title: T0_3_1

city: Chengdu

first: Wei

last: Liu

state: 四川省

address: 林荫街8号

institute: Sichuan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

extract_protocol:
RNA was extracted by trizol and 2.0 μg of total RNA was used for the constuction sequencing libraries
RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® following the manufacturer’s instruction.

value: promyelocyte

value: 10uM amiodarone for 24h


title: T0_2_1

status: Public on Jan 18 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: blca-turt-sample18-rep3

type: RNA

city: Sheffield

first: Jon

last: Griffin

address: Beech Hill Road

department: School of Medicine and Population Health

country: United Kingdom

institute: University of Sheffield

hyb_protocol: Affymetrix hybridisation kit and protocols

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G

data_processing:
SCAN.UPC package from Bioconductor was used
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not applicable

extract_protocol: Areas of viable tumour were annotated by a pathologist.  These areas were macrodissected from 2-4 unstained 4 micron FFPE sections using a sterile 22G needle under RNAse free conditions. RNA was extracted and purified from macrodissected material using RNeasy FFPE kit ((Qiagen, Valencia, CA).

treatment_protocol: Not applicable

tag: lab

value: luminal


title: Pancreatic organoids (passage 5)

city: Rotterdam

first: Kalyan

last: Dulla

address: Postbus 2040

country: Netherlands

institute: Erasmus MC

data_processing:
CLC genomic workbench version 21.0 (Qiagen)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork default parameters
Trimmed sequence reads were mapped to Sus scrofa genome data set assemble 11.1.103 (NCBI) using CLC genomic benchwork default parameters
Read count extraction was performed using CLC genomic benchwork
Assembly: Sus scrofa genome data set assemble 11.1.103 (NCBI)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: Organoids

growth_protocol: Organoids were embedded in extracellular matrix and maintained in medium containing the growth factors Wnt3a, Noggin, R-Spondin 1, FGF10 and EGF (Driehuis et al. 2020. STAR Protoc. 1, 100192).

extract_protocol:
RNA (>5 µg) was extracted using the NucleoSpin RNA kit (Macherey-Nagel).
BGI library construction protocol and sequencing on DNBseq platform

value: Organoids

value: Endodermal; epithelial

tag: genotype

value: WT

tag: passages

tag: time

value: Day 7


title: TiO2_NP_100ug_24H_3

city: Ottawa

first: Sabina

last: Halappanavar

state: ON

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to 8x60K Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (Agilent Technologies, Inc., Santa Clara, USA) slides in a hybridization chamber for 17 h at 65°C rotating at 10 rpm.

scan_protocol: Microarray slides were washed according to manufacturer’s protocol and scanned on an Agilent G4900DA Microarray Scanner (Agilent Technologies, Inc., Santa Clara, USA). Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

organism: Mus musculus

source_name: Immortalized Lung Epithelial cells (FE1)

label_protocol: In brief, 200 ng of total RNA per cell pellet sample or Universal Mouse Reference RNA (UMRR; Agilent Technologies) were used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: FE1 immortalized alveolar lung epithelial cells were cultured as described in Decan et al 2015, in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture F-12HAM (DMEM F12HAM) supplemented with 2 % fetal bovine serum (FBS), 1 ng/mL epidermal growth factor (EGF), 1 U/mL penicillin G, and 1 µg/mL streptomycin and maintained at 37°C, with 5 % CO2.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Boyadzhiev et al., 2021. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol . Total RNA concentration and purity was determined using a NanoDropOne spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system and an Agilent 4200 Tapestation System (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥6 were used for subsequent microarray experiments.

treatment_protocol: Cells were plated at a cell density of 130 000 cells/well in 6-well plates. Following overnight incubation, cells were exposed to 1.8 mL of 0 - 118 ug/mL metal oxide NPs, MPs, or metal chlorides. For all exposures, blank media exposed cells served as negative controls. Following 2, 24, and 48 h of exposure, cell supernatant was harvested, cells were washed with PBS, trypsinized and suspended in fresh cell culture media. An aliquot of cell suspension was used for Trypan Blue dye exclusion staining and the rest of the cells were pelleted by centrifugation (8000 rpm, 10 minutes, 4°C) and frozen at -80°C for microarray analysis. Two to four biological replicates were used for each condition.

tag: strain

value: MutaMouse

value: TiO2 Nanoparticle

tag: time point

value: 24 Hour

tag: dose

value: 100 ug/mL

tag: biological replicate

source_name: Universal Mouse Reference RNA

tag: sample type

value: 11 mouse cell lines


title: T0_1_1


title: Sample 1, Day 7, replicate 1

city: Los Angeles

first: Asha

last: Kar

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

country: USA

institute: University of California Los Angeles

data_processing:
We aligned the reads to the GRCh38 genome with GENCODE v39 annotations using STAR v.2.7.10a, using the two-pass method to account for novel splice junctions (Kar et. al, Genome Medicine 2024).
We filtered the aligned reads to exclude reads mapped to the mitochondrial genome or multiple transcripts (Kar et. al, Genome Medicine 2024).
We used featureCounts v2.0.3 to perform read summarization at the gene level (Kar et. al, Genome Medicine 2024).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes the raw counts for each Sample

molecule: polyA RNA

source_name: cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E).

growth_protocol: Cryopreserved human subcutaneous primary white preadipocytes (Zen-Bio catalog # SP-F-2, lot L120116E) were seeded into PromoCell Pad growth medium (PromoCell C-27410) with 1% Gibco Penicillin-Streptomycin (ThermoFisher 15140122) and cultured according to PromoCell Pad culturing protocols. Cells were maintained in a monolayer culture at 37C and 5% CO2. Cells were propagated for the full experiment and not cultured beyond 5 passages (Kar et. al, Genome Medicine 2024).

extract_protocol:
For the RNA collection, cells were washed with PBS once and then lysed with TriZOL (Invitrogen 15596026), and RNA was purified using Direct-Zol RNA Mini-Prep (Zymo Research R2061) (Kar et. al, Genome Medicine 2024).
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit (Kar et. al, Genome Medicine 2024).

treatment_protocol: To induce adipogenesis, cells were plated at confluency into 12-well plates for both RNA-seq (4 isogenic biological replicates per time point and assay) and the following day, adipogenesis was initiated using preadipocyte differentiation medium (PromoCell C-27436). The 1d and 2d timepoints were collected before any further media changes. For all other differentiation timepoints, 72 hours after the preadipocyte differentiation medium was added, it was replaced with adipocyte nutrition medium (PromoCell C-27438), following PromoCell ASPC differentiation protocols (Kar et. al, Genome Medicine 2024).

tag: tissue

value: subcutaneous adipose tissue

value: primary white preadipocyte


title: TiO2_NP_0ug_24H_3

value: Media Control


title: CK3_1

value: control


title: CK2_1


title: TiO2_NP_100ug_2H_3

value: 2 Hour


title: CK1_1

value: promyelocyte


title: Sample 1, Day 4, replicate 3

value: Day 4


title: blca-turt-sample16-rep3

value: basal-squamous


title: TiO2_NP_0ug_48H_2

value: 48 Hour


title: TiO2_NP_50ug_48H_2

value: 50 ug/mL


title: Sample 1, Day 4, replicate 2


title: Sample 1, Day 4, replicate 4


title: TiO2_NP_100ug_24H_2


title: blca-turt-sample15-rep3

value: luminal-papillary


title: blca-turt-sample13-rep3


title: TiO2_NP_25ug_2H_3

value: 25 ug/mL


title: blca-turt-sample17-rep3


title: TKPT cells, Itgb6-siRNA-3

city: Guangzhou

first: Ruilin

last: Zheng

address: Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
CLC Genomics Workbench V 11.0.1
Assembly: Ensembl_release109
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample

source_name: kidney

growth_protocol: TKPT cells were cultured in DMEM/F-12 (Thermo Fisher Scientific, USA) containing 10% FBS, 1% streptomycin/penicillin, and 0.1% insulin (10 mg/mL).

extract_protocol:
RNA was harvested using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA). The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA)
The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. Polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000

treatment_protocol: TKPT cells were exposed to a hypoxic incubator (1% O2, 5% CO2, 96% N2, 37°C) for 24 h, and then the cells were placed back into a normal oxygen incubator (5% CO2, 37°C) for 12 h. When TKPT cells were cultured in 6-well culture plates to a density of 60%, RNA transfection reagent was used as a carrier to transfect TKPT cells with Itgb6 siRNA.

value: kidney

value: TKPT cells

value: Proximal tubule epithelial cells

value: Itgb6 knockdown


title: TiO2_NP_25ug_24H_2

value: MutaMouse

value: TiO2 Nanoparticle

value: 24 Hour

value: 11 mouse cell lines


title: Sample 1, Day 2, replicate 4

value: subcutaneous adipose tissue

value: primary white preadipocyte

value: Day 2


title: TKPT cells, Scrambled-3

value: WT


title: blca-turt-sample12-rep3

value: basal-squamous


title: TiO2_NP_50ug_24H_2


title: TiO2_NP_100ug_48H_2

value: 48 Hour

value: 100 ug/mL


title: blca-turt-sample14-rep3


title: Sample 1, Day 2, replicate 3


title: TKPT cells, Scrambled-2


title: blca-turt-sample10-rep3


title: blca-turt-sample9-rep3

value: luminal-infiltrated


title: TiO2_NP_25ug_48H_1

value: 25 ug/mL


title: Sample 1, Day 2, replicate 2


title: Sample 1, Day 4, replicate 1

value: Day 4


title: SFFV-T6-61A-TG_WT_rep2

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

data_processing:
Trim_galore (version0.6.6http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming.
Processed reads were remove rRNA and then mapped to mm10 using Hisat2.
gene expressions were counted by featureCount and submitted to DEseq2 to different expression analysis.
Assembly: mm10
Supplementary files format and content: txt

source_name: Hematopoietic stem cells

growth_protocol: hematopoietic stem cells were sorted from bone marrow

extract_protocol:
Lysates were clarified from FACS-sorted  hematopoietic stem cells
First, 200 HSCs (Lineage- Sca-1+ c-kit+ CD34- CD135-) from WT or TG mice were sorted into lysis buffer directly. The transcriptome libraries were prepared using Smart-seq2 method. Then, Agilent Bioanalyzer 2100 system (Agilent Technologies) was used to assess the insertion size, and HiSeq PE Cluster Kit v4-cBot-HS (Illumina) was used to perform the clustering of the index-coded samples according the manufacturer’s instructions. Finally, the libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.

treatment_protocol: To induce the expression of TRMT6/61A, 4-week-old Trmt6/61a-TG mice were received doxycycline in their feed (2g/kg) and drinking water (1g/L doxycycline and 5% sucrose) for 4 weeks.

value: Hematopoietic stem cells

value: dox p.o for 4 weeks


title: Sample 1, Day 2, replicate 1


title: Sample 1, Day 1, replicate 4

value: Day 1


title: SFFV-T6-61A-TG_WT_rep1


title: blca-turt-sample8-rep3

value: luminal-papillary


title: SFFV-T6-61A-TG_TG_rep2

value: OE


title: blca-turt-sample11-rep3

value: luminal


title: TiO2_NP_0ug_48H_1

value: MutaMouse

value: TiO2 Nanoparticle

value: Media Control

value: 11 mouse cell lines


title: blca-turt-sample7-rep3


title: TiO2_NP_25ug_48H_3


title: blca-turt-sample6-rep3

value: neuronal


title: SFFV-T6-61A-TG_TG_rep1


title: blca-turt-sample5-rep3


title: TiO2_NP_50ug_2H_2

value: 2 Hour

value: 50 ug/mL


title: Sample 1, Day 1, replicate 2

value: subcutaneous adipose tissue

value: primary white preadipocyte


title: Overexpression-Atf4-rep5

city: Berlin

first: Rupert

middle: W

last: Overall

state: Berlin

address: Philippstraße 13

country: Germany

institute: Humboldt University of Berlin

data_processing:
Reads were mapped to mouse genome build (mm10) using the STAR algorithm and counts per ENSEMBL gene model prepared using the RSubread package (Liao et al., 2013) in R/BioConductor. Samples were filtered to have at least 1 count per million reads (CPM) in a minimum of 75% of the samples from at least one group. Differential expression analysis was performed using the edgeR package in R/BioConductor (Robinson et al., 2010).
Assembly: mm10
Supplementary files format and content: DCSeq_GeneCounts.tab is tab-delimited text with ENSEMBL gene identifiers in the first column and log2-normalised counts for each sample in subsequent columns

source_name: Hippocampus

growth_protocol: NPCs derived from the hippocampus of female, 6-week-old mice, were maintained as adherent monolayer cultures on poly-D-lysine/laminin-coated tissue culture dishes and cultured in Neurobasal medium (Gibco) supplemented with 1x B27 supplement plus Vitamin A (Gibco), 1x GlutaMAX supplement (Gibco) , 10,000 U/ml Pen/Strep (Gibco), 20 mg/ml human FGF2 (PeproTech) and 20 mg/ml human EGF (PeproTech). An expression cassette containing coding sequences of Atf3 or Atf4 under the control of the TRE3G promoter, a SV40-TetON-3G transactivator and a puromycin selection gene were inserted into the NPC genome using piggyBac technology.  Three stable cell lines were generated: NPCs containing Atf3 coding sequences (Atf3-OE), NPCs containing Atf4 coding sequence (Atf4-OE), and control NPCs (containing the same Tet-ON/puromycin expression cassette but no Atf3 or Atf4).

extract_protocol:
NPCs were collected using cell scratchers and RNA was isolated using Rneasy Mini Kit (QIAGEN) with on-column DNase digest. RNA quality and integrity were controlled using Agilent Technologies 2100 Bioanalyzer.
Libraries were prepared at Novogene using 1 µg of RNA and the NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Libraries were quantified and  controlled using Agilent 2100 Bioanalyzer and sequenced on an Illumina Novaseq Platform (Illumina, San Diego, CA, USA) using a paired-end 150 run (2×150 bases).

treatment_protocol: Differentiation was induced in all NPCs lines by a medium change and withdrawal of the growth factors EGF and FGF from the culture medium. To induce transgene expression, Doxycycline (100 ng/ml) was added to all cultures at the start of differentiation. NPCs were harvested at 10 h after start of differentiation.

value: Hippocampus

value: Neural precursor cell culture

value: Doxycycline at start of differentiation


title: Sample 1, Day 1, replicate 1


title: Sample 1, Day 0, replicate 4

value: Day 0


title: Overexpression-Atf4-rep3


title: blca-turt-sample4-rep3

value: luminal-infiltrated


title: TiO2_NP_0ug_2H_2


title: TiO2_NP_100ug_2H_2

value: 100 ug/mL


title: TiO2_NP_100ug_48H_1

value: 48 Hour


title: TiO2_NP_50ug_48H_1


title: Sample 1, Day 1, replicate 3

value: Day 1


title: blca-turt-sample3-rep3

value: basal-squamous


title: Overexpression-Atf4-rep2


title: blca-turt-sample2-rep3


title: TiO2_NP_0ug_24H_1

value: MutaMouse

value: TiO2 Nanoparticle

value: 24 Hour


title: Sample 1, Day 0, replicate 2


title: Overexpression-Atf4-rep1


title: Overexpression-Atf3-rep5


title: blca-turt-sample1-rep3


title: Overexpression-Atf4-rep4


title: Sample 1, Day 0, replicate 1


title: TiO2_NP_25ug_24H_1

value: 25 ug/mL

value: 11 mouse cell lines


title: blca-turt-sample18-rep2

value: luminal


title: TiO2_NP_25ug_2H_1

value: 2 Hour


title: Overexpression-Atf3-rep4


title: TiO2_NP_100ug_24H_1


title: Sample 1, Day 0, replicate 3

value: subcutaneous adipose tissue

value: primary white preadipocyte


title: Overexpression-Atf3-rep3

value: Hippocampus

value: Neural precursor cell culture


title: blca-turt-sample18-rep1


title: blca-turt-sample17-rep2


title: MDA-MB-231 cells,shRNF20,rep2

city: lexington

first: YADI

last: WU

state: KY

address: 741 S.Limestone

institute: University of kentucky

data_processing:
fastqc version 0.12.1
STAR version 2.7.11a
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).
RNA libraries for RNA-seq were prepared by Novagene.


title: TiO2_NP_50ug_2H_1

value: 50 ug/mL


title: MDA-MB-231 cells,shRNF20,rep1


title: Overexpression-Atf3-rep2

value: Doxycycline at start of differentiation


title: MDA-MB-231 cells,shControl,rep3


title: Overexpression-Atf3-rep1


title: blca-turt-sample17-rep1


title: TiO2_NP_50ug_24H_1


title: TiO2_NP_0ug_2H_1

value: Media Control


title: blca-turt-sample16-rep1


title: MDA-MB-231 cells,shRNF20,rep3


title: Al2O3_NP_0ug_24H_3

value: Al2O3 Nanoparticle


title: Overexpression-control-rep5

value: Overexpression-control


title: blca-turt-sample16-rep2

value: basal-squamous


title: MDA-MB-231 cells,shControl,rep1


title: Overexpression-control-rep4


title: MDA-MB-231 cells,shControl,rep2


title: MDA-MB_231,R90HM2,Chip

library_source: genomic

data_processing:
bowtie2 version 2.5.2
fastqc version 0.12.1
cutadapt version 4.5
samtools version 1.18
picard
macs2 version 2.2.9.1
Assembly: hg38
Supplementary files format and content: BigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented by using micrococcal nuclease (MNase) digestion.
ChIP-seq libraries were prepared by Novagene.


title: TiO2_NP_100ug_2H_1

value: MutaMouse

value: 100 ug/mL


title: blca-turt-sample15-rep2


title: blca-turt-sample15-rep1

value: luminal-papillary


title: Overexpression-control-rep3


title: Overexpression-control-rep2


title: Al2O3_NP_50ug_2H_2


title: Overexpression-control-rep1


title: blca-turt-sample14-rep1


title: MDA-MB_231,control,Input


title: Al2O3_NP_0ug_48H_1

value: 48 Hour


title: blca-turt-sample13-rep2


title: Al2O3_NP_50ug_48H_1

value: 11 mouse cell lines


title: blca-turt-sample14-rep2


title: Barcode sequence, scRNAseq

city: Birsbane

first: Nathan

middle: J.

last: Palpant

state: QLD

address: 306 Carmody Road

country: Australia

institute: University of Queensland

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing data were further processed to generate FASTQ files and the raw count matrix using the CellRanger pipeline
The multiplexed samples were demultiplexed to their original identities by mapping of sample reads to GRCh38 human reference genome and internal barcode sequences
The gene expression count matrix was loaded into Seurat with the barcode matrix added separate from RNA
Assembly: hg38
Supplementary files format and content: tsv. files and mtx. files

source_name: Barcoded WTC-11

extract_protocol:
For each sample, cells were washed with filtered PBS and dissociated using Versene solution containing 0.25% Trypsin and 10 µM ROCK inhibitor Y-27632 followed by RPMI-1640 medium plus FBS at a 1:1 ratio. Cells were then analysed for live/dead cell staining using Zombie NIR™ Fixable Viability Kit (BioLegend). 5 x 105 cells from each live/dead stained sample were collected and pooled. Finally, total of 5 x 105 of single viable cells were sorted from the pooled population using BD FACSymphony™ S6 Cell Sorter.
Library was performed according to the manufacturer's instructions (Chromium Single Cell 3’ Library, Gel Bead and Multiplex Kit). The sorted single cell suspensions were loaded onto 10x Genomics Single Cell 3’ Chips to form single cell gel beads in emulsion (GEMs).

treatment_protocol: Barcoded WTC-11 hiPSCs were seeded onto a T25 flask at a density of 3M cells per flask. Cells were differentiated at day 0 under 1 µM CHIR, 3 µM CHIR, 5 µM CHIR, and 7 µM CHIR in the presence of 500 µg/mL BSA and 213 µg/mL AA.

value: Barcoded WTC-11

value: human iPSCs

value: Internal barcode

value: day 2

value: pooled sample


title: blca-turt-sample13-rep1


title: Gene expression, scRNAseq

description: 10x Genomics


title: MDA-MB_231,shRNF20,Input


title: OXL+GeXIVA 1

city: Haikou

first: Huanbai

last: Wang

state: Hainan

address: Hai Dian Campus of Hainan University, No.58 of Ren Min Road, Mei Lan District, Haikou, Hainan Province,China

department: School of Life Sciences

institute: Hainan University

data_processing:
Data was analysed using NovoMagic platform
fastp (version 0.19.7) was used for quality control
Hisat2 v2.0.5 was used for reads mapping
StringTie (v1.3.3b) was used for novel transcripts prediction
FeatureCounts v1.5.0-p3 was used for count the reads numbers mapped to each gene
Assembly: GRCm39
Supplementary files format and content: table-delimited file includes raw counts for each sample
Supplementary files format and content: table-delimited file includes FPKM values for each sample

source_name: L4-6 spinal cord

extract_protocol:
RNA was extracted using trizol (Ambion, USA)
Libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: L4-6 spinal cord

value: Mice were injected with i.p. 3.5 mg/kg oxaliplatin (OXL) and s.c. GeXIVA[1,2] 1.73 mg/kg 5 times a week for 3 weeks

value: WT


title: OXL+GeXIVA 3


title: Al2O3_NP_25ug_2H_3

value: 2 Hour

value: 25 ug/mL


title: blca-turt-sample12-rep2


title: OXL+GeXIVA 2


title: OXL+NS 3

value: Mice were injected with i.p. 3.5 mg/kg oxaliplatin (OXL) and s.c. normal saline (NS) 5 times a week for 3 weeks


title: MDA-MB_231,CHM2,Chip


title: Al2O3_NP_25ug_48H_1

value: Al2O3 Nanoparticle


title: OXL+NS 2


title: Al2O3_NP_10ug_48H_1

value: MutaMouse

value: 10 ug/mL


title: Al2O3_NP_50ug_2H_1

value: 50 ug/mL


title: Al2O3_NP_25ug_24H_1

value: 24 Hour


title: TiO2_NP_50ug_24H_3

value: TiO2 Nanoparticle

value: 11 mouse cell lines


title: OXL+NS 1


title: blca-turt-sample11-rep2

value: luminal


title: Al2O3_NP_10ug_24H_1


title: blca-turt-sample11-rep1


title: KEO.L35.SK8.CMo.144.1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Novaseq S1 using v3 NovaSeq Control Software v1.7.0 and RTA v3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the hg38 human assembly with the Ensembl version 106 annotation using Salmon version 1.6.0. Gene level summaries were prepared using tximport version 1.24.0
Assembly: hg38 with ensembl 106 annotation
Supplementary files format and content: tab delimited text file with ensemble gene IDs and either integer count data for each sample
Supplementary files format and content: tab delimited text files with ensemble gene IDs and log2 TPM (with a +1 offset) for each sample

source_name: stem-cell derived otic progenitor cells

growth_protocol: Cells were cultured in DFNB basal medium (DMEM/F12 with 1% N2 and 2% B27, Gibco by Life Technologies), supplemented with difluorobenzeneacetamid (DBZ, Tocris Bioscience) at 5 μM

extract_protocol:
RNA was extracted using the Qiagen Rneasy extraction kit following standard procedures
High-throughput ZAPR

treatment_protocol: Infections of OPCs were performed at multiplicities of infection calculated using BHK-21 infectious units for ZIKVPR and HFF infectious units for hCMVGFP. Virus was added to cells in minimal volume and incubated with intermittent rocking for 1 hr at 37o C. Inoculum was then removed and replaced with fresh medium.

value: stem-cell derived otic progenitor cells

tag: virus

value: Mock

tag: agent

value: CMV

tag: heat inactivated_virus

value: No

tag: hours post_infection


title: GS+GeXIVA 3

value: L4-6 spinal cord

value: Mice were injected with i.p. 5 % glucose solution (GS) and s.c. GeXIVA[1,2] 1.73 mg/kg 5 times a week for 3 weeks


title: Al2O3_NP_10ug_2H_1

value: 2 Hour


title: GS+GeXIVA 2

value: WT


title: KEO.L35.SK8.CHI.144.1

tag: cell line

value: TB40/e-UL32-GFP HCMV

value: Yes


title: blca-turt-sample10-rep1

value: basal-squamous


title: GS+GeXIVA 1


title: blca-turt-sample12-rep1


title: KEO.L35.SK8.CMV.144.1


title: GS+NS 3

value: Mice were injected with i.p. 5 % glucose solution (GS) and s.c. normal saline (NS) 5 times a week for 3 weeks


title: blca-turt-sample9-rep1

value: luminal-infiltrated


title: blca-turt-sample9-rep2


title: KEO.L35.SK8.CMo.96.1


title: Al2O3_NP_50ug_24H_1

value: MutaMouse

value: Al2O3 Nanoparticle

value: 24 Hour

value: 50 ug/mL


title: GS+NS 2


title: TKPT cells, Itgb6-siRNA-1

value: kidney

value: TKPT cells

tag: cell type

value: Proximal tubule epithelial cells

value: Itgb6 knockdown


title: Al2O3_NP_0ug_24H_1

tag: treatment

value: Media Control

value: 11 mouse cell lines


title: KEO.L35.SK8.CHI.96.1

value: stem-cell derived otic progenitor cells

value: CMV


title: GS+NS 1

value: L4-6 spinal cord

value: WT


title: Al2O3_NP_25ug_2H_1

value: 2 Hour

value: 25 ug/mL


title: blca-turt-sample8-rep2

tag: lab

value: luminal-papillary


title: KEO.L35.SK8.CMV.96.2

value: TB40/e-UL32-GFP HCMV

value: No


title: Al2O3_NP_10ug_48H_2

value: MutaMouse

value: Al2O3 Nanoparticle

value: 48 Hour

value: 10 ug/mL


title: blca-turt-sample10-rep2

value: basal-squamous


title: blca-turt-sample8-rep1


title: MEF cells, KO4, VSV

city: 武汉

first: zixuan

last: wang

state: 湖北省

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

data_processing:
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads.
The clean reads were then mapped to the mouse genome using HISAT.
Assembly: GRCm39
Supplementary files format and content: file folder includes raw counts for each Sample
Supplementary files format and content: excel file includes FPKM values for each Sample

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs) were maintained in DMEM supplemented with sodium pyruvate (110 mg/l), 10% FBS, 1× non-essential amino acids (VivaCell) and 1% penicillin–streptomycin (VivaCell).

extract_protocol:
Total RNA from cells infected with or without VSV was purified using the RNeasy Mini Kit (QIAGEN NO. 74104).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) accordingly to the manufacturer’s protocol, and index codes were added to assign sequences to each sample.

treatment_protocol: VSV infection

value: MEF

value: Mouse embryonic fibroblasts

tag: genotype

value: EGLN3 knockout

value: VSV infection


title: KEO.L35.SK8.CMo.48.1

value: stem-cell derived otic progenitor cells

value: Mock

value: CMV


title: KEO.L35.SK8.CHI.48.1

value: Yes


title: MEF cells, KO3, VSV

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: EGLN2 knockout


title: MEF cells, KO2, VSV

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: EGLN1 knockout


title: KEO.L35.SK8.CMV.48.1

value: TB40/e-UL32-GFP HCMV


title: MEF cells, WT4, VSV

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: WT


title: KEO.L34.Wi.CMo.144

value: WI

value: No


title: Al2O3_NP_25ug_24H_2

value: MutaMouse

value: Al2O3 Nanoparticle

value: 24 Hour

value: 25 ug/mL

value: 11 mouse cell lines


title: blca-turt-sample7-rep2

value: basal-squamous


title: MEF cells, WT3, VSV

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: MEF

value: Mouse embryonic fibroblasts

value: VSV infection


title: blca-turt-sample6-rep2

value: neuronal


title: Al2O3_NP_0ug_2H_1

value: 2 Hour

value: Media Control


title: Al2O3_NP_0ug_24H_2


title: KEO.L34.Wi.CHI.144

value: stem-cell derived otic progenitor cells

value: CMV

value: Yes


title: blca-turt-sample6-rep1


title: Al2O3_NP_0ug_48H_2

value: 48 Hour


title: MEF cells, WT2, VSV

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: WT


title: KEO.L34.Wi.CMV.144

value: WI

value: TB40/e-UL32-GFP HCMV

value: No


title: blca-turt-sample7-rep1


title: blca-turt-sample5-rep2

value: luminal-papillary


title: MEF cells, KO4

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: EGLN3 knockout

value: no VSV infection


title: blca-turt-sample5-rep1


title: Al2O3_NP_10ug_24H_2

value: MutaMouse

value: Al2O3 Nanoparticle

value: 24 Hour

value: 10 ug/mL

value: 11 mouse cell lines


title: blca-turt-sample4-rep2

value: luminal-infiltrated


title: KEO.L34.Wi.CMo.96

value: stem-cell derived otic progenitor cells

value: Mock


title: blca-turt-sample4-rep1


title: MEF cells, KO3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: MEF

value: Mouse embryonic fibroblasts

value: EGLN2 knockout


title: Al2O3_NP_50ug_48H_3

value: 48 Hour

value: 50 ug/mL


title: Al2O3_NP_50ug_48H_2


title: KEO.L34.Wi.CHI.96

value: WI

value: TB40/e-UL32-GFP HCMV

value: CMV

value: Yes


title: blca-turt-sample3-rep2

value: basal-squamous


title: MEF cells, KO2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: EGLN1 knockout

value: no VSV infection


title: Al2O3_NP_0ug_48H_3

value: MutaMouse

value: Al2O3 Nanoparticle

value: Media Control


title: KEO.L34.Wi.CMV.96

value: stem-cell derived otic progenitor cells

value: No


title: blca-turt-sample3-rep1


title: Al2O3_NP_25ug_48H_2

value: 25 ug/mL

value: 11 mouse cell lines


title: MEF cells, WT4

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

value: MEF

value: Mouse embryonic fibroblasts

value: WT


title: KEO.L34.Wi.CMo.48.1

value: WI

value: Mock


title: KEO.L34.Wi.CHI.48.1

value: TB40/e-UL32-GFP HCMV

value: CMV


title: MEF cells, WT3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所


title: MEF cells, WT2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所


title: KEO.L34.Wi.CMV.48.1


title: KEO.L31.Wi.ZMo.48

value: ZIKA


title: 3-month somatosensory cortex_cKO_rep2

city: wuhan

first: zhao

last: chen

state: Hubei

address: shuiguohu

department: BIOLOGY

institute: wuhan university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameter: )
Trimmed sequence reads were mapped to UCSC genome GrCM38/mm10 using STAR (parameters: default)
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined by DESeq2 as ones with the p value less than 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: somatosensory cortex

extract_protocol:
RNA isolation was performed using the RNAiso Plus (TAKARA) according to manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Somatosensory cortices were dissected and collected from 3 months ctrl and cKO mice.

value: somatosensory cortex

value: cKO

tag: age

value: 3 months


title: KEO.L31.Wi.ZHI.48

value: Yes


title: blca-turt-sample2-rep1

value: basal-squamous


title: blca-turt-sample1-rep2


title: Al2O3_NP_10ug_48H_3

value: MutaMouse

value: Al2O3 Nanoparticle

value: 48 Hour

value: 10 ug/mL


title: Al2O3_NP_0ug_2H_3

value: 2 Hour

value: Media Control

value: 11 mouse cell lines


title: 3-month somatosensory cortex_cKO_rep1


title: blca-turt-sample1-rep1


title: blca-turt-sample2-rep2


title: KEO.L31.Wi.ZV.48

value: stem-cell derived otic progenitor cells

value: WI

value: No


title: Al2O3_NP_25ug_48H_3

value: 25 ug/mL


title: 3-month somatosensory cortex_Ctrl_rep2

value: Ctrl


title: Al2O3_NP_0ug_2H_2


title: Healthy control 9

city: Ann Arbor

first: Sunitha

last: Nagrath

state: Michigan

address: 2800 Plymouth Road

institute: University of Michigan

description: Gene expression data

hyb_protocol: Fragmented and biotinylated ds-cDNA was hybridized following GeneChip ™ 3’ IVT Pico Kit Manual Workflow (applied biosystems,Publication Number 703308; Revision 7 ). The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using applied biosystems GeneChip™ Scanner 3000 7G

data_processing: Standard microarray data processing procedures were followed in R programming environment (4.0.2). Briefly, raw intensities were imported as CEL files using the oligo package. The intensities were then normalized and summarized into gene-wise expression values using a robust multichip average (RMA) method. Quality control plots, including normalized unscaled standard error (NUSE), relative log expression (RLE) as well as principle component analysis (PCA) were generated to discover outliers in the dataset. The probesets were then annotated using clariomshumanhttranscriptcluster.db package. If multiple probes were mapped to the same gene, the one with highest average expression across all samples was selected. Differentially expressed genes were then calculated between different conditions using the limma package.

source_name: white blood cells from healthy control

label_protocol: The labeled cDNA was prepared following the GeneChip ™ 3’ IVT Pico Kit Manual Workflow (applied biosystems,Publication Number 703308; Revision 7 ) by the Thermofisher microarray research services laboratory

growth_protocol: Cell lines used in this study were maintained at 37°C and 5% CO2. Cells were grown to 70 - 80% confluence in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) (Sigma) and 1% Antibiotic-antimycotic (Gibco), before subculturing using 0.05% Trypsin-EDTA (Gibco).

extract_protocol: Following CTC isolation, 100 µL of PicoPure RNA Extraction Buffer was flowed into the chip. The chip was then incubated at 42C for 30 minutes. Following incubation, 100 µL of Ultrapure DEPC-treated water was flowed through the device and was collected in a sterile Eppendorf. This second RNA sample contains the RNA extracted from the CTCs. Each sample was frozen at -80C until purification.To purify, the samples were thawed on ice before purification using the Arcturus® PicoPure® RNA Isolation Kit (Thermo Fisher, Cat# KIT0204). 11µL of the RNA samples were plated into a sterile barcoded PCR plate supplied by Thermo Fisher Microarray Research Services Laboratory . The samples were then shipped their lab and processed following standard 3' IVT Pico Kit protocols.

treatment_protocol: Blood samples from patients or healthy control and cell lines in PBS were processed through the microfluidic graphene oxide (GO) chip. Briefly, GO chips were coated with antibody cocktails, anti-EPCAM, anti-CD133 (Miltenyi), and anti-EGFR (RayBiotech).The chips were then washed with PBS to remove excess antibodies, and blocked with 3% bovine bovine serum albumin (BSA). 1mL of blood was flowed at 1mL/hr through the inlet of the device to isolate CTCs.

value: Blood

value: white blood cells from healthy control

tag: timepoint

value: healthy control

tag: status

value: Healthy

tag: ctc count level

value: low


title: Al2O3_NP_50ug_2H_3

tag: strain

value: MutaMouse

tag: time point

tag: dose

value: 50 ug/mL


title: Al2O3_NP_10ug_2H_3

value: Al2O3 Nanoparticle

tag: biological replicate

tag: sample type


title: 3-month somatosensory cortex_Ctrl_rep1

tag: tissue

value: somatosensory cortex

value: 3 months


title: Al2O3_NP_10ug_2H_2

value: 2 Hour

value: 10 ug/mL


title: KEO.L31.Wi.ZMo.24

value: stem-cell derived otic progenitor cells

tag: virus

value: Mock

tag: agent

value: ZIKA

tag: heat inactivated_virus


title: KEO.L31.Wi.ZHI.24

tag: cell line

value: WI

value: Yes

tag: hours post_infection


title: Al2O3_NP_25ug_24H_3

tag: treatment

value: 24 Hour

value: 25 ug/mL

value: 11 mouse cell lines


title: Healthy control 8

description: Gene expression data

value: Blood

tag: cell type

value: white blood cells from healthy control

value: healthy control

value: Healthy


title: P90, Female, scRNAseq

city: Tel Aviv

first: Mai

last: Eshel

address: Klatzkin 35

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description:
10x Genomics
P90_Fbxo2_F

data_processing:
Genomic alignment, de-multiplexing, and mapping of unique molecular identifiers (UMIs) to each gene was performed using Cell Ranger
Downstream analyses were performed with the Seurat R package (version 4.3.0). Genes detected in at least three nuclei were included in the analysis. We filtered out nuclei with the 10% lowest or 2% highest number of expressed genes and the 2% nuclei with the highest number of unique molecular identifiers (UMI). Nuclei with >10% mitochondrial genes were also excluded from the analysis. We used the R package scDblFinder to exclude doublets and Seurat’s SCTransform to scale and normalize the data. We integrated the male and female datasets employing Seurat’s IntegrateData and performed the next steps on the integrated assay. We ran dimensionality reduction with RunPCA, and the top 40 dimensions were kept. Then we clustered the nuclei using FindNeighbors followed by FindClusters with a resolution of 0.5. We iteratively removed two low quality clusters (identified by high content of mitochondrial genes and low gene count). We annotated the clusters using known marker genes and SingleR.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

molecule: nuclear RNA

source_name: Cochlear duct

extract_protocol:
Three-month-old (P90) heterozygous Fbxo2VHC/+ were euthanized and their temporal bone were removed. The cochlear ducts were removed and snap-frozen on dry ice. Cochlear ducts from 3 animals were pooled for each sex separately and processed for nuclear extraction. The tissue was incubated on ice in 500 ml of lysis buffer (10mM Tris-Hcl pH7.4, 10mM NaCl, 3mM MgCl2, 0.01% NP40, 0.01% Tween20, 1% BSA, 1U/ml RNase Inhibitor) for 30 minutes. The lysis buffer was then gently removed and replaced with 500 ml of DMEM-F12 and the tissue was triturated by pipetting up and down to release the nuclei. The homogenate was passed sequentially through a 70 mm mini cell strainer and a 20mm mini cell strainer (pluriSelect). Following centrifugation at 500 g for 6 minutes at 4oC, the pellet was resuspended in 500 ml of DMEM-F12 and pass through a 10 mm mini cell strainer (pluriSelect). After two more washes with centrifugation and resuspension, Venus positive nuclei were sorted using an Aria II Cell Sorter (BD) to enrich for hair cell and supporting cell nuclei.
The nuclei suspension was captured using the Chromium X with the Single Cell 3' cDNA Kit v3.1 (10x Genomics) to generate libraries.

value: Cochlear duct

tag: strain background

value: FVB/NJ

tag: genotype

value: heterozygous Fbxo2VHC/+

tag: age


title: Healthy control 7

description: Gene expression data

tag: timepoint

tag: status

tag: ctc count level

value: low


title: KEO.L31.Wi.ZV.24

value: No


title: Al2O3_NP_50ug_24H_3

tag: strain

value: MutaMouse

value: Al2O3 Nanoparticle

tag: time point

tag: dose

value: 50 ug/mL


title: Healthy control 6

description: Gene expression data

tag: tissue


title: P90, Male, scRNAseq

description:
10x Genomics
P90_Fbxo2_M


title: KEO.L31.SK8.ZHI.48

value: stem-cell derived otic progenitor cells

tag: virus

value: ZIKA


title: KEO.L31.SK8.ZMo.48

value: Mock

tag: agent


title: Al2O3_NP_25ug_2H_2

value: 2 Hour

value: 25 ug/mL

tag: biological replicate

tag: sample type


title: Al2O3_NP_10ug_24H_3

value: 24 Hour

value: 10 ug/mL

value: 11 mouse cell lines


title: Healthy control 4

description: Gene expression data

value: Blood

value: white blood cells from healthy control

value: healthy control

value: Healthy


title: HAMS, scRNAseq

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Seurat analysis
Cell proliferation analysis
Pathway analysis
Assembly: mm10 reference dataset (GRCm38)

source_name: Pancreatic islets

extract_protocol:
Mouse islets were isolated according to previously published protocol (Schaschkow, A et al, Diabetes, 2021)
Chromium Single Cell 3' Reagent Kits

treatment_protocol: 5-week old NOD mice were treated with HAMS or HAMSAB diet for 5 consequtive weeks

value: Pancreatic islets

value: NOD

value: HAMS


title: HAMSAB, scRNAseq

value: HAMSAB


title: KEO.L31.SK8.ZMo.24

tag: cell line

tag: heat inactivated_virus

value: No

tag: hours post_infection


title: KEO.L31.SK8.ZV.48

value: stem-cell derived otic progenitor cells


title: NiO_NP_5ug_48H_3

value: MutaMouse

tag: treatment

value: NiO Nanoparticle

value: 48 Hour

value: 5 ug/mL


title: KEO.L31.SK8.ZHI.24

value: ZIKA

value: Yes


title: Somatosensory cortex, WGBS, Ctrl, rep1

data_processing:
Image analysis and base calling were performed with Illumina CASAVA pipeline, and finally generated 150 bp paired-end reads.
The reference genome was first transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2.
Clean reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before being aligned to the similarly converted versions of the genome in a directional manner.
The results of methylation extractor were transformed into bigwig format for visualization using IGV browser.
To calculate the methylation level of the sequence, we divided the sequence into multiple bins, with bin site is 10 kb.
The sum of methylated and unmethylated read counts in each window were calculated.
Differentially methylated regions (DMRs) were identified using the DSS software.
Assembly: mm10
Supplementary files format and content: WGBS_cKO_vs_Ctrl_DMR_all_result.txt

source_name: Somatosensory cortex

growth_protocol: Somatosensory cortices were dissected and collected from 2.5 months ctrl and cKO mice.

extract_protocol:
Extracting DNA from tissues using the ctab method
WGBS was performed and analyzed in Novogene (Beijing, China).
The concentration and quality of DNA was assessed on Qubit 2.0 Flurometer (Life Technologies, CA, USA) and an Agilent Bioanalyzer 2100 system (Agilent Technologies), respectively.
Briefly, the genome DNA (100 ng) was randomly broken to 200-300 bp with Covaris S220.
These DNA fragments were treated with bisulfite using Scale Methyl-DNA Lib Prep Kit for Illumina.
Finally, the DNA library was obtained by PCR amplification and adding adaptor.

value: Somatosensory cortex

tag: genotype

value: Ctrl

value: 2.5 months


title: Somatosensory cortex, WGBS, cKO, rep2

value: cKO

tag: age


title: KEO.L31.SK8.ZV.24


title: NiO_NP_10ug_48H_2

value: 10 ug/mL

value: 11 mouse cell lines


title: Healthy control 5

description: Gene expression data

value: Blood

tag: cell type

value: white blood cells from healthy control

tag: timepoint

value: healthy control

value: Healthy

value: low


title: Somatosensory cortex, WGBS, cKO, rep1


title: NiO_NP_0ug_2H_1

value: MutaMouse

value: 2 Hour

value: Media Control


title: NiO_NP_10ug_24H_3

value: NiO Nanoparticle

value: 24 Hour


title: KEO.L30.SK8.CMo.96

value: stem-cell derived otic progenitor cells

value: Mock

value: CMV

value: No


title: Healthy control 1

description: Gene expression data

tag: status

tag: ctc count level


title: NiO_NP_0ug_48H_2

tag: strain

tag: time point

value: 48 Hour


title: H441 cell line, replicate 2

description: Gene expression data

source_name: Lung cancer cell line

tag: tissue

value: Cell line derived from lung tumor

value: Lung cancer cell line

value: cell line control

value: Cell line


title: Somatosensory cortex, WGBS, Ctrl, rep2

value: Somatosensory cortex

value: Ctrl

value: 2.5 months


title: Healthy control 2

description: Gene expression data

value: Blood

value: white blood cells from healthy control

value: healthy control

value: Healthy

value: low


title: Somatosensory cortex, Ctrl, Input, rep3

description: 2_5-month_somatosensory_cortex_Ctrl-H3K36me2_Input_peaks.broadPeak

data_processing:
All ChIP-seq data were detected and remove adaptors using Cutadapt.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.4.4.
we used the macs2 software for peak calling, with the input file as control.
Assembly: UCSC mm10 genome
Supplementary files format and content: macs2 call peak broad peak file

extract_protocol:
Somatosensory cortices were digested into single cells by Papain. Nuclei were extracted in lysis buffer [10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630)]. Nuclear extracts were fixed with 1% formaldehyde for 10 minutes. After digested by micrococcal nuclease, cell lysis was sonicated in EP tubes with power output 100 W, 5 min, 0.5 s on, 0.5 s off on ice.
ChIP-seq libraries were constructed by VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme ND607). 5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were size selected at about 300 bp in length using VAHTS DNA Clean Beads (Vazyme N411). The concentration and quality of DNA was measured with an Agilent 2100 Bioanalyzer.

treatment_protocol: Somatosensory cortices were dissected and collected from 2.5 months ctrl and cKO mice.

tag: chip antibody


title: KEO.L30.SK8.CHI.96

value: stem-cell derived otic progenitor cells

tag: virus

value: TB40/e-UL32-GFP HCMV

tag: agent

value: Yes


title: Somatosensory cortex, Ctrl, Input, rep2


title: NiO_NP_25ug_24H_1

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Boyadzhiev et al., 2021. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol . Total RNA concentration and purity was determined using a NanoDropOne spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system and an Agilent 4200 Tapestation System (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥6 were used for subsequent microarray experiments.

value: MutaMouse

value: NiO Nanoparticle

value: 24 Hour

tag: dose

value: 25 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: KEO.L30.SK8.CMV.96

tag: cell line

value: CMV

tag: heat inactivated_virus

value: No

tag: hours post_infection


title: H441 cell line, replicate 1

description: Gene expression data

value: Cell line derived from lung tumor

value: Lung cancer cell line

value: cell line control

value: Cell line


title: Heatlhy control 3

description: Gene expression data

value: Blood

value: white blood cells from healthy control

value: healthy control


title: H3255 cell line, replicate 2

description: Gene expression data


title: NiO_NP_50ug_48H_2

tag: treatment

value: 48 Hour

value: 50 ug/mL


title: Somatosensory cortex, Ctrl, Input, rep1

value: Somatosensory cortex

tag: genotype

value: Ctrl

tag: age

value: 2.5 months


title: H3255 cell line, replicate 1

description: Gene expression data

tag: cell type

tag: timepoint

tag: status


title: H1650 cell line, replicate 1

description: Gene expression data

tag: ctc count level


title: NiO_NP_25ug_48H_1

tag: strain

value: MutaMouse

value: NiO Nanoparticle

tag: time point


title: KEO.L30.SK8.CMo.48

tag: tissue

value: stem-cell derived otic progenitor cells

tag: virus

value: Mock


title: Somatosensory cortex, Ctrl, H3K36me2, rep3

tag: chip antibody


title: KEO.L30.SK8.CHI.48

value: TB40/e-UL32-GFP HCMV

tag: agent

value: CMV

value: Yes


title: Somatosensory cortex, Ctrl, H3K36me2, rep2


title: KEO.L30.SK8.CMV.48

value: No


title: NiO_NP_5ug_24H_1

value: 24 Hour

tag: dose

value: 5 ug/mL

tag: biological replicate

tag: sample type

value: 11 mouse cell lines


title: Somatosensory cortex, Ctrl, H3K36me2, rep1


title: U2932_shZNF587-417v1_D10_RNA_Rep3

city: Lausanne

first: Filipe

last: Martins

address: Station 19

country: Switzerland

institute: Epfl

description:
U2932_D10_RNA.tab
U2932_D10_RNA_TEs.tab

data_processing:
RNA-seq reads were mapped to the hg19 using hisat v2.1.0
Mapped reads were filtered for uniquely mapping reads (MAPQ > 10)
Read counts on genes and repetitive sequence integrants was performed with featureCounts v2
Assembly: hg19
Supplementary files format and content: U2932_D10_RNA.tab: coma-separated table containing raw read counts on genes
Supplementary files format and content: U2932_D10_RNA_TEs.tab: coma-separated table containing raw read counts on TEs

growth_protocol: RPMI 1640 + 10% FCS + 1% Pen-Strep

extract_protocol:
Total RNA extraction was performed using the NucleoSpin RNA plus kit (Machery-Nagel) according to the manufacturer’s recommendations. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA kit.

treatment_protocol: Lentiviral transduction

tag: cell line

value: Diffuse large B cell lymphoma

value: ZNF587,ZNF417 knockdown

value: Lentiviral transduction

tag: time

value: Day 10


title: Somatosensory cortex, cKO, Input, rep3

description: 2_5-month_somatosensory_cortex_cKO-H3K36me2_Input_peaks.broadPeak

value: Somatosensory cortex

tag: genotype

tag: treatment

value: cKO


title: CTCs from patient 27, baseline

description: Gene expression data

source_name: CTCs from cancer patients

value: Blood

tag: cell type

value: CTCs from cancer patients

value: base

value: Tumor, stable


title: Somatosensory cortex, cKO, Input, rep2

tag: age

value: 2.5 months


title: NiO_NP_0ug_24H_2

source_name: Immortalized Lung Epithelial cells (FE1)

value: MutaMouse

value: NiO Nanoparticle

value: Media Control


title: Somatosensory cortex, cKO, Input, rep1


title: NiO_NP_50ug_24H_2

value: 24 Hour

value: 50 ug/mL

source_name: Universal Mouse Reference RNA


title: U2932_Control_shRNA_D10_RNA_Rep3

description:
U2932_D10_RNA.tab
U2932_D10_RNA_TEs.tab

value: Control


title: U2932_shZNF587-417v1_D10_RNA_Rep1

description:
U2932_D10_RNA.tab
U2932_D10_RNA_TEs.tab

value: Diffuse large B cell lymphoma


title: NiO_NP_10ug_2H_2

value: 2 Hour

value: 10 ug/mL

value: 11 mouse cell lines


title: Somatosensory cortex, cKO, H3K36me2, rep3

value: Somatosensory cortex


title: Somatosensory cortex, cKO, H3K36me2, rep2

value: cKO


title: NiO_NP_10ug_24H_1


title: U2932_Control_shRNA_D10_RNA_Rep2

description:
U2932_D10_RNA.tab
U2932_D10_RNA_TEs.tab

value: Lentiviral transduction

value: Day 10


title: CTCs from patient 27, week10

description: Gene expression data

value: Blood

value: CTCs from cancer patients

tag: timepoint

tag: status


title: CTCs from patient 26, week 10

description: Gene expression data

value: Tumor, stable

tag: ctc count level

value: low


title: NiO_NP_25ug_2H_3

tag: strain

value: MutaMouse

value: NiO Nanoparticle

tag: time point

value: 25 ug/mL


title: NiO_NP_25ug_24H_3

value: 24 Hour


title: CTCs from patient 25, week 4

description: Gene expression data

tag: tissue

value: Tumor, progression


title: CTCs from patient 26, baseline

description: Gene expression data

value: base


title: CTCs from patient 25, baseline

description: Gene expression data


title: U2932_shZNF587-417v1_D10_RNA_Rep2

description:
U2932_D10_RNA.tab
U2932_D10_RNA_TEs.tab

value: Diffuse large B cell lymphoma

value: ZNF587,ZNF417 knockdown


title: NiO_NP_5ug_48H_1

value: 48 Hour

value: 5 ug/mL

value: 11 mouse cell lines


title: U2932_Control_shRNA_D10_RNA_Rep1

description:
U2932_D10_RNA.tab
U2932_D10_RNA_TEs.tab

value: Control

value: Lentiviral transduction


title: Al2O3_NP_50ug_24H_2

value: Al2O3 Nanoparticle

value: 50 ug/mL


title: NiO_NP_50ug_2H_2

value: 2 Hour


title: CTCs from patient 24, week 4

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: Tumor, stable

value: low


title: 2.5 months somatosensory cortex, cKO, rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to UCSC genome mm10 using STAR (parameters: default)
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined by DESeq2.
Assembly: UCSC mm10 genome
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

value: Somatosensory cortex

value: cKO

value: 2.5 months


title: CTCs from patient 24, week 10

description: Gene expression data


title: CRISPR_KMT2A-MLLT3 MPAL, sample3 [RNA-seq]

city: Stanford

first: Feng

last: Pan

address: 265 Campus Drive

department: Pathology

institute: Stanford University School of Medicine

data_processing:
RNA-seq reads were mapped with STAR against the human genome (hg19)
Differential expression analysis and Visualization were carried out with raw counts using RSEM, DESeq2, and iDEP.
Assembly: hg19
Supplementary files format and content: csv files include raw counts for each sample

source_name: CRISPR-engineered

growth_protocol: Gene-edited cells were cultured in vitro (day 0 to day 26) and transplanted (1×106) by IV injection into sub-lethally irradiated (250 cGy) immune-compromised NOD.Cg PrkdcscidIL2rgtm1Wjl/SzJ (NSG) mice.

extract_protocol:
RNA was extracted from control and leukemia cells with RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA-seq libraries were generated and sequenced by Novogene (Sacramento, CA).

treatment_protocol:
N/A
N/A

value: CRISPR-engineered

value: mixed phenotype acute leukemia cells


title: NiO_NP_10ug_48H_3

value: MutaMouse

value: NiO Nanoparticle

value: 48 Hour

value: 10 ug/mL


title: CRISPR_KMT2A-MLLT3 MPAL, sample2 [RNA-seq]


title: 2.5 months somatosensory cortex, cKO, rep2


title: NiO_NP_10ug_2H_1

value: 11 mouse cell lines


title: H1650 cell line, replicate 2

description: Gene expression data

value: Cell line derived from lung tumor

value: Lung cancer cell line

value: cell line control

value: Cell line


title: CRISPR_KMT2A-MLLT3 MPAL, sample1 [RNA-seq]


title: CTCs from patient 24, baseline

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: base


title: 2.5 months somatosensory cortex, cKO, rep1

value: Somatosensory cortex


title: CRISPR_KMT2A-MLLT3 AML, sample3 [RNA-seq]

value: acute myeloid leukemia cells


title: 2.5 months somatosensory cortex, Ctrl, rep3

value: Ctrl

value: 2.5 months


title: NiO_NP_25ug_48H_3

value: 25 ug/mL


title: CRISPR_KMT2A-MLLT3 AML, sample2 [RNA-seq]

value: CRISPR-engineered


title: Somatosensory cortex, cKO, H3K36me2, rep1

value: cKO

tag: chip antibody


title: CTCs from patient 23, week 4

description: Gene expression data

value: Tumor, stable

value: high


title: CRISPR_KMT2A-MLLT3 AML, sample1 [RNA-seq]


title: 2.5 months somatosensory cortex, Ctrl, rep1


title: CRISPR_KMT2A-MLLT3 BCP-ALL, sample2 [RNA-seq]

value: acute lymphoblastic leukemia cells


title: NiO_NP_25ug_2H_2

value: MutaMouse

value: NiO Nanoparticle

value: 2 Hour

value: 11 mouse cell lines


title: CRISPR_KMT2A-MLLT3 BCP-ALL, sample1 [RNA-seq]


title: NiO_NP_5ug_2H_2

value: 5 ug/mL


title: CTCs from patient 23, baseline

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: low


title: CTCs from patient 22, week 4

description: Gene expression data

value: Tumor, progression

value: mid


title: 56740-healthy-CD31

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Alignment of RNAseq reads was performed using STAR v2.7.9a and quantified using RSEM v1.3.3
Murine genome version 39 was used with GENCODE M26 annotation.
FPKM and raw counts of transcripts with the same gene symbol were pooled. Non-protein coding genes, pseudogenes, predicted genes, predicted pseudogenes, and genes with 0 FPKM in all samples were filtered out.
A total of  18,665 genes for mouse were retained and their expression was normalized between samples using the TMM method (edgeR version 3.36.0) and log2 transformed with voom (limma version 3.50.3)
Differential expression was computed using limma. Genes with p.adj value <0.05 and -1>LFC>1 were called significantly differentially expressed in all comparisons.
Assembly: mm10
Supplementary files format and content: tab separated, raw, FPKM and normalized count matrices.

source_name: brain

growth_protocol: We induced experimental metastasis in PDGFRβ-CreERT2; Rosa-tdTomato mice by intracardially injecting brain-homing cancer cells from breast (PyMT-BrM3) and lung (Sv2T3-BrM1) primary origin. To label PDGFRβ expressing cells in this genetic background, mice were treated with 2mg of tamoxifen daily for 5 consecutive days.

extract_protocol:
Mouse endothelial and mural cell populations were sorted into Trizol LS and submitted to the company “GeneWiz from Azenta Life Sciences” for RNA extraction, quality control analysis, library preparation and sequencing. Total RNA was extracted from cells following the Trizol Reagent User Guide and quantified using Qubit 2.0 Fluorometer. Agilent TapeStation 4200  was used to assess RNA integrity. cDNA synthesis and amplification were performed with the SMART-Seq HT Ultra Low Input Kit for Sequencing.
Illumina Nextera XT library preparation kit  was used for sequencing library preparation

treatment_protocol: BrMs and non-tumor samples were processed immediately after resection and single-cell suspensions were subjected to FACS. To isolate the cell populations of interest, we first excluded immune and cancer cells by gating for CD45-CD11B-EPCAM- cells, followed by positive selection with CD31+ and PDGFRβ-tdTom+ markers to isolate endothelial and mural cells respectively.

value: brain

tag: primary origin

value: healthy

tag: condition

value: non-tumor

tag: mouse


title: CTCs from patient 23, week 10

description: Gene expression data


title: NiO_NP_5ug_48H_2

first: Sabina

last: Halappanavar

value: 48 Hour

tag: dose

tag: biological replicate

tag: sample type


title: NiO_NP_50ug_48H_1

value: 50 ug/mL


title: 2.5 months somatosensory cortex, Ctrl, rep2

value: Somatosensory cortex

tag: genotype

value: Ctrl

value: 2.5 months


title: CTCs from patient 22, baseline

description: Gene expression data

value: base


title: 56727-healthy-PDGFRb

value: PDGFRb


title: Patient BCP-ALL, L12 [RNA-seq]

source_name: Primary

tag: cell line

value: Primary

value: acute lymphoblastic leukemia cells

tag: treatment

tag: time


title: 56727-healthy-CD31

tag: cell type


title: Patient BCP-ALL, L04 [RNA-seq]


title: NiO_NP_50ug_24H_1

value: MutaMouse

value: NiO Nanoparticle

value: 24 Hour

value: 11 mouse cell lines


title: NiO_NP_5ug_24H_3

value: 5 ug/mL


title: CTCs from patient 21, week 4

description: Gene expression data

value: Blood

value: CTCs from cancer patients

tag: timepoint

tag: status

value: Tumor, stable

value: low


title: CTCs from patient 21, week 10

description: Gene expression data

tag: ctc count level


title: NiO_NP_10ug_48H_1

tag: strain

tag: time point

value: 48 Hour

value: 10 ug/mL


title: Cas9_control, sample2 [RNA-seq]

value: CRISPR-engineered

value: normal hematopoietic cells

value: WT


title: CTCs from patient 21, baseline

description: Gene expression data

tag: tissue

value: base


title: 56195-56520-lung-PDGFRb

value: brain

tag: primary origin

value: lung

value: PDGFRb

value: BrM


title: SEM, rep2 [RNA-seq]

source_name: SEM

value: SEM

value: acute lymphoblastic leukemia cells


title: NiO_NP_25ug_24H_2

value: MutaMouse

value: NiO Nanoparticle

value: 24 Hour

value: 25 ug/mL

value: 11 mouse cell lines


title: NiO_NP_0ug_24H_3

value: Media Control


title: CTCs from patient 20, week 10

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: Tumor, stable

value: low


title: 56195-56520-lung-CD31

tag: condition


title: CTCs from patient 20, week 4

description: Gene expression data


title: 56740-healthy-PDGFRb-

value: healthy

value: non-tumor

tag: mouse


title: SEM, rep1 [RNA-seq]


title: CTCs from patient 26, week 4

description: Gene expression data


title: MV4-11, rep2 [RNA-seq]


title: 55169-70-lung-PDGFRb

value: brain

value: lung


title: 55169-70-lung-CD31

value: BrM


title: 54957-lung-PDGFRb

value: PDGFRb


title: MV4-11, rep1 [RNA-seq]

value: acute lymphoblastic leukemia cells


title: CTCs from patient 20, baseline

description: Gene expression data

value: base


title: 54957-lung-CD31


title: NiO_NP_0ug_48H_1

value: MutaMouse

value: NiO Nanoparticle

value: 48 Hour

tag: dose


title: Cas9_control, sample1 [RNA-seq]

value: CRISPR-engineered

value: normal hematopoietic cells

value: WT


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day14, sample2 [RNA-seq]


title: 54135-heatlhy-CD31


title: CTCs from patient 18, week 4

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: Tumor, progression


title: 54132-heatlhy-PDGFRb

value: heatlhy


title: NiO_NP_10ug_2H_3

value: 2 Hour

value: 10 ug/mL

tag: biological replicate

value: 11 mouse cell lines


title: CTCs from patient 18, baseline

description: Gene expression data

value: mid


title: CTCs from patient 18, week 10

description: Gene expression data


title: CTCs from patient 19, week 10

description: Gene expression data

value: Tumor, stable

value: high


title: NiO_NP_0ug_2H_2

value: Media Control

tag: sample type


title: NiO_NP_50ug_2H_1

value: MutaMouse

value: 50 ug/mL


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day14, sample1 [RNA-seq]

value: acute lymphoblastic leukemia cells

tag: genotype


title: 54135-healthy-PDGFRb

value: brain

value: non-tumor


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day26, sample2 [RNA-seq]

tag: cell line

value: CRISPR-engineered


title: 54132-healthy-CD31

value: healthy


title: 53680-healthy-PDGFRb

value: PDGFRb


title: NiO_NP_25ug_48H_2

tag: treatment

value: NiO Nanoparticle

value: 48 Hour

value: 25 ug/mL


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day11, sample2 [RNA-seq]

tag: time


title: NiO_NP_5ug_24H_2

value: 24 Hour

value: 5 ug/mL


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day26, sample1 [RNA-seq]

tag: cell type


title: CTCs from patient 16, week 10

description: Gene expression data

value: Blood

value: CTCs from cancer patients

tag: timepoint

value: Tumor, progression


title: 53142-breast-CD31

value: breast

value: BrM


title: NiO_NP_0ug_2H_3

value: MutaMouse

value: 2 Hour

value: Media Control

value: 11 mouse cell lines


title: CTCs from patient 16, week 4

description: Gene expression data

tag: status

value: high


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day11, sample1 [RNA-seq]

value: CRISPR-engineered

value: acute lymphoblastic leukemia cells


title: 53072-breast-PDGFRb

value: brain

value: PDGFRb


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day5, sample2 [RNA-seq]


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day5, sample1 [RNA-seq]


title: NiO_NP_0ug_48H_3

value: NiO Nanoparticle

value: 48 Hour


title: CTCs from patient 17, week 10

description: Gene expression data

value: Tumor, stable

tag: ctc count level

value: low


title: NiO_NP_5ug_2H_3

tag: strain

value: 5 ug/mL


title: NiO_NP_5ug_2H_1

tag: time point


title: 53072-breast-CD31

tag: tissue


title: CTCs from patient 17, baseline

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: base

value: mid


title: CTCs from patient 17, week 4

description: Gene expression data


title: NiO_NP_25ug_2H_1

value: MutaMouse

value: 2 Hour

value: 25 ug/mL


title: CTCs from patient 16, baseline

description: Gene expression data

value: Tumor, progression


title: NiO_NP_50ug_2H_3

value: 50 ug/mL

value: 11 mouse cell lines


title: CTCs from patient 15, week 4

description: Gene expression data


title: NiO_NP_50ug_48H_3


title: CTCs from patient 15, baseline

description: Gene expression data


title: 53680-healthy-CD31

value: brain

tag: primary origin

value: healthy

value: non-tumor


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day0, sample2 [RNA-seq]

value: CRISPR-engineered

value: acute lymphoblastic leukemia cells


title: 52865-breast-PDGFRb

value: breast

value: PDGFRb

tag: condition

value: BrM


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day0, sample3 [RNA-seq]


title: CTCs from patient 14, week 10

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: Tumor, stable

value: high


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day0, sample1 [RNA-seq]


title: NiO_NP_10ug_24H_2

value: MutaMouse

value: NiO Nanoparticle

value: 24 Hour

value: 10 ug/mL


title: CTCs from patient 13, week 10

description: Gene expression data


title: 52865-breast-CD31

tag: mouse


title: CRISPR_KMT2A-MLLT3 MPAL, sample3

description:
atac.a9_10.srt.bw
atac.a9_mpal.narrowpeak

data_processing:
Adapter sequences were trimmed and reads were mapped to Hg19 using Bowtie2.
ATAC-seq peak calling was performed with Genrich (https://github.com/jsh58/Genrich) with default setting.
Bigwig files were generated by deeptools
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Control and tumor cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630). Nuclei were centrifuged at 500 × g for 10 min, 4°C. Nuclei extract were then incubated with Nextera Tn5 Transposase, 2× TD buffer, and nuclease free water at 37°C for 30 min with gentle mixing.
After DNA purification with the MinElute PCR Purification Kit (Qiagen), PCR was performed to amplify the library for additional cycles distinctively according to a quantitative PCR reaction for optimum cycles. The final libraries were sequenced by Novogene.

value: mixed phenotype acute leukemia cells

tag: chip antibody


title: NiO_NP_0ug_24H_1

tag: dose

value: Media Control

tag: biological replicate

value: 11 mouse cell lines


title: CRISPR_KMT2A-MLLT3 MPAL, sample2

description:
atac.a9_9.srt.bw
atac.a9_mpal.narrowpeak


title: CRISPR_KMT2A-MLLT3 MPAL, sample1

description:
atac.a9_8.srt.bw
atac.a9_mpal.narrowpeak


title: 52599-breast-CD31

value: brain


title: ZnO_NP_1ug_48H_3

value: ZnO Nanoparticle

value: 48 Hour

value: 1 ug/mL

tag: sample type


title: CTCs from patient 13, baseline

description: Gene expression data

value: base

value: mid


title: CRISPR_KMT2A-MLLT3 AML, sample3

description:
atac.a9_7.srt.bw
atac.a9_aml.narrowpeak

tag: cell line

value: CRISPR-engineered

value: acute myeloid leukemia cells


title: 51950-breast-PDGFRb

value: breast

value: PDGFRb

value: BrM


title: 51950-breast-CD31


title: CTCs from patient 12, baseline

description: Gene expression data

value: Blood

value: CTCs from cancer patients

value: Tumor, progression


title: CRISPR_KMT2A-MLLT3 AML, sample2

description:
atac.a9_6.srt.bw
atac.a9_aml.narrowpeak


title: ZnO_NP_5ug_48H_3

value: MutaMouse

tag: treatment

value: 5 ug/mL


title: CTCs from patient 12, week 4

description: Gene expression data


title: CRISPR_KMT2A-MLLT3 AML, sample1

description:
atac.a9_3.srt.bw
atac.a9_aml.narrowpeak


title: ZnO_NP_0.5ug_48H_3

value: 0.5 ug/mL

value: 11 mouse cell lines


title: 51697-lung-CD31

value: brain

value: lung


title: ZnO_NP_0ug_48H_3

value: ZnO Nanoparticle

value: 48 Hour

value: Media Control


title: CTCs from patient 11, week 4

description: Gene expression data

value: Tumor, stable

value: low


title: 51435-lung-PDGFRb


title: NiO_NP_50ug_24H_3

value: NiO Nanoparticle

value: 24 Hour

value: 50 ug/mL


title: 52599-breast-PDGFRb

value: breast

value: PDGFRb

value: BrM


title: CRISPR_KMT2A-MLLT3 BCP-ALL, sample2

description:
atac.a9_2.srt.bw
atac.a9_all.narrowpeak

value: CRISPR-engineered

value: acute lymphoblastic leukemia cells


title: CTCs from patient 11, week 10

description: Gene expression data

value: Blood

value: CTCs from cancer patients


title: CTCs from patient 11, baseline

description: Gene expression data

value: base

value: high


title: ZnO_NP_0ug_24H_2

value: MutaMouse

value: ZnO Nanoparticle

value: 11 mouse cell lines


title: ZnO_NP_5ug_2H_3

value: 2 Hour

value: 5 ug/mL


title: CRISPR_KMT2A-MLLT3 BCP-ALL, sample1

description:
atac.a9_1.srt.bw
atac.a9_all.narrowpeak


title: CTCs from patient 10, baseline

description: Gene expression data

value: Tumor, stable


title: Patient BCP-ALL, L12

description:
atac.a4_pt.srt.bw
atac.a4_pt.narrowpeak

value: Primary


title: RNA-seq_EBF1_YmA_rep1

city: Freiburg

first: Nikolay

last: Zolotarev

address: Stübeweg, 51

department: Cellular and Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Quality control and read mapping was done using snakePipes, an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using STAR.
Reads were sorted and indexed using samtools and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools with RPKM normalization.
The expression level of the annotated genes (GRCm38.p4) was calculated by featureCounts (subread v2.0.0).
The differential gene expression was analyzed using the DESeq2 package. Genes with a padj < 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: The count matrix obtained from featureCounts is provided in tab-delimited format (.tsv).
Supplementary files format and content: One bigwig files (.bw) is provided for each sample.
Supplementary files format and content: One table (.csv) with combined DESeq2 results for dC_vs_wt and YmA_vs_wt.

source_name: pro-B cells

growth_protocol: Ebf1-/- fetal liver cells were transduced with EBF1 wt, dC, or YmA. Cells were incubated for 8 days, 50000 CD19+ cells were FACS sorted.

extract_protocol:
Cells were sorted in 70 μl RLT buffer (Qiagen RNeasy Kit). RNA was extracted using Qiagen RNeasy Kit according to the manual. Lysis buffer was added to each sample up to 350 μl and vortexed for 30 sec.
Libraries were prepared using NEBNext Low Input RNA Library Preparation (NEB) according to the manufacturer's protocol.

value: pro-B cells

tag: genotype

value: EBF1 YmA


title: ZnO_NP_0ug_24H_3

city: Ottawa

institute: Health Canada

value: 24 Hour

value: Media Control


title: CTCs from patient 9, week 4

description: Gene expression data

tag: cell type

value: mid


title: RNA-seq_EBF1_dC_rep2

value: EBF1 dC


title: CTCs from patient 10, week 10

description: Gene expression data

value: Blood

tag: timepoint


title: Cas9_control, sample2

description:
atac.a4_cas9.srt.bw
atac.a4_cas9.narrowpeak

value: CRISPR-engineered

value: normal hematopoietic cells


title: RNA-seq_EBF1_dC_rep1


title: Patient BCP-ALL, L04

description:
atac.a4_pt.srt.bw
atac.a4_pt.narrowpeak

value: acute lymphoblastic leukemia cells


title: RNA-seq_EBF1_wt_rep2

value: EBF1 wt


title: ZnO_NP_0.5ug_24H_3

value: MutaMouse

value: ZnO Nanoparticle

value: 0.5 ug/mL


title: SEM, rep1

description:
atac.a4_sem.srt.bw
atac.a4_sem.narrowpeak

value: SEM


title: CTCs from patient 9, week 10

description: Gene expression data

value: CTCs from cancer patients

tag: status

value: Tumor, stable

value: low


title: RNA-seq_EBF1_YmA_rep2

value: pro-B cells

value: EBF1 YmA


title: RNA-seq_EBF1_wt_rep1


title: ZnO_NP_1ug_24H_3

value: 24 Hour

value: 1 ug/mL

value: 11 mouse cell lines


title: CTCs from patient 9, baseline

description: Gene expression data

value: Blood

value: base

tag: ctc count level

value: high


title: SEM, rep2

value: acute lymphoblastic leukemia cells


title: MV4-11, rep2

description:
atac.a4_mv411.srt.bw
atac.a4_mv411.narrowpeak


title: ZnO_NP_1ug_2H_3

tag: strain

value: 2 Hour


title: CTCs from patient 8, week 10

description: Gene expression data

value: Tumor, progression

value: mid


title: ZnO_NP_5ug_24H_3

value: MutaMouse

value: ZnO Nanoparticle

tag: time point

value: 5 ug/mL


title: CTCs from patient 7, week 10

description: Gene expression data

tag: tissue

value: CTCs from cancer patients

value: Tumor, stable


title: YmA_a-Brg1

data_processing:
Quality control and read mapping was done using snakePipes, an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2.
Reads were sorted and indexed using samtools and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools.
We used EBF1 peaks annotation for CTD-dependent and CTD-independent groups from Boller et al. 2016. CTD-dependent peaks were subdivided into YmA-dependent and YmA-independent groups. Peaks were defined as YmA-dependent if they have more than 2-fold higher normalized read count in the wt sample in comparison with YmA.
Assembly: mm10
Supplementary files format and content: One .bed file with EBF1 peaks from Boller et al. 2016 with 3 groups of peaks - YmA-dependent, YmA-independent, and CTD-independent. This file can be used for deeptools visualization.
Supplementary files format and content: One bigwig file (.bw) for each ChIP sample.

growth_protocol: Ebf1-/- fetal liver cells were transduced with EBF1 wt or YmA.

extract_protocol:
EBF1 ChIP was performed according to Boller et al. 2016 protocol with minor changes. Cells were crosslinked with formaldehyde. 4 µg rabbit a-EBF1 (1C) rabbit antibody per sample was used. Cells were harvested and washed with PBS. Cell pellet was resuspended in PBS with 2% FCS (4 mln cells per 1 ml buffer). Fresh formaldehyde mix (50mM HEPES-KOH pH8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 11% (v/v) formaldehyde) was added to the cell suspension to a final concentration of 1% FA. Tubes were incubated on rotator for 10 min at RT. Quenching was performed by adding 2 M Glycine to the final concentration 0.2 M. Cell pellet was resuspended in Lysis buffer (50mM Tris-HCl pH 8.0, 1% (w/v) SDS, 10mM EDTA; PIM) (4 mln cells per 100 μl buffer). Chromatin was sheared the chromatin with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). Fragment size and amount of chromatin was checked. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was mixed with 4 μg of EBF1 antibody or rabbit IgG and incubated on rotator ON at 4°C. Chromatin was incubated with 30 μl of Dynabeads Protein G (ThermoFisherScientific) suspension per sample on rotator for 4 hours at 4°C. Beads were washed 4 times with Wash buffer A (20mM Tris-HCl pH 8.0, 150mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2mM EDTA); once with Final wash buffer A (20mM Tris-HCl pH 8.0, 500mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2mM EDTA). Every wash was on rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were revese crosslinked, treated with RNase A and Proteinase K, and purified with QIAquick PCR Purification Kit.
Brg1 ChIP was performed according to the protocol of Bossen et al., 2015 with the following changes.  Cells were harvested and washed with PBS. The cell pellet was resuspended in 10-20 ml PBS. 150 mM EGS (Sigma-Aldrich) stock solution in DMSO was added 1:100 to the cell suspension. Tubes were incubated on a rotator for 15 min at RT. 37% formaldehyde stock solution was added to the final concentration of 1%. Tubes were incubated on a rotator for 15 min at RT. Quenching was performed by adding 2M Glycine to the final concentration 0.2 M.  The cell pellet was resuspended in 4 ml buffer Lysis buffer 1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; PIM) and incubated on ice for 10 minutes. The cell pellet was resuspended Lysis buffer 3 (10mM Tris-HCl, pH 8.0; 200 mM NaCl; 1 mM EDTA, pH 8.0; 0.5 mM EGTA, pH 8.0; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; PIM) about 1.5-3 x 106 cells per 100 μl buffer.  Chromatin was sheared with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). A small aliquot of chromatin was decrosslinked to check the fragment size on the agarose gel. 30 μl of Dynabeads Protein G (Thermo Fisher) suspension per sample was coupled with 0.5 μg of Brg1 (Abcam, ab110641), or with 2 μg FLAG (M2, Sigma-Aldrich, F1804) antibody, or IgG in 200 μl of PBS with 0.5% BSA. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was added to beads and incubated on rotator ON at 4°C. Beads were washed with Wash buffer I (50 mM Tris-HCl, pH 8.0; 150 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1 % Triton X-100; 1 mM EDTA pH 8.0); Wash buffer II (50 mM Tris-HCl, pH 8.0; 500 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1% Triton X-100; 1 mM EDTA pH 8.0); Wash buffer III (10 mM Tris-HCl, pH 8.0; 250 mM LiCl; 0.5 % NP-40; 0.5 % NaDOC; 1 mM EDTA pH 8.0) and TE buffer. Every wash was on the rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were reverse-crosslinked, treated with 100 μg/ml RNase A and 100 μg/ml Proteinase K, and purified with QIAquick PCR Purification Kit.
NEBNext Ultra II DNA Library Prep Kit for Illumina was used for library preparation according to the manufacturer's protocol.

value: pro-B cells


title: ZnO_NP_0ug_2H_3

value: Media Control


title: MV4-11, rep1


title: ZnO_NP_0.5ug_2H_3

value: 0.5 ug/mL


title: ZnO_NP_0.5ug_48H_2

value: 48 Hour


title: Cas9_control, sample1

value: CRISPR-engineered

value: normal hematopoietic cells


title: YmA_a-EBF1

value: EBF1 YmA


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day26, sample2

description:
atac.a4_d26.srt.bw
atac.a4_CrisprBCP-ALL.narrowpeak


title: CTCs from patient 8, baseline

description: Gene expression data

value: Blood

value: base

value: high


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day26, sample1

value: acute lymphoblastic leukemia cells


title: wt_a-EBF1

value: EBF1 wt


title: input_a-EBF1

value: none (input)


title: CTCs from patient 6, week 10

description: Gene expression data

value: Tumor, progression

value: low


title: EBF1_YmA_rep2

data_processing:
Quality control and read mapping was done using snakePipes, an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2.
Reads were sorted and indexed using samtools and duplicates were removed by sambamba_markdup.
Peak calling was performed using MACS2.
Coverage bigwig files were created using bamCoverage from deeptools.
Assembly: mm10
Supplementary files format and content: One .narrowPeak file containing the MACS2 output for each ATAC sample.
Supplementary files format and content: One bigwig file (.bw) for each sample.

extract_protocol:
Cell pellets were resuspended in 50 ul Tagmentation Mix (10 mM HEPES pH 7.0; 25 mM NaCl; 5 mM MgCl2; 0.01% Digitonin; 0.1% Tween-20; 300 ng loaded Tagmentase) and incubated in the thermoshaker for 30 min, 700 rpm, 37°C. DNA was purified using Zymo DNA Clean and Concentration Kit.
Libraries were amplified using Nextera XT Index Kit v2, 15-17 cycles.


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day14, sample1

description:
atac.a4_d14.srt.bw
atac.a4_CrisprBCP-ALL.narrowpeak


title: input_a-Brg1


title: EBF1_YmA_rep1


title: ZnO_NP_1ug_24H_2

value: MutaMouse

value: ZnO Nanoparticle

value: 24 Hour

value: 1 ug/mL

value: 11 mouse cell lines


title: ZnO_NP_0ug_48H_2

value: 48 Hour

value: Media Control


title: CTCs from patient 5, week 10

description: Gene expression data

value: CTCs from cancer patients

value: Tumor, stable


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day11, sample2

description:
atac.a4_d11.srt.bw
atac.a4_CrisprBCP-ALL.narrowpeak

value: CRISPR-engineered


title: ZnO_NP_0.5ug_24H_2

value: 0.5 ug/mL


title: CTCs from patient 7, baseline

description: Gene expression data

value: Blood

value: base

value: high


title: ZnO_NP_1ug_48H_2


title: ZnO_NP_5ug_48H_2

value: 5 ug/mL


title: EBF1_dC_rep2

value: pro-B cells

value: EBF1 dC


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day14, sample2

value: acute lymphoblastic leukemia cells


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day11, sample1


title: ZnO_NP_5ug_24H_2

value: MutaMouse

value: ZnO Nanoparticle


title: CTCs from patient 5, baseline

description: Gene expression data


title: CTCs from patient 4, week 10

description: Gene expression data


title: CTCs from patient 3, week 10

description: Gene expression data

value: Tumor, progression

value: mid


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day5, sample2

description:
atac.a4_d5.srt.bw
atac.a4_CrisprBCP-ALL.narrowpeak


title: ZnO_NP_0ug_48H_1

value: 48 Hour

value: 11 mouse cell lines


title: CTCs from patient 3, baseline

description: Gene expression data

value: CTCs from cancer patients


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day5, sample1


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day0, sample3

description:
atac.a4_d0.srt.bw
atac.a4_CrisprBCP-ALL.narrowpeak


title: PGC-ESC DKO 3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Raw RNA-Seq reads were aligned against UCSC mm10 and transcript annotations using STAR (2.7.7a; Dobin et al., 2012) with parameter ‘--quantMode GeneCounts’.
Assembly: UCSC mm10
Supplementary files format and content: csv file includes gene count for each Sample

source_name: PGC-ESC

growth_protocol: For routine embryonic stem cell (ESC) culture, cells were maintained on gelatin coated plates (0.2%, G1393, Merk) in 2i/LIF medium. 2i/LIF medium contains 10mg/ml of mouse leukaemia inhibitor factor (LIF) (ESG1107, Merk), 3 mM of GSK3 inhibitor CHIR99021 (SM13-10, Cambridge Bioscience) and 1 mM of MEK inhibitor PD0325901 (72182, Stem Cell Technologies) in N2B27 medium (Mulas et al., 2019). Cells were expanded by single cell dissociation with accutase (SF006, Millipore), 5% BSA quenching and replated every 2 days.

extract_protocol:
Genewiz
Genewiz-Illumina by RNA Poly(A) selection

value: PGC-ESC

value: Puma Noxa DKO


title: CTCs from patient 2, week 10

description: Gene expression data

value: Tumor, stable

value: low


title: ZnO_NP_1ug_48H_1

address: 251 Sir Frederick Banting Driveway

value: 1 ug/mL


title: PGC-ESC DKO 2


title: PGC-ESC DKO 1


title: ZnO_NP_1ug_2H_2

value: 2 Hour


title: Merged_HSC_Y2

first: Xiaoyu

last: Li

data_processing:
Trim_galore (version0.6.6 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the reads length is 25~60nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end.
Processed reads were mapped to mm10 tRNA(http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/mm10-tRNAs.fa) and rRNA.
Count the tRF numbers and submitted to DEseq2 to different expression analysis.
Genome_build: mm10 smallRNA

source_name: Hematopoietic stem cells

extract_protocol:
200 ng small RNA fraction (<200 nt; mainly composed of mature tRNA) was purified from total RNA using MEGAclear Kit (Thermo).
Purified small RNA was deacylated by incubating in 0.1 M Tris-HCl, pH 9 at 37°C for 45 min. Half of the deacylated small RNA fraction was subjected to demethylation treatment by using AlkB in vivo reaction. RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples. 5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel.

value: KSL

tag: age

value: Young(8 weeks)

value: untreated


title: ESC Host 4

source_name: ESC

value: ESC

value: Wildtype


title: Merged_HSC_Y1


title: CTCs from patient 2, baseline

description: Gene expression data

value: Blood

value: base

value: high


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day0, sample1

value: CRISPR-engineered

value: acute lymphoblastic leukemia cells


title: SF529_4

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

description: single-nucleus ATAC-seq, 10x genomics

library_source: genomic single cell

data_processing:
Samples were processed individually using CellRanger ATAC v1.2.0 and aligned to the hg38 reference genome. Files were generated using CellRanger ATAC count.
Spatially delineated samples from the same patient were processed and merged in Signac v1.6.0, thresholded by features present in 10+ cells, peak_region_fragments > 3000, pct_reads_in_peaks > 15, blacklist_ratio < 0.05 and lowmapq < 30000.  and normalized by the mean signal from a randomly selected subpopulation of 5000 peaks.
Data was processed using TF-IDF and LSI in Signac, followed by UMAP construction on components  2:30 with the following parameters: n.neighbours=71L, min.dist=0.4, spread=1.5, repulsion.strength=1.1 followed by Louvain nearest neighbour clustering.
Copy-scAT was used to call copy number alterations and putative ecDNAs, followed by cluster-based averaging. ChromVAR and GeneActivity matrices were generated using Signac and the JASPAR 2021 and Ensembl v86 references respectively.
Assembly: hg38
Supplementary files format and content: Sample-level raw h5 matrix, singlecell.csv metadata file
Supplementary files format and content: Patient-level processed GeneActivity and ChromVAR Matrix (.rdata format), and filtered patient-level metadata file (.tsv)

source_name: multiregional profiling, primary glioblastoma tumour

extract_protocol:
Samples were obtained either as previously cryopreserved extracted nuclei (P519, P521) or as individually snap-frozen tissue fragments (P524, P529). Frozen tissue samples were processed using an iodixanol gradient centrifugation method adapted from Corces et al, with dounce homogenization and centrifugation. Extracted nuclei were washed 1x in 10X wash buffer and resuspended in 100 uL of 0.1X 10X lysis buffer for 2 minutes, followed by a second wash and resuspension into 10X nuclear buffer.
Libraries were constructed as per the 10X protocol usin the Chromium NextGEM Single Cell ATAC Kit v2 (10X genomics), targeting the maximum number of nuclei up to a ceiling of 8000 nuclei. Sequencing was performed on an Illumina NovaSeq 6000 at the Center for Health Genomics and Informatics with paired-end reads with a 2x100 configuration to a targeted depth of 50,000 reads per cell.

value: brain (tumour)

value: glioblastoma


title: EBF1_dC_rep1

value: pro-B cells

value: EBF1 dC


title: EBF1_wt_rep2

value: EBF1 wt


title: CTCs from patient 1, week 10

description: Gene expression data

data_processing: Standard microarray data processing procedures were followed in R programming environment (4.0.2). Briefly, raw intensities were imported as CEL files using the oligo package. The intensities were then normalized and summarized into gene-wise expression values using a robust multichip average (RMA) method. Quality control plots, including normalized unscaled standard error (NUSE), relative log expression (RLE) as well as principle component analysis (PCA) were generated to discover outliers in the dataset. The probesets were then annotated using clariomshumanhttranscriptcluster.db package. If multiple probes were mapped to the same gene, the one with highest average expression across all samples was selected. Differentially expressed genes were then calculated between different conditions using the limma package.

value: CTCs from cancer patients

value: Tumor, progression


title: ZnO_NP_5ug_2H_2

value: MutaMouse

value: ZnO Nanoparticle

value: 2 Hour

value: 5 ug/mL

value: 11 mouse cell lines


title: Merged_HSC_O1

city: Hangzhou

institute: Zhejiang University

value: KSL

value: Old(24 months)

value: untreated


title: SF529_8

description: single-nucleus ATAC-seq, 10x genomics


title: ZnO_NP_0.5ug_2H_2

value: 0.5 ug/mL


title: ZnO_NP_0ug_2H_2

value: Media Control


title: ZnO_NP_5ug_48H_1

value: 48 Hour


title: CTCs from patient 1, baseline

description: Gene expression data

value: Blood

value: base

value: high


title: ZnO_NP_0.5ug_48H_1


title: CRISPR_KMT2A-AFF1 BCP-ALL, Day0, sample2

value: CRISPR-engineered

value: acute lymphoblastic leukemia cells


title: Merged_A_HSC_Y2

value: Young(3 months)

value: AlkB treatment


title: ESC BaxKO 2

value: ESC

value: BaxKO


title: SF529_10

description: single-nucleus ATAC-seq, 10x genomics

value: brain (tumour)

value: glioblastoma


title: ZnO_NP_5ug_2H_1

value: MutaMouse

value: ZnO Nanoparticle

value: 2 Hour

value: 5 ug/mL

value: 11 mouse cell lines


title: CTCs from patient 6, baseline

description: Gene expression data

value: CTCs from cancer patients

value: Tumor, progression


title: Merged_HSC_O2

value: KSL

value: Old(24 months)

value: untreated


title: ZnO_NP_5ug_24H_1

value: 24 Hour


title: EpiLC PGC-ESC DKO 3

source_name: EpiLC

value: EpiLC

value: Puma Noxa DKO


title: SF524

description: single-nucleus ATAC-seq, 10x genomics


title: Merged_A_HSC_Y1

value: Young(3 months)

value: AlkB treatment


title: ESC Host 3

value: ESC

value: Wildtype


title: EpiLC PGC-ESC DKO 2


title: Merged_A_HSC_O2


title: EpiLC PGC-ESC DKO 1


title: ZnO_NP_0.5ug_24H_1

value: MutaMouse

value: 0.5 ug/mL


title: Merged_A_HSC_O1


title: SF521_7

description: single-nucleus ATAC-seq, 10x genomics

value: brain (tumour)

value: glioblastoma


title: SF521_3

description: single-nucleus ATAC-seq, 10x genomics


title: EpiLC Host 4


title: AMY_MDMA_6

city: New York

first: Jennifer

last: Warner-Schmidt

state: NY

address: 220 5th Ave 17th Floor

institute: Transcend Therapeutics

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Assembly: rnor_6.0
Supplementary files format and content: TXT format; Tab-delimited text files include counts.
Supplementary files format and content: CSV format; Data output from DESeq2 on all genes for each sample in the analysis including: ID, log2foldchange, pvalue, padj, gene name and normalized counts for each sample.

organism: Rattus norvegicus

source_name: brain (amygdala)

extract_protocol:
Total RNA was extracted from fresh frozen brain samples (amygdala or frontal cortex) using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 5 lanes of a flowcell.

value: brain (amygdala)

value: MDMA


title: EpiLC Host 3


title: AMY_MDMA_5


title: SF521_2

description: single-nucleus ATAC-seq, 10x genomics


title: ZnO_NP_0.5ug_2H_1

value: ZnO Nanoparticle

value: 2 Hour

value: 11 mouse cell lines


title: PGC-ESC BaxKO 5

value: PGC-ESC

value: BaxKO


title: AMY_MDMA_4


title: ZnO_NP_1ug_24H_1

value: 24 Hour

value: 1 ug/mL


title: PGC-ESC BaxKO 4