title: PAMM1 rep3

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
Mapping and methylation calling of Bisulfite-seq data was performed using Bismark v0.23.1 in PBAT mode against the human GRCh38 genome assembly. Trimmed reads were first aligned to the genome in paired-end mode to be able to detect and discard overlapping parts of the reads while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for positions that were covered more than once. Following methylation extraction, CpG context files from PE and SE runs were used to generate a single coverage file (the "Dirty Harry" procedure).
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage for 50-CpG running windows>
Assembly: GRCh38

source_name: Placenta

extract_protocol:
Low input bisulphite-sequencing libraries were generated using 5,000-100,000 sorted cells, as previously described, using a post-bisulphite adaptor tagging (PBAT) method. In brief, cells were thawed and then lysed in 10mM Tris buffer with 0.5% SDS and proteinase K at 37°C for 1 hour.
In a two-step process, first and second strand synthesis was performed using Klenow Fragment (3’->5’ exo-) enzyme (New England Biolabs) and customised 9bp random sequence containing biotin-conjugated adaptors. Libraries were amplified using 10 amplification cycles with Phusion High-Fidelity DNA polymerase (New England Biolabs). Libraries were quantified using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA). Samples were multiplexed and sequenced using 100 bp paired-end mode on the Illumina NovaSeq.

tag: gestational age

value: 3rd trimester


title: GCN4_DMSO_NOSM_120_C_S27_RNA-seq

status: Public on Aug 01 2023

type: SRA

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Center

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of TFs. Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, Raffinose or Galactose, no heat shock (30°C) or heat shock (37°C)

tag: genotype

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3


title: GCN4_DMSO_SM_30_A_S4_RNA-seq

tag: treatment

value: SM starvation


title: LV treated newborn mouse - rep 3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Raw sequencing data were processed using the 10 Genomics Space Ranger pipeline to generate Fastq files
Sequences were aligned to the mm10 reference genome to produce gene expression counts using Space Ranger's default settings
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of th etissue and spots
Supplementary files format and content: scalefactors_jason.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatual barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were collected and snap frozen in isopentane, then embedded in Killik OCT on dry ice. 5-µm slices were cut using Leica cryostat CM1860 and put on commercial Visium 10X slides
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manifacturer's construction

tag: tissue

value: Liver

tag: age

value: Newborn

value: LV-transduced


title: nme2ko_hghfat_rep4

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Aligment: The sequenced reads from the raw sequence (.fastq files) were aligned on the UCSC mm10 genome using the STAR software (2.7.1a) (Dobin et al. 2013) [PMID:23104886] to produce bam files.
Counts: The aligned reads (.bam files) were counted using HTSeq framework (0.11.2) (Anders et al. 2015) [PMID:25260700], with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none.
Assembly: UCSC mm10
Supplementary files format and content: counts

source_name: liver

extract_protocol:
The RNA was isolated and purified from the liver tissue by NucleoSpin RNA kit (Machery-Nagel- 740955.50). Four independent RNA extractions were performed for each condition.
For each sample, one µg of RNA (RIN = 10) was used for library preparation with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to the manufacturer’s instructions. Each library was quantified on Qubit with the Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
The libraries were then sequenced on the Illumina NextSeq 500 (paired-end 75) at the TGML Platform of Aix-Marseille University (France).

tag: genotype/variation

tag: diet

value: hghfat

value: liver

tag: replicate


title: GCN4_DMSO_NOSM_120_A_S3_RNA-seq


title: LV treated newborn mouse - rep 1


title: nme2ko_hghfat_rep3


title: nme2ko_hghfat_rep2


title: PAMM1 rep1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

value: 1st trimester


title: Foetal mono  rep3

value: Monocytes


title: PAMM1 rep2


title: SG_351_HomoTerminator_E15_5_Input_biol rep 2

city: Grand Rapids

first: Piroska

last: Szabó

state: MI

address: 333 Bostwick Ave NE

department: Department of Epigenetics

institute: Van Andel Insitute

data_processing:
Reads were clipped to 100 bp using Fastp (https://doi.org/10.1002/imt2.107), then aligned using GenPipes’ chip.py pipeline (https://doi.org/10.1093/gigascience/giz037). Visualization tracks were prepared using DeepTools bamCoverage (https://doi.org/10.1093/nar/gkw257).
Assembly: mm10
Supplementary files format and content: bigwig file as summerized alignment

source_name: testis

extract_protocol:
Male germ cells were resuspended in nuclear isolation buffer (Sigma), flash frozen in liquid nitrogen and stored at −80 °C until use. Chromatin was prepared from 100,000 cells and divided into four fractions for H3K36me2, H3K36me3 and H3K27me3 for ULI-NChIP-seq (ref PMID: 25607992). Briefly, the chromatin was fragmented by MNAse digestion (NEB) for 7.5 minutes at 37 degrees, diluted in native ChIP buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 150 mM NaCl; 0.1% Triton X-100) containing 1 mM PMSF (Sigma) and EDTA-free protease inhibitor cocktail (Roche). Each chromatin fraction was incubated overnight at 4 °C with 5 μl of protein A: protein G Dynabeads (ThermoFisher) 1:1 and 0.5 μL of the following antibody: H3K36me2 (Diagenode C15310127 or ActiveMotif 61019), H3K36me3 (Abcam ab9050) or H3K27me3 (Diagenode C15410069).
Antibody-bond chromatin was washed twice in low salt buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 150 mM NaCl; 1% Triton X-100; 0.1% SDS) followed by two washes with high salt buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 500 mM NaCl; 1% Triton X-100; 0.1% SDS) and eluted in 0.1 nM NaCO3 and 1% SDS at 65 °C for 1 h. DNA was purified using SPRI beads (Omega) and used forpaired-end library construction(NEXNext).
Libraries were sequenced (150 bp paired-end) on the NovaSeq 6000 platform.

treatment_protocol: Purification of fetal male germ cells: To obtain homozygous mutant male fetal germ cells, H19Ter+neo/H19Ter+neo or H19Ter/H19Ter females that carry the Oct4-EGFP transgene from the TgOG2 (10) mouse line (Oct4-EGFPTg/Tg) were crossed with males of the same genotype. To obtain heterozygous male fetal germ cells, TgOG2 (10) females were crossed with +/H19Ter+neo or +/H19Ter males. The fetal testicles were dissected and a single cell suspension was prepared by trypsin digestion and trituration as described earlier (10). Up to 8 testes were digested in 150 µl 0.25% trypsin (including 0.5% BSA) at 36 °C for 15 min, tapping gently every 5 min. The trypsin reaction was stopped by adding 450 µl 20% FBS in M2 medium (Sigma Cat. No. M7167). The EGFP+ germ cells were purified by flow cytometry using a Beckman Coulter MoFlo Astrios sorter.

value: testis

tag: cell line

value: fetal male germ cell

tag: date

tag: chip antibody

value: input


title: SG_350_HomoTerminator_E15_5_H3K27me3_biol rep 2

value: H3K27me3 (Diagenode C15410069)


title: GCN4_DMSO_NOSM_120_B_S15_RNA-seq


title: GCN4_DMSO_NOSM_60_B_S14_RNA-seq


title: Foetal mono  rep1


title: Foetal mono  rep2


title: 3rd HBC DRhi rep3

value: Hoffbauer cells (HLA-DR high)


title: SG_349_HomoTerminator_E15_5_H3K36me3_biol rep 2

value: H3K36me3 (Abcam ab9050)


title: nme2ko_hghfat_rep1


title: GCN4_DMSO_NOSM_60_C_S26_RNA-seq


title: GCN4_DMSO_NOSM_30_C_S25_RNA-seq


title: 3rd HBC DRhi rep2


title: SG_347_HomoTerminator_E15_5_H3K36me2_Dia_biol rep 2

value: H3K36me2 (Diagenode C15310127)


title: GCN4_DMSO_NOSM_60_A_S2_RNA-seq


title: SG_346_Control_E15_5_Input_biol rep 2

value: WT


title: 3rd HBC DRhi rep1

value: 3rd trimester


title: GCN4_DMSO_NOSM_30_B_S13_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3


title: SG_345_Control_E15_5_H3K27me3_biol rep 2


title: GCN4_DMSO_NOSM_30_A_S1_RNA-seq


title: GCN4_3IAA_SM_120_C_S36_RNA-seq

value: SM starvation


title: 3rd HBC DRint rep3

value: Hoffbauer cells (HLA-DR intermediate)


title: LV treated newborn mouse - rep 2

value: Liver

value: Newborn

value: LV-transduced


title: 3rd HBC DRint rep2


title: SG_348_HomoTerminator_E15_5_H3K36me2_AM_biol rep 2

value: H3K36me2 (ActiveMotif 61019)


title: SG_344_Control_E15_5_H3K36me3_biol rep 2


title: GCN4_3IAA_SM_120_B_S24_RNA-seq


title: 3rd HBC DRint rep1


title: GCN4_3IAA_SM_120_A_S12_RNA-seq


title: SG_343_Control_E15_5_H3K36me2_AM_biol rep 2


title: 3rd HBC DRneg  rep3

value: Hoffbauer cells (HLA-DR negative)


title: SG_342_Control_E15_5_H3K36me2_Dia_biol rep 2

value: testis


title: SG_341_HomoTerminator_E15_5_Input_biol rep 1

value: fetal male germ cell


title: GCN4_3IAA_SM_60_C_S35_RNA-seq


title: 3rd HBC DRneg rep2


title: 3rd HBC DRneg rep1


title: GCN4_3IAA_SM_60_B_S23_RNA-seq


title: 1st HBC rep3

value: Hoffbauer cells

value: 1st trimester


title: SG_340_HomoTerminator_E15_5_H3K27me3_biol rep 1

value: H3K27me3 (Diagenode C15410069)


title: GCN4_3IAA_SM_60_A_S11_RNA-seq


title: GCN4_3IAA_SM_30_C_S34_RNA-seq


title: GCN4_3IAA_SM_30_B_S22_RNA-seq


title: 1st HBC rep2


title: SG_337_HomoTerminator_E15_5_H3K36me2_Dia_biol rep 1


title: SG_338_HomoTerminator_E15_5_H3K36me2_AM_biol rep 1


title: GCN4_3IAA_SM_30_A_S10_RNA-seq


title: SG_336_Control_E15_5_Input_biol rep 1

value: input


title: cfRNA_MOF_B_500uL_comparation_2_serum

city: wuhan

first: shuang

last: peng

address: wuhan university

country: China

institute: wuhan university

data_processing:
Adapter seqeucnes were trimmed by using trim_galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' and ‘-e 10' to remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR 2.7.5a; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
The raw counts of each gene was calculated with featureCounts v2.0.1.
Assembly: hg38

source_name: serum

extract_protocol:
cfRNA RNA and cfDNA was extracted by QIAamp ccfDNA/RNA Kit or a new method developed on MOF materials by ourselves
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian following manufacturer's protocols; cfDNA libraries for genome-seq were prepared using  NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocols.

value: serum


title: GCN4_3IAA_NOSM_120_C_S33_RNA-seq


title: cfRNA_MOF_A_500uL_comparation_2_serum


title: SG_335_Control_E15_5_H3K27me3_biol rep 1

value: WT


title: cfRNA_Kit_500uL_comparation_2_serum


title: GCN4_3IAA_NOSM_120_A_S9_RNA-seq


title: GCN4_3IAA_NOSM_120_B_S21_RNA-seq


title: cfRNA_Kit_2500uL_comparation_2_serum


title: SG_334_Control_E15_5_H3K36me3_biol rep 1

value: H3K36me3 (Abcam ab9050)


title: SG_339_HomoTerminator_E15_5_H3K36me3_biol rep 1


title: GCN4_3IAA_NOSM_60_C_S32_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3


title: SG_332_Control_E15_5_H3K36me2_Dia_biol rep 1

value: H3K36me2 (Diagenode C15310127)


title: GCN4_3IAA_NOSM_60_B_S20_RNA-seq


title: cfRNA_Kit_1000uL_comparation_2_serum


title: GCN4_3IAA_NOSM_60_A_S8_RNA-seq


title: MOF_1_cfRNA_comparation_1_plasma

source_name: plasma

value: plasma


title: 1st HBC rep1


title: GEX-TTP-KO

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) functions mkfastq and count were used to align to the mm10 genome and demultiplex the sequencing data and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Cell ranger output files

source_name: SI LP

extract_protocol:
ILCs (Live CD45+ Lin- CD3- CD90.2+ CD127+ TCRβ-) were sorted from the SI LPs of 4 WT and 4 Zfp36 151 -/- mice and pooled per genotype prior to encapsulation for scRNAseq.
Cells were loaded on the Chromium Controller (10x Genomics) and Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: ILCs

value: SI LP

tag: strain

tag: library type

value: GEX


title: no Glutamine-24h, 3

city: New York

first: Joel

last: Encarnacion-Rosado

state: New York

address: 550 First Avenue

department: Radiation Oncology

institute: NYU Grossman School of Medicine

data_processing:
Bulk RNA-seq libraries, raw data collection (FASTQ (fq)), alignment (HISAT2), mapping, differential expression analysis (DESeq2) were performed according to manufacturer’s instructions by Novogene52.
Ilumina Casava sifrware was used for basecalling perfomed by Novogene
Sequencing reads were mapped using STAR v2.5 with a mismatch parameter of m=2 (performed by Novogene), reads with adaptor contamination were removed, reads with uncertain nucleotids for more than 10% of either read were removed, reads with low quality nucleotides (base quality < 20) for more than 50% of read were removed
Differential gene expression was performed using DESeq2
Bulk RNA-seq libraries, raw data collection (FASTQ (fq)), alignment (HISAT2), mapping, differential expression analysis (DESeq2) were performed according to manufacturer’s instructions by Novogene52.
Assembly: GRCm39 C57BL/6J
Supplementary files format and content: differential expression analysis (DESeq2)

source_name: pancreatic cancer

growth_protocol: 2D growth in 10% FBS DMEM and orthotopic tumor in the pancreata of B6J

extract_protocol: Total  RNA was extracted from tumor and tumor cells using PuTotal RNA from cell cultures and tumors were obtained using TRizol (Thermo, 15596026) and PureLink RNA Midi Kit (Thermo, 12183025) kit according to the manufacturer’s instructionsreLink RNA Minit Kit (Thermo Scientific)

value: pancreatic cancer

value: tumor

value: KRASmut,p53 mut

value: no Glutamine-24h


title: no Glutamine-24h, 2


title: GCN4_3IAA_NOSM_30_B_S19_RNA-seq


title: MOF_1_cfRNA_comparation_1_plasma_beirui


title: no Glutamine-24h, 1


title: GEX-WT

description: 10x Genomics


title: MOF-3_cfRNA_comparation_1_plasma


title: GAT2_DMSO_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GAT2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GAT2-3xV5 IAA7::URA3


title: GCN4_3IAA_NOSM_30_A_S7_RNA-seq


title: SG_333_Control_E15_5_H3K36me2_AM_biol rep 1

value: testis

value: fetal male germ cell

value: H3K36me2 (ActiveMotif 61019)


title: Kit_1_cfRNA_comparation_1_plasma


title: DON 25 uM-24h, 3

value: DON 25 uM-24h


title: Kit-4-cfRNA_comparation_1_plasma


title: GAT2_DMSO_B_S50_RNA-seq


title: MOF_3_cfRNA_comparation_1_plasma_beirui


title: cfDNA_4 _with_kit

data_processing:
Adapter seqeucnes were trimmed by using trim_galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' and ‘-e 10' to remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR 2.7.5a; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
The raw counts of each gene was calculated with featureCounts v2.0.1.
Assembly: hg38
Library strategy: genome-seq

value: serum


title: GAT2_DMSO_A_S49_RNA-seq


title: DON 25 uM-24h, 1


title: HY19-CNT, 3

value: CNT


title: cfDNA_2_with_MOF


title: GAT2_3IAA_C_S54_RNA-seq


title: DON 25 uM-24h, 2


title: cfDNA_3_with_MOF


title: GCN4_3IAA_NOSM_30_C_S31_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3


title: HY19-CNT, 2


title: GAT2_3IAA_B_S53_RNA-seq


title: GAT2_3IAA_A_S52_RNA-seq


title: HY19-CNT, 1


title: GAT1_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GAT1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GAT1-3xV5 IAA7::URA3


title: DRP-104, 3


title: cfDNA_1_with_MOF


title: HK-2 cells, Phosphoramidon, t24h, rep3

city: Taipei city

first: Hung-Jin

last: Huang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human kidney

growth_protocol: HK-2 cells were maintained kept in Keratinocyte-serum-free medium (K-SFM) with bovine pituitary extract and human recombinant EGF (Invitrogen, CA), cultured at 37 °C/5% CO2

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded 24 hours before treatment on 6-cm dish at a density of 6x10^5 cells per well with 4 ml of medium per dish. Cells were treated at ~90% confluency with the required doses for the required timepoints.

value: immortalized human renal proximal tubular epithelial cells

value: treated with phosphoramidon for 24 hours


title: HK-2 cells, Phosphoramidon, t24h, rep2


title: GAT1_DMSO_B_S2_RNA-seq


title: DRP-104, 2


title: GAT1_DMSO_A_S1_RNA-seq


title: DRP-104, 1


title: HY19-VEH3

value: VEH


title: HK-2 cells, CSE, t24h, control sample, rep3

value: untreated


title: GAT1_3IAA_C_S6_RNA-seq


title: HK-2 cells, CSE, t24h, control sample, rep2


title: HY19-VEH2

value: pancreatic cancer


title: GAT1_3IAA_B_S5_RNA-seq


title: GAT1_3IAA_A_S4_RNA-seq


title: HK-2 cells, CSE, t24h, control sample, rep1


title: GAL80_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GAL80-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GAL80-3xV5 IAA7::URA3


title: PANBRP (TCR-seq)

city: Jerusalem

first: Miriam

middle: I.

last: Rosenberg

address: Edmond Safra Campus

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem, Givat Ram

description: TCRseq (TCR beta) from gDNA from fresh frozen tumor

data_processing:
Library strategy: TCR-seq
All data analysis provided by Adaptive Biotechnologies, after proprietary sequence processing steps, in their sequence viewer interface, immunoSEQ Analyzer, were exported as a summary .tsv file for each patient.
TCRbeta gene segment locus calls were made using the Adaptive pipeline as part of their automated data processing pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Each patient repertoire is provided as a .tsv file containing the data obtained from Adaptive including rearranged sequences detected, their total number, and their frequencies in our samples.

source_name: Neuroblastoma tumor

growth_protocol: Tumor genomic DNA were prepared from fresh-frozen tumor collected during tumor resection or biopsy.

extract_protocol:
Genomic DNA was extracted from fresh frozen tumor using Qiagen Genomic Tip or Qiagen All prep.
Genomic DNA was processed through the Adaptive ImmunoSeq pipeline, including multiplex PCR and sequencing according to their proprietary platform. Targeted loading was 500ug gDNA per assay (TCRbeta/IgH) though not all samples reached this target.
ImmunoSeq (https://www.immunoseq.com/assays/)

tag: patient subgroup

value: High risk non-OMAS

tag: disease state

value: neuroblastoma

value: fresh frozen tumor


title: HY19-VEH1

value: tumor

value: KRASmut,p53 mut


title: PANEYN (TCR-seq)


title: GAL80_DMSO_B_S44_RNA-seq


title: RNAseq_E17.5_Pou3F1_KO.2

city: Montreal

first: Benoit

middle: Charles

last: Boulan

state: Quebec

address: 110, avenue des Pins Ouest

country: Canada

institute: IRCM

description:
collection at stage E17.5
E14_HET_vs_KO_Pou3f1.csv

data_processing:
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Assembly: mm10
Supplementary files format and content: Bigwig tracks files and MACS2 peaks bed files for scored peaks in CUT&RUN

source_name: retina

extract_protocol: RNA-seq: RNA extraction was performed as detailed by manufactorer (RNeasy mini kit, Qiagen).

value: retina

value: whole retina

tag: mouse line

value: homorozygous

tag: condition


title: RNAseq_E17.5_Pou3F1_KO.5


title: RNAseq_E17.5_Pou3F1_HET.6

value: heterozygous


title: GAL80_DMSO_A_S43_RNA-seq

tag: genotype


title: PALVXB (TCR-seq)


title: HK-2 cells, Phosphoramidon, t24h, rep1

tag: treatment


title: GAL80_3IAA_C_S48_RNA-seq


title: RNAseq_E17.5_Pou3F1_HET.1

tag: tissue


title: RNAseq_ P1-14D_Pou3f1_6

description:
in vivo transfection at P1, collection of cells by FACS with Gfp after 14 days
RNAseq_Pou3f1_OE_14D.csv

growth_protocol: In vivo electroporation of P1 eyes was performed as described previously (de Melo et al. 2011) using plasmid DNA at 3ug/ul

treatment_protocol: The electroporated eyes were collected after 48hrs or at post-natal day 14 and processed for dissection, dissociation and FACS sorting. Multiple sorted GFP+ cells samples were combined to obtain 150 000 cells per replicate

value: about 150 000 sorted GFP cells

value: WT


title: GAL80_3IAA_B_S47_RNA-seq


title: GAL80_3IAA_A_S46_RNA-seq


title: RNAseq_ P1-14D_Pou3f1_4


title: PAWTLL (TCR-seq)


title: PAUGCI (TCR-seq)


title: RNAseq_ P1-14D_Pou3f1_3


title: GAL4_gal_DMSO_C_S35_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-GAL4

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-GAL4

value: Galactose induction


title: Validation_set_Normal_S8

value: serum

value: normal


title: PALNHZ (TCR-seq)


title: RNAseq_ P1-14D_Pou3f1_2


title: Validation_set_Normal_S7


title: RNAseq_ P1-14D_Pou3f1_1


title: PAWTLU (TCR-seq)


title: RNAseq_ P1-14D_Ctrl_4

value: Gfp


title: PAWTMX (TCR-seq)


title: Validation_set_Normal_S6


title: GAL4_gal_3IAA_C_S36_RNA-seq


title: PAMBYG (TCR-seq)


title: Validation_set_Normal_S5


title: PAWTBP (TCR-seq)


title: GAL4_gal_DMSO_A_S23_RNA-seq


title: GAL4_gal_3IAA_B_S30_RNA-seq


title: PAWKRA (TCR-seq)


title: RNAseq_ P1-14D_Ctrl_3


title: Validation_set_Normal_S4


title: RNAseq_ P1-14D_Ctrl_2


title: PAPKVS (TCR-seq)


title: GAL4_gal_3IAA_A_S24_RNA-seq


title: Validation_set_Normal_S9


title: RNAseq_ P1-14D_Ctrl_1


title: Validation_set_Normal_S1


title: GAL4_DMSO_no_gal_C_S31_RNA-seq


title: PARLEZ (TCR-seq)

value: Low risk non-OMAS


title: GAL4_DMSO_no_gal_B_S25_RNA-seq


title: RNAseq_ P1-48H Pou3F1.4

description:
in vivo transfection at P1, collection of cells by FACS with Gfp after 48hrs
RNAseq_Pou3f1_OE_48h.csv


title: GAL4_gal_DMSO_B_S29_RNA-seq


title: Validation_set_HCC_S9

value: HCC


title: PAPKPC (TCR-seq)

value: neuroblastoma


title: RNAseq_ P1-48H Pou3F1.3


title: GAL4_DMSO_C_S9_RNA-seq


title: Validation_set_HCC_S11


title: PARBGB (TCR-seq)

value: fresh frozen tumor


title: RNAseq_ P1-48H Pou3F1.2


title: PARPWX (TCR-seq)


title: RNAseq_ P1-48H Ctrl.4


title: Validation_set_Normal_S3


title: Validation_set_HCC_7


title: GAL4_DMSO_B_S8_RNA-seq


title: PAWJAD (TCR-seq)

value: High risk non-OMAS


title: GAL4_DMSO_A_S7_RNA-seq


title: RNAseq_ P1-48H Ctrl.3


title: Validation_set_HCC_3


title: Validation_set_HCC_5


title: PAPXAM (TCR-seq)


title: PAUBMJ (TCR-seq)


title: Validation_set_HCC_2


title: GAL4_3IAA_no_gal_C_S33_RNA-seq


title: PAVHIP (TCR-seq)


title: rIgG_E14

data_processing:
CUT&RUN: NGS data were preprocessed withTrimmomatic tool for sequence trimming and adapter removal. Fastq reads were aligned using bowtie2 mm10 genome on Galaxy platform. MACS2 was used for peak calling using default parameters  (FDR = 0.05) . Bamcoverage was used to generate bigwig files.
Assembly: mm10
Supplementary files format and content: Bigwig tracks files and MACS2 peaks bed files for scored peaks in CUT&RUN
Library strategy: CUT&RUN

source_name: Retina

extract_protocol:
CUT&RUN: Genomic DNA extraction was performed as per manufactorers guidelines (QIAquick Nucleotide Removal Kit).
CUT&RUN: Libraries were prepared with the KAPA DNA HyperPrep Kit (Roche 07962363001 - KK8504). This protocol includes an End-Repair/A-tailing step and an adapter ligation step followed by a PCR amplification (enrichment) of ligated fragments.
CUT&RUN: The adapters used for ligation were IDT for Illumina TruSeq UD Indexes (Illumina - 20022371). The final enriched product (library, after PCR) was purified using KAPA purification beads (Roche 07983298001 - KK8002) and a dual-SPRI size selection was performed (with KAPA beads) to select fragments between 180-500 bp. Libraries were then quantified using a Nanodrop microvolume spectrophotometer (ng/l) and quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent -5067-4626) on a Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted, pooled equimolar and sequenced in pair end 50 cycles (PE50) on a S1 flowcell (Illumina - 20012863) of the Illumina NovaSeq 6000 System.

value: Retina

value: Retinal cells

tag: antibody

value: rabbit IgG


title: GAL4_3IAA_no_gal_B_S27_RNA-seq


title: Validation_set_HCC_1


title: GAL4_3IAA_no_gal_A_S21_RNA-seq


title: Validation_set_CHB_S4

value: CHB


title: POU3F1_E14


title: GAL4_DMSO_no_gal_A_S19_RNA-seq


title: PAWPXJ (TCR-seq)


title: PAWLRY (TCR-seq)


title: GAL4_3IAA_C_S12_RNA-seq


title: Validation_set_CHB_S3


title: Hmox2-/- _MAEC_3

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

department: Medicine

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using Kallisto v.0.44.0
The Kallisto index was made with default parameters and the GENCODE (Release 39 (GRCh38.p13) and was run in quant mode with default parameters
Assembly: Mm10
Supplementary files format and content: tsv

source_name: Aorta

growth_protocol: Room Air

extract_protocol:
Total aortic EC RNA was isolated from aortic ECs using, TRI Reagent (Zymo Research, R2050-1-200) and Zymo Direct-zol RNA Miniprep Kit (Zymo Research, catalog number R2053). Heart tissue total RNA was isolated from fast-frozen whole heart. Tissue was pulverized under liquid nitrogen in a stainless-steel mortar and pestle and the frozen tissue powder quantitatively transferred to test tubes. Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen, 74134).
Oligo-dT mRNA directional

treatment_protocol: Hmox2+/+ vs Hmox2-/-

value: Aorta

value: Endotheial cells

value: Hmox2 Knock_out

value: Room Air


title: GAL4_3IAA_B_S11_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-GAL4


title: PAWTKW (TCR-seq)


title: Hmox2-/- _MAEC_2


title: PAPJLU (TCR-seq)


title: GAL4_3IAA_A_S10_RNA-seq


title: RNAseq_ P1-48H Ctrl.2

value: retina

value: about 150 000 sorted GFP cells

value: WT


title: Validation_set_CHB_S1

value: serum


title: Hmox2-/- _Heart_3

source_name: Heart

value: Heart

value: Tissue


title: Training_set_Normal_9

value: normal


title: Validation_set_CHB_6


title: Training_set_Normal_6


title: FZF1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 FZF1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 FZF1-3xV5 IAA7::URA3


title: PAVEAC (TCR-seq)

value: Low risk non-OMAS

value: neuroblastoma

value: fresh frozen tumor


title: FZF1_DMSO_B_S38_RNA-seq


title: PARFKR (TCR-seq)

value: OMAS


title: PAWKII (TCR-seq)


title: FZF1_DMSO_A_S37_RNA-seq


title: Hmox2-/- _Heart_2


title: Hmox2-/- _Heart_1


title: Hmox2+/+ _MAEC_3

value: Aorta

value: Hmox2 WT


title: FZF1_3IAA_C_S42_RNA-seq


title: PAPRIP (TCR-seq)


title: PAPSTN (TCR-seq)


title: Training_set_Normal_5


title: Training_set_Normal_14


title: Training_set_Normal_13


title: Hmox2+/+ _MAEC_2

value: Endotheial cells


title: Hmox2-/- _MAEC_1

value: Hmox2 Knock_out

value: Room Air


title: PAPPEB (TCR-seq)


title: FZF1_3IAA_B_S41_RNA-seq


title: Training_set_Normal_12


title: PAPGFB (TCR-seq)


title: FZF1_3IAA_A_S40_RNA-seq


title: Hmox2+/+ _Heart_4


title: Training_set_Normal_11


title: FHK2_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-FKH2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-FKH2


title: PATVYZ (TCR-seq)


title: Hmox2+/+ _MAEC_1


title: Hmox2+/+ _Heart_2


title: FHK2_DMSO_A_S43_RNA-seq


title: PASDZS (TCR-seq)


title: Training_set_Normal_10


title: Hmox2+/+ _Heart_3


title: Hmox2+/+ _Heart_1


title: Training_set_HCC_S7

value: HCC


title: FHK2_3IAA_C_S48_RNA-seq


title: PANSDX (TCR-seq)


title: FHK2_3IAA_B_S47_RNA-seq


title: SPL_PX2_citeseq

city: New Haven

first: Alicia

middle: J

last: Little

state: CT

address: 333 Cedar St, PO Box 208059

department: Dermatology

institute: Yale University

description:
Splenocytes, ADT-derived cDNA
Mus musculus (MRL/lpr)
Antibody-derived oligonucleotide library

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline (5.0.1) where ADT sequences were concatenated and treated as Custom library with default settings (v5.0.1) and aligning to the mm10 genome build.
Further processing was done with Seurat v4.1.1 (cell and gene filtering, ADT identification, clustering, differential gene expression analysis)
Assembly: mm10
Supplementary files format and content: 10X genomics output files (*.h5 files)

source_name: spleen

extract_protocol:
Dorsal interscapular lesional skin and spleens of 20-week-old MRL/lpr mice were harvested one day after a 5-day treatment course with either PBS (vehicle) or PX-478 at the dose of 30 mg/kg daily. After preparation and staining of single-cell suspensions from skin, live CD45+ and CD45- single cells were sorted and admixed at a 50:50 ratio. These cells and whole splenocytes were then stained for surface protein (Feature Barcoding Technology) per BioLegend protocol with 0.5 mg of each oligonucleotide-tagged TotalSeqTM-C antibody: anti-mouse CD4 (BioLegend, Cat #100571), anti-mouse CD8a (BioLegend, Cat #100785), and anti-mouse CD45RB (BioLegend, Cat #103321). Cells were then submitted immediately for 10X single-cell RNA sequencing (5'v2).
Library preparation was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

value: spleen

value: multiple

value: ADT

tag: antibodies/tags

value: anti-CD45RB/TotalSeqC #103321, anti-CD4/TotalSeqC #100571, anti-CD8a/TotalSeqC #100785

value: PX478 (HIF1 inhibitor)


title: Training_set_HCC_S4

source_name: serum

value: serum


title: PAUWXL (TCR-seq)


title: FHK2_3IAA_A_S46_RNA-seq


title: SPL_PX1_citeseq


title: PAUPWX (TCR-seq)


title: SPL_PBS2_citeseq

value: vehicle (PBS)


title: FKH1_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-FKH1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-FKH1


title: Training_set_HCC_S2


title: PAUKNU (TCR-seq)

value: neuroblastoma

value: fresh frozen tumor


title: FKH1_DMSO_B_S44_RNA-seq


title: SPL_PBS1_citeseq


title: FHK2_DMSO_B_S44_RNA-seq


title: Training_set_HCC_S1


title: FKH1_DMSO_A_S43_RNA-seq


title: SKIN_PX2_citeseq

description:
Live CD45+-enriched skin cells,  ADT-derived cDNA
Mus musculus (MRL/lpr)
Antibody-derived oligonucleotide library

source_name: skin (dorsal interscapular)

value: skin (dorsal interscapular)


title: Training_set_HCC_S8


title: PATXKK (TCR-seq)

value: OMAS


title: PANUTJ (TCR-seq)


title: FKH1_3IAA_C_S48_RNA-seq


title: SKIN_PX1_citeseq


title: Training_set_HCC_S10


title: Training_set_HCC_8


title: PATWIL (TCR-seq)


title: SKIN_PBS1_citeseq


title: FKH1_3IAA_A_S46_RNA-seq


title: Training_set_HCC_S3


title: PATRNS (TCR-seq)


title: FHL1_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 FHL1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 FHL1-3xV5 IAA7::URA3


title: SPL_PX2

description:
Splenocytes, mRNA-derived cDNA
Mus musculus (MRL/lpr)
5' mRNA library

value: mRNA


title: PAUHXD (TCR-seq)


title: PATADI (TCR-seq)


title: Training_set_HCC_6


title: SPL_PX1


title: FHL1_DMSO_B_S32_RNA-seq


title: Training_set_HCC_S15


title: PANNNX (TCR-seq)


title: FHL1_DMSO_A_S31_RNA-seq


title: Training_set_HCC_1


title: Training_set_HCC_10


title: SKIN_PBS2_citeseq


title: PASJDC (TCR-seq)


title: PASLAE (TCR-seq)


title: SPL_PBS1


title: PATTTS (TCR-seq)


title: FHL1_3IAA_C_S36_RNA-seq


title: FHL1_3IAA_B_S35_RNA-seq


title: FKH1_3IAA_B_S47_RNA-seq


title: Training_set_CHB_S9

value: CHB


title: Training_set_HCC_7


title: SKIN_PX2

description:
Live CD45+-enriched skin cells, mRNA-derived cDNA
Mus musculus (MRL/lpr)
5' mRNA library


title: PASIUC (TCR-seq)


title: FHL1_3IAA_A_S34_RNA-seq


title: SKIN_PX1


title: PASDYT (TCR-seq)


title: Training_set_CHB_S8


title: ERT1_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ERT1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ERT1-3xV5 IAA7::URA3


title: Training_set_CHB_S7


title: SKIN_PBS2


title: PASCCV (TCR-seq)


title: SPL_PBS2


title: SKIN_PBS1


title: ERT1_DMSO_B_S26_RNA-seq


title: PASAKL (TCR-seq)


title: Training_set_HCC_4

value: HCC


title: ERT1_DMSO_A_S25_RNA-seq


title: Training_set_CHB_S6


title: Training_set_CHB_S5


title: M4SPL8

description:
Mus musculus (MRL/lpr)
Sorted live CD8+ T cells from spleen (mouse #4)

data_processing:
Sequence alignment to mouse genome MM9 was done by using STAR 2.5.3 and TopHat 2.1.0 on the Partek Flow® platform. The differentially regulated genes were analyzed by DEseq2
Assembly: mm9
Supplementary files format and content: tab-delimited text file - output of DESeq2

extract_protocol:
Skin-infiltrating and splenic CD4+ and CD8+ T cells were isolated and sorted from lesional skin and spleens of 20-week-old MRL/lpr mice, and mRNA isolated (RNeasy Plus Micro Kit, Qiagen, 74034).
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa, 634893) was used to construct the sequencing library. Samples were sequenced on an Illumina HiSeq 2000 with 100-bp paired ends.

value: spleen

value: CD8+ T cells

value: WT MRL/lpr


title: ERT1_3IAA_C_S30_RNA-seq


title: ERT1_3IAA_B_S29_RNA-seq


title: Training_set_CHB_S2


title: PASAHC (TCR-seq)


title: M234SK8

description:
Mus musculus (MRL/lpr)
Sorted live CD8+ T cells from skin (pooled: mouse #2, 3, 4)

source_name: skin

value: skin


title: PARTZY (TCR-seq)


title: Training_set_CHB_S12


title: ERT1_3IAA_A_S28_RNA-seq


title: M4SK4

description:
Mus musculus (MRL/lpr)
Sorted live CD4+ T cells from skin (mouse #4)

value: CD4+ T cells


title: M4SPL4

description:
Mus musculus (MRL/lpr)
Sorted live CD4+ T cells from spleen (mouse #4)


title: PANJHR (TCR-seq)


title: PARJPI (TCR-seq)


title: Training_set_CHB_S11

value: serum


title: Training_set_CHB_S10


title: DIG2_DMSO_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 DIG2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 DIG2-3xV5 IAA7::URA3


title: PAUDKX (TCR-seq)


title: DIG2_DMSO_B_S50_RNA-seq


title: M3SPL4

description:
Mus musculus (MRL/lpr)
Sorted live CD4+ T cells from spleen (mouse #3)


title: PAPRHG (TCR-seq)


title: DIG2_DMSO_A_S49_RNA-seq


title: Training_set_CHB_9


title: M3SK4

description:
Mus musculus (MRL/lpr)
Sorted live CD4+ T cells from skin (mouse #3)


title: PANBRP (BCR-seq)

description: BCRseq (IgH locus) from gDNA from fresh frozen tumor

data_processing:
Library strategy: BCR-seq
All data analysis provided by Adaptive Biotechnologies, after proprietary sequence processing steps, in their sequence viewer interface, immunoSEQ Analyzer, were exported as a summary .tsv file for each patient.
Genome_build: hg19
Supplementary_files_format_and_content: Each patient repertoire is provided as a .tsv file containing the data obtained from Adaptive including rearranged sequences detected, their total number, and their frequencies in our samples.

extract_protocol:
Genomic DNA was extracted from fresh frozen tumor using Qiagen Genomic Tip or Qiagen All prep. DNA was processed through the Adaptive ImmunoSeq pipeline, including multiplex PCR and sequencing according to their proprietary platform. Targeted loading was 500ug gDNA per assay (IgH) though not all samples reached this target.
ImmunoSeq (https://www.immunoseq.com/assays/)

value: High risk non-OMAS


title: DIG2_3IAA_C_S54_RNA-seq


title: M1SPL8

description:
Mus musculus (MRL/lpr)
Sorted live CD8+ T cells from spleen (mouse #1)


title: Training_set_CHB_7


title: PANEYN (BCR-seq)

value: neuroblastoma


title: M3SPL8

description:
Mus musculus (MRL/lpr)
Sorted live CD8+ T cells from spleen (mouse #3)


title: M1SPL4

description:
Mus musculus (MRL/lpr)
Sorted live CD4+ T cells from spleen (mouse #1)


title: Training_set_CHB_5


title: DIG2_3IAA_B_S53_RNA-seq


title: PAMBYG (BCR-seq)

value: fresh frozen tumor


title: PALVXB (BCR-seq)


title: Training_set_CHB_4


title: DIG2_3IAA_A_S52_RNA-seq


title: DIG1_DMSO_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 DIG1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 DIG1-3xV5 IAA7::URA3


title: M1SK4

description:
Mus musculus (MRL/lpr)
Sorted live CD4+ T cells from skin (mouse #1)


title: Training_set_CHB_3


title: PAWTLL (BCR-seq)

source_name: Neuroblastoma tumor


title: M1SK8

description:
Mus musculus (MRL/lpr)
Sorted live CD8+ T cells from skin (mouse #1)


title: DIG1_DMSO_B_S50_RNA-seq


title: Training_set_CHB_2


title: DIG1_DMSO_A_S49_RNA-seq


title: ICA (C12)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM19)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: oral squamous cell carcinoma

extract_protocol:
Total RNA was isolated by using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany)
Library was prepared using the TruSeq stranded mRNA sample preparation kit in accordance with the manufacturer’s protocol.

treatment_protocol: Six-week-old male C57BL/6J mice were fed with 4NQO dissolved in drinking water (100 ug/mL) was admisistered to the mice for 10 weeks to induce OSCC carcinogenesis.

value: oral squamous cell carcinoma

tag: pathological stage

value: Invasive carcinoma


title: PAUGCI (BCR-seq)


title: Training_set_CHB_1


title: Training_set_CHB_8


title: PAPKVS (BCR-seq)


title: ICA (C08)


title: DIG1_3IAA_C_S54_RNA-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis


title: PALNHZ (BCR-seq)


title: DIG1_3IAA_B_S53_RNA-seq


title: ICA (C06)


title: larval_CNS-delta-POZ1

city: Princeton

first: Michael

last: Levine

state: New Jersey

address: Icahn lab, Princeton University

institute: Princeton University

description: Micro-C raw

library_source: other

data_processing:
The raw data were mapped onto the Dm6 reference genome as described by bwa (Li and Durbin, 2009).
Validated paired reads were filtered and finalized using pairtools (Goloborodko et al., 2019)
They were further processed into multi-resolution matrix by Cooler (Abdennur and Mirny, 2020)
Focal contacts in wing imaginal discs expressing Halo-GAF were detected by SIP (Rowley et al., 2020) using newly created Micro-C maps. The parameters were set as -g 4.0 -min 2.0 -max 2.0 -mat 5000 -d 15 -res 400 -sat 0.01 -t 2800 -nbZero 4 -factor 2 -fdr 0.1 -del true -cpu 16 -isDroso false. The called loops were further filtered with a “value” > 4.25 and with enough micro-C data coverage (filtered out anchors with marginals < 500). The loops were further filtered by removing loops associated with high CP190 (>10000) (Kyrchanova et al., 2021) by intersecting with BEDtools (Quinlan and Hall, 2010). The loops were first mapped to transcription start sites within 2500 bp of the loop anchor center using BEDtools (Quinlan and Hall, 2010). They were subsequently manually inspected to determine whether linked promoters correspond to paralogs.
The dumped matrix with 100bp bin size from the cooler files were compared with the standard loop list with anchors normalized to 1.6kb for embryos and 3.2kb for discs using the pairToPair function from BEDtools (Quinlan and Hall, 2010).
The reads were summed for each standard loop and summarized into a count table. The count tables were imported for differential looping analysis with DESeq2 (Love et al., 2017).
genome build/assembly: dm6
processed data files format and content: cooler, contact matrix
Library strategy: Micro-C

molecule: other

organism: Drosophila melanogaster

source_name: larval CNS

extract_protocol:
For wing imaginal discs or larval CNS, yw or homozygous delta-POZ wandering 3rd instar larvae were collected and dissected in PBS. 90 discs or 45 CNS were collected for each biological replicate and two replicates for each genotype were prepared. For adult CNS, 45 CNS were collected from 2-5 days adult head for each replicate. Tissues were incubated in 500 µL 1% formaldehyde/PBST for 15 min, passively rotating at room temperature.
The fixation was terminated by addition of 370 µL 2 M Tris-HCl pH 7.5. Secondary fixations with 3 mM DSG (Thermo Fisher Scientific) and EGS (Thermo Fisher Scientific) were performed as previously described (Levo et al., 2022).

value: larval CNS

value: delta-POZ


title: PAWTMX (BCR-seq)


title: ICA (C05)


title: DAL81_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 DAL81-3xV5 IAA7::URA3

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 DAL81-3xV5 IAA7::URA3


title: PAWTLU (BCR-seq)


title: ICA (C03)


title: adult_CNS1

description: Micro-C raw

source_name: adult CNS

value: adult CNS

value: y w


title: DIG1_3IAA_A_S52_RNA-seq


title: larval_CNS2

description: Micro-C raw


title: PAWKRA (BCR-seq)


title: DAL81_DMSO_A_S19_RNA-seq


title: PAWTBP (BCR-seq)


title: CIS (C10)

value: Carcinoma in situ


title: DAL81_DMSO_B_S20_RNA-seq


title: larval_CNS1

description: Micro-C raw


title: ICA (C09)


title: PAWJAD (BCR-seq)


title: adult_CNS2

description: Micro-C raw


title: wing_disc2

description: Micro-C raw

source_name: wing imaginal disc

value: wing imaginal disc


title: CIS (C11)


title: wing_disc1

description: Micro-C raw


title: CIS (C04)


title: larval_CNS-delta-POZ2

description: Micro-C raw


title: PARLEZ (BCR-seq)

value: Low risk non-OMAS


title: DAL81_3IAA_A_S22_RNA-seq


title: PAPKPC (BCR-seq)


title: DAL81_3IAA_C_S24_RNA-seq


title: CIS (C02)


title: nolo[deltaA23] larval CNS, replicate 1, scRNAseq

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v6.1.12
UMI count matrices (h5 files filtered_feature_bc_matrix.h5) were imported and analysed using the R package Seurat (v3.1.5).
Log-normalize counts were calculated using the NormalizeData method implemented in Seurat with a scale factor set to 10'000.
Assembly: dm6
Supplementary files format and content: Comma-separated table of log-normalized counts, genes x cells, for the 3 samples integrated (all3Integrated_RNA_normData.csv.gz)

source_name: central nervous system

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
15 wandering third instar larvae were dissected in ice-cold Schneider’s medium supplemented with 10% fetal bovine serum, washed in Rinaldini solution (0.36 mM NaH2PO4*H2O, 11.9 mM NaHCO3, 137 mM NaCl, 2.7 mM KCl, 5.6 mM glucose*H2O), dissociated in 2 µg/µl collagenase I (Sigma C2674) and 2 µg/µl papain (Sigma P4762) for 50 minutes at room temperature, and dissociated into single cells by pipeting up and down several times. The cell suspension was washed in PBS with 1% BSA and RNase inhibitor (Sigma 3335399001), passed through a 35 µm cell strainer, resuspended in PBS with 1% BSA and RNase inhibitor, filtered again through a 0.35 µm cell strainer, counted and assessed for viability on a Moxi V instrument (Witec MXV102), and diluted to 1000 cells/µl. 20 µl (20000 cells) were processed according to the instructions of 10x Genomics Chromium Next GEM sc 3’ reagent kits v3.1 dual index (CG000315 RevC August 2021).
Library preparation was performed according to the manufacter’s instructions (10x Genomics Chromium Next GEM sc 3' reagent kits v3.1 dual index (CG000315 RevC August 2021).

treatment_protocol: animals were not subjected to any particular treatment

value: nolo[deltaA23] homozygote

value: central nervous system

tag: age

value: third instar larva


title: CYC8_DMSO_120_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-CYC8

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-CYC8


title: PARBGB (BCR-seq)

value: neuroblastoma


title: CYC8_DMSO_120_B_S9_RNA-seq


title: CIS (C01)


title: PAPXAM (BCR-seq)

value: fresh frozen tumor


title: WT larval CNS, replicate 1, scRNAseq

description: 10x Genomics

value: wildtype


title: DYS (B06)

value: oral squamous cell carcinoma

value: Dysplasia


title: PARPWX (BCR-seq)


title: CIS (C07)


title: DYS (B07)


title: CYC8_DMSO_60_C_S14_RNA-seq


title: PAUBMJ (BCR-seq)


title: DYS (B05)


title: CYC8_DMSO_120_A_S3_RNA-seq


title: Wildtype D. mel. adult CNS, Hi-C rep2

description:
assembly: dm6
Hi-C library

data_processing:
FASTQ files were mapped to the reference genome using distiller v0.3.3 (https://github.com/open2c/distiller-nf). The following reference genomes were used: dm6 for Drosophila melanogaster and GSE120751_Dvir_HiC.fa.gz downloaded from ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120751/suppl/ for Drosophila virilis.
For each biological replicate, unique pairs of reads with MAPQ ≥ 30 on both sides were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
For each sample, unique pairs of reads with MAPQ ≥ 30 on both sides from all replicates were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
Supplementary files format and content: Multi-resolution cooler file format (mcool): unique pairs of reads with MAPQ ≥ 30 on both sides, aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction (cooler v0.8.11, https://github.com/open2c/cooler).

extract_protocol:
20 larval CNSs or 10 adult CNSs or 1 million FACS-purified nuclei per replicate were homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting with Csp6I and MseI restriction enzymes.
Illumina sequencing libraries were prepared with a standard protocol.

treatment_protocol: animals were not subjected to any particular treatment.

value: adult

value: Wildtype


title: DAL81_3IAA_B_S23_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 DAL81-3xV5 IAA7::URA3


title: Wildtype D. mel. adult CNS, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: CYC8_DMSO_60_B_S8_RNA-seq


title: PAVHIP (BCR-seq)


title: DYS (B04)


title: nolo[deltaA23] homozygous knock-out D. mel. larval CNS, Hi-C rep3

description:
assembly: dm6
Hi-C library

value: nolo[deltaA23] homozygote KO


title: DYS (B03)


title: nolo[deltaA23] homozygous knock-out D. mel. larval CNS, Hi-C rep2

description:
assembly: dm6
Hi-C library


title: PAVEAC (BCR-seq)


title: CYC8_DMSO_60_A_S2_RNA-seq


title: CYC8_DMSO_30_C_S13_RNA-seq


title: PAWPXJ (BCR-seq)


title: DYS (B02)


title: nolo[deltaA23] homozygous knock-out D. mel. larval CNS, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: beatIV[deltaA65] larval CNS, replicate 1, scRNAseq

description: 10x Genomics

value: beatIV[deltaA65] homozygote

value: beat-IV[deltaA65] homozygote


title: PAWLRY (BCR-seq)


title: beat-IV[deltaA65] homozygous knock-out D. mel. larval CNS, Hi-C rep3

description:
assembly: dm6
Hi-C library


title: DYS (B01)


title: CYC8_DMSO_30_A_S1_RNA-seq


title: PAWTKW (BCR-seq)


title: beat-IV[deltaA65] homozygous knock-out D. mel. larval CNS, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: PAPJLU (BCR-seq)


title: HYP (A08)

value: Hyperplasia


title: beat-IV[deltaA65] homozygous knock-out D. mel. larval CNS, Hi-C rep2

description:
assembly: dm6
Hi-C library


title: PAWKII (BCR-seq)

value: Low risk non-OMAS


title: CYC8_3IAA_120_C_S18_RNA-seq


title: HYP (A07


title: CYC8_3IAA_120_B_S12_RNA-seq


title: PARFKR (BCR-seq)

value: OMAS


title: HYP (A05)


title: Wildtype D. mel. larval CNS, Hi-C rep3

description:
assembly: dm6
Hi-C library

value: central nervous system


title: HYP (A06)


title: CYC8_3IAA_120_A_S6_RNA-seq


title: Wildtype D. mel. larval CNS, Hi-C rep2

description:
assembly: dm6
Hi-C library

value: third instar larva


title: CYC8_3IAA_60_C_S17_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-CYC8


title: PAPSTN (BCR-seq)

value: neuroblastoma


title: HYP (A04)


title: HYP (A03)


title: Wildtype D. mel. larval CNS, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: Wildtype D. mel. 14-16 hour old embryo FACS-purified neurons, Hi-C rep2

description:
assembly: dm6
Hi-C library

source_name: neuron

value: OregonR

value: neuron

value: 14-16 hour old embryo


title: PAPRIP (BCR-seq)

value: fresh frozen tumor


title: CYC8_3IAA_60_B_S11_RNA-seq


title: CYC8_DMSO_30_B_S7_RNA-seq


title: CYC8_3IAA_60_A_S5_RNA-seq


title: HYP (A02)

value: oral squamous cell carcinoma


title: CYC8_3IAA_30_C_S16_RNA-seq


title: CYC8_3IAA_30_B_S10_RNA-seq


title: PAPGFB (BCR-seq)


title: CYC8_3IAA_30_A_S4_RNA-seq


title: PANSDX (BCR-seq)


title: Normal (D03)

value: Normal


title: Normal (D02)


title: Normal (D01)


title: CUP9_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CUP9-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CUP9-3xV5 IAA7::URA3


title: Wildtype D. mel. 14-16 hour old embryo FACS-purified glia, Hi-C rep1

description:
assembly: dm6
Hi-C library

source_name: glia

value: glia

value: Wildtype


title: Wildtype D. mel. 14-16 hour old embryo FACS-purified neuroblasts, Hi-C rep2

description:
assembly: dm6
Hi-C library

source_name: neuroblast

value: neuroblast


title: PANUTJ (BCR-seq)


title: PAUWXL (BCR-seq)


title: NK cells, HD IL-15, anti-NK1.1, YFP+, M4 [m4_yfp.pos]

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: tab-delimited text file include log2CPM gene count values for each sample

source_name: natural killer

extract_protocol:
RNA was harvested using Rneasy Plus Micro kit (Qiagen).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

tag: cell type

value: natural killer

value: mut/mut

tag: time

value: 6 hours


title: Wildtype D. mel. 14-16 hour old embryo FACS-purified neuroblasts, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: CUP9_DMSO_B_S14_RNA-seq


title: PAUPWX (BCR-seq)

value: OMAS


title: PAUKNU (BCR-seq)


title: CUP9_DMSO_A_S13_RNA-seq


title: CUP9_3IAA_C_S18_RNA-seq


title: NK cells, HD IL-15, unstimulated, M4 [m4_unstim]

value: unstimulated


title: Wildtype D. mel. 10-12 hour old embryo FACS-purified neurons, Hi-C rep1

description:
assembly: dm6
Hi-C library

value: 10-12 hour old embryo


title: PAPPEB (BCR-seq)

value: neuroblastoma


title: Wildtype D. mel. 10-12 hour old embryo FACS-purified neurons, Hi-C rep2

description:
assembly: dm6
Hi-C library

value: OregonR


title: Wildtype D. mel. 14-16 hour old embryo FACS-purified neurons, Hi-C rep1

description:
assembly: dm6
Hi-C library

value: neuron


title: HYP (A01)

value: Hyperplasia


title: PAUHXD (BCR-seq)

value: fresh frozen tumor


title: NK cells, HD IL-15, anti-NK1.1, YFP-, M4 [m4_yfp.neg]


title: Wildtype D. mel. 10-12 hour old embryo FACS-purified glia, Hi-C rep2

description:
assembly: dm6
Hi-C library


title: Wildtype D. mel. 14-16 hour old embryo FACS-purified glia, Hi-C rep2

description:
assembly: dm6
Hi-C library

value: 14-16 hour old embryo


title: PATXKK (BCR-seq)


title: CUP9_3IAA_B_S17_RNA-seq


title: NK cells, HD IL-15, anti-NK1.1, YFP+, M3 [m3_yfp.pos]


title: PATWIL (BCR-seq)


title: NK cells, HD IL-15, anti-NK1.1, YFP-, M3 [m3_yfp.neg]


title: PATTTS (BCR-seq)


title: Wildtype D. mel. 10-12 hour old embryo FACS-purified neuroblasts, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: NK cells, HD IL-15, unstimulated, M3 [m3_unstim]


title: Wildtype D. mel. 10-12 hour old embryo FACS-purified neuroblasts, Hi-C rep2

description:
assembly: dm6
Hi-C library


title: CUP2_DMSO_C_S9_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CUP2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CUP2-3xV5 IAA7::URA3


title: PATRNS (BCR-seq)


title: NK cells, HD IL-15, anti-NK1.1, YFP+, M2 [m2_yfp.pos]


title: PATADI (BCR-seq)


title: CUP2_DMSO_A_S7_RNA-seq


title: NK cells, HD IL-15, anti-NK1.1, YFP-, M2 [m2_yfp.neg]


title: Wildtype D. mel. 6-8 hour old embryo FACS-purified neurons, Hi-C rep1

description:
assembly: dm6
Hi-C library

value: 6-8 hour old embryo


title: Wildtype D. mel. 6-8 hour old embryo FACS-purified glia, Hi-C rep2

description:
assembly: dm6
Hi-C library

value: glia


title: PASLAE (BCR-seq)


title: CUP2_3IAA_C_S12_RNA-seq


title: CUP2_3IAA_B_S11_RNA-seq


title: NK cells, HD IL-15, unstimulated, M2 [m2_unstim]


title: PASJDC (BCR-seq)


title: NK cells, HD IL-15, anti-NK1.1, YFP-, F [f2_yfp.neg]


title: CUP9_3IAA_A_S16_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CUP9-3xV5 IAA7::URA3


title: Wildtype D. mel. 6-8 hour old embryo FACS-purified neurons, Hi-C rep2

description:
assembly: dm6
Hi-C library

value: Wildtype


title: Wildtype D. mel. 6-8 hour old embryo FACS-purified neuroblasts, Hi-C rep1

description:
assembly: dm6
Hi-C library

value: neuroblast


title: PANNNX (BCR-seq)


title: CST6_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CST6-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CST6-3xV5 IAA7::URA3


title: Wildtype D. mel. 10-12 hour old embryo FACS-purified glia, Hi-C rep1

description:
assembly: dm6
Hi-C library


title: CUP2_3IAA_A_S10_RNA-seq


title: PASGHN (BCR-seq)


title: PASDYT (BCR-seq)


title: NK cells, HD IL-15, unstimulated, F [f2_unstim]

value: natural killer

value: mut/mut


title: NK cells, LD IL-15, rep2 [ATAC-seq]

data_processing:
ATAC-seq data were first processed using the AIAP pipeline. As a part of the pipeline: reads were aligned to the mm10 genome using bwa; locations of Tn5 insertion events were inferred from properly paired, non-PCR duplicate reads with MAPQ >= 10; each Tn5 insertion event was extended from insertion site up and down 75 bp to generate a 150 bp “pseudo read”; pseudo reads were piled up to generate an ATAC signal profile, which was subsequently normalized against both sequencing depth and sample quality, similar to the getGroupBW() function of the ArchR package. Briefly, sample quality was calculated as the fraction of reads mapped to promoters (transcription start sites ± 1 Kb. frac.pro); a sequencing depth scaling factor (depth.fac) was calculated for each sample as the ratio of the sequencing depth of that sample over the median sequencing depth of all samples; each ATAC-seq profile (bigWig track) was then divided by frac.pro and depth.fac to obtain normalized signals; normalized ATAC-seq signals were divided by 3 because the typical value of depth.fac is 0.3 - 0.4. ATAC-seq data were visualized using WashU Epigenome Browser.
ATAC-seq peaks for each sample were called as a part of the AIAP pipeline, using macs2 with FDR cutoff at 0.01. After manual inspection of the peaks called, we further filtered the resulting narrowPeak files for peaks with -log10FDR >= 8. To call differentially accessible regions (DARs), we merged all overlapping peaks to create a union peakset. We then formed a peak-sample matrix with each entry corresponding to the number of Tn5 insertion sites in each peak for each sample. We filtered out peaks where any sample has no reads, since we cannot properly normalize zero values. DARs were called using DESeq25 (v1.26.0), with the design formula ~ replicate + type. “Type” represents high or low dose IL15 treatment. The cutoff for DARs were set at log2FoldChange >= 1 & FDR <= 0.05.
For motif enrichment in DARs, up (high dose > low dose) and down (low dose > high dose) DARs were separately ranked by p value and the top 1000 peaks in each category were used for motif enrichment. For each DAR used for motif enrichment, its 25 closest non-DARs in the Euclidean space constructed from low dose samples were selected without replacement as background peaks. We used HOMER (v4.11.1) for motif enrichment in DARs relative to background peaks (findMotifsGenome.pl up_or_down_DAR.bed mm10.fa out_dir -bg up_or_down_DAR_background.bed -nomotif -size given).
Assembly: mm10
Supplementary files format and content: bigWig: normalized ATAC-seq signals

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. Aliquots of approximately 75,000 cells (LD/HD IL-15) were used as input per biological replicate. Transposase reaction occurred at 37C for 30 minutes. DNA was purified with the Qiagen MinElute PCR Purification kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext Ultra 2xMastermix (NEB) and Illumina UD Indexes (10 bp).The libraries were quantified using the universal library quantification kit (KAPA Biosystems). The product was purified using Qiagen MinElute PCR Purification kit, followed by AMPure bead selection.
ATAC-Seq libraries profiles were visualized using High Sensitivity D1000 ScreenTape on the Tapestation (Agilent).

value: WT

value: LD IL-15, 72 hours

value: 72 hours


title: CST6_DMSO_A_S1_RNA-seq


title: NK cells, LD IL-15, rep1 [ATAC-seq]


title: PASCCV (BCR-seq)

value: OMAS

value: neuroblastoma


title: CST6_DMSO_B_S2_RNA-seq


title: NK cells, HD IL-15, anti-NK1.1, YFP+, F [f2_yfp.pos]

value: 6 hours


title: NK cells, HD IL-15, rep2 [ATAC-seq]

value: HD IL-15, 72 hours


title: CST6_3IAA_C_S6_RNA-seq


title: CST6_3IAA_B_S5_RNA-seq


title: NK cells, HD IL-15, rep1 [ATAC-seq]


title: PASAHC (BCR-seq)

value: fresh frozen tumor


title: CST6_3IAA_A_S4_RNA-seq


title: CRZ1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CRZ1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CRZ1-3xV5 IAA7::URA3


title: PARJPI (BCR-seq)


title: PASIUC (BCR-seq)


title: miniSOX_SL_rep1

city: hong kong

first: Haoqing

last: Hu

address: No.21 Pokflam road, L412

institute: The University of Hong Kong

data_processing:
Raw reads in fastq format were aligned to the mm10 transcriptome using RSEM (Bo Li et al., 2011) and bowtie 2.0 (Langmead et al., 2012) (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3 (Hutchins et al., 2014).
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq (Risso et al., 2011). GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
The table was used to inspect individual gene expression, generate correlation heatmaps, perform principal components analysis (PCA) and analyze differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names(name). The rest of the columns contain the normalized RNA expression gene counts.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, #15596018) following the user guide quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. ffective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

tag: cell line

value: Embryonic stem cell

value: miniSOX_lentivirus transduced with endogeouns SOX2 silienced

value: DOX


title: CRZ1_DMSO_B_S38_RNA-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

address: 1100 FAIRVIEW AVE N

institute: Fred Hutchinson Cancer Center


title: Wildtype D. mel. 6-8 hour old embryo FACS-purified glia, Hi-C rep1

description:
assembly: dm6
Hi-C library

value: OregonR

value: glia

value: 6-8 hour old embryo

value: Wildtype


title: PARTZY (BCR-seq)


title: CUP2_DMSO_B_S8_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CUP2-3xV5 IAA7::URA3


title: PAPRHG (BCR-seq)


title: miniSOX_2i_rep2


title: miniSOX_SL_rep2


title: miniSOX_2i_rep1


title: PANJHR (BCR-seq)


title: CRZ1_DMSO_A_S37_RNA-seq


title: PASFHI (BCR-seq)


title: SO2_2i_biol_rep3

value: SOX2_lentivirus transduced with endogeouns SOX2 silienced


title: CRZ1_3IAA_C_S42_RNA-seq


title: FNV_2i_biol_rep3

value: SOX17FNV_lentivirus transduced with endogeouns SOX2 silienced


title: PARSCY (BCR-seq)


title: PAPNAI (BCR-seq)


title: PASAKL (BCR-seq)


title: FNV_2i_biol_rep2


title: CRZ1_3IAA_A_S40_RNA-seq


title: CRZ1_3IAA_B_S41_RNA-seq


title: SO2_2i_biol_rep2


title: NTC_2i_biol_rep2

value: WT


title: PASPIH (BCR-seq)

value: OMAS


title: COM2_DMSO_A_S1_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 COM2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 COM2-3xV5 IAA7::URA3


title: COM2_DMSO_B_S2_RNA-seq


title: PAUHDK (BCR-seq)

source_name: Neuroblastoma tumor

value: neuroblastoma


title: SOX2_biol_rep2

data_processing:
Reads were trimmed to 35 bp length to remove Tn5 transposase sequence and then mapped to mouse genome assembly mm10 using bowtie2 (--very-sensitive --end-to-end --no-unal --no-mixed -X 2000).
Mapped reads were filtered to removed low quality reads and sorted using samtools (Danecek et al., 2021) (samtools view -q 35 | sort).
Mitochondrial reads were removed afte alignment (grep -v chrM).
PCR duplicates were removed using samtools (rmdup) and only uniquely mapped reads were kept.
The BAM files of replicates of each sample were merged with samtools (merge).
Assembly: mm10
Supplementary files format and content: Peak files were generated with MACS2 (Zhang et al., 2008) (with option -g mm -f BAMPE --call-summits).

extract_protocol:
Cells were collected with 0.05% Trypsin, washed with DPBS, pelleted for use.
9x10^5 cells were used as starting cells. Libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Small Kit (#20034197), amplified using KAPA HiFi plus dNTPs - commercial kit (#KK2102) using indexes from the TruePrep Index Kit V2 for Illumina (#TD202). Post amplification libraries were size seleced with Agencourt AMPure XP - Beckman Coulter using 0.55x/1.5x ptotocol. Library concentrations were confirmed with Qubit™ dsDNA HS Assay Kit (#Q32854) and quality were validated by Agilent 2100 Bioanalyzer.


title: COM2_DMSO_C_S3_RNA-seq


title: PAUXJB (BCR-seq)


title: COM2_3IAA_B_S5_RNA-seq


title: FNV_biol_rep2


title: SOX2_biol_rep1


title: PASIBJ (BCR-seq)


title: FNV_biol_rep1


title: PANBRP (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

data_processing:
Raw FASTQs from both the OMAS/LR/HR cohort and NCI TARGET (Pugh TJ et al 2013) datasets were processed using fastq-mcf (https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/ FastqMcf.md; parameters used were: http://expressionanalysis.github.io/ea-utils/; parameters: --max-ns 4 –qual-mean 25 -H -p 5 -q 7 -l 25).
[Alignment and isoform quantification] Clipped reads were aligned to the human reference genome hg19 using STAR v2.4 (Dobin et al 2013) and a UCSC reference transcriptome supplemented with lincRNAs from Ensembl. RSEM v1.2.14 (https://github.com/ExpressionAnalysis/STAR-SEQR) was used for both gene and isoform quantification
[RNA fusion event detection]  RNA fusion events were detected using STAR-SEQR v0.6.5  (Ritchie et al 2014) parameters: -m 1).
[Differential expression analysis]  Differential expression analysis was performed using Q2 Solutions’ ensemble two group comparisons suite. This method summarizes the differential expression p-values and classification probabilities from five tools—t-test, limma4, DESeq2 ((Ritchie et al 2014), edgeR (Anders and Huber, 2010) and EBSeq (Robinson MD, McCarthy DJ, Smyth GK 2010)—to produce a new p-value for differential expression.
[p-value calculation]  For any given gene, the p-values of each constituent model are input into a logistic regression model, which estimates the probability that the gene is differentially expressed. This probability is transformed into a p-value for differential expression by comparing it against its empirical cumulative distribution as estimated by bootstrap resampling of TCGA data from various cancer types.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM files given for gene counts

growth_protocol: Tumor total RNA and tumor genomic DNA were prepared from fresh-frozen tumor collected during tumor resection or biopsy.

extract_protocol:
Fresh tumor was frozen on dry ice and stored until further processing. RNA was extracted using Trizol reagent as per manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Access kit (now called TruSeq RNA Exome).  Briefly

value: High risk non-OMAS


title: CHA4_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CHA4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CHA4-3xV5 IAA7::URA3


title: middle-aged, NLRP3i-treated, rep8 [26122-P]

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

description:
26122-P
DESEQ2_normalized_counts

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore! in Galaxy (Galaxy Version 0.6.7+galaxy0)  using the default parameters
Sequence reads were aligned to mouse genome (GrCM38/mm10) using Bowtie2 in Galaxy (Galaxy Version 2.4.2+galaxy0)  using the default parameters
Read count extraction using FeatureCounts in Galaxy (Galaxy Version 2.0.1+galaxy2) using the default parameters
Read count were normalized using DESeq2 in Galaxy (Galaxy Version 2.11.40.7+galaxy1)
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited text file including the normalized counts for each sample in a matrix table

source_name: Kidney

extract_protocol:
mRNA was isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD) as per the manufacturer’s instructions.
Library generation \was performed \using TruSeq RNA Library Prep Kits (Illumina, San Diego, CA, USA)

treatment_protocol: The podocyte fraction was MACS-sorted as the following. Kidney tissue (w/o the kidney capsule and surrounding fat) was placed into ice cold RPMI 1640 medium, (w/o L-glutamine and phenol red, GE Healthcare Bio-Sciences, Pittsburgh, PA). After removal of the medulla the remaining cortex was minced into fine pieces and digested in 0.2 mg/ml Liberase™ TL (Sigma-Aldrich, St. Louis, MO), 100 U/ml DNAse I (Sigma-Aldrich, St. Louis, MO) in RPMI 1640 medium (w/o L-glutamine and phenol red) by shaking at 37oC for 30 minutes. The digest was passed through an 18G needle (Becton Dickenson, Franklin Lakes, NJ) 10 times and enzymes were inactivated by adding 5 ml of RPMI 1640 medium (w/o L-glutamine and phenol red) supplemented with 1 mM sodium pyruvate (ThermoFisher Scientific, Waltham, MA), 9% Nu-Serum™ IV Growth Medium Supplement (Corning Incorporated - Life Sciences, Durham, NC) and 100U/ml Penicillin-Streptomycin (ThermoFisher Scientific, Waltham, MA). The cell suspension was passed through a 100 µm and a 40 µm cell strainer (BD Biosciences, San Jose, CA) and pelleted by centrifugation at 200G at 4oC for 5 minutes. Cells were were resuspended in media containing two rabbit anti-Nephrin antibodies (36) (1:100, Abcam, Cambridge, MA). After 1 hour at 4oC cells were pelleted, washed in media and incubated with anti-rabbit microbeads (Miltenyi Biotec, Auburn, CA) along with Alexa Fluor 594-conjugated AffiniPure Donkey Anti-Rabbit IgG 1:200 (in order to visualize binding of the Nephrin antibodies to the podocytes) for 30 minutes at 4oC. Cells were pelleted and washed in PBS with 0.5% BSA and 2mM EDTA and applied to MACS LS columns (Miltenyi Biotec, Auburn, CA) to gently separate microbead-bound podocytes from the other kidney cells. Cells not retained by the magnetic field were collected, pelleted and designated non-podocyte (NP) fractions. LS columns were removed from the magnetic field then washed with PBS with 0.5% BSA and 2mM EDTA and podocytes were collected. A small aliquot of each fraction imaged using an EVOS FL Cell Imaging System to verify podocyte isolation, based on the presence of Nephrin antibody. Additionally, qRT-PCR for a panel of podocyte genes was performed in both podocyte and non-podocyte fractions to confirm cell type identity. Only fractions with significant podocyte expression or absence thereof were moved along for subsequent analysis as podocytes or non-podocytes, respectively.

value: Kidney

value: podocyte

value: wildtype


title: CHA4_DMSO_B_S2_RNA-seq


title: middle-aged, NLRP3i-treated, rep7 [26121-P]

description:
26121-P
DESEQ2_normalized_counts


title: PALVXB (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: fresh frozen tumor


title: PATNJJ (BCR-seq)


title: middle-aged, NLRP3i-treated, rep6 [26120-P]

description:
26120-P
DESEQ2_normalized_counts


title: CHA4_DMSO_A_S1_RNA-seq


title: CHA4_3IAA_C_S6_RNA-seq


title: CHA4_3IAA_B_S5_RNA-seq


title: PAUGCI (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PAMBYG (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: COM2_3IAA_C_S6_RNA-seq


title: middle-aged, NLRP3i-treated, rep4 [26118-P]

description:
26118-P
DESEQ2_normalized_counts


title: middle-aged, NLRP3i-treated, rep3 [26117-P]

description:
26117-P
DESEQ2_normalized_counts


title: PAPKVS (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: CBF1_DMSO_120_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CBF1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CBF1-3xV5 IAA7::URA3


title: PALNHZ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: middle-aged, NLRP3i-treated, rep1 [26115-P]

description:
26115-P
DESEQ2_normalized_counts


title: COM2_3IAA_A_S4_RNA-seq


title: PAWTMX (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: CBF1_DMSO_120_B_S45_RNA-seq


title: PANEYN (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: CBF1_DMSO_60_C_S50_RNA-seq


title: CBF1_DMSO_120_A_S39_RNA-seq


title: middle-aged, saline-treated, rep6 [26192-P]

description:
26192-P
DESEQ2_normalized_counts

value: saline-treated


title: middle-aged, saline-treated, rep7 [26193-P]

description:
26193-P
DESEQ2_normalized_counts


title: PAWTLL (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PAWTBP (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: middle-aged, NLRP3i-treated, rep5 [26119-P]

description:
26119-P
DESEQ2_normalized_counts


title: CBF1_DMSO_60_B_S44_RNA-seq


title: CBF1_DMSO_60_A_S38_RNA-seq


title: PAWKRA (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: CHA4_3IAA_A_S4_RNA-seq


title: PAWJAD (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: middle-aged, saline-treated, rep3 [26189-P]

description:
26189-P
DESEQ2_normalized_counts


title: CBF1_DMSO_30_B_S43_RNA-seq


title: middle-aged, NLRP3i-treated, rep2 [26116-P]

description:
26116-P
DESEQ2_normalized_counts


title: PARLEZ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: Low risk non-OMAS


title: middle-aged, saline-treated, rep2 [26186-P]

description:
26186-P
DESEQ2_normalized_counts


title: CBF1_DMSO_30_A_S37_RNA-seq


title: CBF1_3IAA_120_C_S54_RNA-seq


title: PARPWX (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PARBGB (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: young, untreated, rep6 [26470-P]

description:
26470-P
DESEQ2_normalized_counts

value: untreated


title: PAPXAM (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: young, untreated, rep5 [26469-P]

description:
26469-P
DESEQ2_normalized_counts


title: middle-aged, saline-treated, rep1 [26185-P]

description:
26185-P
DESEQ2_normalized_counts


title: CBF1_3IAA_120_A_S42_RNA-seq


title: middle-aged, saline-treated, rep5 [26191-P]

description:
26191-P
DESEQ2_normalized_counts


title: young, untreated, rep4 [26466-P]

description:
26466-P
DESEQ2_normalized_counts


title: PAUBMJ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: CBF1_3IAA_120_B_S48_RNA-seq


title: PAWTLU (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: middle-aged, saline-treated, rep4 [26190-P]

description:
26190-P
DESEQ2_normalized_counts


title: PAVHIP (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: young, untreated, rep3 [26465-P]

description:
26465-P
DESEQ2_normalized_counts


title: young, untreated, rep2 [26462-P]

description:
26462-P
DESEQ2_normalized_counts


title: CBF1_3IAA_60_B_S47_RNA-seq


title: CBF1_DMSO_30_C_S49_RNA-seq


title: CBF1_3IAA_60_C_S53_RNA-seq


title: CBF1_3IAA_60_A_S41_RNA-seq


title: PAVEAC (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PAWPXJ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: young, untreated, rep1 [26461-P]

description:
26461-P
DESEQ2_normalized_counts


title: CBF1_3IAA_30_C_S52_RNA-seq


title: CBF1_3IAA_30_B_S46_RNA-seq


title: PAPKPC (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PAWLRY (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: CBF1_3IAA_30_A_S40_RNA-seq


title: PAPJLU (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: ABF1_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-ABF1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-ABF1


title: ABF1_DMSO_A_S1_RNA-seq


title: PAPSTN (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PAPRIP (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: S37 104885-001-050

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: liver

growth_protocol: Animal care and experimental procedures were approved by The Netherlands Central Authority for Scientific Procedures on Animals (CCD; project license AVD5010020172064) and an independent Animal Welfare Body of The Netherlands Organization for Applied Scientific Research (IvD TNO; TNO-489). Ldlr-/-.Leiden mice were bred and housed at the SPF animal facility at TNO (TNO Metabolic Health Research, Leiden, The Netherlands). Male mice were chosen because of their increased susceptibility for developing obesity and inflammation in comparison to female mice.

extract_protocol:
For next generation sequencing the RNA-Bee total-RNA isolation kit (Bio-Connect, Huissen, The Netherlands) was used to isolate total RNA from individual liver samples (lobus sinister lateralis) and RNA integrity was determined with the RNA 6000 Nano Lab-on-a-Chip kit and bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands). Total RNA's were processed into tagged random sequence libraries.
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from total-RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7760S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 v1.5 system (Illumina, New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-35 million reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: Mice (10-17 weeks old) were group-housed in a temperature-controlled room on a 12h light-dark cycle at 50-60% humidity and with free access to heat-sterilized water and food. Body weight, food intake per cage and clinical signs were monitored regularly. One group of mice (n=8) received the healthy grain-based chow diet (Ssniff Spezialdiäten GmbH, Soest, Germany) and a total of 45 mice received fast food diet (FFD) containing 41 kCal% fat from milk fat, 44 kCal% from carbohydrates (mainly fructose) and 14 kCal% casein (Research Diets, New Brunswick, NJ, USA) to induce advanced NASH and hepatic fibrosis. At t=0, after a 25-week run-in period on FFD, mice were matched on body weight, glucose, cholesterol and triglycerides into three groups of 15 mice each. Appropriate group sizes were calculated a priori by power analysis (GPower), with a minimal effect size of 30%, using a two-sided test with 95% confidence interval, power of 90% and α of 0.05. One group of n=15 mice served as FFD reference and was sacrificed at t=0 to indicate NASH and atherosclerosis severity at the start of the treatment. Comparison of semaglutide-treated mice with this reference group indicated whether semaglutide treatment could reduce NASH, hepatic fibrosis and atherosclerosis below levels at the start of treatment or blocked further progression. The second group (n=15) received daily subcutaneous saline injections for twelve weeks (FFD control). The third group (n=15) received daily subcutaneous semaglutide injections (100 µL, Ozempic®, Novo Nordisk, Bagsværd, Denmark) for twelve weeks. The dose was escalated over five days at a rate of 0.024 (20%), 0.048 (40%), 0.072 (60%), 0.096 (80%) mg/kg/day until the final dose of 0.120 mg/kg/day was reached and maintained until the study endpoint (based on weekly body weight measurement). Animals were sacrificed non-fasted by gradual-fill CO2 asphyxiation after the 25-week run-in period (t=0; FFD reference) or twelve weeks after the run-in period (t=12; other groups) and organs were collected for further analysis.

tag: treatmentperiod

tag: mousenr

value: m50 sema


title: S37 104885-001-053

value: m53 sema


title: S37 104885-001-052

value: m52 sema


title: ABF1_DMSO_B_S2_RNA-seq


title: ABF1_3IAA_B_S5_RNA-seq


title: ABF1_3IAA_A_S4_RNA-seq


title: S37 104885-001-049

value: m49 sema


title: S37 104885-001-051

value: m51 sema


title: S37 104885-001-048

value: m48 sema


title: S37 104885-001-047

value: m47 sema


title: PAPPEB (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: OMAS

value: neuroblastoma


title: S37 104885-001-046

value: m46 sema


title: S37 104885-001-045

value: m45 sema


title: PAPGFB (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

value: fresh frozen tumor


title: PAUXJB (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: ABF1_B_ChEC-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary files format and content: Processed data is provided in a bigwig format and contains spike-in normalized signal per base pair.
Library strategy: ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ABF1-MNase::TRP1

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or SM, Raffinose or Galactose.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ABF1-MNase::TRP1


title: ABF1_3IAA_C_S6_RNA-seq


title: PAWTKW (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PATVYZ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: ABF1_C_ChEC-seq


title: PAWKII (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PARFKR (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PATNJJ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASIBJ (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASFHI (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: PASDZS (RNA-seq)

description: RNAseq from fresh frozen tumor RNA


title: Rep2 Ded1-RNA X-link grown in SD+LEU medium

city: Paris

first: N.

middle: Kyle

last: Tanner

state: Ile de France

address: 13 rue Pierre et Marie Curie

department: Microbial Gene Expression

institute: Université de Paris-Cité & CNRS

data_processing:
The Illumina adapters were de-multiplexed using the bcl2fastq2 tool (version 2.18.12)
Adapters were removed with Cutadapt (adapter trimming, version 1.15).
The quality of the reads was verified using the FastQC tool (version v0.11.5)
BWA tool (version 0.7.12) was usedto do a local alignment with the following parameter : bwa mem -t 40 –c 1000 index .fasta read-file.fastq > sample.sam.
Samtools tool (version 1.9) was used according to the following parameter: samtools view -bt index.fasta sample.sam - o sample.bam.
PCR duplications were eliminated using the following parameter: samtools rmdup -s sample.bam -o sample-rmdup.bam.
File sorted by genomic coordinates using the yeast genome in general feature format (GFF) available from SGD (genome.gff) using the following parameters: samtools sort sample-rmdup.bam > sample-rmdup-sorted.bam and samtools index sample-rmdup-sorted.bam.
The counting table of each reads was obtained using the Bedtools tool (version 2.3.0) according to the following parameters: bedtools multicov -S -D -bams sample- rmdup-sorted.bam -bed genome.gff > sens-counts.txt and bedtools multicov -s -D -bams sample-rmdup-sorted.bam -bed genome.gff > antisens-counts.txt.
Assembly: Yeast S. cerevisiae (S288C) genome was indexed (index.fasta).
Supplementary files format and content: *RMdup_bedtools.txt:
column 1: NCBI locus
column 2: keywords
column 3: Feature
column 4: coordinate start
column 5: coordinate end
column 6: ND
column 7: Orientation
column 8: Merged features
column 9: Identification
column 10: Reads

growth_protocol: The wild type BY4742 yeast strain with the DED1 gene under its own promoter and terminator in the YCplac111 plasmid was grown at 30°C in SD-LEU to an OD600 of ~0.4 (exponential phase). The cultures were then made 300 µM in 4-thiouracil. Cultures were incubated to an OD600 of 1.8-2.0 (~5 hours). Some cultures were subjected to glucose depletion by growing 10 min in medium lacking glucose prior to irradiation.

extract_protocol:
Cells were lysed by vortexing in a FastPrep-24, clarified by centrifugation, and then bound to Protein A-Sepharose beads with Ded1 IgG, washed extensively and digested with nuclease S1
The 3' adapter was added directly to the Protein-Sepharose-bound Ded1-RNA complex, eluded, the 5' adapter was added, the Ded1-RNA complex was eluted, digested with protease K, the RNA was phenol/chloroform extracted, ethanol precipitated and then subjected to RT-PCR. The PCR products were combined and concentrated with a NucleoSpin Gel and PCR Clean-up kit amplification, purified on 6% PAGE and material migrating between ~120 and ~200 residues were recovered.

treatment_protocol: Cells with ~1.3% 4-thiouridine incorporated were concentrated to an OD600 of ~32 and irradiate 2X 10 min with UV light centered at 365 nm with a flux of ~7 Joules/cm^2 in a polystyrene petri dish with lid and on ice.

tag: strain

value: Normal (WT) growth conditions

tag: molecule subtype

value: Ded1 bound RNA


title: Rep1 Ded1-RNA X-link grown in SD+LEU medium

value: with the DED1 gene under its own promoter and terminator in the YCplac111 plasmid


title: PARSCY (RNA-seq)

description: RNAseq from fresh frozen tumor RNA

tag: patient subgroup

tag: disease state