title: circ-seq_ THP-1 cells infected by H37Ra_rep3

first: Yifan

last: Zhu

address: Huazhong Agricultural University, Wuhan, China

institute: HZAU

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: GRCh37 hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: The culture of M. tb and infected cells was performed in an animal biosafety level-3 facility at Huazhong Agricultural University. The M.tb 1458 and H37Ra strain (clinic strain isolated from cattle) (GenBank accession no. GCA_001855255.1) was grown in Middlebrook 7H9 broth supplemented with 10% oleic acid-albumin-dextrose-catalase (OADC) (BD PharMingen, USA) and 0.05% Tween-80 (Sigma, USA) at 37°C.       THP-1 human monocytic cell line (ATCC® TIB-202TM) was maintained in RPMI-1640 medium (HyClone, Logan, UT, USA) with 10% FBS (FBS, Gibco, Grand Island, NY, USA) at 37°C with 5% CO2. Before infection, THP-1 cells were stimulated with 40 ng/mL phorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich, St. Louis, MO, USA) for 12 h.

extract_protocol:
RNA was harvested using Magen Hipure Total RNA Mini Kit, 2ug of total RNA was used for the construction of sequencing libraries.
RNA  libraries for circRNA-seq were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR).

treatment_protocol: PMA differentiated THP-1 cells were infected with M.tb 1458 or H37Ra at an MOI of 10 , and then incubated for 12 h (defined as -12 h), followed by thoroughly washing with fresh medium with 10% FBS and 100μg/mL gentamycin. This time point was set as a starting point (0 h). Then continued culturing cells in complete me-dium with 100μg/mL Gentamicin for 12 h and collected the cells for fur-ther analysis.

value: macrophages

value: infected by M.tb. H37Ra


title: NGP cells, STM, 3D, 3h, rep2

status: Public on Apr 10 2024

type: SRA

city: Chicago

first: Susan

middle: L

last: Cohn

state: IL

address: 5721 S. Maryland Ave.

department: Pediatrics

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
Raw read quality for all sequencing data was assessed with fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to trim leading and trailing bases below quality 3 and remove reads less than 36 base pairs in length
Reads were aligned to GRCh38 using Hisat2 (version 2.1.0).
Reads were counted across exons (-exon flag) using featureCounts of subread (version 1.5.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: NGP

growth_protocol: Kelly and NGP cells were grown at 5% CO2 in RPMI1640 (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was harvested from cells using the TRIzol reagent (Invitrogen). Poly(A) RNA was extracted using the Dynabeads mRNA DIRECT Purification kit following the manufacturer's protocol.
RNA was purified by RNA Clean & Concentrator Kits (Zymo Research) and cDNA libraries were constructed using the SMART® cDNA Library Construction Kit (Takara) following the manufacturer’s instructions.

treatment_protocol: Kelly and NGP cells were treated with either 8 uM STM2457 or DMSO for 3 or 6 days. Kelly and NGP cells were then treated with Actinomycin D (Sigma A1410) at a concentration of 10 μg/ml for 0, 3, or 6 hours. Total RNA was then extracted as below.

tag: cell line

value: NGP

tag: cell type

value: neuroblastoma cell line, MYCN-amplified

tag: genotype

value: WT

tag: treatment

tag: time

value: 3h actinomycin D


title: Clone5_Plus [ATAC-seq]

city: Boston

first: David

middle: T

last: Scadden

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

description: ATAC-Seqdata in ER-Hoxb8 cells

library_source: genomic

data_processing:
Illumina software used for basecalling.
Raw sequences of ATAC-seq data were mapped with a Bowtie2 mapper with a default setting to the mouse genome (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: peaks

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Bone Marrow ER-Hoxb8 GMP cells

growth_protocol: ER-HoxB8 cells were maintained in RPMI medium supplemented with 10% FBS, penicillin/streptomycin, and SCF.

extract_protocol: ATAC-seq samples were performed as previously described (Buenrostro et al., 2015)

value: ER-Hoxb8 cells


title: osino80_H2AZ_rep1, ChIP-seq

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

country: China

institute: Fudan University

description:
Oryza sativa Nipponbare
osino80_H2AZ_rep1

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the nuclear genome were preserved and SAMtools was used to obtain high quality alignments.
After deduplication, SICER was used to call peaks by comparing the IP and the input.
Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: bigWig

organism: Oryza sativa Japonica Group

source_name: 14-day-old seedlings

growth_protocol: Rice were grown in artificial growth chambers under an SD photoperiod for 14 days.

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: tissue

value: 14-day-old seedlings

tag: cultivar

value: Nipponbare

value: no treatment

tag: antibody


title: circ-seq_ THP-1 cells infected by H37Ra_rep2

city: Wuhan


title: NGP cells, DMSO, 3D, 6h, rep1

value: DMSO

value: 6h actinomycin D


title: NGP cells, DMSO, 3D, 6h, rep2


title: circ-seq_ THP-1 cells infected by H37Ra_rep1


title: NGP cells, DMSO, 3D, 3h, rep2


title: osino80_H2Aub_rep1, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H2Aub_rep1


title: osino80_H3K27me3_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H3K27me3_rep2


title: GCs,ob,control, rep1

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
Base calling software.  Quality of raw reads was evaluated by means of FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
After adapter and quality trimming using Trim Galore (v0.6.2), RNA-seq data was mapped to mouse genome GRCm38 using HISAT2 v2.1.0.
Assembly: GRCm38
Supplementary files format and content: Raw counts per gene were calculated in R using the org.Mmu.eg.db package.

molecule: polyA RNA

source_name: Ovaries

extract_protocol:
RNA was harvested using G&T protocol - beads for poly A tail pooled down the RNA, followed by reverse transcription and amplification
All libraries were prepared from 100-200 pg of cDNA using the Nextera XT Kit (Illumina) following manufacturer's protocol.

value: Ovaries

value: Granulosa cells (GCs)

tag: developmental stage

value: GCs from Antral follicle

value: ob/ob +/+

tag: state

value: Wild type


title: NGP cells, STM, 3D, 0h, rep2

value: 0h actinomycin D


title: circ-seq_ THP-1 cells infected by M.tb 1458_rep3

value: macrophages

value: infected by M.tb 1458


title: osino80_H2A, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H2A


title: NGP cells, STM, 3D, 0h, rep1

value: NGP

value: neuroblastoma cell line, MYCN-amplified


title: NGP cells, DMSO, 3D, 0h, rep2

value: WT


title: NGP cells, DMSO, 3D, 3h, rep1

value: 3h actinomycin D


title: WT_rep4, BS-seq

description:
Oryza sativa Nipponbare
WT_BS_rep4
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)

data_processing:
Cutadapt was used to trim paired-end reads to obtain high-quality reads (q ≥ 20) with no adapter.
Bismark was used to map filtered reads to the rice reference genome (MSU7) and to obtain DNA methylation regions (DMRs) from filtered mapping results.
The DNA methylation levels were extracted and visualized by using ViewBS.
Assembly: MSU7
Supplementary files format and content: Bismark coverage files containing DNA methylation calls.

extract_protocol:
14-day-old rice seedlings were harvested and total genomic DNA was extracted using the DNeasy plant maxi kit (QIAGEN).
Sodium bisulfite treatment, library construction, and sequencing were performed via the custom service of GENERGY BIO (Shanghai, China).

value: 14-day-old seedlings

value: wild-type


title: WT_rep3, BS-seq

description:
Oryza sativa Nipponbare
WT_BS_rep3
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)

value: Nipponbare

value: no treatment


title: circ-seq_ THP-1 cells-control_rep3

value: control


title: circ-seq_ THP-1 cells infected by M.tb 1458_rep1


title: osino80_H2Aub_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
osino80_H2Aub_rep2


title: circ-seq_ THP-1 cells-control_rep2


title: WT_rep2, BS-seq

description:
Oryza sativa Nipponbare
WT_BS_rep2
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)


title: Kelly cells, DMSO, 6D, 6h, rep2

source_name: Kelly

value: Kelly

value: DMSO

value: 6h actinomycin D


title: Kelly cells, DMSO, 6D, 6h, rep1


title: WT_rep1, BS-seq

description:
Oryza sativa Nipponbare
WT_BS_rep1
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)


title: NGP cells, STM, 3D, 3h, rep1


title: Kelly cells, STM, 6D, 6h, rep1


title: Kelly cells, STM, 6D,  3h, rep1


title: osino80_rep4, BS-seq

description:
Oryza sativa Nipponbare
osino80_BS_rep4
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)


title: Kelly cells, DMSO, 6D,  3h, rep2


title: shHMGB1_2

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13).
The short reads less than 16 nt were also dropped. After that, clean reads were aligned to the GRCh38 genome by Tophat2 allowing 4 mismatches. Uniquely mapped reads were used to calculate reads number and FPKM value (fragments per kilobase of transcript per million fragments mapped) for each gene.
The DESeq2 was utilized to screen out the differentially expressed genes (DEGs). A false discovery rate <0.05 and fold change>1.5 or < 2/3 were set as the cut-off criteria for identifying DEGs.
To predict the gene function and calculate the functional category distribution frequency, Gene Ontology (GO) analyses and enriched KEGG pathway were identified using KOBAS 2.0 server. Hypergeometric test and Benjamin-Hochberg FDR controlling procedure were used to define the enrichment of each pathway (corrected p-value<0.05).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa cells

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (Bio-Rad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and a tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bp were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified, and stored at -80℃ before sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 NT paired-end sequencing.

value: HeLa cells

value: transfected with HMGB1 shRNA


title: Kelly cells, STM, 6D, 0h, rep2

value: 0h actinomycin D


title: circ-seq_ THP-1 cells infected by M.tb 1458_rep2

value: macrophages


title: circ-seq_ THP-1 cells-control_rep1


title: shHMGB1_1


title: Kelly cells, DMSO, 6D, 0h, rep2


title: osino80_rep3, BS-seq

description:
Oryza sativa Nipponbare
osino80_BS_rep3
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)


title: GCs,ob,control, rep3

value: Ovaries

value: Granulosa cells (GCs)

value: GCs from Antral follicle

value: ob/ob +/+

value: Wild type


title: NGP cells, DMSO, 3D, 0h, rep1

value: NGP

value: neuroblastoma cell line, MYCN-amplified

value: WT


title: osino80_rep2, BS-seq

description:
Oryza sativa Nipponbare
osino80_BS_rep2
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)

value: 14-day-old seedlings

value: Nipponbare

value: no treatment


title: Kelly cells, STM, 6D, 6h, rep2

value: Kelly


title: Kelly cells, STM, 6D, 3h, rep2

value: 3h actinomycin D


title: Kelly cells, DMSO, 6D, 0h, rep1

value: DMSO


title: Kelly cells, STM, 3D, 6h, rep2

value: 6h actinomycin D


title: shCtrl_2

value: HeLa cells

value: transfected with empty vector


title: osino80_rep1, BS-seq

description:
Oryza sativa Nipponbare
osino80_BS_rep1
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)


title: Kelly cells, STM, 3D, 6h, rep1


title: shCtrl_1


title: Kelly cells, DMSO, 3D, 6h, rep2


title: Kelly cells, STM, 3D, 3h, rep2


title: human sample 12s [miRNA]

city: Cheonan-si

first: Seongho

last: Ryu

address: 25 Bongjeong-ro Dongnam-gu

country: South Korea

institute: Soonchunhyang University

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4). Adapters are not trimmed away from the reads.
Data Pre-processing & Quality Check: Filtering → Signal+1 → Logarithm → Quantile Normalization
Statistical Test: Fold Change, Paired T-test. Criteria for Significant Result : |fc|≥2 & raw.p<0.05
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, and RPM values for each sample

source_name: kidney

extract_protocol:
miRNA was extracted from human tissues by miRNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using the SMARTer smRNA-Seq Kit from Illumina

value: kidney

tag: tumor stage

value: normal


title: human sample 10s [miRNA]


title: Kelly cells, DMSO, 3D, 3h, rep2


title: Kelly cells, STM, 3D, 3h, rep1


title: Kelly cells, DMSO, 3D, 6h, rep1


title: human sample 9s [miRNA]


title: Kelly cells, DMSO, 6D, 3h, rep1


title: Kelly cells, STM, 3D, 0h, rep1

value: 0h actinomycin D


title: Kelly cells, DMSO, 3D, 3h, rep1


title: HMGB1_NC_2

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue = 0 Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: hela cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: HMGB1 overexpression plasmid transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

value: hela cell (control plasmid)


title: Kelly cells, STM, 3D, 0h, rep2


title: Kelly cells, STM, 6D, 0h, rep1


title: HMGB1_1

value: HMGB1 overexpression in hela cell


title: HMGB1_2


title: human sample 5s [miRNA]


title: Kelly cells, DMSO, 3D, 0h, rep2


title: Brunello FITC peptide high 15%-round 2

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description: Screening.xlsx

data_processing:
SMART-seq: The SMART-seq NGS data was firstly removed adapters and aligned to the pre-designed oligonucleotide sequence using bowtie2. The nucleotides with the range of the 12-nt random sequences were further visualized using WebLogo
10x Genomics: The sequencing data of the scRNA-seq libraries were processed by Cell Ranger (provided by 10x Genomics Inc.). Each transcript was first assigned with a 10x Cell Barcode. Transcripts with the same Cell Barcode were considered to originate from the same cell and were used to determine the cell type identity of that cell. For each cell, we further counted the sequencing reads aligned to the CellIDs, which were further normalized as z-scores. And the most dominant CellID, which exhibited the highest z-score, determines the representative CellID of that cell. Thus, for each cell in our analysis, the classification performance of CellID can be evaluated by the cell type identity.
Screening: The CRISPR screening NGS libraries were sequenced as 150-bp paired-end. The sequencing reads were firstly undergone adapter removal by ‘cutadapter’ with parameters ‘-n 1 -e 0.11 -O 15 -m 16’. The sequences were then aligned to the designed CRISPR library sequences using bowtie2 with ‘–np 0 –n-ceil L,0,0.2 –very-sensitive’. We counted the reads number of each gRNA from the Brunello CRISPR library in both the mgSrtA labeled sample and the control sample (starting reference). The reads numbers were then normalized according to the sequencing depth of each NGS library, and an enrichment score was calculated for each gRNA (thus the targeted gene) using MAGeCK.
Library strategy: Screening

growth_protocol: K562 and Jurkat cells  were cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. 293T, HeLa, A549, MC-38, Hepa1-6 and C2C12 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
OligoFITC.noSrtA and OligoFITC.SrtA library: Oligonucleoides were captured using SMART-seq and enriched with 2X beads selection, followed by two round PCR amplification.
scFB4 library: Library was prepared using Chromium Single Cell3' v3 (10x Genomics)
FB4.PA library: CellID-derived cDNA were enriched after cDNA amplification with 2X beads selection and amplified by one round PCR amplification.
Screening library: Genomic DNA (gDNA) was extracted from the sorted cells.The gRNA cassette was amplified  from the gDNA.

value: myelogenousleukemiacell

value: Cells derived from first round sorting with high 20% MFI were labeled by FITC modified peptide again and the one with high 15% MFI were sorted.


title: human sample 4s [miRNA]


title: Kelly cells, DMSO, 3D, 0h, rep1

value: neuroblastoma cell line, MYCN-amplified

value: WT


title: Brunello FITC peptide high 20%-round 1

description: Screening.xlsx

value: Cells labeled by FITC modified peptide with high 20% MFI were sorted.


title: human sample 3s [miRNA]


title: 54645, nonpregnant

city: Gainesville

first: Peter

last: Hansen

state: Florida

address: 2250 Shealy Drive

department: Department of Animal Sciences

institute: University of Florida

data_processing:
Trimming with cutadapt (v.3.4); phred-like score <20 and reads <65 bases
Mapped with STAR package (v2.7.9) to ARS-UCD1.3
Mapped reads processed with HTSeq, samtools, and scripts to remove PCR duplicates and to count uniquely mapped reads
Read counts normalized by library size
Assembly: Bos taurus (ARS-UCD1.3)
Supplementary files format and content: Txt data file includes Gene ID in first column. Expression data in reads per million

organism: Bos taurus

source_name: Endometrial cells from uterine body

extract_protocol:
Qiagen Rneasy Microkit with prior tissue homogenization using beads
NEBNext Ultra II Directional RNA Library Prep Kit and SPT Labtech mosquito LV liquid handling instrument

value: Endometrial cells from uterine body


title: HMGB1_NC_1


title: Brunello FITC oligo high 15%-round 2

description: Screening.xlsx

value: Cells derived from first round sorting with high 20% MFI were labeled by FITC modified oligonucleotide again and the one with high 15% MFI were sorted.


title: human sample 2s [miRNA]


title: 54610, pregnant


title: 54611, pregnant


title: Brunello FITC oligo high 20%-round 1

description: Screening.xlsx

value: Cells labeled by FITC modified oligonucleotide with high 20% MFI were sorted.


title: Brunello FITC oligo low 20%-round 1

description: Screening.xlsx

value: Cells labeled by FITC modified oligonucleotide with low 20% MFI were sorted.


title: human sample 1s [miRNA]


title: human sample 12, stage 4 [miRNA]

value: tumor stage 4

tag: disease

value: clear cell renal cell carcinoma


title: human sample 8s [miRNA]


title: 54524, pregnant


title: human sample 10, stage 2 [miRNA]

value: tumor stage 2


title: cell&oligo without SrtA

description:
oligonucleotides
library for oligonucleotides non-specific binding on cells
SMARTSeq.xlsx

library_source: other

data_processing:
SMART-seq: The SMART-seq NGS data was firstly removed adapters and aligned to the pre-designed oligonucleotide sequence using bowtie2. The nucleotides with the range of the 12-nt random sequences were further visualized using WebLogo
10x Genomics: The sequencing data of the scRNA-seq libraries were processed by Cell Ranger (provided by 10x Genomics Inc.). Each transcript was first assigned with a 10x Cell Barcode. Transcripts with the same Cell Barcode were considered to originate from the same cell and were used to determine the cell type identity of that cell. For each cell, we further counted the sequencing reads aligned to the CellIDs, which were further normalized as z-scores. And the most dominant CellID, which exhibited the highest z-score, determines the representative CellID of that cell. Thus, for each cell in our analysis, the classification performance of CellID can be evaluated by the cell type identity.
Screening: The CRISPR screening NGS libraries were sequenced as 150-bp paired-end. The sequencing reads were firstly undergone adapter removal by ‘cutadapter’ with parameters ‘-n 1 -e 0.11 -O 15 -m 16’. The sequences were then aligned to the designed CRISPR library sequences using bowtie2 with ‘–np 0 –n-ceil L,0,0.2 –very-sensitive’. We counted the reads number of each gRNA from the Brunello CRISPR library in both the mgSrtA labeled sample and the control sample (starting reference). The reads numbers were then normalized according to the sequencing depth of each NGS library, and an enrichment score was calculated for each gRNA (thus the targeted gene) using MAGeCK.

molecule: other

value: cells incubated with oligo


title: cell&oligo with SrtA

description:
oligonucleotides
library for oligonucleotides labeled on cells
SMARTSeq.xlsx

value: cells incubated with oligo and mgSrtA


title: 54539, pregnant


title: Brunello start reference-peptide

description:
start reference
Screening.xlsx

value: K562-Cas9 cells were infected with Brunello sgRNA library.


title: human sample 9, stage 4 [miRNA]

value: kidney


title: IRE-KMS27-TAZ-003-R-05-23

city: Rome

first: Giacomo

last: Corleone

address: via chianesi 43

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

data_processing:
Sequencing quality of each sample was assessed with FASTQC v0.11.91 and summarized with MultiQC v.1.92
RNA-seq wereanalyzed by using the Kallisto v.0.46.0(Bray et al, 2016) and Sleuth v.0.30.0 (Pimentel et al, 2017) pipeline.
Read quantification was performed with the function quant of Kallisto tool (parameters: -b 100
The Kallisto results were processed and normalized through the function sleuth_prep using transcript mode. The gene-transcripts correspondence map was retrieved through the functions useMart and getBM of biomaRT R package (Durinck et al, 2009). Those correspondences were annotated based on grch37 of Ensembl release 103(Yates et al, 2020)
Differential analysis was conducted by fitting full and reduced models through the function sleuth_fit with the formula parameter, respectively, set to full and reduced. The processed reads counts were converted in transcript per million measurements through the function sleuth_to_matrix of Sleuth (Pimentel et al, 2017) R package
Assembly: GRCh37
Supplementary files format and content: The sleuth_Diff_analysis_rna_seq_wald_HA-taz_06023.csv represents the differential analysis transcript based
Supplementary files format and content: the HA_TAZ_tpm.csv represent show the TPM counts associated at each probed transcript

source_name: Plasma Cells

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated in triplicate using the same amount of RNA for each sample according to the Illumina Stranded Total RNA Prep kit with an initial ribosomal depletion step using Ribo-Zero Plus (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2x100 bp) with NovaSeq 6000 (Illumina, CA)

value: Plasma Cells

value: HA-TAZ


title: Brunello FITC peptide low 15%-round 2

description: Screening.xlsx

value: myelogenousleukemiacell

value: Cells derived from first round sorting with low 20% MFI were labeled by FITC modified peptide again and the one with low 15% MFI were sorted.


title: Brunello start reference-oligo

description:
start reference
Screening.xlsx


title: IRE-KMS27-TAZ-001-R-05-23


title: Brunello FITC peptide low 20%-round 1

description: Screening.xlsx

value: Cells labeled by FITC modified peptide with low 20% MFI were sorted.


title: IRE-KMS27-TAZ-002-R-05-23


title: 54513, pregnant


title: Brunello FITC oligo low 15%-round 2

description: Screening.xlsx

value: Cells derived from first round sorting with low 20% MFI were labeled by FITC modified oligonucleotide again and the one with low 15% MFI were sorted.


title: 54494, nonpregnant

value: Endometrial cells from uterine body


title: IRE-KMS27-HA-002-R-05-23

value: wild type


title: IRE-KMS27-HA-001-R-05-23


title: human sample 5, stage 1 [miRNA]

value: tumor stage 1


title: BALL1MPRA004

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas pl.

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt

data_processing:
Following next-generation sequencing, the MPRA sequence data was trimmed to contain only barcode sequences without allowing for any mismatches and read counts were determined for all barcodes. To identify significant allele-specific effects mpralm (69) was performed on RNA and DNA barcode counts after merging RNA or DNA counts across all barcodes for each allele.
Assembly: .txt file containing SNV-barcode associations
Supplementary files format and content: .txt file containing SNV-barcode associations
Supplementary files format and content: .txt file containing analysis of all cell lines x all SNVs MPRA data
Library strategy: MPRA

growth_protocol: RPMI 1640 + 10% serum

extract_protocol: MPRA Oligo design :Oligo libraries were designed by following previous work with modified protocols (1-4). MPRA oligos ordered from Agilent (230 bp) were structured as follows: 5'-Primer1-enh-Kpnl-Xbal-barcode-primer2-3' where primer1 and primer2 are universal primer sites, enh denotes the 175bp variant containing region to test for enhancer activity, Kpnl and Xbal denote recognition sequences for cut sites, and barcode denotes 10-bp tag sequence (see Sup File 6). Agilent oligos were resuspended in 100 ul nuclease free water. All 10-bp barcodes for each variant allele used in MPRA are provided in Supplemental File 7. MPRA Plasmid Cloning-Input (DNA) Library construction: For plasmid cloning, oligo libraries were amplified by 20 cycles of emulsion PCR (Micellula DNA Emulsion & Purification Kit #E3600, EURx Molecular Biology Products) using Herculase II fusion DNA polymerase (#600675, Agilent), forward and reverse primers (see Sup File 3) to introduce SfiI restriction enzyme sites (GGCCNNNNNGGCC) (NEB) and homology arms to the pMPRA1 plasmid (Cat: #49349, Addgene). Purified PCR products were separated on a 2-4% agarose gel to verify the expected amplification size of 281bp. The pMPRA1 backbone vector was Sfil digested overnight and size selected on a 1% agarose gel. Vector backbone gel extraction was done with the Qiagen gel extraction kit and QIAquick PCR purification kit (28706X4 and 28104).  Gibson assembly was used to clone oligos into vector using 79 ng of inserts, 100 ng of digested vector, and 20 ul Gibson assembly 2x master mix (# E2611S, NEB). The reaction was purified using MinElute PCR purification column (Qiagen), and drop analysis was performed with Millipore filters (Type VSWP 0.25 um Millipore #VSWP02500). For the transformation step, we aimed to obtain 10x CFU bacterial cells than the distinct promoter-tag combinations (unique sequences) in the oligo library. We transformed the Gibson assembly reactions into MegaX DH10B electrocompetent bacteria (#C6400-03, Invitrogen) using GenePulser II electroporator (Bio-Rad). Plasmids were extracted with Qiagen Maxi Prep Kit. For quality control studies, an aliquot of the isolated plasmid library was digested with SfiI and run on 1 % agarose gel to confirm the presence of inserts. To generate linear enhancer-barcode backbone sequences for reporter insertion, 2 ug of plasmid was digested with KpnI/XbaI. A minimal promoter + truncated eGFP was then ligated to the linearized enhancer-barcode backbone and purified using the Qiagen MilEute PCR purification kit. The ligation was then transformed into 1 vial of MegaX electrocompetent bacteria (#C6400-03, Invitrogen) as before. Plasmids were then extracted using a Qiagen Maxiprep kit as before and the elution was verified as a single size band by gel electrophoresis. MPRA library transfection and sequencing MPRA plasmid library (10 µg) transfections were done in 10 ALL cell lines having at >95% cell viability (45 million cells x 4 replicates x 10 cell lines) using electroporation with the Neon Transfection system (Thermofisher). Next day, RNA-was harvested using the RNeasy plus mini kit (Cat: #74134, Qiagen) using 4 columns per sample. Once the RNA was isolated, we performed additional DNase digestion using RQ1 RNase-free DNase (Cat: # M6101, Promega). All tubes from the same replicates were combined and added 1 volume of 70% ethanol to the combined lysate and mixed well by pipetting. The DNase treated RNA was again purified with RNeasy mini kit and eluted in 60 ul RNase free water. Total RNA was quantified using DeNovix Ds-11 FX instrument. We yielded 16µg-112µg of total RNA from each replicate depending on the cell line used. mRNA purification was performed using Dynabeads mRNA purification kit (Cat: #61006, Invitrogen). mRNA concentration was measured using Qubit HS RNA (Cat: #Q32852, Invitrogen). We yielded from 0.75-2 ug of mRNA in average from each replicate. cDNA was synthesized using three primers (2 uM) cDNA P1, cDNA P4, and cDNA 6, with the Superscript III first-strand synthesis system (Cat: #18080051, Invitrogen) (see Sup File 6). Final multiplexing of 50ng cDNA and input plasmid DNA (4 aliquots of MPRA plasmid pool that were independently prepared for next-generation sequencing) was carried out using Q5 Hot Start 2x Master Mix (NEB #M0494S), index primers, and Multiplexing primer 1 for 15 cycles of PCR. The reactions were size selected using AMPure XP beads (Cat: #A63881, Beckman Coulter, Indianapolis, IN) and eluted in 20 ul nuclease free water. The final library concentration was measured using Qubit DNA HS. 20-40 ng of each library was sequenced on the Illumina NovaSeq (200 million x 150bp paired-end reads per sample) at the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital. MPRA sequencing analysis Following next-generation sequencing, the MPRA sequence data was trimmed to contain only barcode sequences without allowing for any mismatches and read counts were determined for all barcodes. To identify significant allele-specific effects mpralm (5) was performed on RNA and DNA barcode counts after merging RNA or DNA counts across all barcodes for each allele.  1. P. Kheradpour et al., Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 23, 800-811 (2013).  2. A. Melnikov et al., Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature biotechnology 30, 271-277 (2012).  3. A. Melnikov, X. Zhang, P. Rogov, L. Wang, T. S. Mikkelsen, Massively parallel reporter assays in cultured mammalian cells. JoVE (Journal of Visualized Experiments), e51719 (2014).  4. J. Choi et al., Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nat Commun 11, 2718 (2020).  5. L. Myint, D. G. Avramopoulos, L. A. Goff, K. D. Hansen, Linear models enable powerful differential activity analysis in massively parallel reporter assays. BMC Genomics 20, 209 (2019).


title: 54488, pregnant


title: human sample 4, stage 1 [miRNA]


title: BALL1MPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 54451, pregnant


title: BALL1MPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 54522, pregnant


title: human sample 3, stage 3 [miRNA]

value: tumor stage 3


title: REHMPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt

source_name: REH

value: REH


title: human sample 2, stage 1 [miRNA]

value: clear cell renal cell carcinoma


title: 54401, pregnant


title: BALL1MPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: REHMPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 54397, pregnant


title: human sample 8, stage 3 [miRNA]


title: REHMPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 54385, pregnant


title: human sample 12s

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4). Adapters are not trimmed away from the reads.
Original raw data: Cufflinks -G option
Data Pre-processing & Quality Check: Filtering → Signal+1 → Logarithm → Quantile Normalization
Statistical Test: Fold Change, Paired T-test. Criteria for Significant Result : |fc|≥2 & raw.p<0.05
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample, and FPKM values for each sample

extract_protocol:
RNA was extracted from human tissues by miRNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using the SMARTer smRNA-Seq Kit from Illumina

value: normal


title: 54687, nonpregnant


title: P12-IchikawaMPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: REHMPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: IRE-KMS27-HA-003-R-05-23


title: P12-IchikawaMPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 1, stage 2 [miRNA]

value: tumor stage 2


title: 54233, nonpregnant


title: P12-IchikawaMPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 697MPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 10s


title: 54204, pregnant


title: human sample 9s


title: 697MPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 53932, nonpregnant


title: RS411MPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 697MPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 697MPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 54172, nonpregnant


title: RS411MPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: RS411MPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 5s


title: 53890, pregnant


title: RS411MPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: SEMMPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt

source_name: SEM

value: SEM


title: 53868, nonpregnant


title: P12-IchikawaMPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: SEMMPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 53726, nonpregnant


title: SEMMPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 53703, nonpregnant


title: SEMMPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 3s


title: human sample 2s


title: human sample 1s


title: Nalm6MPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: Nalm6MPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 53667, pregnant


title: human sample 12, stage 4

value: tumor stage 4


title: Nalm6MPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: Nalm6MPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 52851, nonpregnant


title: SUPB15MPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 4s

value: kidney


title: human sample 10, stage 2


title: human sample 9, stage 4


title: SUPB15MPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 52400, nonpregnant


title: CEMMPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt

source_name: CEM

value: CEM


title: 52265, nonpregnant


title: human sample 8, stage 3


title: 52338, pregnant


title: SUPB15MPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: CEMMPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 52216, pregnant


title: CEMMPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: JurkatMPRA003

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt

source_name: Jurkat

value: Jurkat


title: JurkatMPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 5, stage 1


title: 52173, nonpregnant


title: JurkatMPRA004

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 4, stage 1


title: JurkatMPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: human sample 3, stage 3


title: 52084, pregnant


title: NALM6_polII_rep1

data_processing:
Reads were quality checked using fastqc (v0.11.5)
and trimmed using trimgalore (v0.4.4)
before being mapped to the hg19 reference genome using bowtie2 (v2.2.9).
Sam files were converted to bam format using samtools (v1.2),
which were sorted using picard (v1.141).
Duplicates were removed using picard
and mitochondrial reads were removed using samtools.
For visualization, bam files from replicates were merged using samtools
and converted to bigwig format using deeptools (v3.5.0).
For peak calling, we used macs2 (v2.1.1), and only considered peaks called in both samples.
Assembly: HG19
Supplementary files format and content: .bigwig for coverage from merged replicates
Supplementary files format and content: .narrowpeak for PU.1 peaks called

extract_protocol: RNA polymerase II ChIP-seq data were generated by first fixing 20 million Nalm6 cells in 1% formaldehyde (diluted from sigma F87750) at room temp for 10 minutes. Crosslinking was stopped with the addition of 2.5M glycine to a concentration of 0.125M, and the cells were then washed in ice-cold PBS. 5mg anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody [4H8] (ab5408, lot: GR3264797-1) was prebound to 200ul of protein G dynabeads (invitrogen 10003D) overnight in 0.5% BSA in PBS. Fixed cell pellets (20M cells) were suspended in 1ml Farnham lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP40, 1x protease inhibitors (Roche 11836170001)) and passed through a 18G needle 10x. Nuclei were pelleted and resuspended in 275ul of RIPA buffer (1x PBS, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS, 1x protease inhibitors) and sonicated on high power in 1.5ml tubes for 25 minutes (30s on/ 30s off) using a Diagenode Bioruptor Plus. 5% Input samples were taken from sonicated material and the remaining sonicated material was added to the pre-bound antibody/protein G beads to rotate overnight at 4C. The next day the supernatant was discarded, and the beads were washed 5x with ice cold LiCl buffer (100mM Tris pH 7.5, 500mM LiCL, 1% NP40, 1% sodium deoxycholate) and 1x with ice cold TE buffer (10mM Tris pH 7.5, 1mM EDTA). Samples were eluted from the washed beads using room temperature IP elution buffer (1% SDS, 0.1 M NaHCO3) at 65C for 1hr, vortexing every 15 minutes. The elution was then incubated at 65C overnight to reverse crosslinks. The next day DNA was purified using the QIAquick PCR purification kit (Qiagen 28104). DNA quantification was performed using the PicoGreen assay (Molecular Probes, Eugene, OR, P-7581). Sequencing libraries were generated from ChIP and input DNA by using the KAPA Hyper Prep kit (Roche, Basel, Switzerland, # 7962363001) according to the included manufacturer’s specifications, and quality was determined by using the Agilent TapeStation with D1000 screentape. Then, >50M 50-bp paired-end reads per sample were generated on the NovaSeq 6000.

tag: read length


title: human sample 2, stage 1


title: NALM6_polII_rep2


title: SUPB15MPRA002

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: ATAC_BALL1_2

data_processing:
Data were analyzed as in (https://doi.org/10.1038/s41375-022-01685-z), GSE161501, and GSE129066.
Assembly: HG19
Supplementary files format and content: .bw for coverage
Supplementary files format and content: .narrowpeak for accessible regions
Library strategy: CUT & RUN

extract_protocol: Fast-ATAC in fresh primary ALL cells from patients and in a subset of ALL cell lines (BALL1, CEM, Jurkat and P12-Ichikawa) was performed on 10,000 cells as described in (https://doi.org/10.1038/ng.3646) and (https://doi.org/10.1038/s41375-022-01685-z). Paired-end Illumina next-generation sequencing of Fast-ATAC libraries was performed at the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children’s Research Hospital. Data were analyzed as in (https://doi.org/10.1038/s41375-022-01685-z).


title: ATAC_BALL1_1


title: human sample 1, stage 2


title: SEM_PCap_HiC

data_processing:
Analysis of Promoter capture HiC data was performed using the Arima CHiC pipeline (v1.5, https://github.com/ArimaGenomics/CHiC). Briefly, this pipeline uses HiCUP v0.8.0 for mapping and quality assessment of promoter capture HiC data and CHiCAGO to identify significant looping interactions in the promoter capture HiC data using 5kb resolution and adj. p < 0.05.
Assembly: HG19
Supplementary files format and content: bedpe for significant loops called at 5kb resolution used to determine if SNVs were in a looping genomic region

extract_protocol:
Arima promoter capture HiC (Arima: A510008, A303010, A302010) was performed according to the manufacturers provided instructions using unspecified proprietary buffers, solutions, enzymes, and reagents. Briefly, 10 million ALL cells were harvested, suspended in 5ml RT PBS which was brought to 2% formaldehyde by adding 37% methanol-stabilized paraformaldehyde for a 10-minute fixation. The amount of fixed cell suspension equal to 5mg of cell DNA was used for HiC. Cells were lysed with Lysis Buffer and conditioned with Conditioning Solution before their DNA was digested in a cocktail consisting of Buffer A, Enzyme 1, and Enzyme 2. The digested, fixed chromatin was biotinylated using using Buffer B and Enzyme B before being ligated using Buffer C and Enzyme C. The fixed, biotinylated, ligated DNA was then subjected to reversal of crosslinking and digestion of proteins before being purified. 100ul containing 1500ug of purified large proximally ligated DNA was fragmented for 24 cycles (30s on/ 30s off) using a Diagenode Bioruptor Plus bath sonicator. The fragmented DNA was then subjected to two-sided size selection targeting fragments between 200-600bp using AMPure XP DNA purification beads. Size selected DNA was then subjected to biotin enrichment using T1 streptavidin beads. Bead bound, enriched HiC DNA was then subjected to Arima library prep. Briefly, the sample underwent end repair followed by adapter ligation, at which point the sample was then subjected to 10 cycles of PCR amplification. The library DNA was then purified using AMPure XP DNA purification beads. The HiC library was then subjected to Arima promoter capture enrichment. The library was precleared of biotinylated DNA using T1 streptavidin beads before being subjected to promoter enrichment with biotinylated RNA probes. After washing, the captured fragments were then amplified an additional 13 PCR cycles. These libraries were submitted for deep sequencing on an Illumina Nova-seq where >200M 150bp paired-end reads were obtained.
Promoter capture Hi-C
read length: 150bp

value: ALL


title: NALM6_input


title: 52058, pregnant


title: UWB1.289_DMSO_24h_rep3

city: Heidelberg

first: Stephan

last: Gade

address: Meyerhofstrasse  1

country: Germany

institute: GSK - Cellzome

data_processing:
Reads were aligned with STAR,
Sequence reads were trimmed for adaptor sequence/low-quality sequence, aligned with STAR on Hg38 genome.
Read count extraction was done using FeatureCounts R package
Assembly: hg38
Supplementary files format and content: tab delimited text file with 3 columns: Geneid, sample and count. The column count contains the raw counts

growth_protocol: Cells were cultured at 37°C, 5% CO2 in 1:1 RPMI:MEGM (Lonza, #CC-3151), 3% fetal bovine serum (FBS,Gibco), MEGM SingleQuots supplements (Lonza, #CC-4136) used without gentamycin-amphotericin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra DNA

treatment_protocol: For the Olaparib (CAS: 763113-22-0) treatment, three 15 cm dishes per condition were prepared by seeding 3‒4 x 106 cells per plate; 24 hours later medium was removed and 25 ml fresh medium containing dimethylsulfoxide (DMSO) (Sigma) or 4uM Olaparib was applied to the cells. Cells were incubated for indicated time (24 hours) at 37°C, 5% CO2

value: WT

value: DMSO


title: 52073, pregnant


title: CEMMPRA001

description:
MPRA_ALL_CELL_LINES.txt
barcodes.txt


title: 52030, pregnant


title: 52055, nonpregnant


title: UWB1.289_DMSO_24h_rep1


title: REH_PCap_HiC


title: 52024, pregnant


title: RS411_PCap_HiC


title: CEM_PCap_HiC


title: Nalm6_PCap_HiC


title: UWB1.289_Olaparib_4uM_24h_rep3

value: Olaparib 4uM


title: BALL1_PCap_HiC


title: 51983, nonpregnant

value: Endometrial cells from uterine body


title: NALM6_PU1

data_processing:
The Nextflow CUT and RUN pipeline (v2.0) was used in spike-in mode to assess quality and map reads to the HG19 (human) and K12-MG1655 (E. coli) reference genomes (72, 73).
The spike-in normalized .bam files from Nextflow were exported to Easeq (v1.111), where peaks were called against the IgG sample using adaptive local thresholding (p < 1x10-5, FDR < 1x10-5, Log2(Fold Change) > 1, merge within = 100bp, window size = 100bp) (74).
Data shown are spike-in normalized bigwig files generated in Nextflow.
Assembly: HG19
Supplementary files format and content: .bigwig for coverage
Supplementary files format and content: .txt for PU.1 peaks called
Library strategy: CUT & RUN

extract_protocol: CUT and RUN data were generated using the Epicypher Cutana CUT&RUN kit v3.0 (14-1048) according to the manufacturers provided instructions. Briefly 500k NALM6 cells per reaction were bound to 10ml of provided activated ConA beads in 0.2ml PCR tubes. Bead-bound cells were suspended in Antibody Buffer (Wash buffer with 0.1% digitonin, 0.5mM Spermidine, 2mM EDTA, and 1x HALT protease inhibitors) and incubated with 1ul PU.1 antibody (Cell Signaling 2258) or IgG (Epicypher 13-0042k) overnight on a nutator mixer at 4C. The next day after washing, pAG MNase was bound and targeted digestion was carried out for 2 hours at 4C. Digestion was stopped using 33ml Stop buffer + 1ml (0.5ng) E.coli spike-in DNA and then cleaved DNA were released for 10 minutes at 37C. DNA were then purified for library preparation using the included purification kit. >30M 75bp paired end reads were generated per sample using the Illumina Novaseq.


title: 697_PCap_HiC


title: UWB1.289_Olaparib_4uM_24h_rep2


title: NALM6_igg

value: IgG


title: UWB1.289_Olaparib_4uM_24h_rep1


title: 51990, nonpregnant


title: PFOA_0.25_2 [CTTGTTGG-CTATGATC-2]

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

data_processing:
Sequencing read quality was assessed via FastQC and MultiQC.
Reads were aligned to a splice junction aware build of the human genome (GRCh38) using STAR.
Aligned reads were assigned to genes using featureCounts, where multimapping and multi-overlapping reads were not counted.
Assembly: GRCh38
Supplementary files format and content: Tab deliminted files containnig the read counts per sample

growth_protocol: MCF10A cells were cultured and expanded at passage 105 for all rounds of cell culture. Cells were plated in black, clear flat bottom 384 well plates (Corning, Corning, NY, USA) using a 2.5-125uL multi-channel pipette. First, 10uL of plain media was added to pre-warmed plates. 500 cells in 30 uL of media were added to each well at a slow speed to make up a final volume of 40 uL. The cells were left undisturbed to allow the cells to attach and distribute uniformly over the well. Each microplate was incubated at 37oC humidified incubator with 5% CO2 for 24 hours prior to dosing.

extract_protocol:
To conduct high throughput RNA-sequencing, we developed an adapted version of the plexWell (SeqWell, Beverly, MA, USA) plate-based sequencing method to make the method applicable for high throughput in vitro toxicological analysis. In the plexWell protocol, sequencing reactions are prepared in custom 96 well plates, where each well contains a unique oligo barcode. Plates are also assigned a unique oligo barcode. Cells are lysed and cDNA is directly prepared from the cellular lysate.
A tagmentation reaction adds the well specific barcode to the cDNA from each well. The tagmented cDNAs are then pooled prior to library preparation, where plate specific barcodes can also be incorporated for ultrahigh sample multiplexing prior to sequencing. For example, 384 wells of treated samples would be processed across 4 custom 96 well plates, where each of the samples receives a well specific barcode and each of the 4 plates receives a plate specific barcode. This leads to each of the 384 samples receiving a unique combination of well and plate barcodes, which can be bioinformatically deconvoluted following sequencing.
Libraries were sequenced at Illumina NovaSeq 6000 l at the Advanced Genomics Core.

treatment_protocol: Cells were then exposed to test chemicals for 48 hours with 4 biological replicates per dose. Doses are in micromolar in the "treatment" column

value: Nontumorigenic breast

value: PFOA 0.25

value: 48 hrs

tag: control flags

value: Water

tag: plate id


title: UWB1.289_DMSO_24h_rep2


title: 51918, pregnant


title: PFNA_0.025_3 [CCTACACA-CTATGATC-2]


title: Copper_25_1 [CCATTGCG-ATAGAGAG-2]

value: Copper 25


title: wt-replicate D [D]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Total RNA was extracted from WT (METTL1 expressing) cells. RNAs were not further treated with NaBH4+Aniline.

data_processing:
FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers.
We used bowtie to align the reads against the human genome (GRCh38/UCSC hg38), with the option "-v 2 - m 500" to allow for 2 mismatches and multiple mapping of tRNA fragments, and htseq-count with the "-samout" option to flag alignment reads. tRNA fragments were extracted from the alignment files using custom PERL scripts. Statistical significance of differential expression was evaluated using the R DESeq2 package.
Assembly: GRCh38/UCSC hg38
Supplementary files format and content: read counts and especific tRNAs' sequences

growth_protocol: DU145 were cultured in DMEM with L-Glutamine and pyruvate (Gibco) supplemented with 10% FBS (Gibco) and 1% Penicillin/streptomycin, a humidified atmosphere at 37°C and 5% CO2. Cell cultures were tested for mycoplasma monthly and maintained mycoplasma-free.

extract_protocol:
Total RNA was extracted from cells. Small RNA was size-selected and treated or not treated with NaBH4+Aniline (that induces RNA chain cleavage at methylated guanosines).
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

treatment_protocol: tRNAs were de-aminoacylated with a solution containing 1mM EDTA and 0.1M Tris-HCl pH 9.0 for 30 min at 37°C. For identifying the m7G deposition position, 1-2 mg of tRNAs were treated with Buffer A (0.2 M Tris-HCl pH, 0.01 M MgCl2, 0.2 M KCl) supplemented with 10 μg of m7GTP (NEB) per 10 μg of tRNAs for 5 min at 85ºC. Freshly prepared NaBH4 was added to a final concentration of 0.5 M and samples were incubated for 30 min on ice. Treated tRNAs were desalted with Micro Bio-Spin 6 columns (Biorad) and ethanol precipitated. To induce complete ꞵ-elimination and cleavage of RNA at methylated guanines, reduced RNAs were treated with aniline/acetate/water solution (1:3:7) (Sigma). All small RNAs were treated with T4 PNK (NEB) to ensure phosphorylated 5’ ends and 3’OH ends, followed by heat inactivation and ethanol precipitation.

value: prostate cancer cells

tag: molecule type

value: small RNA


title: PCB153_25_4 [ATGACACC-CCATAGGG-2]


title: wt-replicate D [D_BH4]

description: Total RNA was extracted from WT (METTL1 expressing) cells. RNAs were treated with NaBH4+Aniline.


title: 51945, pregnant


title: 51901, pregnant


title: PFDA_25_3 [CACAGTCT-CTATGATC-2]

value: PFDA 25


title: PFOS_25_4 [CAGGCCAT-CTATGATC-2]

value: PFOS 25


title: SUPB15_PCap_HiC


title: wt-replicate NoD [NoD_BH4]


title: 51896, nonpregnant


title: Control_0_2 [CCTTATGT-ATAGAGAG-2]

value: Control 0


title: Control_0_8 [CTGTACGC-ATAGAGAG-2]


title: wt-replicate NoD [NoD]


title: 51853, pregnant


title: PFOA_0.025_1 [CTCGTACA-CTATGATC-2]


title: Copper_25_4 [TCCTATCT-ATAGAGAG-2]


title: Copper_25_3 [ATGGTCCG-ATAGAGAG-2]


title: rat injected with HepLPCs rep3

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA from liver tissue was isolated using TRIzol® Reagent (Invitrogen). DNase I (TaKara) was used to remove genomic DNA. The concentration and purity of RNA samples was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
Library preparation, and Illumina Hiseq xten/Nova seq 6000 Sequencing RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: Cirrhosis rats injected with PBS or HepLPCs

value: liver

tag: strain

value: Sprague-Dawley rat

tag: age

value: 5 months

value: wild type

value: HepLPCs injection


title: 51844, pregnant

tag: cell type

value: Endometrial cells from uterine body


title: BPA_25_3 [CAGGAAGG-ATATGAGA-2]

tag: cell line

tag: genotype

value: WT

value: BPA 25

value: DMSO


title: Control_0_1 [ACTCACCG-ATAGAGAG-2]

value: Nontumorigenic breast

tag: treatment

tag: time

value: 48 hrs


title: 51836, pregnant


title: Thiram_0.025_2 [AACCAATC-CCATAGGG-2]

value: Thiram 0.025


title: rat injected with HepLPCs rep1

tag: tissue


title: 51821, nonpregnant


title: Lead_25_2 [CAGAAGAA-ATAGAGAG-2]

value: Lead 25

value: Water


title: MPB_25_2 [TTGGCTGC-ATATGAGA-2]

value: MPB 25


title: rat injected with PBS rep3

value: PBS injection


title: PFNA_2.5_1 [TGTTGCAC-CTATGATC-2]

value: PFNA 2.5


title: PCB153_2.5_1 [TGTTGCAC-CCATAGGG-2]


title: 51805, pregnant


title: rat injected with PBS rep2

value: liver


title: 51795, nonpregnant


title: rat injected with PBS rep1

value: Sprague-Dawley rat


title: PFOS_25_2 [ACATCCTT-CTATGATC-2]

value: PFOS 25


title: Lead_25_4 [CGTCTGAA-ATAGAGAG-2]


title: PCB153_0.25_1 [ATGGAACA-CCATAGGG-2]


title: 51752, nonpregnant


title: Normal rat rep3

value: 5 months

value: wild type

value: no treatmet


title: Control_0_45 [CTATTCCA-CTATGATC-2]

value: WT

value: Control 0


title: 51667, pregnant

value: Endometrial cells from uterine body


title: rat injected with HepLPCs rep2

value: HepLPCs injection


title: Arsenic_0.25_3 [CACCGCAA-ATAGAGAG-2]

value: Nontumorigenic breast

value: Arsenic 0.25

value: 48 hrs


title: PPB_2.5_4 [ATGCCGCT-ATATGAGA-2]

value: PPB 2.5

value: DMSO


title: 51628, pregnant


title: Control_0_11 [GTTATCGA-ATAGAGAG-2]

value: Water


title: Normal rat rep1


title: 51589, nonpregnant


title: Lead_0.025_4 [TGAATGTG-ATAGAGAG-2]


title: 51562, nonpregnant


title: Phenanthrene_2.5_4 [CCTGTTAC-CTATGATC-2]

value: Phenanthrene 2.5


title: 51565, nonpregnant


title: Control_0_58 [CTAAGGCG-CCATAGGG-2]


title: 51505, pregnant


title: BPS_0.25_4 [TGCTCCGT-ATATGAGA-2]


title: DCP_25_0.025_3 [ATTCGCAG-CCATAGGG-2]


title: Control_0_34 [CCTTATGT-CTATGATC-2]


title: 51516, nonpregnant


title: DCB_14_25_3 [CACAGTCT-CCATAGGG-2]


title: Thiram_0.25_3 [AAGTACCT-CCATAGGG-2]

value: Thiram 0.25


title: Normal rat rep2

value: liver

value: Sprague-Dawley rat


title: BPA_25_2 [CAGAAGAA-ATATGAGA-2]

value: BPA 25


title: 51494, pregnant


title: PFOS_2.5_3 [GTGCGAGT-CTATGATC-2]

value: PFOS 2.5


title: 51489, pregnant


title: PFDA_0.25_3 [CACCGCAA-CTATGATC-2]

value: PFDA 0.25


title: MPB_0.025_3 [CCTACACA-ATATGAGA-2]

value: WT


title: PFOA_0.25_4 [CTGGTCGT-CTATGATC-2]

value: PFOA 0.25


title: DCB_14_0.25_1 [ACGAAGCG-CCATAGGG-2]


title: PCB153_0.025_4 [CGCGTGAT-CCATAGGG-2]


title: 51424, nonpregnant

value: Endometrial cells from uterine body


title: BPF_25_1 [CCATTGCG-ATATGAGA-2]

value: BPF 25


title: Copper_2.5_2 [GGTGTGAC-ATAGAGAG-2]

value: Nontumorigenic breast

value: Copper 2.5


title: 51340, pregnant


title: MPB_0.25_3 [CCATACTC-ATATGAGA-2]

value: 48 hrs


title: Thiram_0.025_3 [TCTATTGG-CCATAGGG-2]

value: Thiram 0.025


title: DCB_14_2.5_1 [AACGCTTG-CCATAGGG-2]

value: DMSO


title: human sample 8s

value: kidney

value: normal


title: 51297, nonpregnant


title: DCB_14_0.25_4 [TGCTCCGT-CCATAGGG-2]


title: 51284, nonpregnant


title: Arsenic_0.025_2 [ACCGTTCC-ATAGAGAG-2]

value: Arsenic 0.025

value: Water


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk2_gene37

type: RNA

city: Bethesda

first: Michelle

last: Bylicky

state: Maryland

address: 10 Center Drive

department: Radiation Oncology Branch

institute: National Cancer Institute

description: Gene expression 2 weeks post treatment start, Animals received 2 weeks of Onalespib (5 days per week, 55mg/kg) and 1 week of radiation (3 x 2 Gy).

hyb_protocol: mRNA: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Human 8x60 (v3) Gene Expression Microarrays Design ID 072363 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 42° C for 30 min, and stained with Streptavidin-Alexa555.     miRNA: labeled target was applied to Agilent Human miRNA 8x60 v21.0 arrays (design ID 070156) in hybridization buffer.  Arrays were hybridized at 55° C for 20 hrs in a rotating incubator, washed at 37° C for 10 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: FaDu human squamous cell carcinoma

label_protocol: mRNA: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA).  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.   miRNA: Total RNA samples were dephosphorylated, denatured, and end-labeled with Cy-3.

growth_protocol: The human squamous cell carcinoma from the pharynx (FaDu) was used for this study. Prior to injection FaDu cells were cultured in DMEM, 10% FBS. These cells were injected into right flank of athymic mice at a concentration of 1 x 10^6 cells.

extract_protocol: Tumor samples were bathed in liquid nitrogen and pulverized into a fine powder using a mortar and pestle. Approximately 100 µg of powdered sample was lysed with 700 µl of QIAzol lysis buffer (Cat # 79306, QIAGEN) and homogenized by passing the solution through QIAshredder spin columns (Cat # 79654, QIAGEN). RNA isolation was performed using standard miRNeasy mini kits (Cat # 217004, QIAGEN) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a DeNovix DS-11 nanodrop spectrophotometer (DeNovix, DE, US) and Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA). by spectrophotometry and on the Agilent Bioanalyzer.

treatment_protocol: Six-week old Athymic nude nu/nu female mice were injected with FaDu cells in right flank. FaDu cells were allowed to grow to tumor size 200mm3 before treatment started. Mice were divided into 4 groups beyond the initial Control on D1: Untreated (UT), x-ray irradiation only (Rad), Onalespib drug treated only (Drug), and both (Rad + Drug). Mice received i.p injections 5 days per week of control vehicle or Onalespib. Mice received Drug through week 1 and week 2. Mice in the Drug+Rad group had a second week of Drug. In animals receiving Onalespib and radiation, animals were injected with Onalespib 2-3 hours prior to radiation. Mice in Rad groups received 6Gy total radiation 2Gy every other day (2Gy x 3) for the first week. Mice receiving treatments were euthanized at the end of week 1 and at the end of week 2. Animals receiving radiation were euthanized approximately 4 hours post radiation. Control mice were euthanized at the beginning of treatment (D1), and Untreated (vehicle only) at the end of week 1 and Day 8 of treatment schedule due to excessive tumor size. Tumor samples were analyzed at Day 1 at end of Week 1 and Week 2 (indicated in figure 1A, below). Additional mice were followed for tumor growth delay. Longer term tumor samples were not available as this was not the primary purpose of this study.

tag: tumor type

value: Head and Neck Squamous cell tumor

tag: tumor origin

value: hypopharyngeal

tag: mouse strain

value: Athymic nude mice (nu/nu)

tag: biological sex

value: Female

tag: age of mice

value: 6 weeks old

value: Drug+XRT


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk2_gene35


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk2_gene36


title: Homo sapiens xenograft in Mus musculus, XRT_Wk2_gene33

description: Gene expression 2 weeks after treatment start, mice received radiation the 1st week (3 x 2 Gy) and no subsequent treatment the second week

value: XRT


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk2_gene34


title: Homo sapiens xenograft in Mus musculus, XRT_Wk2_gene32


title: Arsenic_0.25_2 [CTCTCAGG-ATAGAGAG-2]

value: WT

value: Arsenic 0.25


title: Homo sapiens xenograft in Mus musculus, Drug_Wk2_gene29

description: Gene expression 2 weeks after treatment start, animals received IP injection of Onalespib 55mg/kg for 5 days on both weeks including day of euthanasia

value: Drug


title: 51280, nonpregnant

value: Endometrial cells from uterine body


title: Homo sapiens xenograft in Mus musculus, XRT_Wk2_gene30


title: Homo sapiens xenograft in Mus musculus, Drug_Wk2_gene28


title: Lead_0.25_1 [GTTGACAG-ATAGAGAG-2]

value: Nontumorigenic breast

value: Lead 0.25

value: 48 hrs


title: PCB153_25_2 [TTGGCTGC-CCATAGGG-2]

value: DMSO


title: 51276, nonpregnant


title: PFDA_0.25_1 [ACGAAGCG-CTATGATC-2]

value: PFDA 0.25


title: DCB_14_0.025_4 [CAAGTGAC-CCATAGGG-2]


title: Homo sapiens xenograft in Mus musculus, Drug_Wk2_gene27


title: Phenanthrene_2.5_3 [ACTTCAAC-CTATGATC-2]

value: Phenanthrene 2.5


title: PFOA_0.25_3 [TGTAAGAC-CTATGATC-2]

value: PFOA 0.25

value: Water


title: Cadmium_25_1 [CATCTTCT-ATAGAGAG-2]

value: Cadmium 25


title: Mercury_25_2 [TTGGCTGC-ATAGAGAG-2]

value: Mercury 25


title: 51133, pregnant


title: 51149, nonpregnant


title: Homo sapiens xenograft in Mus musculus, Drug_Wk2_gene26

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old


title: DCB_14_0.025_2 [ACCGTTCC-CCATAGGG-2]

value: WT


title: Homo sapiens xenograft in Mus musculus, XRT_Wk2_gene31

description:
Gene expression 2 weeks after treatment start, mice received radiation the 1st week (3 x 2 Gy) and no subsequent treatment the second week

This sample set was not used in the final analysis.

value: XRT


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk2_gene25

description: Gene expression 10 days post treatment start in sham animals, early euthanasia due to tumor size

value: Ctrl


title: Lead_2.5_3 [ACTTCAAC-ATAGAGAG-2]

value: Nontumorigenic breast

value: Lead 2.5


title: 51098, nonpregnant

value: Endometrial cells from uterine body


title: PCB187_0.25_2 [ACGCTGCA-CCATAGGG-2]

value: 48 hrs

value: DMSO


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk2_gene23


title: BPS_2.5_2 [ATTCCGTA-ATATGAGA-2]

value: BPS 2.5


title: DCP_25_2.5_4 [TCAGATAC-CCATAGGG-2]


title: 51034, nonpregnant


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk2_gene24


title: 51162, pregnant


title: 51027, nonpregnant


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk2_gene22


title: PCB153_0.25_4 [TCCTTGGC-CCATAGGG-2]


title: 51006, pregnant


title: Copper_0.25_4 [CTGGTCGT-ATAGAGAG-2]

value: Copper 0.25

value: Water


title: 50988, pregnant


title: Arsenic_2.5_3 [CGCTCTTG-ATAGAGAG-2]

value: Arsenic 2.5


title: PFDA_2.5_3 [CGCTCTTG-CTATGATC-2]

value: PFDA 2.5


title: Lead_0.025_1 [GTTAAGCA-ATAGAGAG-2]


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk1_gene20

description: Gene expression 1 week post Onalespib (5 days, 55mg/kg) and radiation treatment (3 x 2 Gy)

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Drug+XRT


title: PFDA_0.025_4 [CAAGTGAC-CTATGATC-2]


title: 50947, pregnant


title: PCB187_2.5_2 [ACCGACCA-CCATAGGG-2]


title: Arsenic_2.5_2 [ATTCCGTA-ATAGAGAG-2]


title: Control_0_41 [TTCCATTC-CTATGATC-2]

value: Control 0


title: DCB_14_2.5_3 [CGCTCTTG-CCATAGGG-2]

value: WT


title: 50886, nonpregnant


title: PFDA_25_1 [GTTCGTCT-CTATGATC-2]

value: PFDA 25


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene18

description: Gene expression 1 week after treatment start, animals received radiation every other day for 3 days, 2 Gy each day, total 6Gy. Animals irradiated day of euthanasia

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old

value: XRT


title: BPF_25_3 [ATGGTCCG-ATATGAGA-2]

value: Nontumorigenic breast

value: BPF 25

value: 48 hrs


title: PPB_0.25_3 [CGATGGCA-ATATGAGA-2]

value: DMSO


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk1_gene19


title: 50833, pregnant

value: Endometrial cells from uterine body


title: BPF_0.25_4 [CTGGTCGT-ATATGAGA-2]


title: 50819, pregnant


title: DCP_25_0.25_4 [CTGGTCGT-CCATAGGG-2]


title: 50776, nonpregnant


title: Control_0_28 [TGGACAAC-ATATGAGA-2]


title: Homo sapiens xenograft in Mus musculus, Drug+XRT_Wk1_gene21


title: PFNA_2.5_4 [CTTCTGGC-CTATGATC-2]

value: PFNA 2.5


title: PFOA_0.025_4 [ACCTGAGC-CTATGATC-2]

value: Water


title: Control_0_29 [CTATTCCA-ATATGAGA-2]


title: Copper_2.5_1 [CACATGGT-ATAGAGAG-2]

value: Copper 2.5


title: Arsenic_0.025_3 [TCAAGGAT-ATAGAGAG-2]

value: Arsenic 0.025


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene16

value: Head and Neck Squamous cell tumor

value: hypopharyngeal


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene17


title: Control_0_50 [CCTTATGT-CCATAGGG-2]

value: WT

value: Control 0


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene14

description: Gene expression 1 week after treatment start, animals received IP injection of Onalespib 55mg/kg for 5 days including day of euthanasia

value: Athymic nude mice (nu/nu)

value: Drug


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene15

value: Female

value: 6 weeks old


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene13


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene12


title: 50537, nonpregnant


title: Homo sapiens xenograft in Mus musculus, Drug_Wk1_gene11


title: 50635, pregnant


title: 50855, nonpregnant


title: BPS_25_3 [CACAGTCT-ATATGAGA-2]

value: Nontumorigenic breast

value: BPS 25


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk1_gene10

description: Gene expression in untreated tumors 1 week post treatment start, sham animals

value: Ctrl


title: 50751, nonpregnant


title: Control_0_33 [ACTCACCG-CTATGATC-2]

value: 48 hrs

value: DMSO


title: 50259, pregnant

value: Endometrial cells from uterine body


title: DCP_25_2.5_2 [GGTGTGAC-CCATAGGG-2]


title: Control_0_6 [CCGAGTTA-ATAGAGAG-2]

value: Water


title: Control_0_37 [TGGTGACT-CTATGATC-2]


title: Arsenic_0.025_4 [CAAGTGAC-ATAGAGAG-2]


title: 49884, nonpregnant


title: Mercury_2.5_1 [TGTTGCAC-ATAGAGAG-2]

value: Mercury 2.5


title: BPF_0.25_3 [TGTAAGAC-ATATGAGA-2]


title: 49876, pregnant


title: PFDA_0.025_3 [TCAAGGAT-CTATGATC-2]


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk1_gene8


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk1_gene9


title: Control_0_48 [GTGCGTTC-CTATGATC-2]


title: 49836, pregnant


title: PFOS_0.025_1 [TCAACTGA-CTATGATC-2]


title: Lead_25_1 [GGCTCCTA-ATAGAGAG-2]

value: Lead 25


title: Thiram_2.5_2 [GTACCAGC-CCATAGGG-2]

value: Thiram 2.5


title: Thiram_2.5_3 [ACTTCAAC-CCATAGGG-2]


title: BPA_0.025_1 [GTTAAGCA-ATATGAGA-2]


title: Thiram_25_1 [GGCTCCTA-CCATAGGG-2]

value: Thiram 25


title: 49830, pregnant


title: 50036, nonpregnant


title: PPB_25_1 [CATCTTCT-ATATGAGA-2]

value: WT

value: PPB 25


title: Homo sapiens xenograft in Mus musculus, Ctrl_Day1_gene5

description: Gene expression Day 1 of experiment

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)


title: PFOA_2.5_2 [GGTGTGAC-CTATGATC-2]

value: PFOA 2.5


title: Arsenic_25_4 [TGGTACAG-ATAGAGAG-2]

value: Nontumorigenic breast

value: Arsenic 25


title: 49746, pregnant


title: 49662, nonpregnant


title: Homo sapiens xenograft in Mus musculus, Ctrl_Day1_gene6

description: Gene expression Day 1 of experiment

value: Female

value: 6 weeks old

value: Ctrl


title: Phenanthrene_25_3 [CAGGAAGG-CTATGATC-2]

value: Phenanthrene 25

value: 48 hrs

value: DMSO


title: Homo sapiens xenograft in Mus musculus, Ctrl_Wk1_gene7


title: Homo sapiens xenograft in Mus musculus, Ctrl_Day1_gene2

description: Gene expression Day 1 of experiment


title: Control_0_52 [GGAGCTAT-CCATAGGG-2]

value: Control 0


title: 49655, pregnant

value: Endometrial cells from uterine body


title: Control_0_56 [CTGTACGC-CCATAGGG-2]


title: Homo sapiens xenograft in Mus musculus, Ctrl_Day1_gene3

description: Gene expression Day 1 of experiment


title: CCh12_male_children_digit_chondrocyte

city: Tokyo

first: Makii

last: Fukami

address: 2-10-1 Okura, Setagaya

department: Department of Molecular Endocrinology

country: Japan

institute: National Research

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Microarrays were scanned by Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent). The data were analyzed using GeneSpring software (version 14.9, Agilent Technologies).

source_name: chondrocyte

label_protocol: Labeling was performed using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent Technologies)

extract_protocol: Cartilage tissues were stored in RNAlater. Frozen tissue specimens were homogenized and subjected to total RNA extraction with the TRIzol reagent. Total RNA of chrondrocytes was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN).  Quantity and quality of the extracted RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male

tag: developmental stage

value: child

value: chondrocyte


title: Homo sapiens xenograft in Mus musculus, Ctrl_Day1_gene4

description: Gene expression Day 1 of experiment

value: Head and Neck Squamous cell tumor


title: PFOA_2.5_1 [CACATGGT-CTATGATC-2]

value: WT

tag: control flags

value: Water

tag: plate id


title: 49787, nonpregnant


title: 49614, pregnant


title: CCh11_male_children_digit_chondrocyte


title: PPB_2.5_2 [ACCGACCA-ATATGAGA-2]

value: PPB 2.5


title: 49499, pregnant


title: 49553, nonpregnant


title: BPA_2.5_3 [ACTTCAAC-ATATGAGA-2]

value: Nontumorigenic breast

value: BPA 2.5


title: PFDA_25_2 [CCAGGTAA-CTATGATC-2]

value: PFDA 25


title: PPB_0.25_1 [TCCTCAGA-ATATGAGA-2]


title: CCh10_male_children_digit_chondrocyte


title: Control_0_44 [TGGACAAC-CTATGATC-2]


title: BPA_0.025_3 [TCTATTGG-ATATGAGA-2]


title: PFDA_0.25_4 [TGCTCCGT-CTATGATC-2]

value: PFDA 0.25


title: Copper_0.025_4 [ACCTGAGC-ATAGAGAG-2]

value: Copper 0.025


title: 49515, pregnant


title: 49541, pregnant


title: PFOS_0.025_4 [CTAGCCGA-CTATGATC-2]


title: Control_0_59 [GTTATCGA-CCATAGGG-2]


title: Control_0_64 [GTGCGTTC-CCATAGGG-2]


title: PCB153_2.5_2 [ATTCTCCA-CCATAGGG-2]


title: PFOS_0.025_3 [GTGTCCAT-CTATGATC-2]


title: 49452, nonpregnant


title: BPS_0.025_1 [CGAGCATT-ATATGAGA-2]


title: 49496, nonpregnant


title: PPB_0.25_4 [CAACCGTG-ATATGAGA-2]


title: 49401, nonpregnant


title: BPS_2.5_3 [CGCTCTTG-ATATGAGA-2]

value: BPS 2.5


title: MPB_25_1 [CAGAGTGG-ATATGAGA-2]

value: MPB 25

value: 48 hrs


title: 49332, nonpregnant


title: PFNA_0.025_1 [TCACTCAC-CTATGATC-2]

value: DMSO


title: CCh08_male_children_digit_chondrocyte


title: CCh09_male_children_digit_chondrocyte


title: CCh07_male_children_digit_chondrocyte


title: CCh05_female_children_digit_chondrocyte

value: female


title: CCh06_female_children_digit_chondrocyte


title: 49281, nonpregnant

value: Endometrial cells from uterine body


title: CCh03_female_children_digit_chondrocyte

value: child


title: 49238, nonpregnant


title: PCB187_2.5_4 [ATGCCGCT-CCATAGGG-2]


title: PFNA_0.25_4 [TCCTTGGC-CTATGATC-2]

value: PFNA 0.25


title: Copper_0.025_2 [CGTAATTC-ATAGAGAG-2]


title: BPS_0.025_3 [TCAAGGAT-ATATGAGA-2]


title: 49235, pregnant


title: PPB_0.025_4 [CTAGCCGA-ATATGAGA-2]


title: Mercury_0.25_4 [TCCTTGGC-ATAGAGAG-2]

value: Mercury 0.25


title: 49195, nonpregnant


title: Cadmium_2.5_2 [ACCGACCA-ATAGAGAG-2]

value: WT

value: Cadmium 2.5


title: CCh02_female_children_digit_chondrocyte

value: chondrocyte


title: CCh01_female_children_digit_chondrocyte


title: 49160, nonpregnant


title: Phenanthrene_0.025_4 [TGAATGTG-CTATGATC-2]

value: Nontumorigenic breast

value: Phenanthrene 0.025


title: CCh04_female_children_digit_chondrocyte


title: 49119, nonpregnant


title: ACa07_male_adult_knee_cartilage

source_name: cartilage

value: male

value: adult

value: cartilage


title: ACa08_male_adult_knee_cartilage


title: ACa02_female_adult_knee_cartilage


title: Thiram_0.25_2 [AATGTGCC-CCATAGGG-2]

value: Thiram 0.25


title: DCP_25_0.025_4 [ACCTGAGC-CCATAGGG-2]


title: ACa01_female_adult_knee_cartilage


title: Pooled EPS brains, mScarlet+ve Sorted Cells

city: Toronto

first: Madeline

middle: Nicole

last: Hayes

state: Ontario

address: 72 Elm St

department: DSCB

country: Canada

institute: Sickkids Research

data_processing:
Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy-aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k-mers length of 23, with entries manually added for GFP, mScarlet, EGFRviii, KRAS, and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: -r, --seqBias, --mp -3, --validateMappings, --rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited .csv file including raw counts for all conditions.

organism: Danio rerio

source_name: Sorted Cells

growth_protocol: Zebrafish were housed and reared following approved animal use protocol

extract_protocol:
Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations
Sequence ready polyA-enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina, according to manufacturer’s recommendations

treatment_protocol: Fertilized embryos injected with either EPS or KPG construct mix

tag: strain

value: CG1 p53null

value: Sorted Cells


title: EGFRviii, PI3KCAH1047R, mScarlet tumor negative control brain 2

source_name: Whole Brain

value: Whole Brain


title: PCB153_0.025_3 [CCTACACA-CCATAGGG-2]

value: 48 hrs

value: DMSO


title: Thiram_0.025_1 [GTTAAGCA-CCATAGGG-2]

value: Thiram 0.025


title: Cadmium_2.5_4 [ATGCCGCT-ATAGAGAG-2]

value: Water


title: PFOS_0.25_4 [CAACCGTG-CTATGATC-2]

value: PFOS 0.25


title: EGFRviii, PI3KCAH1047R, mScarlet tumor positive whole brain 3


title: PPB_2.5_3 [GTGCGAGT-ATATGAGA-2]

value: WT

value: PPB 2.5


title: PFDA_2.5_1 [AACGCTTG-CTATGATC-2]

value: PFDA 2.5


title: 49101, nonpregnant

value: Endometrial cells from uterine body


title: 49095, pregnant


title: Control_0_26 [CTAAGGCG-ATATGAGA-2]

value: Nontumorigenic breast

value: Control 0


title: Homo sapiens xenograft in Mus musculus, Ctrl_Day1_gene1

description: Gene expression Day 1 of experiment

value: Head and Neck Squamous cell tumor

value: hypopharyngeal

value: Athymic nude mice (nu/nu)

value: Female

value: 6 weeks old

value: Ctrl


title: DCB_14_25_1 [GTTCGTCT-CCATAGGG-2]

value: 48 hrs


title: KRAS,PI3KCAH1047R, GFP tumor negative control brain

value: CG1 p53null

value: Whole Brain


title: 49013, pregnant


title: DCB_14_0.25_2 [CTCTCAGG-CCATAGGG-2]

value: DMSO


title: Control_0_18 [CCTTATGT-ATATGAGA-2]


title: EGFRviii, PI3KCAH1047R, mScarlet tumor positive whole brain 2


title: EGFRviii, PI3KCAH1047R, mScarlet tumor negative control brain 1


title: Control_0_14 [CTGCGAAC-ATAGAGAG-2]

value: Water


title: 49059, nonpregnant


title: 49082, nonpregnant


title: EGFRviii, PI3KCAH1047R, mScarlet tumor positive whole brain 1


title: Phenanthrene_25_2 [CAGAAGAA-CTATGATC-2]

value: WT

value: Phenanthrene 25


title: Control_0_46 [CTGCGAAC-CTATGATC-2]


title: 48991, pregnant


title: Lead_0.25_3 [AAGTACCT-ATAGAGAG-2]

value: Lead 0.25


title: 49014, nonpregnant

value: Endometrial cells from uterine body


title: PPB_2.5_1 [CAACTCCG-ATATGAGA-2]

value: Nontumorigenic breast

value: PPB 2.5


title: KRAS,PI3KCAH1047R, GFP tumor positive whole brain 2


title: Mercury_2.5_4 [CTTCTGGC-ATAGAGAG-2]

value: Mercury 2.5


title: DCP_25_0.025_1 [CTCGTACA-CCATAGGG-2]


title: KRAS,PI3KCAH1047R, GFP tumor positive whole brain 3


title: MPB_2.5_1 [TGTTGCAC-ATATGAGA-2]

value: MPB 2.5


title: Phenanthrene_25_4 [CGTCTGAA-CTATGATC-2]


title: KRAS,PI3KCAH1047R, GFP tumor positive whole brain 1


title: 48988, pregnant


title: 48983, pregnant


title: PCB187_0.025_1 [TCAACTGA-CCATAGGG-2]


title: Copper_0.025_3 [ATTCGCAG-ATAGAGAG-2]

value: Copper 0.025


title: 48943, nonpregnant


title: Control_0_40 [CTGTACGC-CTATGATC-2]

value: Control 0


title: 49007, nonpregnant


title: siUSF1 MLPS+IFNγ control, biol rep 5

city: Sheffield

first: Endre

last: Kiss-Toth

state: South Yorkshire

address: The Medical School, Beech Hill Road

department: Division of Clinical Medicine

institute: University of Sheffield

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequences using trimmomatic PE (parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Trimmed sequence reads were mapped to hg38 using Salmon v 0.11.4
Read count extraction and normalization were performed using STAR
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes TPM and  NumReads values for each sample

source_name: Blood

extract_protocol:
RNA was harvested using ReliaPrep RNA Cell miniprep system (Promega)
RNA libraries for RNAseq were prepared by Novogene using polyA enrichment library preparation

value: Blood

value: Monocyte-derived macrophage

value: USF1 knockdown

value: MLPS+IFNgamma


title: siUSF1 MLPS+IFNγ control, biol rep 6


title: PFOA_0.025_2 [CGTAATTC-CTATGATC-2]

value: 48 hrs


title: siUSF1 MLPS+IFNγ control, biol rep 4


title: PCB153_0.025_1 [TCACTCAC-CCATAGGG-2]

value: DMSO


title: DCP_25_0.025_2 [CGTAATTC-CCATAGGG-2]


title: siUSF1 MLPS+IFNγ control, biol rep 3


title: 48902, pregnant

data_processing:
Trimming with cutadapt (v.3.4); phred-like score <20 and reads <65 bases
Mapped with STAR package (v2.7.9) to ARS-UCD1.3
Mapped reads processed with HTSeq, samtools, and scripts to remove PCR duplicates and to count uniquely mapped reads
Read counts normalized by library size
Assembly: Bos taurus (ARS-UCD1.3)
Supplementary files format and content: Txt data file includes Gene ID in first column. Expression data in reads per million


title: PCB187_25_2 [ACATCCTT-CCATAGGG-2]


title: Control_0_49 [ACTCACCG-CCATAGGG-2]


title: PFOA_25_3 [ATGGTCCG-CTATGATC-2]

value: PFOA 25

value: Water


title: PFOS_2.5_2 [ACCGACCA-CTATGATC-2]

value: WT

value: PFOS 2.5


title: siUSF1 MLPS+IFNγ control, biol rep 2


title: 48761, nonpregnant

value: Endometrial cells from uterine body


title: PCB153_2.5_4 [CTTCTGGC-CCATAGGG-2]

value: Nontumorigenic breast


title: Lead_0.025_2 [AACCAATC-ATAGAGAG-2]


title: MLPS+IFNγ control, biol rep 6

value: Control


title: PFDA_0.025_1 [CGAGCATT-CTATGATC-2]


title: 48661, nonpregnant


title: 48859, nonpregnant


title: BPF_0.025_2 [CGTAATTC-ATATGAGA-2]


title: 48871, nonpregnant


title: PCB187_0.25_1 [TCCTCAGA-CCATAGGG-2]


title: 48624, nonpregnant


title: PPB_25_3 [ACACAACA-ATATGAGA-2]

value: PPB 25


title: Mercury_0.025_1 [TCACTCAC-ATAGAGAG-2]

value: Mercury 0.025


title: 48617, nonpregnant


title: MLPS+IFNγ control, biol rep 4


title: Cadmium_0.025_2 [CAAGTAGT-ATAGAGAG-2]

value: Cadmium 0.025


title: MLPS+IFNγ control, biol rep 5


title: MLPS+IFNγ control, biol rep 3


title: PFOA_25_1 [CCATTGCG-CTATGATC-2]


title: 48614, nonpregnant


title: 48578, nonpregnant


title: MPB_2.5_3 [CGCAACAG-ATATGAGA-2]

value: MPB 2.5


title: Copper_0.25_1 [TACAGAGT-ATAGAGAG-2]

value: Copper 0.25


title: PFNA_0.025_2 [CAGGCTTC-CTATGATC-2]


title: MLPS+IFNγ control, biol rep 2

value: Blood

value: Monocyte-derived macrophage


title: 48476, nonpregnant


title: MPB_2.5_2 [ATTCTCCA-ATATGAGA-2]


title: MLPS+IFNγ control, biol rep 1

value: MLPS+IFNgamma


title: Arsenic_2.5_1 [AACGCTTG-ATAGAGAG-2]

value: Arsenic 2.5

value: 48 hrs


title: Lead_2.5_2 [GTACCAGC-ATAGAGAG-2]

value: Lead 2.5


title: siUSF1 MLPS+IFNγ control, biol rep 1

value: USF1 knockdown


title: Mercury_2.5_2 [ATTCTCCA-ATAGAGAG-2]

value: WT

value: Mercury 2.5

value: Water


title: 48461, nonpregnant

value: Endometrial cells from uterine body


title: siUSF1 M0, biol rep 6


title: Control_0_3 [ATAGATCC-ATAGAGAG-2]

value: Nontumorigenic breast

value: Control 0


title: BPF_0.025_1 [CTCGTACA-ATATGAGA-2]

value: DMSO


title: 48454, pregnant


title: Control_0_31 [GCCAGTGT-ATATGAGA-2]


title: 48243, nonpregnant


title: siUSF1 M0, biol rep 5


title: BPS_2.5_1 [AACGCTTG-ATATGAGA-2]

value: BPS 2.5


title: siUSF1 M0, biol rep 4


title: Cadmium_0.025_3 [GTGTCCAT-ATAGAGAG-2]

value: Cadmium 0.025


title: 48161, nonpregnant


title: siUSF1 M0, biol rep 3


title: Mercury_0.025_2 [CAGGCTTC-ATAGAGAG-2]

value: Mercury 0.025


title: Mercury_0.025_4 [CGCGTGAT-ATAGAGAG-2]


title: 48154, pregnant


title: siUSF1 M0, biol rep 2

value: Blood


title: MPB_25_3 [GATGAGAA-ATATGAGA-2]

value: MPB 25


title: BPA_25_1 [GGCTCCTA-ATATGAGA-2]

value: BPA 25


title: siUSF1 M0, biol rep 1

value: Monocyte-derived macrophage


title: Phenanthrene_0.25_3 [AAGTACCT-CTATGATC-2]

value: Phenanthrene 0.25

value: 48 hrs


title: siMYC M0, biol rep 6

value: MYC knockdown


title: 47928, nonpregnant


title: PFDA_2.5_4 [TGAACTCT-CTATGATC-2]

value: WT

value: PFDA 2.5


title: 47905, nonpregnant


title: Phenanthrene_0.025_3 [TCTATTGG-CTATGATC-2]

value: Phenanthrene 0.025


title: BPS_25_2 [CCAGGTAA-ATATGAGA-2]

value: BPS 25


title: BPF_0.025_4 [ACCTGAGC-ATATGAGA-2]

value: Nontumorigenic breast


title: Copper_0.25_3 [TGTAAGAC-ATAGAGAG-2]

value: Copper 0.25

value: Water


title: 47524, nonpregnant

value: Endometrial cells from uterine body


title: siMYC M0, biol rep 5


title: Cadmium_0.025_1 [TCAACTGA-ATAGAGAG-2]

value: Cadmium 0.025


title: siMYC M0, biol rep 4


title: PCB153_2.5_3 [CGCAACAG-CCATAGGG-2]

value: DMSO


title: 47520, pregnant


title: siMYC M0, biol rep 3

value: Blood


title: DCB_14_0.25_3 [CACCGCAA-CCATAGGG-2]


title: BPS_0.025_4 [CAAGTGAC-ATATGAGA-2]


title: 47992, pregnant


title: 47226, pregnant


title: siMYC M0, biol rep 2


title: Mercury_2.5_3 [CGCAACAG-ATAGAGAG-2]

value: Mercury 2.5


title: siMYC M0, biol rep 1


title: Control_0_57 [TTCCATTC-CCATAGGG-2]

value: Control 0


title: 47034, pregnant


title: Cadmium_25_4 [CTGCGAAC-CCATAGGG-2]

value: Cadmium 25


title: 47013, pregnant


title: Thiram_25_4 [CGTCTGAA-CCATAGGG-2]

value: Thiram 25


title: Control_0_13 [CTATTCCA-ATAGAGAG-2]

value: 48 hrs


title: M0 control, biol rep 6

value: Monocyte-derived macrophage

value: Control


title: 46966, nonpregnant


title: Control_0_54 [CCGAGTTA-CCATAGGG-2]

value: WT


title: Control_0_21 [TGGTGACT-ATATGAGA-2]


title: M0 control, biol rep 5


title: PFDA_0.025_2 [ACCGTTCC-CTATGATC-2]


title: Arsenic_0.25_1 [ACGAAGCG-ATAGAGAG-2]

value: Arsenic 0.25


title: MPB_0.025_4 [CGCGTGAT-ATATGAGA-2]


title: PFOS_2.5_1 [CAACTCCG-CTATGATC-2]

value: PFOS 2.5


title: 46847, nonpregnant


title: MPB_25_4 [ATGACACC-ATATGAGA-2]

value: Nontumorigenic breast

value: MPB 25


title: 46829, pregnant


title: Lead_25_3 [CAGGAAGG-ATAGAGAG-2]

value: Lead 25

value: Water


title: M0 control, biol rep 4


title: DCP_25_2.5_3 [CCACAATG-CCATAGGG-2]


title: 47146, nonpregnant

value: Endometrial cells from uterine body


title: M0 control, biol rep 2


title: M0 control, biol rep 3


title: PCB187_2.5_1 [CAACTCCG-CCATAGGG-2]

value: DMSO


title: M0 control, biol rep 1

value: Blood


title: BPA_0.025_4 [TGAATGTG-ATATGAGA-2]


title: 46672, nonpregnant


title: Phenanthrene_0.25_2 [AATGTGCC-CTATGATC-2]

value: Phenanthrene 0.25


title: Control_0_53 [TGGTGACT-CCATAGGG-2]

value: Control 0


title: E2A_PBX1_rep3 (PDX_ATAC)

description: ATAC-seq on ALL patient derived xenografts (PDX_ATAC)

data_processing:
Data were analyzed as in (https://doi.org/10.1038/s41375-022-01685-z), GSE161501, and GSE129066.
Assembly: HG19
Supplementary files format and content: .narrowpeak for accessible regions

source_name: PDX

value: PDX

tag: disease state

tag: disease subgroup


title: Control_0_15 [GCCAGTGT-ATAGAGAG-2]

tag: cell line

tag: cell type


title: E2A_PBX1_rep1 (PDX_ATAC)


title: MPB_0.25_1 [ATGGAACA-ATATGAGA-2]

tag: genotype

tag: treatment


title: BPS_25_1 [GTTCGTCT-ATATGAGA-2]

value: BPS 25

tag: time


title: 46590, pregnant


title: E2A_PBX1_rep2 (PDX_ATAC)


title: 46538, pregnant


title: Cadmium_0.025_4 [CTAGCCGA-ATAGAGAG-2]

value: Cadmium 0.025

value: 48 hrs


title: MLL_AF4_Rep2 (PDX_ATAC)


title: PCB187_0.025_4 [CTAGCCGA-CCATAGGG-2]


title: 46362, nonpregnant


title: Control_0_43 [GTTATCGA-CTATGATC-2]


title: 46313, nonpregnant


title: MLL_AF4_Rep1 (PDX_ATAC)


title: Thiram_0.25_1 [GTTGACAG-CCATAGGG-2]

value: Thiram 0.25


title: 46249, nonpregnant


title: BPA_2.5_2 [GTACCAGC-ATATGAGA-2]

value: WT

value: BPA 2.5


title: Control_0_60 [TGGACAAC-CCATAGGG-2]


title: 46262, pregnant


title: 46633, nonpregnant


title: BPS_25_4 [TGGTACAG-ATATGAGA-2]


title: Pooled EPS brains, mScarlet-ve Sorted Cells

value: CG1 p53null

tag: tissue

value: Sorted Cells


title: TALL_Rep1 (PDX_ATAC)


title: PCB187_25_1 [CATCTTCT-CCATAGGG-2]

value: Nontumorigenic breast


title: Control_0_51 [ATAGATCC-CCATAGGG-2]


title: PPB_25_2 [ACATCCTT-ATATGAGA-2]

value: PPB 25


title: Cadmium_25_2 [ACATCCTT-ATAGAGAG-2]

value: Cadmium 25

value: Water


title: DCB_14_0.025_1 [CGAGCATT-CCATAGGG-2]

value: DMSO


title: ATAC_HSB2_2


title: MPB_0.025_2 [CAGGCTTC-ATATGAGA-2]


title: 45808, pregnant

value: Endometrial cells from uterine body


title: Control_0_55 [TGGTGGAA-CCATAGGG-2]


title: ATAC_DND41_2


title: BPF_0.25_2 [CTTGTTGG-ATATGAGA-2]


title: ATAC_Loucy_2

source_name: Loucy

value: Loucy


title: TALL_Rep2 (PDX_ATAC)


title: 45796, nonpregnant


title: Control_0_32 [GTGCGTTC-ATATGAGA-2]

value: Control 0


title: DCP_25_2.5_1 [CACATGGT-CCATAGGG-2]


title: ATAC_CEM_2

value: CEM


title: Control_0_22 [CCGAGTTA-ATATGAGA-2]


title: ATAC_MOLT16_2


title: PFNA_25_4 [ATGACACC-CTATGATC-2]

value: PFNA 25


title: 46174, nonpregnant


title: Mercury_25_4 [ATGACACC-ATAGAGAG-2]

value: Mercury 25


title: BPS_0.025_2 [ACCGTTCC-ATATGAGA-2]

value: 48 hrs


title: 45523, nonpregnant


title: PFOS_0.25_1 [TCCTCAGA-CTATGATC-2]

value: PFOS 0.25


title: 45354, pregnant


title: ATAC_P12_2


title: 46026, pregnant


title: ATAC_Jurkat_2

value: Jurkat


title: 45248, nonpregnant


title: BPF_2.5_1 [CACATGGT-ATATGAGA-2]

value: WT

value: BPF 2.5


title: PPB_25_4 [CAGGCCAT-ATATGAGA-2]


title: Mercury_0.025_3 [CCTACACA-ATAGAGAG-2]

value: Mercury 0.025


title: 45799, nonpregnant


title: DCP_25_25_4 [TCCTATCT-CCATAGGG-2]

value: Nontumorigenic breast


title: MPB_0.25_2 [CTAACAAC-ATATGAGA-2]


title: ATAC_DND41_1


title: PFOA_2.5_4 [TCAGATAC-CTATGATC-2]

value: PFOA 2.5


title: Cadmium_0.25_1 [TCCTCAGA-ATAGAGAG-2]

value: Cadmium 0.25


title: ATAC_HSB2_1


title: Thiram_0.25_4 [CGACTAGC-CCATAGGG-2]

value: Thiram 0.25


title: 45169, nonpregnant


title: 44344, nonpregnant


title: 44059, nonpregnant


title: PFOS_0.025_2 [CAAGTAGT-CTATGATC-2]

value: DMSO


title: ATAC_Loucy_1


title: BPA_0.25_3 [AAGTACCT-ATATGAGA-2]


title: ATAC_CEM_1


title: BPF_25_2 [TTCACACT-ATATGAGA-2]

value: BPF 25


title: ATAC_MOLT16_1


title: DCP_25_25_2 [TTCACACT-CCATAGGG-2]


title: 43838, pregnant

value: Endometrial cells from uterine body


title: 43726, pregnant


title: MPB_2.5_4 [CTTCTGGC-ATATGAGA-2]

value: MPB 2.5


title: BPS_0.25_2 [CTCTCAGG-ATATGAGA-2]


title: ATAC_P12_1


title: Control_0_61 [CTATTCCA-CCATAGGG-2]

value: Control 0


title: ATAC_Jurkat_1


title: 45244, nonpregnant


title: 43267, nonpregnant


title: PFNA_0.25_2 [CTAACAAC-CTATGATC-2]

value: PFNA 0.25


title: PFOS_25_1 [CATCTTCT-CTATGATC-2]

value: PFOS 25


title: Control_0_20 [GGAGCTAT-ATATGAGA-2]

value: 48 hrs


title: PFNA_2.5_2 [ATTCTCCA-CTATGATC-2]

value: PFNA 2.5


title: 43096, pregnant


title: Phenanthrene_2.5_2 [GTACCAGC-CTATGATC-2]

value: Phenanthrene 2.5


title: S3_blood_13

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

data_processing:
Data was mapped against a cDNA library using a pseudo-aligner approach (kallisto v0.46.1)
Assembly: GRCm38
Supplementary files format and content: Processed data contains length-scaled TPM values.

extract_protocol:
Total RNA from bone marrow derived murine neutrophils and monocytes, or whole blood, from control and treated mice was purified using the RNeasy Plus Mini kit (QIAGEN, Germany) following the manufacturer’s instructions.
Library was prepared using a 250-300 bp insert cDNA library (low-input). mRNA was enriched using oligo (dT) beads and randomly fragmented in fragmentation buffer followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment.

value: Blood

tag: condition

value: PBS


title: 43599, nonpregnant

extract_protocol:
Qiagen Rneasy Microkit with prior tissue homogenization using beads
NEBNext Ultra II Directional RNA Library Prep Kit and SPT Labtech mosquito LV liquid handling instrument


title: S3_blood_10_ivig

value: IVIG


title: BPS_0.25_1 [ACGAAGCG-ATATGAGA-2]

value: Nontumorigenic breast

value: WT


title: Control_0_10 [CTAAGGCG-ATAGAGAG-2]

value: Water


title: m4_stimul_Ics_6h

source_name: Ics

value: Ics


title: m2_stimul_Ics_6h


title: Control_0_17 [ACTCACCG-ATATGAGA-2]

value: DMSO


title: PFOA_0.25_1 [TACAGAGT-CTATGATC-2]

value: PFOA 0.25


title: PFDA_0.25_2 [CTCTCAGG-CTATGATC-2]

value: PFDA 0.25


title: Lead_0.25_2 [AATGTGCC-ATAGAGAG-2]

value: Lead 0.25


title: PFNA_0.25_1 [ATGGAACA-CTATGATC-2]


title: 40560, pregnant

value: Endometrial cells from uterine body


title: 43077, nonpregnant


title: m3_stimul_Ics_6h


title: 43185, nonpregnant


title: 40550, nonpregnant


title: S3_blood_9