25039_MM_O_EM_F_MYC.MIRnull_mc31257_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk24095 de novo tumor harvested from spleen

description:
Vk24095_MM_O_EM_M_MYC.MDRhet_mc28332_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk23589 de novo tumor harvested from spleen

description:
Vk23589_MM_O_EM_F_MYC.MIRnull_mc27636_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: Yes


title: SC5314_HMA1_KO_37_Rep3_RPF

value: SC5314 - hma1delta/hma1delta


title: Russian_healthy_3180

description: Study subject, 3180_R cell sample


title: WXS of Vk23631 passaged in vivo harvested from spleen

description:
Vk23631_MM_R_EM_M_MYC_mc31901_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: plasma cell

value: multiple myeloma


title: Russian_asthmatic_3179

description: Study subject, 3179_R cell sample

value: asthmatic


title: WXS of Vk24094 de novo tumor harvested from spleen

description:
Vk24094_MM_O_EM_M_MYC.MDRhet_mc28331_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: spleen


title: WXS of Vk28158 passaged in vivo harvested from spleen

description:
Vk28158_MM_R_EM_M_MYC_29731b_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: Transplant recipient

value: MYC


title: SC5314_HMA1_KO_37_Rep2_RPF


title: WXS of Vk23117 de novo tumor harvested from spleen

description:
Vk23117_MM_O_EM_F_MYC.MIRnull_mc28334_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk22633 de novo tumor harvested from spleen

description:
Vk22633_MM_O_EM_M_MYC.MDRnull_mc28330_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: male


title: WXS of Vk22428 de novo tumor harvested from spleen

description:
Vk22428_MM_O_EM_F_MYC.MIRhet_mc31258_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk22304 de novo tumor harvested from spleen

description:
Vk22304_MM_O_EM_F_MYC.MIRnull_mc28336_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: SC5314_HMA1_KO_37_Rep1_RPF


title: Russian_healthy_3177

description: Study subject, 3177_R cell sample

value: healthy


title: WXS of Vk22182 de novo tumor harvested from spleen

description:
Vk22182_MM_O_EM_M_MYC.MIRnull_mc28333_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: SC5314_HMA1_KO_30_Rep3_RPF


title: WXS of Vk14750 growing in vitro

description:
Vk14750_MM_V_V_M_MYC_mc32168_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: in vitro

value: in vitro tumor

value: No


title: Russian_healthy_3148

description: Study subject, 3148_R cell sample

value: Russian


title: WXS of Vk14451 passaged in vivo harvested from spleen

description:
Vk14451_MM_R_EM_M_MYC.EGFP_mc31644_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: SC5314_WT_30_Rep1_RPF

value: SC5314 - wild type


title: WXS of Vk12653 passaged in vivo harvested from spleen 2

description:
Vk12653_MM_R_EM_M_MYC.AIDhet_mc26382_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: SC5314_HMA1_KO_30_Rep1_RPF


title: Russian_healthy_3147

description: Study subject, 3147_R cell sample


title: WXS of Vk12653 passaged in vivo harvested from spleen 1

description:
Vk12653_MM_R_EM_M_MYC.AIDhet_26382_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WXS of Vk12598 passaged in vivo harvested from spleen

description:
Vk12598_MM_R_EM_M_MYC.AIDhet_23916_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: Russian_healthy_3146

description: Study subject, 3146_R cell sample

value: Male


title: WXS of of Vk26784 passaged in vivo harvested from spleen

description:
Vk26784_MM_R_EM_M_MYC_27456_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection


title: WGS of VkMYC mouse Vk34578 tail germline genomic DNA

description:
Tail.Vk34578_N_O_Tail_M_MYC_35363_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

data_processing:
Sequenced reads were trimmed for adaptor sequences with fastp version 0.22 and mapped to genome using bwa. Copy number was determined using GATK4 ModelSegments with penalty of 0 and 5. SNV were called using Mutect 2. Identical SNV in unrelated tumor samples were assumed to be germline and removed.
processed data files format and content: Tab deliminated text file with segmented copy number data and binary vcf.gz summarizing structural variants and single nucleotide variants
Assembly: GRCm38 with addition of DNA sequences for VkMYC transgene, CRE, FGFR3_IRES_GFP, and human CRBN BAC containing IL5Ra, TRNT, CRBN

source_name: Tail

value: Tail

value: original de novo tumor

value: tail

value: germline

value: yes


title: Russian_healthy_3143

description: Study subject, 3143_R cell sample

value: Female


title: WGS of VkMYC mouse Vk32908 tail germline genomic DNA

description:
Tail.Vk32908_N_O_Tail_M_MYC.CrbnNull.CRBN_34574_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

data_processing:
Sequenced reads were trimmed for adaptor sequences with fastp version 0.22 and mapped to genome using bwa. Copy number was determined using GATK4 ModelSegments with penalty of 0 and 5. Structural variants were called using Lumpy as implemented in Smoove release 19. Identical SV in unrelated tumors were assumed to be germline and removed. SNV were called using Mutect 2. Identical SNV in unrelated tumor samples were assumed to be germline and removed.
processed data files format and content: Tab deliminated text file with segmented copy number data and binary vcf.gz summarizing structural variants and single nucleotide variants
Assembly: GRCm38 with addition of DNA sequences for VkMYC transgene, CRE, FGFR3_IRES_GFP, and human CRBN BAC containing IL5Ra, TRNT, CRBN


title: Russian_healthy_3178

description: Study subject, 3178_R cell sample


title: WGS of VkMYC mouse Vk32829 tail germline genomic DNA

description:
Tail.Vk32829_N_O_Tail_F_MYC.Nsd2Null_34573_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: female


title: RNA_RA_6h_dTAG13_rep2

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

institute: MPI Molecular Genetics

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2010) with the following arguments: -u -no-effective-length-correction -b.
Assembly: mm10
Supplementary files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: embryonic stem cells

value: Sox2 KO

tag: treatment

value: neural differentiation


title: WXS of Vk22284 passaged in vivo harvested from spleen

description:
Vk22284_MM_R_EM_M_MYC.CRE_23185b_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: male

value: spleen

value: Transplant recipient

value: plasma cell

value: multiple myeloma

value: Yes


title: WGS of Vk39885 growing in vitro

description:
Vk39885_MM_V_V_F_MYC.CrbnNull.CRBN_40056_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro

value: in vitro tumor

value: No


title: Russian_asthmatic_3142

description: Study subject, 3142_R cell sample

tag: gender

value: Russian

value: asthmatic


title: Russian_healthy_3176

description: Study subject, 3176_R cell sample

value: Male

tag: nationality

value: healthy


title: WXS of Vk21598 de novo tumor harvested from spleen

description:
Vk21598_MM_O_EM_M_MYC.MDRnull_mc27635_wxs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
snv_wxs.vcf
Hybrid Selection

value: original de novo tumor


title: RNA_RA_3h_dTAG13_rep2

value: embryonic stem cells


title: WGS of Vk39337 growing in vitro

description:
Vk39337_MM_V_V_F_MYC.CrbnNull.CRBN_40022_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: female


title: Russian_healthy_3141

description: Study subject, 3141_R cell sample

value: Female

tag: diagnosis


title: SC5314_HMA1_KO_30_Rep2_RPF

tag: strain

value: SC5314 - hma1delta/hma1delta


title: WGS of Vk38975 growing in vitro

description:
Vk38975_MM_V_V_M_MYC_40066_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

tag: Sex

value: male

value: MYC


title: RNA_RA_24h_DMSO_rep2

value: WT

value: neural differentiation


title: WGS of Vk38525 growing in vitro

description:
Vk38525_MM_V_V_M_MYC_38923_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: plasma cell

value: multiple myeloma

value: Yes


title: WGS of Vk38862 growing in vitro

description:
Vk38862_MM_V_V_F_MYC_39683_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro

value: in vitro tumor


title: RNA_RA_24h_dTAG13_rep2

value: Sox2 KO


title: Russian_healthy_3128

description: Study subject, 3128_R cell sample

value: Russian


title: RNA_RA_12h_DMSO_rep2


title: RNA_RA_12h_dTAG13_rep2


title: WGS of Vk38150 growing in vitro

description:
Vk38150_MM_V_V_M_MYC.CrbnNull.CRBN_39515_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: RNA_RA_3h_DMSO_rep2


title: Russian_healthy_3113

description: Study subject, 3113_R cell sample

value: healthy


title: WGS of Vk37553 passaged in vivo harvested from spleen

description:
Vk37553_MM_R_EM_M_MYC.CrbnNull.CRBN_38839_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: spleen

value: Transplant recipient

value: No


title: WGS of Vk38291 growing in vitro

description:
Vk38291_MM_V_V_F_MYC_39684_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: female


title: Russian_healthy_3112

description: Study subject, 3112_R cell sample

value: Female


title: WGS of Vk37783 growing in vitro 1

description:
Vk37783_MM_V_V_F_MYC.Omo.rtTA_39274_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk37296 growing in vitro 1

description:
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40052_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: male


title: Russian_asthmatic_3109

description: Study subject, 3109_R cell sample

value: asthmatic


title: WGS of Vk37553 growing in vitro

description:
Vk37553_MM_V_V_M_MYC.CrbnNull.CRBN_39481_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: RNA_UT_rep2

value: embryonic stem cells

value: WT

value: untreated


title: WGS of Vk36973 passaged in vivo harvested from spleen

description:
Vk36973_MM_R_EM_F_MYC.CrbnNull.CRBN_37409_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: plasma cell

value: multiple myeloma


title: WGS of Vk39227 growing in vitro

description:
Vk39227_MM_V_V_M_MYC.CrbnNull.CRBN_39482_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro

value: Yes


title: WGS of Vk37296 growing in vitro 2

description:
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40057_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro tumor


title: ChIP_Oct4_RA_6h_dTAG13

data_processing:
For ChIP-Seq, reads were trimmed to 50 bp length. The trimmed reads were aligned to the reference genome using bowtie2 (version 2.2.4) (Langmead, 2012) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
Assembly: mm10
Supplementary files format and content: bigWig files representing read density

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10minutes. The solubilized chromatin was then pooled and mixed thoroughly. The chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at-80°C until use. 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 6 washing steps (9 for T) with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.

value: Sox2 KO


title: ChIP_Oct4_RA_6h_DMSO


title: Russian_healthy_3108

description: Study subject, 3108_R cell sample

value: Male

value: Russian

value: healthy


title: RNA_RA_6h_DMSO_rep2

value: neural differentiation


title: Russian_healthy_3101

description: Study subject, 3101_R cell sample


title: WGS of Vk36679 passaged in vivo harvested from spleen

description:
Vk36679_MM_R_EM_M_MYC.CrbnNull.CRBN_36984_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: spleen

value: Transplant recipient


title: WGS of Vk36574 passaged in vivo harvested from spleen

description:
Vk36574_MM_R_EM_M_MYC.CrbnNull.CRBN_38943_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: male

value: yes


title: Russian_healthy_3092

description: Study subject, 3092_R cell sample


title: ChIP_Nanog_RA_6h_DMSO

value: embryonic stem cells


title: Russian_healthy_3116

description: Study subject, 3116_R cell sample


title: WGS of Vk38290 growing in vitro

description:
Vk38290_MM_V_V_F_MYC.CrbnNull.CRBN_39878_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: female

value: No


title: ChIP_Nanog_RA_6h_dTAG13

value: untreated


title: WGS of Vk36387 passaged in vivo harvested from spleen

description:
Vk36387_MM_R_EM_F_MYC.CrbnNull.CRBN_39020_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: plasma cell

value: multiple myeloma


title: Russian_healthy_3090

description: Study subject, 3090_R cell sample

value: Female


title: WGS of Vk37783 growing in vitro 2

description:
Vk37783_MM_V_V_F_MYC.Omo.rtTA_39522_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro

value: in vitro tumor


title: WGS of Vk36040 de novo tumor harvested from spleen

description:
Vk36040_MM_O_EM_F_MYC.CrbnNull.CRBN_36064_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: original de novo tumor


title: WGS of Vk35707 growing in vitro

description:
Vk35707_MM_V_V_F_MYC.CrbnNull.CRBN_37200_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: Russian_healthy_3079

description: Study subject, 3079_R cell sample

value: Male

value: Russian


title: WGS of Vk34286 growing in vitro

description:
Vk34286_MM_V_V_F_MYC.Omo.rtTA_35681_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk34635 passaged in vivo harvested from spleen

description:
Vk34635_MM_R_EM_M_MYC.CrbnNull.CRBN_36608_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: Russian_healthy_3072

description: Study subject, 3072_R cell sample

value: healthy


title: WGS of Vk33982 passaged in vivo harvested from spleen

description:
Vk33982_MM_R_EM_F_MYC.CrbnNull.CRBN_37049_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: spleen


title: WGS of Vk33883 passaged in vivo harvested from spleen

description:
Vk33883_MM_R_EM_M_MYC.CrbnNull.CRBN_38052_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: Transplant recipient


title: Russian_healthy_3071

description: Study subject, 3071_R cell sample


title: WGS of Vk32976 passaged in vivo harvested from bone marrow

description:
Vk32976_MM_R_BM_F_MYC_34625_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: bone marrow

value: MYC

value: no


title: WGS of Vk32908 passaged in vivo harvested from spleen

description:
Vk32908_MM_R_EM_M_MYC.CrbnNull.CRBN_34444_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: male


title: Russian_healthy_3070

description: Study subject, 3070_R cell sample


title: WGS of Vk36040 passaged in vivo harvested from spleen

description:
Vk36040_MM_R_EM_F_MYC.CrbnNull.CRBN_36724_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: female

value: yes


title: WGS of Vk32829 passaged in vivo harvested from spleen

description:
Vk32829_MM_R_EM_F_MYC.Nsd2Null_33590_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: plasma cell


title: Russian_healthy_3057

description: Study subject, 3057_R cell sample


title: WGS of Vk32642 passaged in vivo harvested from spleen

description:
Vk32642_MM_R_EM_M_MYC.CrbnNull_34117_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: multiple myeloma


title: WGS of Vk32366 de novo tumor harvested from spleen

description:
Vk32366_MM_O_EM_F_MYC.Nsd2het_34522_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: IPAH-Adventitia-UM003-Full ROI-UM003-IPAH_WTA-009

city: Aurora

first: Rubin

middle: M

last: Tuder

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado

description: Adventitia

scan_protocol: GeoMx Digital Spatial Profiler

data_processing: Gene expression was normalised with RUVIII (Molania et al. 2019) (v0.9.7.1, k=5). The set of control genes with lowest variation across pseudobiological replicates was identified in a two-step approach, first running RUVIII across log2 transformed counts with all genes as controls, then choosing the 100 genes with the least variation to use for the normalisation.

source_name: IPAH Lung

extract_protocol: rna kit

tag: individuial

tag: batch


title: WGS of Vk32269 passaged in vivo harvested from spleen

description:
Vk32269_MM_R_EM_F_MYC.CrbnHet.CRBN_36110_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: Russian_healthy_3052

description: Study subject, 3052_R cell sample

value: Female


title: Russian_healthy_3051

description: Study subject, 3051_R cell sample


title: WGS of Vk31803 passaged in vivo harvested from bone marrow

description:
Vk31803_MM_R_BM_F_MYC_35001_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk31159 passaged in vivo harvested from spleen

description:
Vk31159_MM_R_EM_F_MYC_342935_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk31159 growing in vitro

description:
Vk31159_MM_V_V_F_MYC_38842_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro


title: Russian_healthy_3050

description: Study subject, 3050_R cell sample


title: IPAH-Intima+Media-UM003-Full ROI-UM003-IPAH_WTA-007

description: Intima+Media


title: WGS of Vk33880 passaged in vivo harvested from bone marrow

description:
Vk33880_MM_R_BM_M_MYC.CrbnNull.CRBN_36199_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: IPAH-Intima+Media-UM003-Full ROI-UM003-IPAH_WTA-008

description: Intima+Media


title: IPAH-Adventitia-UM003-Full ROI-UM003-IPAH_WTA-008

description: Adventitia


title: IPAH-Intima+Media-UM003-Full ROI-UM003-IPAH_WTA-009

description: Intima+Media


title: Russian_healthy_3048

description: Study subject, 3048_R cell sample


title: WGS of Vk28158 passaged in vivo harvested from spleen

description:
Vk28158_MM_R_EM_M_MYC_29806_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk33369 passaged in vivo harvested from spleen

description:
Vk33369_MM_R_EM_F_MYC.CrbnNull.CRBN_37289_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk23053 passaged in vivo harvested from spleen

description:
Vk23053_MM_R_EM_M_MYC.Traf3Null.CRE.BCL6_34772_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS of Vk14750 growing in vitro

description:
Vk14750_MM_V_V_M_MYC_33411_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM

value: in vitro tumor


title: Russian_healthy_3047

description: Study subject, 3047_R cell sample


title: IPAH-Adventitia-UM003-Full ROI-UM003-IPAH_WTA-007

description: Adventitia


title: WGS of Vk12653 growing in vitro

description:
Vk12653_MM_V_V_M_MYC.AIDhet_35960_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: Russian_healthy_3024

description: Study subject, 3024_R cell sample


title: WGS of Vk12598 growing in vitro

description:
Vk12598_MM_V_V_M_MYC.AIDhet_35084_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: WGS low pass mate pair of Vk32642 passaged in vivo harvested from spleen

description:
Vk32642_MM_R_EM_M_MYC.CrbnNull_32642_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair

data_processing:
Sequenced reads were trimmed for adaptor sequences with fastp version 0.22 and mapped to genome using bwa. Copy number was determined using GATK4 ModelSegments with penalty of 0 and 5. Structural variants were called using Lumpy as implemented in Smoove release 19. Identical SV in unrelated tumors were assumed to be germline and removed.
processed data files format and content: Tab deliminated text file with segmented copy number data and binary vcf.gz summarizing structural variants
Assembly: GRCm38 with addition of DNA sequences for VkMYC transgene, CRE, FGFR3_IRES_GFP, and human CRBN BAC containing IL5Ra, TRNT, CRBN

extract_protocol:
CD138-selected cells were used to extract DNA using PureGene
DNA libraries were constructed using Nextera mate Pair Library Preparation Kit


title: Russian_healthy_3023

description: Study subject, 3023_R cell sample


title: WGS low pass mate pair of Vk32245 growing in vitro 2

description:
Vk32245_MM_V_V_F_MYC_32245cl-D_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair

extract_protocol:
Cells were used to extract DNA using PureGene
DNA libraries were constructed using Nextera mate Pair Library Preparation Kit


title: IPAH-Oblit-UM003-Full ROI-UM003-IPAH_WTA-003

description: Obliterative Lesion


title: IPAH-Oblit-UM003-Full ROI-UM003-IPAH_WTA-005

description: Obliterative Lesion


title: WGS low pass mate pair of Vk32245 growing in vitro 1

description:
Vk32245_MM_V_V_F_MYC_30482cl-C_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: IPAH-Plx-UM003-Full ROI-UM003-IPAH_WTA-004

description: Plexifirm lesion


title: WGS of Vk31080 growing in vitro

description:
Vk31080_MM_V_V_F_MYC.CRE_35260_wgs
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
snv_wgs.vcf
RANDOM


title: IPAH-Plx-UM003-Full ROI-UM003-IPAH_WTA-002

description: Plexifirm lesion


title: WGS low pass mate pair of Vk32052 passaged in vivo harvested from spleen

description:
Vk32052_MM_R_EM_F_MYC.CrbnNull.CRBN_32052_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: WGS low pass mate pair of Vk29790 passaged in vivo harvested from spleen

description:
Vk29790_MM_R_EM_F_MYC.CrbnHet.CRBN_29790d_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: IPAH-Plx-UM003-Full ROI-UM003-IPAH_WTA-006

description: Plexifirm lesion


title: WGS low pass mate pair of Vk29087 passaged in vivo harvested from spleen

description:
Vk29087_MM_R_EM_M_MYC.CRE_29087_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: Russian_healthy_3020

description: Study subject, 3020_R cell sample


title: Russian_healthy_3021

description: Study subject, 3021_R cell sample


title: WGS low pass mate pair of Vk28158 passaged in vivo harvested from spleen

description:
Vk28158_MM_R_EM_M_MYC_28158_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: WGS low pass mate pair of Vk27181 passaged in vivo harvested from spleen

description:
Vk27181_MM_R_EM_M_MYC_27181_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: WGS low pass mate pair of Vk26784 passaged in vivo harvested from spleen

description:
Vk26784_MM_R_EM_M_MYC_26784b_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: Control-Adventitia-AH014-Full ROI-AH014-CTRL_WTA-006

description: Adventitia

source_name: Control Lung


title: WGS low pass mate pair of Vk23631 passaged in vivo harvested from spleen

description:
Vk23631_MM_R_EM_M_MYC_23631_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: Control-Intima+Media-AH014-Full ROI-AH014-CTRL_WTA-006

description: Intima+Media


title: WGS low pass mate pair of Vk22284 passaged in vivo harvested from spleen

description:
Vk22284_MM_R_EM_M_MYC.CRE_22284b_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: Control-Intima+Media-AH014-Full ROI-AH014-CTRL_WTA-005

description: Intima+Media


title: Control-Adventitia-AH014-Full ROI-AH014-CTRL_WTA-005

description: Adventitia


title: Russian_healthy_3019

description: Study subject, 3019_R cell sample


title: WGS low pass mate pair of Vk14750 growing in vitro

description:
Vk14750_MM_V_V_M_MYC_14750cl-C_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: Russian_asthmatic_3022

description: Study subject, 3022_R cell sample

value: asthmatic


title: Russian_healthy_3017

description: Study subject, 3017_R cell sample

value: Male


title: WGS low pass mate pair of Vk14451 passaged in vivo harvested from spleen

description:
Vk14451_MM_R_EM_M_MYC.EGFP_14451_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: WGS low pass mate pair of Vk12653 passaged in vivo harvested from spleen

description:
Vk12653_MM_R_EM_M_MYC.AIDhet_12653c_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: WGS low pass mate pair of Vk12598 growing in vitro

description:
Vk12598_MM_V_V_M_MYC.AIDhet_12598cl-D_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair


title: Russian_healthy_3016

description: Study subject, 3016_R cell sample

value: Russian


title: Russian_healthy_3015

description: Study subject, 3015_R cell sample

value: healthy


title: WGS low pass mate pair of Vk12598 passaged in vivo harvested from spleen

description:
Vk12598_MM_R_EM_M_MYC.AIDhet_12598c_mp
igv_cna_penalty_0.seg.txt
igv_cna_penalty_5.seg.txt
sv.vcf
OTHER - Mate Pair

value: spleen


title: RNA-Seq of Vk40173 growing in vitro

description:
Vk40173_MM_V_V_M_MYC_40383_rna
Vk40173_MM_V_V_M_MYC_40383_rna

data_processing:
Sequenced reads were trimmed for adaptor sequences with fastp version 0.22 and mapped to genome using salmon version 1.8 with parameters  --gcBias --validateMappings  --reduceGCMemory. The salmon index was created using GENCODE m23 GTF
For TPM_filtered the salmon index was created after removing from the GENCODE m23 GTF file mitochondrial gene transcripts, ribosomal RNA transcripts, and immunoglobulin transcripts, and after addition to the GTF  of RNA transcripts for CRE, GFP, human FGFR3, human CRBN, human IL5Ra, human TRNT, and the VkMYC transgene
Assembly: GRCm38 with addition of  DNA sequences for VkMYC transgene, CRE, FGFR3_IRES_GFP, and human CRBN BAC containing IL5Ra, TRNT, CRBN
Supplementary files format and content: Tab deliminated text file containing TPM summarized per gene

extract_protocol: Cells were placed in TriZol (Invitrogen), and following extraction were further purified on Purelink Micro-Minicolumns (Invitrogen) with an on-column DNAse digestion step


title: RNA-Seq of Vk40264 growing in vitro

description:
Vk40264_MM_V_V_F_MYC_40613_rna
Vk40264_MM_V_V_F_MYC_40613_rna


title: Russian_healthy_3014

description: Study subject, 3014_R cell sample


title: Russian_healthy_3013

description: Study subject, 3013_R cell sample


title: RNA-Seq of Vk39885 growing in vitro 1

description:
Vk39885_MM_V_V_F_MYC.CrbnNull.CRBN_40054_rna
Vk39885_MM_V_V_F_MYC.CrbnNull.CRBN_40054_rna


title: RNA-Seq of Vk39687 growing in vitro 2

description:
Vk39687_MM_V_V_F_MYC.CrbnNull.CRBN_40590_rna
Vk39687_MM_V_V_F_MYC.CrbnNull.CRBN_40590_rna


title: RNA-Seq of Vk39885 growing in vitro 2

description:
Vk39885_MM_V_V_F_MYC.CrbnNull.CRBN_40199_rna
Vk39885_MM_V_V_F_MYC.CrbnNull.CRBN_40199_rna


title: Control-Adventitia-AH014-Full ROI-AH014-CTRL_WTA-003

description: Adventitia


title: Control-Intima+Media-AH014-Full ROI-AH014-CTRL_WTA-004

description: Intima+Media


title: RNA-Seq of Vk39687 growing in vitro 1

description:
Vk39687_MM_V_V_F_MYC.CrbnNull.CRBN_40258_rna
Vk39687_MM_V_V_F_MYC.CrbnNull.CRBN_40258_rna


title: Russian_healthy_3012

description: Study subject, 3012_R cell sample


title: Control-Adventitia-AH014-Full ROI-AH014-CTRL_WTA-004

description: Adventitia


title: Russian_healthy_3011

description: Study subject, 3011_R cell sample


title: IPAH-Oblit-UM003-Full ROI-UM003-IPAH_WTA-001

description: Obliterative Lesion


title: Control-Intima+Media-AH014-Full ROI-AH014-CTRL_WTA-003

description: Intima+Media


title: RNA-Seq of Vk39336 passaged in vivo harvested from spleen

description:
Vk39336_MM_R_EM_M_MYC.CrbnNull.CRBN_39872_rna
Vk39336_MM_R_EM_M_MYC.CrbnNull.CRBN_39872_rna

extract_protocol:
CD138-selected cells were placed in TriZol (Invitrogen), and following extraction were further purified on Purelink Micro-Minicolumns (Invitrogen) with an on-column DNAse digestion step
cDNA libraries were prepared using NEBNext Ultra II RNA library Prep Kit (New England Biolabs)

value: Transplant recipient


title: Control-Intima+Media-AH014-Full ROI-AH014-CTRL_WTA-002

description: Intima+Media


title: RNA-Seq of Vk39227 growing in vitro

description:
Vk39227_MM_V_V_M_MYC.CrbnNull.CRBN_39393_rna
Vk39227_MM_V_V_M_MYC.CrbnNull.CRBN_39393_rna


title: Control-Adventitia-AH014-Full ROI-AH014-CTRL_WTA-002

description: Adventitia


title: Russian_healthy_3010

description: Study subject, 3010_R cell sample


title: RNA-Seq of Vk38975 growing in vitro 3

description:
Vk38975_MM_V_V_M_MYC_40653_rna
Vk38975_MM_V_V_M_MYC_40653_rna


title: Control-Adventitia-AH014-Full ROI-AH014-CTRL_WTA-001

description: Adventitia


title: RNA-Seq of Vk38975 growing in vitro 2

description:
Vk38975_MM_V_V_M_MYC_40065.1_rna
Vk38975_MM_V_V_M_MYC_40065.1_rna


title: RNA-Seq of Vk38975 growing in vitro 1

description:
Vk38975_MM_V_V_M_MYC_40065_rna
Vk38975_MM_V_V_M_MYC_40065_rna


title: Russian_healthy_3009

description: Study subject, 3009_R cell sample


title: Russian_healthy_3008

description: Study subject, 3008_R cell sample


title: RNA-Seq of Vk38951 growing in vitro

description:
Vk38951_MM_V_V_F_MYC_40241_rna
Vk38951_MM_V_V_F_MYC_40241_rna


title: RNA-Seq of Vk38975 passaged in vivo harvested from spleen

description:
Vk38975_MM_R_EM_M_MYC_39671_rna
Vk38975_MM_R_EM_M_MYC_39671_rna


title: Control-Intima+Media-AH014-Full ROI-AH014-CTRL_WTA-001

description: Intima+Media


title: IPAH-Adventitia-BA021-Full ROI-BA021-IPAH_WTA-010

description: Adventitia


title: RNA-Seq of Vk39337 growing in vitro

description:
Vk39337_MM_V_V_F_MYC.CrbnNull.CRBN_40060_rna
Vk39337_MM_V_V_F_MYC.CrbnNull.CRBN_40060_rna


title: RNA-Seq of Vk38951 passaged in vivo harvested from spleen

description:
Vk38951_MM_R_EM_F_MYC_39876_rna
Vk38951_MM_R_EM_F_MYC_39876_rna


title: WT M HNF1b

data_processing:
first, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
next, samples were aligned to mm10 genome with bowtie2  (Langmead et al., Nature methods, 2012)
next, MASC2 was used to visualize peaks (Zhang et al., Genome Biology, 2008)
next,  .tdf files were generated using IGV and IGVTools (Robinson et al., Nature Biotechnology 2011)
Assembly: mm10
Supplementary files format and content: .tdf files containing tracks with respective histone modification peak heights and locations
Supplementary files format and content: .bedgraph files containing tracks with respective histone modification peak heights and locations

extract_protocol:
Snap-frozen kidneys of 12-14 weeks old mice were ground into powder in liquid nitrogen. After 15 min Chromatin cross-linking in 1% formaldehyde at room temperature the reaction was quenched with 0.125M Glycine. Cells were then lysed using Farnham Lysis Buffer and homogenized on ice. After filtering through a 70um filter, chromatin was sonicated until majority of the fragments were below 1000bp length as assessed by electrophoresis of small aliquots.
Sheared chromatin (>600ug per sample) was incubated with H3K27ac (Active Motif, 39133), H3K4me3 (Millipore, CS200580), and HNF1b (Invitrogen, 720259) antibodies. Libraries for next generation sequencing were prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) and sequenced on a NovaSeq 6000 or HiSeq 3000 machine (Illumina).

value: Kidney

value: WT

tag: antibody

value: Invitrogen, 720259


title: Russian_healthy_3007

description: Study subject, 3007_R cell sample

data_processing:
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 50%. Replicate control probes were combined by their median values.
Log2 transformation and quantile normalization.


title: Russian_healthy_3006

description: Study subject, 3006_R cell sample


title: Mouse, kidney, E1WT, rep4

data_processing:
first, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
subsequently, samples were aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013).
Finally, HTSeq (Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Assembly: mm10
Supplementary files format and content: .tabular files with raw read counts

value: Klotho E1 WT

value: male


title: Mouse, kidney, E1WT, rep3


title: IPAH-Intima+Media-BA021-Full ROI-BA021-IPAH_WTA-009

description: Intima+Media


title: IPAH-Adventitia-BA021-Full ROI-BA021-IPAH_WTA-009

description: Adventitia


title: Russian_healthy_3005

description: Study subject, 3005_R cell sample


title: RNA-Seq of Vk38911 passaged in vivo harvested from spleen

description:
Vk38911_MM_R_EM_F_MYC.CrbnNull.CRBN_40602_rna
Vk38911_MM_R_EM_F_MYC.CrbnNull.CRBN_40602_rna

value: female

tag: tumor type

value: no


title: RNA-Seq of Vk38862 growing in vitro

description:
Vk38862_MM_V_V_F_MYC_39623_rna
Vk38862_MM_V_V_F_MYC_39623_rna

value: plasma cell

tag: disease

value: multiple myeloma

value: MYC

value: yes


title: IPAH-Adventitia-BA021-Full ROI-BA021-IPAH_WTA-008

description: Adventitia


title: RNA-Seq of Vk38526 de novo tumor harvested from spleen

value: original de novo tumor

value: B cell

value: Burkitt Lymphoma

value: MYCfl

tag: myc transgene_stop_codon_reversion


title: Russian_healthy_3004

description: Study subject, 3004_R cell sample

value: Male

value: Russian

value: healthy


title: Mouse, kidney, E1WT, rep1

value: Kidney


title: Mouse, kidney, E1WT, rep2


title: Russian_healthy_3002

description: Study subject, 3002_R cell sample


title: RNA-Seq of Vk38525 growing in vitro

description:
Vk38525_MM_V_V_M_MYC_39247_rna
Vk38525_MM_V_V_M_MYC_39247_rna

value: in vitro

value: in vitro tumor

tag: cell line


title: IPAH-Intima+Media-BA021-Full ROI-BA021-IPAH_WTA-008

description: Intima+Media


title: RNA-Seq of Vk38523 passaged in vivo harvested from spleen

description:
Vk38523_MM_R_EM_M_MYC.Nsd2Null_39897_rna
Vk38523_MM_R_EM_M_MYC.Nsd2Null_39897_rna

value: male

value: spleen

value: Transplant recipient

tag: cell type


title: Mouse, kidney, E1KO, rep4

tag: genotype

value: Klotho E1 KO


title: Mouse, kidney, E1KO, rep3

tag: tissue


title: Replicate 2 Knockdown 8hpf

city: Ithaca

first: Jonathan

last: Wells

state: NY

address: 216 Biotechnology Building

institute: Cornell University

data_processing:
filter low-quality reads and adaptors
read mapping with STAR
read counting with Tecounts
Assembly: GRCz11
Supplementary files format and content: read counts

molecule: polyA RNA

organism: Danio rerio

source_name: whole embryos

extract_protocol:
Qiagen RNAeasy
directional mRNA poly-A enrichment

treatment_protocol: injection with LNA at 0hpf

value: whole embryos

tag: time

value: WT

value: Bik-1 LNA


title: IPAH-Intima+Media-BA021-Full ROI-BA021-IPAH_WTA-007

description: Intima+Media


title: RNA-Seq of Vk38291 growing in vitro

description:
Vk38291_MM_V_V_F_MYC_39622_rna
Vk38291_MM_V_V_F_MYC_39622_rna

value: female

value: plasma cell

value: multiple myeloma

value: MYC

value: yes


title: Replicate 2 Knockdown 18hpf

tag: treatment


title: IPAH-Oblit-BA021-Full ROI-BA021-IPAH_WTA-006

description: Obliterative Lesion


title: RNA-Seq of Vk38291 passaged in vivo harvested from spleen

description:
Vk38291_MM_R_EM_F_MYC_39200_rna
Vk38291_MM_R_EM_F_MYC_39200_rna


title: IPAH-Oblit-BA021-Full ROI-BA021-IPAH_WTA-005

description: Obliterative Lesion


title: Replicate 2 Knockdown 14hpf


title: Mouse, kidney, E1KO, rep2


title: IPAH-Oblit-BA021-Full ROI-BA021-IPAH_WTA-004

description: Obliterative Lesion


title: RNA-Seq of Vk38290 growing in vitro 2

description:
Vk38290_MM_V_V_F_MYC.CrbnNull.CRBN_39900_rna
Vk38290_MM_V_V_F_MYC.CrbnNull.CRBN_39900_rna


title: C.reinhardtii, short Fe timecourse, 240 min, rep 2

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

data_processing:
Reads were mapped to the C.reinhardtii reference assembly with STAR (v2.4.1.d) using STAR --outFilterMismatchNoverLmax 0.04  --alignIntronMax 10000  --readFilesCommand zcat  --outFilterType BySJout
Normalized expression estimates were calculated with cuffdiff (v2.0.2) with cuffdiff  --multi-read-correct --max-bundle-frags 1000000000
Assembly: The Chlamydomonas reinhardtii reference genome assembly and annotations (v5.6) available from Phytozome at (https://phytozome-next.jgi.doe.gov/)
Supplementary files format and content: The processed data file, Fe_timecourses.FPKMs.tsv, includes normalized expression estimates in terms of fragments per kb of gene per million mapped reads (FPKMs) for all C.reinhardtii nuclear genes in all samples. The mean of two biologicial replicates is presented.

organism: Chlamydomonas reinhardtii

source_name: cultured cells

growth_protocol: Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.

extract_protocol:
Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA).
RNA-Seq libraries compatible with the Illumina HiSeq platform were constructed using standard kits and protocols from Illumina.

treatment_protocol: Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times.

value: cultured cells

tag: time point

value: 240 min

value: iron deprevation

tag: cultured in

value: TAP medium without Fe-EDTA 240 min


title: Replicate 2 Knockdown 11hpf


title: RNA-Seq of Vk38290 growing in vitro 1

description:
Vk38290_MM_V_V_F_MYC.CrbnNull.CRBN_38473_rna
Vk38290_MM_V_V_F_MYC.CrbnNull.CRBN_38473_rna

value: in vitro

value: in vitro tumor


title: Replicate 2 Control 8hpf

value: Scrambled LNA


title: IPAH-Plx-BA021-Full ROI-BA021-IPAH_WTA-003

description: Plexifirm lesion


title: RNA-Seq of Vk38227 passaged in vivo harvested from spleen

description:
Vk38227_MM_R_EM_F_MYC.CrbnNull.CRBN_40281_rna
Vk38227_MM_R_EM_F_MYC.CrbnNull.CRBN_40281_rna

value: spleen

value: Transplant recipient


title: C.reinhardtii, short Fe timecourse, 240 min, rep 1


title: C.reinhardtii, short Fe timecourse, 120 min, rep 2

value: 120 min

value: TAP medium without Fe-EDTA 120 min


title: Replicate 2 Control 18hpf

value: whole embryos

value: WT


title: RNA-Seq of Vk38150 growing in vitro

description:
Vk38150_MM_V_V_M_MYC.CrbnNull.CRBN_39280_rna
Vk38150_MM_V_V_M_MYC.CrbnNull.CRBN_39280_rna

value: male

value: plasma cell


title: IPAH-Plx-BA021-Full ROI-BA021-IPAH_WTA-002

description: Plexifirm lesion


title: IPAH-Plx-BA021-Full ROI-BA021-IPAH_WTA-001

description: Plexifirm lesion


title: Replicate 2 Control 14hpf


title: RNA-Seq of Vk37783 growing in vitro

description:
Vk37783_MM_V_V_F_MYC.Omo.rtTA_39273_rna
Vk37783_MM_V_V_F_MYC.Omo.rtTA_39273_rna

value: female

value: multiple myeloma

value: Yes


title: IPAH-Adventitia-VA010-Full ROI-VA010-IPAH_WTA-010

description: Adventitia


title: Replicate 2 Control 11hpf


title: C.reinhardtii, short Fe timecourse, 60 min, rep 2

value: cultured cells

value: 60 min

value: TAP medium without Fe-EDTA 60 min


title: IPAH-Intima+Media-VA010-Full ROI-VA010-IPAH_WTA-009

description: Intima+Media


title: IPAH-Intima+Media-VA010-Full ROI-VA010-IPAH_WTA-008

description: Intima+Media


title: C.reinhardtii, short Fe timecourse, 60 min, rep 1

value: iron deprevation


title: RNA-Seq of Vk37553 growing in vitro

description:
Vk37553_MM_V_V_M_MYC.CrbnNull.CRBN_39392_rna
Vk37553_MM_V_V_M_MYC.CrbnNull.CRBN_39392_rna

value: in vitro

value: in vitro tumor

value: yes


title: Mouse, kidney, E1KO, rep1

value: Kidney

value: Klotho E1 KO


title: RNA-Seq of Vk37553 passaged in vivo harvested from spleen

description:
Vk37553_MM_R_EM_M_MYC.CrbnNull.CRBN_38838_rna
Vk37553_MM_R_EM_M_MYC.CrbnNull.CRBN_38838_rna

value: spleen

value: Transplant recipient


title: Replicate 1 Knockdown 18hpf

value: whole embryos

value: WT

value: Bik-1 LNA


title: C.reinhardtii, short Fe timecourse, 30 min, rep 2

value: 30 min

value: TAP medium without Fe-EDTA 30 min


title: IPAH-Plx-VA010-Full ROI-VA010-IPAH_WTA-007

description: Plexifirm lesion


title: IPAH-Plx-VA010-Full ROI-VA010-IPAH_WTA-006

description: Plexifirm lesion


title: C.reinhardtii, short Fe timecourse, 30 min, rep 1


title: RNA-Seq of Vk37296 growing in vitro 3

description:
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40061_rna
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40061_rna

value: male

value: plasma cell

value: multiple myeloma


title: C.reinhardtii, short Fe timecourse, 120 min, rep 1

value: cultured cells

value: 120 min

value: TAP medium without Fe-EDTA 120 min


title: RNA-Seq of Vk37296 growing in vitro 4

description:
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40061.1_rna
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40061.1_rna

value: in vitro

value: in vitro tumor


title: Replicate 1 Control 8hpf

value: Scrambled LNA


title: Replicate 1 Knockdown 11hpf


title: RNA-Seq of Vk37296 growing in vitro 1

description:
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40053_rna
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40053_rna

value: yes


title: C.reinhardtii, short Fe timecourse, 15 min, rep 1

value: 15 min

value: iron deprevation

value: TAP medium without Fe-EDTA 15 min


title: RNA-Seq of Vk37296 growing in vitro 2

description:
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40058_rna
Vk37296_MM_V_V_M_MYC.CrbnNull.CRBN_40058_rna


title: Replicate 1 Control 18hpf

value: whole embryos

value: WT


title: IPAH-Intima+Media-VA010-Full ROI-VA010-IPAH_WTA-003

description: Intima+Media


title: IPAH-Oblit-VA010-Full ROI-VA010-IPAH_WTA-005

description: Obliterative Lesion


title: C.reinhardtii, short Fe timecourse, 10 min, rep 2

value: 10 min

value: TAP medium without Fe-EDTA 10 min


title: Replicate 1 Control 14hpf


title: Replicate 1 Knockdown 8hpf

value: Bik-1 LNA


title: RNA-Seq of Vk37296 passaged in vivo harvested from spleen

description:
Vk37296_MM_R_EM_M_MYC.CrbnNull.CRBN_39698_rna
Vk37296_MM_R_EM_M_MYC.CrbnNull.CRBN_39698_rna

value: male

value: spleen

value: Transplant recipient

value: plasma cell


title: C.reinhardtii, short Fe timecourse, 10 min, rep 1

value: cultured cells


title: IPAH-Adventitia-VA010-Full ROI-VA010-IPAH_WTA-003

description: Adventitia


title: RNA-Seq of Vk37236 passaged in vivo harvested from spleen

description:
Vk37236_MM_R_EM_F_MYC.Nsd2Null_38746_rna
Vk37236_MM_R_EM_F_MYC.Nsd2Null_38746_rna

value: female

value: multiple myeloma


title: IPAH-Adventitia-VA010-Full ROI-VA010-IPAH_WTA-002

description: Adventitia


title: Replicate 1 Control 11hpf

value: Scrambled LNA


title: C.reinhardtii, short Fe timecourse, 15 min, rep 2


title: C.reinhardtii, short Fe timecourse, 5 min, rep 2

value: 5 min

value: TAP medium without Fe-EDTA 5 min


title: RNA-Seq of Vk37234 passaged in vivo harvested from spleen

description:
Vk37234_MM_R_EM_F_MYC_37768_rna
Vk37234_MM_R_EM_F_MYC_37768_rna

value: MYC

value: yes


title: Replicate 1 Knockdown 14hpf

value: whole embryos