title: A08_12H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv

value: seeding


title: A08_CT_5

status: Public on Apr 13 2021

type: SRA

city: Nanjing

first: wang

last: yinying

state: Jiangsu

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

department: College of Agriculture

country: China

institute: Nanjing Agricultural University

description: count.csv

library_source: transcriptomic

data_processing:
alignment: Hisat2 software version 2.1.0
assemble: stringtie software version 1.3.5
Genome_build: B73 AGPv4.59 reference genome
Supplementary_files_format_and_content: format: csv, content: genes reads count

molecule: total RNA

organism: Zea mays

source_name: seedling stalk

growth_protocol: K09 (resistant) and A08 (susceptible) seedling  are planted at a temperature at 26 ± 2 °C during a 14/10 h light/dark cycle, with the light density of 600 LUX, a  humidity approximately 75%.

extract_protocol:
RNA was extracted from the seedling stems at different time points inoculated with F. graminearum using TRIzol reagent (Invitrogen), then purified with the RNeasy
RNA samples were subject to quality control prior to the library construction using Illumina TruSeq RNA library prep kit v2

treatment_protocol: 20 μl of 1.0ⅹ10 6 /ml Fusarium graminearum  spore suspensions  in 0.001% Tween-20 were inoculated to the K09 (resistant) and A08 (susceptible)， seedling stem，and the seedling stalk of K09 and A08 were  harvested at 6h，12h，24h，48h and 72h. with non-infected materials at 6h as control.

tag: tissue

value: stem

tag: developmental stage

tag: treatment

value: MOCK

tag: hours post inoculated

tag: genotype

value: wild type


title: NHP_Group2_202_5

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

library_source: genomic

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

molecule: genomic DNA

organism: Macaca fascicularis

source_name: whole liver lysate

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. For HepG2 cells, the base editor and sgRNA was inroduced by NEON electroporation. In vivo treatment was delivery by AAV or LNP mediated delivery via tail vein injection.

value: on-target

value: intravenous

value: targeted amplicon sequencing

value: base-edited PCSK9


title: FlatCoatedRetriever40

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

country: USA

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on an Illumina iScan.

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Flatcoated Retriever


title: YPB-rep1

city: Harbin

first: Guangyue

last: Li

state: heilongjang

address: No.26 Hexing Road Xiangfang District

department: College of Life Science

institute: Northeast Forestry University

data_processing:
ChIP-seq reads were quality and adapter trimmed with Cutadapt (version 1.14), before being aligned to the human hg38 genome with bowtie2 (version 2.3.5) using default parameters.
Resulting BAM files were sorted and indexed with samtools and PCR duplicates were filtered with picard tools MarkDuplicates (version 2.18.26) and MultiBamSummary and PlotCorrelation programs in DeepTools were used to complete correlation analysis of repeated samples.
Peaks were called on filtered input and control BAM files with MAC2 set to broadPeak with the following command line parameters: macs2 callpeak -t Input.bam -c Control.bam -f BAMPE -g hs -n CPP2 --broad --broad-cutoff 0.05 -q 0.05 --outdir . --keep-dup all
High confidence peak screening between samples was performed using Bedtools (v2.29.2) and BigWig coverage files were generated using bedGraphToBigWig (version 4) from MACS2 resulting bedgraphs.
Peaks were annotated by ChipSeeker package and the differences of each group on the Peaks were analyzed by DiffBind package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Bigwig files of histone marks

organism: Homo sapiens

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640, supplemented with 10% fetal bovine serum (FBS) (Biological Industries USA, Inc.), and maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7645S) from New England Biolabs Inc. (Ipswich, MA). The following steps were followed for library preparation: end repair, 5’ phosphorylation, dA-tailing, adapter ligation, U excision, cleanup of adaptor-ligated DNA without size selection, and library amplification for 12 to 13 cycles followed by clean-up with Agencourt AMPure XP. The quality of the libraries was assessed using the Agilent High Sensitivity DNA kit (cat# 5067-4626) on the Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified using the NEBNext Library Quant kit for Illumina (cat# E7630S) from New England Biolabs Inc

treatment_protocol: Cells were individually treated with 30 μM of YPB, OPB and a control peptide for 48 h

tag: cell type

value: triple negative breast cancer (TNBC) cell lines

tag: chip antibody

value: YPB


title: FlatCoatedRetriever35


title: NHP_Group1_103_5


title: FlatCoatedRetriever34


title: YPB-Input

value: untreated


title: A08_48H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group1_102_5


title: FlatCoatedRetriever33


title: A08_12H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group1_101_5


title: A08_CT_4

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever32


title: Panc6.03

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Trim adapters with trim_galore
Align reads with STAR to hg38 genome with option --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited files with raw counts from STAR --quantMode GeneCounts

growth_protocol: cell lines were cultured in RPMI-1640 supplemented with 5% fetal bovine serum, 2 mM L-Glutamine, and 100 IU/ml penicillin/streptomycin. The cells were grown at 37 °C in a humidified atmosphere supplemented with 5% (v/v) CO2.

extract_protocol:
Trizol (Invitrogen) was used to isolate total RNA by following the instruction provided by the company.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp.
Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 75 bp, paired end sequencing was performed on an Illumina NextSeq 500 sequencer using a 150 bp HO sequencing kit (v2) (Illumina Inc., San Diego, CA, USA), with all libraries sequenced to a minimum read depth of 40M read pairs per library

treatment_protocol: Cell line samples for RNAseq were not subjected to treatment. The main comparison is differential expression between glycan phenotypes of the samples.

tag: cell line

value: pancreatic cancer cell

tag: glycan

value: Both


title: CFPAC1


title: FlatCoatedRetriever31


title: NHP_Group4_403_4


title: FlatCoatedRetriever30


title: FlatCoatedRetriever36


title: Capan2


title: SW1990


title: NHP_Group4_402_4


title: NHP_Group4_401_4


title: SU8686


title: FlatCoatedRetriever29


title: A08_CT_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: PANC203


title: K09_72H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group3_303_4


title: FlatCoatedRetriever27


title: NHP_Group3_302_4


title: K09_72H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: K09_72H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever26


title: NHP_Group3_301_4


title: PL45


title: PANC10.05


title: FlatCoatedRetriever25


title: NHP_Group2_203_4


title: K09_24H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: K09_6H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever24


title: Colo357


title: A08_48H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: L3.3


title: NHP_Group2_202_4


title: NHP_Group2_201_4


title: K09_6H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever28


title: FlatCoatedRetriever23


title: K09_6H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group1_103_4


title: K09_CT_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: PaTu-8988T


title: NHP_Group1_102_4


title: FlatCoatedRetriever21


title: Panc8.13


title: PANC1


title: K09_CT_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: K09_CT_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever19


title: NHP_Group4_403_3


title: MiaPaCa-2


title: FlatCoatedRetriever20


title: A08_72H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever18


title: NHP_Group4_403_2


title: L36PL


title: BX-PC3


title: NHP_Group4_403_1


title: FlatCoatedRetriever17


title: PANC2.13

value: sTRA


title: FlatCoatedRetriever22


title: Panc4.03


title: FlatCoatedRetriever16


title: NHP_Group4_402_3


title: A08_24H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group4_402_2


title: FlatCoatedRetriever15


title: NHP_Group4_402_1


title: NHP_Group1_101_4


title: Panc3.27


title: FlatCoatedRetriever13


title: NHP_Group4_401_3


title: FlatCoatedRetriever12


title: A08_72H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: PaTu-8988S


title: A08_6H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group4_401_2


title: HPAF2


title: A08_CT_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: PV3

city: Hangzhou

first: Yongli

last: Ji

state: Zhejiang

address: Jiefang Road 88

institute: Zhejiang University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample,Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: adipose derived stem cells

growth_protocol: Stem cells were isolated from mice subcutaneous, abdominal and perivascular adipose tissue,and then cultured in stem cell culture medium

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose derived stem cells

tag: strain

value: perivascular adipose


title: A08_72H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv

value: seeding


title: NHP_Group4_401_1


title: A08_CT_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv

value: stem


title: NHP_Group3_303_3


title: HPAC

source_name: HPAC

value: HPAC


title: PV2


title: Capan1


title: NHP_Group3_303_2


title: FlatCoatedRetriever14


title: A08_6H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv

value: wild type


title: PANC504


title: NHP_Group3_303_1

value: on-target


title: PSN1


title: A08_6H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: PV1


title: Hs-766T


title: X1.2.uM.Phenanthrene.quinone_6_PE50_BG_Rep6

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

data_processing:
Raw fastq files were trimmed if necessary to remove adaptor sequences or basepairs with a phred score below 25
Each fastq file was aligned to the Genome Reference Consortium Zebrafish Build 11 (GRCz11) (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/) using the Star Aligner (Dobin et al. 2013) with default settings
Resulting SAM files were then used to count reads aligning to genes using HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/) along with the gff file for the Z11 genome (GCF_000002035.6_GRCz11_genomic.gff)
This led to a file of 39,701 genes with raw counts assigned to them.  From this file any gene that had a count of ‘0’ in at least 43/170 (more than 25% of the datasets had a ‘0’ for that gene), was removed from further analysis.  This led to a dataset of 21,854 genes across 170 datasets.
Raw counts were normalized with DESEQ2.  This program was also used to identify fold changes and associated adjusted p-values for those fold changes
Genome_build: GRCz11
Supplementary_files_format_and_content: .csv, Normalized gene expression levels

organism: Danio rerio

growth_protocol: To collect zebrafish embryos spawning funnels were placed in the tanks at night and the following morning embryos were collected and age staged (Kimmel et al. 1995; Westerfield 2007). Embryos were maintained in embryo medium (EM) in an incubator at 28°C until further processing. EM consisted of 15 mM NaCl, 0.5 mM KCl, 1 mMMgSO4, 0.15 mMKH2PO4, 0.05 mM Na2HPO4, and 0.7 mMNaHCO3.

extract_protocol:
Following exposure, 48-hpf whole embryos were homogenized using RNAzol (Molecular Research Center, Inc).  RNA was isolated via phenol guanidine extraction.
50 bp sequencing was conducted using an Illumina HiSeq 2000 sequencer
mRNAs were enriched by polyA selection. Libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems)

treatment_protocol: Embryos were exposed to chemicals above and RNA was harvested at 48 hpf

value: 48 hour post fertilization embryo

tag: chemical

value: Phenanthrene-quinone

tag: concentration


title: X1.2.uM.Phenanthrene.quinone_5_PE50_BG_Rep5


title: AB3

value: abdominal adipose


title: X1.2.uM.Phenanthrene.quinone_4_PE50_BG_Rep4


title: NHP_Group3_302_3

value: intravenous

value: targeted amplicon sequencing

value: base-edited PCSK9


title: AB2


title: NHP_Group3_302_2


title: X1.2.uM.Phenanthrene.quinone_3_PE50_BG_Rep3


title: ASPC1


title: AB1


title: X1.2.uM.Phenanthrene.quinone_2_PE50_BG_Rep2


title: X1.2.uM.Phenanthrene.quinone_1_PE50_BG_Rep1


title: WTC

city: Mexico City

first: Jorge

last: Melendez-Zajgla

address: Periferico Sur 4809 Col. Arenal Tepepan

country: Mexico

institute: Instituto Nacional de Medicina Genomica

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed for adapters, low complexity and low quality bases using trimmomatic ver. 0.33
Conserved paired reads were aligned with STAR ver 2.4.2 using GRCh38 and genocode GTF ver. 24
Transcript abundance was determined using RSEM ver. 1.2.29
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file that includes normalized count values for each sample

source_name: Breast cancer cell line

growth_protocol: MCF7 cells were cultured in EMEM supplemented with 5% Fetal Bovine Serum and were transiently transfected with an expression vector containing the ORF of IKKe using Xfect (clontech) . An expression vector containing the ORF of Lacz was employed as a control. The cells were analyzed for IKKe expression 48 hours after transfection by qRTPCR and found a 200 fold increase expression in MCF7 IKKe overexpressing cells

extract_protocol:
RNA was isolated with Trizol
Library was constructed using TruSeq stranded total RNA Illumina
RNAseq 2x 76 Paired End

value: MCF7 cells

value: Transfected with an IKKe overexpressing vector

tag: type of transfection

value: Transient


title: WTB


title: SUB2

value: subcutaneous adipose


title: DMSO_7_PE50_AK_Rep7

value: DMSO


title: SUB1

value: adipose derived stem cells


title: V3

value: Transfected with a control vector


title: NHP_Group3_301_2


title: NHP_Group3_301_1


title: DMSO_6_PE50_AK_Rep6


title: DMSO_5_PE50_AK_Rep5


title: V2


title: NHP_Group2_203_3


title: V1


title: DMSO_4_PE50_AK_Rep4


title: NHP_Group2_203_2


title: invivo_LNP_48h_Rep2

data_processing:
Raw reads were trimmed and filtered using fastp version version 0.20.0
Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
variants were called using HaplotypeCaller (GATK version 4.1.2.0)
Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
Supplementary_files_format_and_content: Variant call format (VCF)

source_name: primary hepatocytes

growth_protocol: for in vitro:DMEM growth medium supplemented with 10% FBS and 1% P/S; in vivo samples were isolated from C58BL/6J animals

extract_protocol:
in vitro: Detachment with TryplE, wash with PBS, lysis in RLT buffer and RNA isolation following RNAeasy protocol; in vivo: primary hepatocyte isolation
total RNA

treatment_protocol: in vitro: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000; in vivo: LNP- or AAV-mediated delivery

value: tail vein

value: ABEmax7.10, LNP, 48h

value: primary hepatocytes


title: invivo_LNP_48h_Rep1


title: invivo_LNP_48h_Rep3


title: NHP_Group2_203_1

value: on-target


title: DMSO_3_PE50_AK_Rep3

value: 48 hour post fertilization embryo


title: invivo_LNP_Rep3

value: ABEmax7.10, LNP


title: NHP_Group3_302_1


title: DMSO_2_PE50_AK_Rep2


title: SUB3


title: POLG D7 PerMac_LPS_rep1

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Sample 15

data_processing:
Illumina BaseSpace FASTQ Generation | Version: 1.0.0
Illumina BaseSpace RNA-Seq Alignment | Version: 2.0.0; Incroporates STAR Aligner (Version: 2.6.1a) and Salmon Quantification (Version 0.11.2)
Genome_build: Mus_musculus (UCSC mm10)

growth_protocol: For BMDMs, bone marrow was isolated from the femurs and tibiae of mice. After red blood cell lysis using ACK buffer, marrow cells were then cultured for 6 days in the presence of 30% conditioned media harvested from L929 cells (a source of MCSF) to enrich for macrophages. On day 6, cells were lifted and re-plated into well dishes in 5% L929 conditioned media for LPS challenge experiments (Da7 seven post harvest). For PerMacs, 1.5 ml of 3% Brewer's thioglycollate media was injected i.p. into mice.  Four days later, peritoneal exudate cells were harvested by gavage and plated on tissue culture dishes for subsequent treatment. DMEM media (Sigma D5796) supplemented with 10% FBS (screened for low endotoxin; VWR 97068-085) was used throughout.  Standard culture at 37C, 5% CO2 in a humidified incubator.

extract_protocol:
Total cellular RNA from WT and POLG BMDMs and PerMacs was prepared using the Quick-RNA microprep kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were left untreated (Mock) or stimulated with 200 ng/ml Ultrapure E. coli 055:B5 LPS (Invivogen tlrl-pb5lps) for 6 hours.

tag: Sex

value: female

tag: age

value: 12 months old

value: POLG D257A/D257A (POLG mutator)

value: 200 ng/ml Ultrapure E. coli 055:B5 LPS

tag: time

value: 6 hours


title: POLG D7 PerMac_LPS_rep2

description: Sample 16


title: WTA

value: MCF7 cells

value: Transfected with an IKKe overexpressing vector


title: NHP_Group3_301_3

value: intravenous

value: targeted amplicon sequencing

value: base-edited PCSK9


title: invivo_LNP_Rep2


title: DMSO_1_PE50_AK_Rep1

tag: tissue

value: DMSO


title: NHP_Group2_202_2


title: DMSO_8_PE50_BG_Rep8


title: NHP_Group2_202_1


title: invivo_LNP_Rep1

value: tail vein


title: invivo_AAV_Rep3

value: ABEmax7.10, AAV


title: DMSO_7_PE50_BG_Rep7


title: NHP_Group2_201_3


title: POLG D7 PerMac_mock_rep2

description: Sample 14

value: Mock


title: WT D7 PerMac_LPS_rep2

description: Sample 12

value: POLG +/+ (WT)


title: POLG D7 PerMac_mock_rep1

description: Sample 13


title: WT D7 PerMac_LPS_rep1

description: Sample 11


title: invivo_AAV_Rep2

value: primary hepatocytes


title: DMSO_6_PE50_BG_Rep6

value: 48 hour post fertilization embryo


title: WT D7 PerMac_mock_rep2

description: Sample 10

value: female


title: NHP_Group2_201_2

value: on-target


title: invivo_AAV_Rep1


title: WT D7 PerMac_mock_rep1

description: Sample 9

value: 12 months old


title: NHP_Group1_103_3


title: NHP_Group2_201_1


title: Control_invivo_Rep4

value: control


title: NHP_Group2_202_3


title: Control_invivo_Rep3


title: POLG D7 BMDM_LPS_rep2

description: Sample 8

source_name: MCSF-differentiated bone marrow-derived macrophage

value: 9 months old

value: POLG D257A/D257A (POLG mutator)

value: 200 ng/ml Ultrapure E. coli 055:B5 LPS

value: 6 hours


title: Control_invivo_Rep2


title: DMSO_3_PE50_BG_Rep3


title: DMSO_4_PE50_BG_Rep4


title: DMSO_5_PE50_BG_Rep5


title: NHP_Group1_103_1

value: intravenous

value: targeted amplicon sequencing


title: DMSO_2_PE50_BG_Rep2

value: DMSO


title: NHP_Group1_103_2

value: base-edited PCSK9


title: POLG D7 BMDM_LPS_rep1

description: Sample 7


title: POLG D7 BMDM_mock_rep2

description: Sample 6


title: Control_invivo_Rep1

value: tail vein


title: DMSO_1_PE50_BG_Rep1


title: POLG D7 BMDM_mock_rep1

description: Sample 5

value: Mock


title: pro B cells isolated from lactoferrin knockout mouse (KO2)

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description:
Expression data for pro-B cells isolated from lactoferrin knockout mice
KO2_B

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mouse genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: mouse bone marrow

growth_protocol: Mice were maintained in Central Sourth University Animal Facility according to the Institutional Animal Care Guidelines. All animals were housed in plastic cages (5 mice/cage) with free access to distilled water and a standard diet under specific-pathogen free (SPF) conditions of humidity (50±10%), lightning (12-h light/dark cycle) and temperature (24±0.5℃).

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: No special treatment in this protocol

value: lactoferrin knockout

value: pro B


title: NHP_Group1_102_2


title: NHP_Group1_102_3


title: pro B cells isolated from lactoferrin knockout mouse (KO1)

description:
Expression data for pro-B cells isolated from lactoferrin knockout mice
KO1_B


title: X10.uM.Dibenzo.a.l..pyrene_5_PE50_AK_Rep5

value: 48 hour post fertilization embryo

value: Dibenzo(a,l) pyrene

value: 10 uM


title: X10.uM.Dibenzo.a.l..pyrene_4_PE50_AK_Rep4


title: WT D7 BMDM_LPS_rep2

description: Sample 4

value: female

value: POLG +/+ (WT)


title: NHP_Group1_102_1

value: on-target


title: pre-pro B cells isolated from lactoferrin knockout mouse (KO2)

description:
Expression data for pre-pro-B cells isolated from lactoferrin knockout mice
KO2_A

value: pre-pro B


title: WT D7 BMDM_LPS_rep1

description: Sample 3

value: 9 months old

value: 200 ng/ml Ultrapure E. coli 055:B5 LPS


title: NHP_Group1_101_2

value: intravenous


title: WT D7 BMDM_mock_rep2

description: Sample 2

value: 6 hours


title: NHP_Group1_101_3

value: targeted amplicon sequencing


title: pro B cells isolated from wild type mice (WT2)

description:
Expression data for pro-B cells isolated from wild type mice
WT2_B

value: wild type


title: X10.uM.Dibenzo.a.l..pyrene_3_PE50_AK_Rep3


title: WT D7 BMDM_mock_rep1

description: Sample 1


title: X10.uM.Dibenzo.a.l..pyrene_1_PE50_AK_Rep1


title: pro B cells isolated from wild type mice (WT1)

description:
Expression data for pro-B cells isolated from wild type mice
WT1_B


title: X10.uM.Benzo.a.pyrene_8_PE50_AK_Rep8

value: Benzo(a)pyrene


title: pre-pro B cells isolated from wild type mice (WT2)

description:
Expression data for pre-pro-B cells isolated from wild type mice
WT2_A


title: X10.uM.Benzo.a.pyrene_7_PE50_AK_Rep7


title: TAFE4_tam: Isolated single nuclei from hippocampus of 9-month-old P301S-floxed APOE4 mice treated with tamoxifen

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10+ human APOE
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

extract_protocol:
Mice were aged to 9 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: mouse genotype

value: P301S APOE4 fl/fl Aldh1la1CreERT

value: tamoxifen

value: nuclei of brain


title: TAFE4_oil: Isolated single nuclei from hippocampus of 9-month-old P301S-floxed APOE4 mice treated with oil

tag: treatment

value: oil


title: p11_3: LT_CD112high_3_ATAC

city: Toronto

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Reads were mapped against the hg19 human reference genome using BWA with default parameters.
All duplicate reads, and reads mapped to mitochondria, chrY, an ENCODE blacklisted region  (ENCODE Project Consortium 2012) or an unspecified contig were removed
MACS 2.0.10 was used to call peaks with a uniform extension size of 147 bp
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files of peaks called in each given cell population

source_name: cord blood pool 3

extract_protocol:
as in Buenrostro et al. Nat Methods 2013
Library preparation for ATAC-Seq was performed on 2000 cells with Nextera DNA Sample Preparation kit (Illumina).
4 ATAC-seq libraries were sequenced per lane in HiSeq 2500 System (Illumina) to generate paired-end 50-bp reads

value: human cord blood hematopoietic stem cells


title: p11_2: LT_CD112high_2_ATAC

source_name: cord blood pool 2


title: p11_1: LT_CD112high_1_ATAC

source_name: cord blood pool 1


title: TAFE3_tam: Isolated single nuclei from hippocampus of 9-month-old P301S-floxed APOE3 mice treated with tamoxifen

value: P301S APOE3 fl/fl Aldh1la1CreERT


title: X10.uM.Benzo.a.pyrene_6_PE50_AK_Rep6

value: 48 hour post fertilization embryo

value: 10 uM


title: RNA_Tumor_FlFl_S3

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description:
RNA-seq in mouse tumoral keratinocytes from Zfp36 fl/fl sample
FeatureCount.txt
Tumor_FlFl_vs_Mock_FlFl_pval0.05_log2FC1.xlsx
Tumor_FlFl_vs_Treated_FlFl_pval0.05_log2FC1.xlsx

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome mm10 by using STAR_2.5.3 software with default parameters
Reads from the alignment were sorted and indexed according to chromosomes
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1
Raw read counts were normalized and a differential expression analysis was performed with DESeq2 by applying an adjusted p-value <0.05 and an absolute log2-ratio larger than 1
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing differential expression analysis results and tab-separated file containing normalized read counts for each sample and gene

source_name: Whole skin

extract_protocol:
Total RNA from treated but non-tumoral skin was isolated by pestle homogenization using a TRIzol and chloroform method according to the manufacturer’s instructions (Invitrogen). Total RNA from sorted epidermal cells (isolated from mock-treated skin, DMBA/TPA-treated adjacent skin and papillomas) was extracted using an RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared using Ovation® SoLo RNA-Seq system (NuGEN Technologies)

value: tumoral keratinocytes

tag: condition

value: Zfp36 fl/fl


title: p10_3: LT_CD112low_3_ATAC


title: RNA_Tumor_FlFl_S2


title: TAFE3_oil: Isolated single nuclei from hippocampus of 9-month-old P301S-floxed APOE3 mice treated with oil

value: P301S APOE3/fl/fl Aldh1la1CreERT


title: FE4: Isolated single nuclei from hippocampus of 9-month-old floxed APOE4 mice

value: APOE4 fl/fl


title: pre-pro B cells isolated from wild type mice (WT1)

description:
Expression data for pre-pro-B cells isolated from wild type mice
WT1_A

tag: genotype

value: pre-pro B


title: p10_2: LT_CD112low_2_ATAC


title: X10.uM.Dibenzo.a.l..pyrene_2_PE50_AK_Rep2

value: Dibenzo(a,l) pyrene


title: pre-pro B cells isolated from lactoferrin knockout mouse (KO1)

description:
Expression data for pre-pro-B cells isolated from lactoferrin knockout mice
KO1_A

value: lactoferrin knockout


title: NHP_Group1_101_1

value: on-target

value: intravenous

value: targeted amplicon sequencing

value: base-edited PCSK9


title: Day-20-TN3

city: Los Angeles

first: Reza

last: Ardehali

state: CA

address: 675 Charles E Young dr

department: Cardiology

institute: UCLA

data_processing:
RNA-seq data was mapped with OLego (v.1.1.5) and normalized by using TPM (transcripts per millions) analysis
Total number of reads mapped to a known transcript annotation was estimated using featureCounts version v1.5.0-p2
Expression levels for each transcript were determined by normalizing the counts returned by featureCounts using a custom Perl script
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: Raw feature counts for each sample

extract_protocol:
as described in paper
as described in paper
single cell RNA-seq

value: embryonic stem cell


title: RNA_Tumor_FlFl_S1


title: RNA_Tumor_DK14_S3

description:
RNA-seq in mouse tumoral keratinocytes from Zfp36 ΔK14 sample
FeatureCount.txt
Tumor_DK14_vs_Mock_DK14_pval0.05_log2FC1.xlsx
Tumor_DK14_vs_Treated_DK14_pval0.05_log2FC1.xlsx

value: Zfp36 ΔK14


title: RNA_Tumor_DK14_S2


title: RNA_Tumor_DK14_S1


title: Day-20-TN1


title: Day-20-TN2


title: X1.uM.Benzo.a.pyrene_5_PE50_AK_Rep5

value: Benzo(a)pyrene

value: 1 uM


title: X1.uM.Benzo.a.pyrene_3_PE50_AK_Rep3

value: 48 hour post fertilization embryo


title: X1.uM.Benzo.a.pyrene_4_PE50_AK_Rep4


title: X10.uM.Benzo.a.pyrene_4_PE50_AK_Rep4

value: 10 uM


title: RNA_Treated_FlFl_S3

description:
RNA-seq in mouse treated tumoral keratinocytes from Zfp36 fl/fl sample
FeatureCount.txt
Treated_FlFl_vs_Mock_FlFl_pval0.05_log2FC1.xlsx
Tumor_FlFl_vs_Treated_FlFl_pval0.05_log2FC1.xlsx

value: treated tumoral keratinocytes


title: Day-10-TN3


title: X1.uM.Benzo.a.pyrene_6_PE50_AK_Rep6


title: X10.uM.Benzo.a.pyrene_5_PE50_AK_Rep5


title: X10.uM.Benzo.a.pyrene_2_PE50_AK_Rep2


title: Day-10-TN2


title: RNA_Treated_FlFl_S2

value: Zfp36 fl/fl


title: AnnexinV-negative_rep1

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

description:
AnnexinV-
SAM24376373

data_processing:
Illumina v1.8 software used for basecalling
Reads were demultiplexed based on perfect matches to expected cell barcodes.
Transcript reads were aligned to the mouse reference genome using GSNAP.
Reads aligning uniquely to exons were counted to each gene, and size-factor normalization was used to calculating nRPKM statistic
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include abundance measurements for each sample

source_name: Corpus Callosum

extract_protocol:
Mice were perfused with cold PBS and the corpus callosum dissected from the brain. Tissues were dissociated with Miltenyi Neural Tissue Dissociation Kit (P).
Tru-seq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: 4 weeks of 0.2% Cuprizone chow (Cuprizone_4w)

value: Corpus Callosum

tag: type

value: AnnexinV-negative

tag: timepoint


title: AnnexinV-positive_rep1

description:
AnnexinV+
SAM24376371

value: AnnexinV-positive


title: AnnexinV-positive_rep2

description:
AnnexinV+
SAM24376372


title: KO_Cuprizone_4+3w_rep3

description:
KO_Cuprizone_4+3w
SAM24369070

data_processing:
Illumina v1.8 software used for basecalling
Reads were demultiplexed based on perfect matches to expected cell barcodes.
Transcript reads were aligned to the mouse reference genome using GSNAP.
Transcript counts for a given gene were based on the number of unique molecular identifiers (UMIs) for reads overlapping exons in sense orientation. To account for sequencing or PCR errors, one mismatch was allowed when collapsing UMI sequences.
Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Cells with less than 1000 total UMIs were discarded.
Data was further analyzed using Seurat R package.
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include abundance measurements for each sample

extract_protocol:
Mice were perfused with cold PBS and the corpus callosum dissected from the brain. Tissues were dissociated with Miltenyi Neural Tissue Dissociation Kit (P).
10X libraries were prepared using Chromium Single Cell 3' Library Prep Kit (v2)

treatment_protocol: No treatment (Baseline), 4 weeks of 0.2% Cuprizone chow (Cuprizone_4w), 4 weeks of 0.2 Cuprizone chow followed by 3 weeks of normal chow (Cuprizone_4+3w)

tag: batch


title: RNA_Treated_FlFl_S1

tag: cell type


title: X10.uM.Benzo.a.pyrene_1_PE50_AK_Rep1


title: FE3: Isolated single nuclei from hippocampus of 9-month-old floxed APOE3 mice

value: APOE3 fl/fl

value: nuclei of brain


title: Day-10-TN1


title: WT_Cuprizone_4+3w_rep3

description:
WT_Cuprizone_4+3w
SAM24369069

value: Mertk-WT


title: AnnexinV-negative_rep2

description:
AnnexinV-
SAM24376374


title: Day-20-N3


title: RNA_Treated_DK14_S3

description:
RNA-seq in mouse treated tumoral keratinocytes from Zfp36 ΔK14 sample
FeatureCount.txt
Treated_DK14_vs_Mock_DK14_pval0.05_log2FC1.xlsx
Tumor_DK14_vs_Treated_DK14_pval0.05_log2FC1.xlsx


title: Day-20-N2


title: KO_Cuprizone_4w_rep4

description:
KO_Cuprizone_4w
SAM24369068


title: X1.uM.Benzo.a.pyrene_1_PE50_AK_Rep1


title: X10.uM.Benzanthrone_6_PE50_BG_Rep6

value: Benzanthrone


title: Day-20-N1


title: RNA_Treated_DK14_S1


title: RNA_Mock_FlFl_S3

description:
RNA-seq in mouse keratinocytes from Zfp36 fl/fl sample
FeatureCount.txt
Treated_FlFl_vs_Mock_FlFl_pval0.05_log2FC1.xlsx
Tumor_FlFl_vs_Mock_FlFl_pval0.05_log2FC1.xlsx

value: keratinocytes


title: X10.uM.Benzanthrone_5_PE50_BG_Rep5


title: KO_Cuprizone_4w_rep3

description:
KO_Cuprizone_4w
SAM24369066


title: X1.uM.Benzo.a.pyrene_2_PE50_AK_Rep2


title: WT_Cuprizone_4w_rep3

description:
WT_Cuprizone_4w
SAM24369065


title: Day-10-N3


title: X10.uM.Benzanthrone_2_PE50_BG_Rep2


title: Day-10-N2


title: KO_Baseline_rep3

description:
KO_Baseline
SAM24369064

value: Baseline


title: Day-10-N1

value: embryonic stem cell


title: WT_Baseline_rep3

description:
WT_Baseline
SAM24369063


title: X10.uM.Benzanthrone_1_PE50_BG_Rep1


title: RNA_Mock_FlFl_S1


title: RNA_Mock_FlFl_S2


title: RNA_Mock_DK14_S3

description:
RNA-seq in mouse keratinocytes from Zfp36 ΔK14 sample
FeatureCount.txt
Treated_DK14_vs_Mock_DK14_pval0.05_log2FC1.xlsx
Tumor_DK14_vs_Mock_DK14_pval0.05_log2FC1.xlsx

value: Zfp36 ΔK14


title: Day-7-T-neg3

source_name: Day 7, TBX5 -, 3


title: X10.uM.Benz.a.anthracene.7.12.dione_6_PE50_BG_Rep6


title: KO_Cuprizone_4+3w_rep2

description:
KO_Cuprizone_4+3w
SAM24360689


title: X10.uM.Benz.a.anthracene.7.12.dione_5_PE50_BG_Rep5


title: Day-7-T-neg2

source_name: Day 7, TBX5 -, 2


title: WT_Cuprizone_4+3w_rep2

description:
WT_Cuprizone_4+3w
SAM24360688


title: RNA_Mock_DK14_S2


title: RNA_Treated_DK14_S2


title: WT_Cuprizone_4w_rep4

description:
WT_Cuprizone_4w
SAM24369067


title: X10.uM.Benz.a.anthracene.7.12.dione_4_PE50_BG_Rep4


title: RNA_Mock_DK14_S1


title: Day-7-T-neg1

source_name: Day 7, TBX5 -, 1


title: KO_Cuprizone_4w_rep2

description:
KO_Cuprizone_4w
SAM24360687


title: Day-7-T-pos3

source_name: Day 7,TBX5 +, 3


title: Day-7-T-pos2

source_name: Day 7,TBX5 +, 2


title: X10.uM.Benz.a.anthracene.7.12.dione_3_PE50_BG_Rep3


title: Wt1CreERT2:Rosa26mTmG:DspW/F_2

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

description:
Single cell RNA
sample 5

data_processing:
Seurat
Genome_build: GRCm38 with dTomato and EGFP
Supplementary_files_format_and_content: UMI count matrix
Supplementary_files_format_and_content: Genes file
Supplementary_files_format_and_content: Barcodes file

source_name: epicardial derived cells

extract_protocol:
Whole heart was digested with Collagenase II through  the Langendorff perfusion system. The isolated non-cardiac myocytes fraction was subjected to the Fluorescence Activated Cell Sorting system to generate the EGFP positive epicardial derived cells. Single vialbe EGFP positive cell was loaded onto the 10X Genomics Chromium Single cell Gene expression Solution at the density recommended by the manufacturer and barcoded according to the standard protocol.
Libraries were sequenced on an Illumina platform using 75-bp pair-end sequencing on a NovaSeq6000 instrument

value: heart

value: 3-6 months


title: WT_Cuprizone_4w_rep2

description:
WT_Cuprizone_4w
SAM24360686


title: KO_Cuprizone_4+3w_rep1

description:
KO_Cuprizone_4+3w
SAM24360685


title: X10.uM.Benz.a.anthracene.7.12.dione_1_PE50_BG_Rep1

value: 48 hour post fertilization embryo


title: Wt1CreERT2:Rosa26mTmG:DspW/F_3

description:
Single cell RNA
sample 6


title: X10.uM.Benz.a.anthracene.7.12.dione_2_PE50_BG_Rep2

value: 10 uM


title: KO_Cuprizone_4w_rep1

description:
KO_Cuprizone_4w
SAM24360683


title: Wt1CreERT2:Rosa26mTmG:DspW/F_1

description:
Single cell RNA
sample 4


title: Day-0-4

source_name: Undifferentiated hESC 3


title: Day-0-2

source_name: Undifferentiated hESC 2


title: GUIDE-Seq SG7

city: Madrid

first: Oscar

last: Quintana Bustamante

state: Spain

address: Av Complutense 40

country: Spain

institute: CIEMAT/CIBERER/IIS-FJD

data_processing:
Library strategy: GUIDE-Seq
Data Processing using GUIDE-seq analysis package (https://github.com/aryeelab/guideseq) using an optimized alignment (Needleman-Wunch).
also see following publication (https://pubmed.ncbi.nlm.nih.gov/27153277/)
also see following publication ((https://pubmed.ncbi.nlm.nih.gov/25513782/)
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files

source_name: HEK293 cells

growth_protocol: Standard culture conditions for HEK293 cells stably expressing Cas9

extract_protocol:
Genomic DNA was isolated (QuickExtract) followed by fragmentation and adapter ligation using the LOTUS™ DNA Library Prep Kit (IDT).
Libraries were generated by two rounds of amplification, followed by Illumina-based NGS. Illumina sequencing was carried out on a MiSeq using V2 chemistry and 2x150 paired-end reads

treatment_protocol: gRNA complexes were generated using Alt-R® CRISPR-Cas9 crRNA XT and Alt-R®CRISPR-Cas9 tracrRNA, and transfected with a dsODN tag into HEK293 cells stably expressing Cas9 using the Nucleofector system (Lonza, Basel).

tag: cell line

value: HEK293 cells

value: HEK293 cells stably expressing Cas9

value: nucleofected with SG7 gRNA


title: GUIDE-Seq SG4

value: nucleofected with SG4 gRNA


title: Wt1CreERT2:Rosa26mTmG_3

description:
Single cell RNA
sample 3

tag: strain


title: WT_Cuprizone_4+3w_rep1

description:
WT_Cuprizone_4+3w
SAM24360684

value: Corpus Callosum


title: GUIDE-Seq SG3

value: nucleofected with SG3 gRNA


title: Wt1CreERT2:Rosa26mTmG_1

description:
Single cell RNA
sample 1


title: Day-0-1

source_name: Undifferentiated hESC 1


title: KO_Baseline_rep2

description:
KO_Baseline
SAM24360681


title: WT_Baseline_rep2

description:
WT_Baseline
SAM24360680


title: GUIDE-Seq SG2

value: nucleofected with SG2 gRNA


title: HPV-.2, scRNA-Seq

first: Fei

last: Quan

address: Baojian Road 157

institute: Harbin Medical University

data_processing:
The BD Whole Transcriptome Analysis (WTA) Rhapsody analysis pipeline was used to process sequencing data (.fastq file), including alignment and generation of gene/barcode matrix.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized UMI count values for each cell

source_name: Cervical cancer

extract_protocol:
Fresh specimens of HPV+ and HPV- CC were collected at the time of cervical biopsy and stored in 1ml Cryopreservation protection fluid from SINOTECHTM tissue sample Cryopreservation kit (JZ-SC-58202, Sinomics Genomics, China) in the gradient freezer at -80℃ overnight, and then stored in the liquid nitrogen to facilitate subsequent single cell RNA sequencing and analysis. Single Cell preparation, library construction, and sequencing were performed by the Shanghai Sinomics Corporation of China.
scRNA-Seq

value: Cervical cancer samples

tag: hpv status

value: HPV-

tag: Stage

tag: cancer type

value: squamous cell carcinoma, SCC


title: HPV-.1, scRNA-Seq

value: IIB


title: KO_Baseline_rep1

description:
KO_Baseline
SAM24359738

value: Baseline


title: GUIDE-Seq SG8

value: nucleofected with SG8 gRNA


title: OPSCC311

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to the NCBI reference sequence database to identify human coding genes with Bowtie v1.2.2.
Transcripts Per Million (TPM) were calculated. The read counts of  one gene were normalized by the average length of all isoforms and by the size of the all mapped mRNA reads.
Genome_build: NCBI reference sequence database
Supplementary_files_format_and_content: Tab-delimited text file includes TPM-normalized gene counts for all samples

source_name: Oropharyngeal squamous cell carcinoma

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were collected for pathologic analysis from biopsy or primary surgical resection.
Ribosomal RNA (rRNA) was removed with the RiboMinus kit (Life Technologies) and custom DNA oligonucleotide probes. The RNA was used to construct RNA-seq libraries with the NEBNext Ultra mRNA Library Prep kit (New England BioLabs). The resulting cDNA libraries were PCR amplified and subject to sequencing with Illumina HiSeq 3000 at Washington University Genome Technology Access Center.

value: HPV+

value: FFPE

tag: cohort

value: WashU cohort


title: OPSCC310


title: Day-7-T-pos1

source_name: Day 7,TBX5 +, 1

value: embryonic stem cell


title: OPSCC309


title: HPV+.2, scRNA-Seq


title: HPV+.1, scRNA-Seq


title: GUIDE-Seq SG1

value: HEK293 cells

value: nucleofected with SG1 gRNA


title: WT_Baseline_rep1

description:
WT_Baseline
SAM24359737

value: Mertk-WT


title: WT_Cuprizone_4w_rep1

description:
WT_Cuprizone_4w
SAM24360682


title: OPSCC308


title: OPSCC307


title: iGUIDE  human MOCK

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

institute: UZH Zurich

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

source_name: HEK cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation

value: Electroporation MOCK

value: Electroporation with dsODN only

value: iGUIDE

value: Untreated


title: CHANGE-seq  human

value: in situ gDNA digest

value: Cas9 digest with sgRNA-hP01

value: CHANGE-seq

value: Cas9-KO PCSK9


title: Wt1CreERT2:Rosa26mTmG_2

description:
Single cell RNA
sample 2

value: heart

tag: age

value: 3-6 months


title: OPSCC306

value: HPV+


title: RSA_6

city: Shanghai

first: Sha

last: Xu

address: Songhu Road 2005

institute: Fudan University

data_processing:
FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool， which was used to merge paired-end reads
Fastq to fasta format step was then  processed using the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads with fasta format were mapped to targeted Bisulfite Genome (hg19) by Blast
Unmapped reads were filtered and mapped reads with coverage greater than 90% and identity greater than 95% were kept as effective reads and were used for following statistics. Sequencing depth for each amplicon per sample was calculated   by blasting the effective reads against the targeted genome region. Reads less than 10-fold were removed and overall sequencing depth for each sample were evaluated
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include methylation values for each Sample

source_name: Villi

extract_protocol:
Genomic DNA was extracted from frozen samples using Genomic Tip-500 columns (Qiangen, Valencia, CA, USA) and from bisulfite-converted samples using an EZ DNA Methylation™-GOLD Kit (Zymo Research, CA, USA) according to the manufacturer’s instructions.
Libraries from different samples were quantified and pooled together, followed by sequencing on the Illumina HiSeq platform according to manufacturer's protocols. Sequencing was performed with a 2x150bp paired-end mode.
Targeted Bisulfite-Seq

tag: disease

value: RSA patients

value: extravillous trophoblast

value: bisulfite-converted


title: iGUIDE  human target; sgRNA-hP01

value: Electroporation sgRNA-hP01

value: Cas9 with sgRNA-hP01 and dsODN


title: RSA_7

tag: tissue


title: KI4

city: Durham

first: Perry

last: Blackshear

state: NC

address: 111 T W Alexander Drive

institute: NIH/NIEHS

data_processing:
Sequenced reads were filtered for low-quality sequence, then mapped to mm10 whole genome using STAR (V2.5.2b).
The featureCounts per gene were calculated using the featureCounts command available from Subread (v1.5.0-p1).
Differential expression analysis was peformed with R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include featureCounts values for each Sample.

source_name: skin

extract_protocol:
Skin was removed, flash frozen in liquid nitrogen, and homogenized into a powder by mortar and pestle. RNA was extracted using Trizol reagent and the GE Healthcare Illustra RNAspin mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed by EA | Q² Solutions with Illumina HiSeq 2500 instruments.

treatment_protocol: Shaved back skin of anesthetized mice was treated with a single topical application of 400 nmol of 7,12-dimethylbenz[a]anthracene (DMBA) in 0.2 ml acetone. Starting one week later, the same patch of skin was subjected to twice weekly treatments with 10 nmol of 12-0 tetradecanoylphorbol-13-acetate (TPA) in 0.2 ml acetone.  These applications were continued for 20 weeks.

value: skin

value: TTP delta ARE


title: KI3


title: OPSCC305

value: FFPE

value: WashU cohort


title: CIRCLE-seq  human control

value: Cas9 digest without sgRNA

value: CIRCLE-seq

value: Untreated


title: KI2


title: OPSCC304


title: CIRCLE-seq  human target

value: in situ gDNA digest

value: Cas9 digest with sgRNA-hP01


title: RSA_5


title: RSA_4


title: KI5


title: OPSCC302


title: invitro_human_control_mP01_Rep2

source_name: direct cell lysis HepG2

value: on-target, NEON electroporation

value: targeted amplicon sequencing


title: invitro_human_control_mP01_Rep3


title: RSA_1


title: WT5

value: wild type


title: RSA_2

value: RSA patients


title: OPSCC303

value: HPV+


title: KI1


title: WT3


title: WT4


title: invitro_human_control_mP01_Rep1


title: OPSCC300


title: Normal_thirdtrimester_3

value: Normal pregnancy

value: extravillous trophoblast

value: bisulfite-converted


title: WT2

value: skin


title: Normal_thirdtrimester_2


title: invitro_human_ABEmax_sgRNA_mP01_Rep2

value: ABEmax, sgRNA-hP01

value: base-edited PCSK9


title: OPSCC301

value: FFPE

value: WashU cohort


title: WT1


title: OPSCC299


title: invitro_human_ABEmax_sgRNA_mP01_Rep1


title: OPSCC298


title: Normal_thirdtrimester_1


title: Normal_secondtrimester_3


title: OPSCC297


title: RSA_3


title: OPSCC296


title: Normal_secondtrimester_2


title: invitro_human_ABEmax_sgRNA_mP01_Rep3


title: OPSCC295


title: Normal_secondtrimester_1


title: Normal_firsttrimester_7


title: OPSCC294


title: OPSCC293


title: OPSCC292


title: Normal_firsttrimester_6


title: OPSCC291


type: RNA

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: 3D engineered muscles at  5 h after a 30-min acute EPS (electrical plus stimulation)

hyb_protocol: Purified Cy3-labeled cRNAs (1650 ng) from from pooled individual WT or DBA/2 mice were then hybridized on the microarrays. Washing, scanning, and gene analysis with Agilent’s Whole Mouse Genome Microarray (4x44K v2) were conducted according to the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent Feature Extraction software (v. 9.5.1) was used to assess spot quality and extract feature intensity statistics.

data_processing: The Subio Platform and Subio Basic Plug-in (v1.11; Subio Inc., Aichi, Japan) was then used to calculate the between-sample fold change.

label_protocol: Microarray analyses were performed as single-color hybridizations. Total RNAs obtained from mouse leukocytes were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and MMLV-RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNAs were prepared from 3D engineered muscles by acid guanidinium–phenol–chloroform extraction and the quality of RNA samples was determined using an RNA 6000 Nano LabChip Kit (p/n 5065-4476) on an Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies).

value: skeletal muscle

tag: time point

value: 5 h after after


title: Normal_firsttrimester_3

tag: treatment


title: Normal_firsttrimester_4


description: 3D engineered muscles at 0 min after a 30-min acute EPS (electrical plus stimulation)

value: 0 min after after


title: OPSCC290


title: Cell_line_Braf-Pten-Brn2-hom_3

city: Orsay

first: Lionel

last: Larue

address: Bat 110, Centre universitaire

department: UMR3347 CNRS - U1021 INSERM, Institut Curie

country: France

institute: Institut Curie

hyb_protocol: Complementary RNA (cRNA) was synthesized using the GeneChip 3′IVT Plus reagent Kit, according to the manufacturer’s protocol. Then 11μg cRNA were hybridized to mouse MOE430 gene expression Affymetrix microarrays

scan_protocol: After washing and staining, using the Affymetrix fluidics station 450, the probe arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Data processing was done using R/Bioconductor. CEL files were read using the oligo package and normalized using the RMA - Robust Multichip Average algorithm. The highest-IQR probe for each gene was retained.

label: biotin

source_name: cell line derived from mouse melanoma tumor

label_protocol: not provided

growth_protocol: Murine Braf-Pten-Brn2-wt, Braf-Pten-Brn2-het & Braf-Pten-Brn2-hom melanoma cell line were established respectively from melanoma arising from Braf-Pten-Brn2-wt, Braf-Pten-Brn2-het & Braf-Pten-Brn2-hom mice. Small pieces (≈10 mm3) of primary tumors were cleaned, washed in PBS, and subcutaneously implanted into the neck pad of C57BL/6 mice. Once the implanted tumor reached a volume of ≈1 cm3, it was removed from the mouse, tumors were dissociated as single cells prior to establishing them in culture as previously  described (Gallagher et al., 2011).

extract_protocol: total RNA was extracted using the miRneasy, Qiagen extraction kit according to the manufacturer's instructions.

value: Tyr::CreERT2::BrafV600E F/+ Pten F/+ BRN2 F/F

tag: Sex

value: female

tag: rin

tag: designation

tag: mouseid


title: Cell_line_Braf-Pten-Brn2-hom_2

value: cell line derived from mouse melanoma tumor

tag: genotype


title: Normal_firsttrimester_2


description: 3D engineered muscle at  5 h with no acute EPS (electrical plus stimulation)

value: 5 h after


title: Normal_firsttrimester_5


title: Cell_line_Braf-Pten-Brn2-hom_1


description: 3D engineered muscle at 0 min with no acute EPS (electrical plus stimulation)

value: 0 min after


title: OPSCC289

value: HPV+


title: Irradiation 3Gy 24h, biological rep 1

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: 08 3 Gy 24h

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Affymterix GeneChip Human Genome U219 ArrayStrip (16 h, 45°C).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: hiPSCs_Irradiation 3Gy 24h

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were used to form EBs. After 7 days, the EBs were differentiated into a chondrogenic lineage in a defined medium supplemented with TGF-β (10 ng/ml).

extract_protocol: Total RNA isolation was performed using the modified Chomczynski method with the use of TRI Reagent (Sigma, St Louis, MO, USA) and the RNeasy Mini Elute Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: Treatment plans were prepared using volumetric modulated arc therapy (VMAT) technique using 2 co-planar arcs. The goal of the plans was to cover at least 95% of the PTV with the planned prescription dose: 1, 2 and 3 Gy.

tag: cell type

value: Irradiation 3Gy 24h


title: Cell_line_Braf-Pten-Brn2-het_2

value: Tyr::CreERT2::BrafV600E F/+ Pten F/+ BRN2 F/+


title: Irradiation 2Gy 24h, biological rep 1

description: 07 2 Gy 24h

source_name: hiPSCs_Irradiation 2Gy 24h

value: Human induced pluripotent stem cells (hiPSCs)

value: Irradiation 2Gy 24h


title: Irradiation 1Gy 24h, biological rep 2

description: 06 1 Gy 24h_2

source_name: hiPSCs_Irradiation 1Gy 24h

value: Irradiation 1Gy 24h


title: Irradiation 3Gy 24h, biological rep 2

description: 08 3 Gy 24h_2


title: Control 24h, biological rep 2

description: 05 ctrl 24h_2

source_name: hiPSCs_Control 24h

value: Control 24h


title: Irradiation 1Gy 24h, biological rep 1

description: 06 1 Gy 24h


title: Control 24h, biological rep 1

description: 05 ctrl 24h


title: Irradiation 3Gy 1h, biological rep 2

description: 04 3 Gy 1h_2

source_name: hiPSCs_Irradiation 3Gy 1h

value: Irradiation 3Gy 1h


title: Irradiation 2Gy 24h, biological rep 2

description: 07 2 Gy 24h_2


title: OPSCC288

value: FFPE

value: WashU cohort


title: Cell_line_Braf-Pten-Brn2-wt_4

value: Tyr::CreERT2::BrafV600E F/+ Pten F/+ BRN2 +/+


title: OPSCC285


title: OPSCC287


title: Cell_line_Braf-Pten-Brn2-het_1


title: OPSCC284

value: HPV-


title: Irradiation 2Gy 1h, biological rep 2

description: 03 2 Gy 1h_2

source_name: hiPSCs_Irradiation 2Gy 1h

value: Irradiation 2Gy 1h


title: Irradiation 2Gy 1h, biological rep 1

description: 03 2 Gy 1h


title: Normal_firsttrimester_1

value: Normal pregnancy

value: extravillous trophoblast

value: bisulfite-converted


title: K562-PLVX-vector-rep1

first: Peng

last: Liu

address: Dong An Road, 131

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

growth_protocol: K562 cells were cultured in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gibco) and 50 μg/ml of penicillin/streptomycin

extract_protocol:
Stable cells were harvested with TRIzol reagent (Invitrogen) and kept at -80 °C . RNA extraction was performed by Shanghai Majorbio.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: chronic myeloid leukemia cell line

tag: infection

value: Lentiviruses carrying PLVX-vector


title: K562-PLVX-Flag-CM-rep2


title: K562-PLVX-Flag-CM-rep3


title: K562-PLVX-vector-rep3


title: K562-PLVX-Flag-CM-rep1


title: OPSCC282

tag: hpv status

value: HPV+


title: Cell_line_Braf-Pten-Brn2-wt_2

value: cell line derived from mouse melanoma tumor

value: female


title: Cell_line_Braf-Pten-Brn2-wt_3


title: Cell_line_Braf-Pten-Brn2-wt_1


title: BRN2_HOM_TUM_8

source_name: Primary tumor

label_protocol: The IVT reaction was carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labelling.

growth_protocol: Newborn mice were treated dorsally with 0.4 μg/day/mouse tamoxifen from P1 to P3. Developing skin excrescences > 3 mm diameter were considered to be melanomas, and validated after growth. Mice were sacrificed and autopsied four weeks after tumor appearance or once the tumors reached 2 cm3. Only melanoma having a volume of 1cm^3 were used for the transcriptomic analysis. For mice harbouring multiple melanome, only the biggest melanomas on each mouse was harvested. Tumors were then excised, rinsed in cold PBS and snap-frozen in liquid nitrogen.

value: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 F/F

tag: category


title: Irradiation 3Gy 1h, biological rep 1

description: 04 3 Gy 1h

value: Human induced pluripotent stem cells (hiPSCs)


title: Phase 1-3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description:
P1_3
processed data file: counts.matrix.norm.txt

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Arabidopsis genome version TAIR10 (version 34) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: counts.matrix.norm.txt: Tab-delimited text file includes library size normalized counts per sample.

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Arabidopsis thaliana was cultivated at 21°C (500 W m-2) for 13 h and 18°C (0 W m-2) for 11 h in growth chamber. Plant was cultivated in water culture including 1mM KH2PO4, 0.25 mM K2SO4, 1mM MgSO4•7H2O, 2 mM Ca(NO3)2•4H2O, 50 μM KCl, 5 μM MnSO4•H2O, 1 μM ZnSO4•7H2O, 1 μM CuSO4•5H2O, 0.1 μM NiSO4•6H2O, 0.7 μM (NH4)6Mo7O24•4H2O, 30 μM H3BO3, and 100 μM FeNaEDTA.

extract_protocol:
The total RNA was isolated using RNeasy Plant Mini Kit (Qiagen). On-column DNase digestion (RNase-Free DNase Set, Qiagen) was conducted according to manufacturer protocols to avoid genomic DNA contamination.
4µg of total RNA was used as input for TruSeq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in average of 30M reads per library with 1x75bp single end setup.

treatment_protocol: Phase 0 samples (rosette leaves) were harvested 1 hour later from 105 mM NaCl salt shock treatment; Phase 1 samples (rosette leaves) were harvested 2 days later after reaching 90 mM NaCl by a stepwise addition (15 mM NaCl per day).

tag: ecotype/background

value: 5 weeks

value: rosette leaves

value: salt stress


title: BRN2_HOM_TUM_9

value: male


title: OPSCC286

value: FFPE

tag: cohort

value: WashU cohort


title: BRN2_HOM_TUM_10


title: Irradiation 1Gy 1h, biological rep 2

description: 02 1 Gy 1h_2

source_name: hiPSCs_Irradiation 1Gy 1h

value: Irradiation 1Gy 1h


title: Phase 1-2

description:
P1_2
processed data file: counts.matrix.norm.txt

tag: age


title: K562-PLVX-vector-rep2


title: OPSCC283


title: OPSCC278


title: Control 1h, biological rep 1

description: 01 ctrl 1h

source_name: hiPSCs_Control 1h

value: Control 1h


title: K562-PLKO-shRunx1-rep1

value: Lentiviruses carrying PLKO-shRunx1


title: Control 1h, biological rep 2

description: 01 ctrl 1h_2


title: K562-PLKO-shRunx1-rep3


title: OPSCC281

source_name: Oropharyngeal squamous cell carcinoma


title: OPSCC280


title: K562-PLKO-shRunx1-rep2


title: K562-PLKO-shDNMT3A-rep2

value: Lentiviruses carrying PLKO-shDNMT3A


title: K562-PLKO-shDNMT3A-rep1

value: chronic myeloid leukemia cell line


title: OPSCC276


title: BRN2_HOM_TUM_7


title: Irradiation 1Gy 1h, biological rep 1

description: 02 1 Gy 1h


title: BRN2_HOM_TUM_6


title: BRN2_HET_TUM_7

value: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 F/+


title: OPSCC279

value: HPV+


title: BRN2_HET_TUM_6


title: Phase 1-1

description:
P1_1
processed data file: counts.matrix.norm.txt


title: K562-PLKO-shDNMT3A-rep3


title: Phase 0-3

description:
P0_3
processed data file: counts.matrix.norm.txt

value: salt shock


title: K562-PLKO-vector-rep2

value: Lentiviruses carrying PLKO-vector


title: Phase 0-2

description:
P0_2
processed data file: counts.matrix.norm.txt


title: OPSCC277


title: OPSCC273


title: Phase 0-1

description:
P0_1
processed data file: counts.matrix.norm.txt


title: BRN2_HET_TUM_10


title: Control-3

description:
CTRL_3
processed data file: counts.matrix.norm.txt

value: control


title: K562-PLKO-vector-rep3


title: BRN2_HET_TUM_9


title: OPSCC275


title: BRN2_HOM_TUM_5

value: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 F/F

value: female


title: BRN2_HOM_TUM_4


title: OPSCC274


title: Control-2

description:
CTRL_2
processed data file: counts.matrix.norm.txt

value: 5 weeks

value: rosette leaves


title: BRN2_WT_TUM_5

value: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 +/+


title: Control-1

description:
CTRL_1
processed data file: counts.matrix.norm.txt


title: BRN2_HOM_TUM_3


title: BRN2_HET_TUM_8

value: male


title: OPSCC271

value: FFPE

value: WashU cohort


title: K562-PLKO-vector-rep1


title: OPSCC270


title: OPSCC272


title: OPSCC268


title: OPSCC267


title: OPSCC269


title: OPSCC266


title: OPSCC264


title: BRN2_HOM_TUM_2


title: OPSCC265


title: BRN2_HET_TUM_5


title: BRN2_HET_TUM_4


title: BRN2_HET_TUM_2


title: BRN2_HET_TUM_3


title: OPSCC263


title: KPC-Snail;Twist cKO YFP+ cancer cells from lung - mouse 586P

first: Raghu

last: Kalluri

state: TX

address: 1881 East Road

department: Cancer Biology

institute: MD Anderson Cancer Center

hyb_protocol: whole transcriptome analysis was performed using the WT Plus Assay (Applied Biosystems) according to the manufacturer's instructions.

scan_protocol: Mouse Clariom D array (Applied Biosystems)

data_processing: TAC4.0 version 2 software

source_name: mouse KPC-ST YFP+ pancreatic cancer cells

extract_protocol: total RNA was extracted by the PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer's instructions.

treatment_protocol: tissue was minced with scissors in a 1.5 mL tube, and incubated at 37°C in 4 ug/mL Collagenase IV (Gibco, 17104019) and 4 ug/mL Dispase II (Gibco, 17105041) in serum-free RPMI in a 6well dish for 1 hour. Cells were resuspended in 10 mL of complete media (RPMI with 20% FBS and 1% PSA) and strained through a 70 um strainer and pelleted to removed digestion media. the pelleted cells were washed twice in PBS, resuspended in FACS buffer (PBS with 2% FBS) and sorted for YFP positivity by flow cytometry (BD FACSAria IIIu Cell Sorter).

tag: eartag

tag: gender

value: Pdx1-Cre; KrasG12D; p53R172H/+; Snai1F/F; Twist1F/F ; Rosa26-LSL-EYFPF/F

tag: tumor type

value: metastatic


title: KPC-Snail;Twist cKO YFP+ cancer cells from liver - mouse 583P

label_protocol: whole transcriptome analysis was performed using the WT Plus Assay (Applied Biosystems) according to the manufacturer's instructions.

value: Pdx1-Cre; KrasG12D; p53R172H/+; Snai1F/F; Twist1F/F ; Rosa26-LSL-EYFPF/+


title: KPC-Snail;Twist cKO YFP+ cancer cells from lung - mouse 583P


title: BRN2_HET_TUM_1


title: KPC-Snail;Twist cKO YFP+ cancer cells from primary tumor - mouse 586P

value: primary


title: KPC-Snail;Twist cKO YFP+ cancer cells from liver - mouse 586P


title: KPC-Snail;Twist cKO YFP+ cancer cells from primary tumor - mouse 583P


title: KPC-Snail;Twist cKO YFP+ cancer cells from lung - mouse 407P

value: Pdx1-Cre; KrasG12D; p53R172H/+; Snai1F/F; Twist1F/F ; Rosa26-LSL-EYFPF/F; αSMA-RFP


title: KPC-Snail;Twist cKO YFP+ cancer cells from liver - mouse 404P

value: Pdx1-Cre; KrasG12D; p53R172H/+; Snai1F/F; Twist1F/F ; Rosa26-LSL-EYFPF/+; αSMA-RFP


title: KPC-Snail;Twist cKO YFP+ cancer cells from lung - mouse 404P


title: OPSCC262

value: HPV+

tag: tissue


title: OPSCC260


title: BRN2_WT_TUM_2

tag: Sex


title: KPC-Snail;Twist cKO YFP+ cancer cells from primary tumor - mouse 404P


title: BRN2_WT_TUM_1

tag: rin


title: OPSCC261


title: OPSCC257


title: OPSCC259

value: HPV-


title: OPSCC258


title: OPSCC254


title: BRN2_WT_TUM_4


title: TCPP_4_FRC_Rep4

city: Richland

first: Ryan

last: McClure

address: 11829272 Battelle for the US DOE, 790 6th Street

institute: Pacific Northwest National Laboratory

data_processing:
Raw fastq files were trimmed if necessary to remove adaptor sequences or basepairs with a phred score below 25
Each fastq file was aligned to the Genome Reference Consortium Zebrafish Build 11 (GRCz11) (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/) using the Star Aligner (Dobin et al. 2013) with default settings
Resulting SAM files were then used to count reads aligning to genes using HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/) along with the gff file for the Z11 genome (GCF_000002035.6_GRCz11_genomic.gff)
This led to a file of 39,701 genes with raw counts assigned to them.  From this file any gene that had a count of ‘0’ in at least 43/170 (more than 25% of the datasets had a ‘0’ for that gene), was removed from further analysis.  This led to a dataset of 21,854 genes across 170 datasets.
Raw counts were normalized with DESEQ2.  This program was also used to identify fold changes and associated adjusted p-values for those fold changes
Genome_build: GRCz11
Supplementary_files_format_and_content: .csv, Normalized gene expression levels

extract_protocol:
Following exposure, 48-hpf whole embryos were homogenized using RNAzol (Molecular Research Center, Inc).  RNA was purified using the Direct-zol MiniPrep kit (Zymo Research) and included the optional in-column DNase 1 digestion treatment for 15 minutes
100 bp sequencing was conducted using an Illumina HiSeq 3000 sequencer
mRNAs were enriched by polyA selection. Libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems)

value: 48 hour post fertilization embryo

tag: chemical

tag: concentration

value: 85 uM


title: BRN2_WT_TUM_3

tag: genotype

value: female

tag: mouseid


title: OPSCC255


title: OPSCC256


title: OPSCC253


title: KPC Control YFP+ cancer cells from liver - mouse H410

source_name: mouse KPC YFP+ pancreatic cancer cells

value: Pdx1-Cre; KrasG12D; p53R172H/+; Rosa26-LSL-EYFPF/+


title: KPC Control YFP+ cancer cells from primary tumor - mouse H444

value: Pdx1-Cre; KrasG12D; p53R172H/+; Rosa26-LSL-EYFPF/+;


title: OPSCC251


title: KPC-Snail;Twist cKO YFP+ cancer cells from primary tumor - mouse 407P


title: TCPP_1_FRC_Rep1


title: M_P6_Kir2.1_rep4

city: Fukuoka

first: Takeshi

last: Imai

address: Maidashi3-1-1, Higashi-ku

department: Graduate School of Medical Sciences

institute: Kyushu University

hyb_protocol: Cy3-labeled cRNA (600 ng) was fragmented with 10x Blocking Agent and 25x Fragmentation Buffer at 60°C for 30 min. After fragmentation, the solution was immediately transferred on ice and 25 µL of 2x GE Hybridization Buffer HI-RPM was added. The hybridization solution was mixed gently and hybridized with the SuperPrint G3 Mouse GE 8x60K Microarray (G4852A) for 17 hours at 65°C in a rotating hybridization oven (10 rpm). After hybridization, the microarray slide was washed sequentially in Wash Buffer 1 for 1 min at room temperature and Wash Buffer 2 for 1 min at 37°C.

scan_protocol: The microarray slides were scanned using an Agilent DNA microarray scanner G2505C  using one color scan setting for 8x60k array slides  (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned imaged were analyzed with Feature Extraction Software 10.7.3.1 with the following parameters: Grid Template, 028005_D_F_20110614, and FE protocol, GE1_107_Sep09. The extracted data were processed using Microsoft Excel.

source_name: Mitral cell,P6,Kir2.1,replicate 4

label_protocol: Single-cell cDNA synthesis and amplification was performed as described previously (Imai et al., 2009). Briefly, a T7 promoter was attached to the 3’-end and the total cDNA was PCR-amplified (30 cycles). The quality of PCR-amplified cDNA was assessed by agarose gel electrophoresis. Samples with sufficient yields, containing EYFP and pcdh21 transcripts (determined by secondary PCR for EYFP and pcdh21) were used in subsequent analyses. Samples from 10 neurons were pooled for each hybridization experiment. cRNA was amplified and labeled using Agilent Low RNA Input Linear Amplification Kit following the manufacturer’s instructions, followed by RNAeasy Mini column purification (QIAGEN). cRNA yields were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: At P3 or P6, olfactory bulbs were minced in Ca2+-free Ringer’s solution (138mM NaCl, 2mM MgCl2, 2mM sodium pyruvate, 9.4mM glucose, 2mM EGTA, and 5mM HEPES, pH7.4). Minced OB was incubated with 0.88 U/mL Dispase (Invitrogen) and, 200 U/mL Collagenase type II and 0.1 mg/mL DNase I (Roche) for 20 minutes at 37 ℃. The sample was centrifuged at 1k rpm for 5 minutes and the pellet was resuspended in Ca2+-free Ringer’s solution. After repeating this washing procedure, the pellet  was suspended in 0.1% bovine serum albumin and 0.05 mg/mL DNase I solution and mixed gently. The cell suspension was placed on a coverslip and the EYFP-expressing mitral cells were collected manually with a glass capillary, a micro-manipulator, TransferMan NK2 (Eppendolf), and a microinjector, CellTram vario (Eppendolf), equipped to an inverted fluorescence microscope, DMI6000B (Leica). The picked single cell was rinsed in a drop of 0.1% bovine serum albumin/ Ringer’s solution (Ca2+-free Ringer’s solution contained 2mM CaCl2), transferred to 0.4 μL of RNase free H2O in a PCR tube, snap-frozen in liquid nitrogen, and stored at -80 ℃ until use.

treatment_protocol: pCAG-EYFP alone, or pCAG-EYFP and pCAG-Kir2.1 was introduced in mitral cells using in utero electroporation at E12.

tag: strain

value: ICR

value: Olfactory bulb

tag: cell

value: Mitral cell

value: Postnatal day 6

tag: treatment

value: EYFP and Kir2.1 expression by in utero electroporation


title: M_P6_Kir2.1_rep1

source_name: Mitral cell,P6,Kir2.1,replicate 1


title: KPC Control YFP+ cancer cells from Lung - mouse 978U

value: Pdx1-Cre; KrasG12D; p53R172H/+; Rosa26-LSL-EYFPF/F

value: metastatic


title: M_P6_Kir2.1_rep2

source_name: Mitral cell,P6,Kir2.1,replicate 2


title: KPC-Snail;Twist cKO YFP+ cancer cells from liver - mouse 407P


title: TCPP_2_FRC_Rep2

description: lane2-s020-indexRPI14-AGTTCC-26_S20_L002


title: OPSCC252

tag: hpv status

value: FFPE

value: WashU cohort


title: M_P6_Kir2.1_rep3

source_name: Mitral cell,P6,Kir2.1,replicate 3


title: M_P6_Control_rep2

source_name: Mitral cell,P6,Control,replicate 2

value: EYFP expression by in utero electroporation


title: KPC Control YFP+ cancer cells from liver - mouse H444


title: M_P6_Control_rep4

source_name: Mitral cell,P6,Control,replicate 4


title: M_P6_Control_rep1

source_name: Mitral cell,P6,Control,replicate 1


title: M_P3_Kir2.1_rep4

source_name: Mitral cell,P3,Kir2.1_replicate4

value: Postnatal day 3


title: KPC Control YFP+ cancer cells from primary tumor - mouse H410

value: primary


title: KPC Control YFP+ cancer cells from primary tumor - mouse 978U


title: M_P6_Control_rep3

source_name: Mitral cell,P6,Control,replicate 3


title: KPC Control YFP+ cancer cells from lung - mouse H410


title: TCEP_4_FRC_Rep4

description: lane2-s030-indexRPI44-TATAAT-72_S30_L002

value: 48 hour post fertilization embryo

value: Tris(2-chloroethyl) phosphate


title: TCEP_2_FRC_Rep2

description: lane2-s029-indexRPI42-TAATCG-70_S29_L002

value: 85 uM


title: TCEP_3_FRC_Rep3

description: lane3-s044-indexRPI43-TACAGC-71_S44_L003


title: OPSCC248

value: HPV+


title: OPSCC249


title: OPSCC250


title: TCEP_1_FRC_Rep1

description: lane1-s015-indexRPI41-GACGAC-69_S15_L001


title: OPSCC247


title: OPSCC245


title: TDBPP_3_FRC_Rep3

description: lane3-s037-indexRPI23-GAGTGG-47_S37_L003

value: Tris(2,3-dibromopropyl) phosphate

value: 3 uM


title: OPSCC246


title: TDBPP_4_FRC_Rep4

description: lane3-s038-indexRPI24-GGTAGC-48_S38_L003


title: M_P3_Kir2.1_rep1

source_name: Mitral cell,P3,Kir2.1_replicate1

value: ICR

value: Olfactory bulb


title: M_P3_Kir2.1_rep3

source_name: Mitral cell,P3,Kir2.1_replicate3

value: Mitral cell


title: M_P3_Control_rep4

source_name: Mitral cell,P3,Control,replicate 4


title: OPSCC244

value: HPV-


title: TDBPP_2_FRC_Rep2

description: lane2-s023-indexRPI22-CGTACG-46_S23_L002


title: TPP_4_FRC_Rep4

description: lane3-s042-indexRPI36-CCAACA-60_S42_L003

value: Triphenyl phosphate

value: 8 uM


title: OPSCC242

value: FFPE


title: T47D CAPER KD H3K4 ChIP B [18301X30]

first: Yao

last: Yu

address: 1155 Pressler

institute: UT MD Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.7.15-r1140 with the following configurations: -q 5 -l 32 -k 2
Data were filtered by removing duplicates and unmapped reads using samtools version 1.9
peaks were called using macs version 2 with the following setting: -B -q 0.05
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using bedGraphToBigWig version 4

source_name: T47D CAPER KD H3K4 ChIP

growth_protocol: T47D and PME cells were maintained in RPMI and HMEC complete medium respecteivley as per the procedure mentioned on ATCC website.

extract_protocol:
RBM39, MLL1 and H3K4me3 bound DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: RBM39 KD was perfomed by the Neon Trasnfection system as per the procedure mentioned on ThermoFischer Scietific.

tag: cell line

tag: tissue source

value: Mammary Gland, Derived from metastatic site, Pleural effusion

tag: tissue type

value: Mammary gland, Ductal carcinoma

tag: cell type

value: Epithelial

tag: passages

value: 15th passage

tag: chip antibody


title: T47D Control KD H3K4 ChIP B [18301X28]

source_name: T47D Control KD H3K4 ChIP


title: TDBPP_1_FRC_Rep1

tag: tissue

value: 48 hour post fertilization embryo


title: TPP_3_FRC_Rep3

description: lane3-s041-indexRPI35-CATTTT-59_S41_L003


title: M_P3_Kir2.1_rep2

source_name: Mitral cell,P3,Kir2.1_replicate2

tag: age

value: Postnatal day 3

value: EYFP and Kir2.1 expression by in utero electroporation


title: M_P3_Control_rep3

source_name: Mitral cell,P3,Control,replicate 3

value: EYFP expression by in utero electroporation


title: T47D CAPER KD H3K4 ChIP A [18301X29]


title: T47D Control KD H3K4 ChIP A [18301X27]


title: PME MLL1 B [18301X26]

source_name: PME MLL1

value: PME

value: Breast

value: Adherent Epithelial from Breast

value: 4th passage


title: M_P3_Control_rep2

source_name: Mitral cell,P3,Control,replicate 2

value: ICR

value: Olfactory bulb

value: Mitral cell


title: OPSCC240

source_name: Oropharyngeal squamous cell carcinoma

value: HPV+

tag: cohort

value: WashU cohort


title: TPP_2_FRC_Rep2

description: lane2-s027-indexRPI34-CATGGC-58_S27_L002

tag: chemical

value: Triphenyl phosphate

value: 8 uM


title: OPSCC239

value: FFPE


title: OPSCC241


title: M_P3_Control_rep1

source_name: Mitral cell,P3,Control,replicate 1


title: OPSCC238


title: IPP_4_FRC_Rep4

description: lane2-s026-indexRPI32-CACTCA-56_S26_L002

value: Triisopropylated phenyl phosphate

tag: concentration


title: TPP_1_FRC_Rep1

description: lane1-s012-indexRPI33-CAGGCG-57_S12_L001

value: 48 hour post fertilization embryo


title: OPSCC243


title: IPP_3_FRC_Rep3

description: lane3-s040-indexRPI31-CACGAT-55_S40_L003


title: PME CAPER A [18301X23]

source_name: PME CAPER

value: Epithelial

value: CAPER


title: OPSCC237


title: PME CAPER B [18301X24]


title: TiBP_4_FRC_Rep4

description: lane1-s010-indexRPI28-CAAAAG-52_S10_L001

value: Triisobutyl phosphate


title: PME Input A [18301X21]

source_name: PME Input

value: PME


title: PME Input B [18301X22]

value: Breast


title: T47D CAPER KD Input A [18301X3]

source_name: T47D CAPER KD Input

value: Mammary Gland, Derived from metastatic site, Pleural effusion

value: Mammary gland, Ductal carcinoma

value: 15th passage


title: TBBPA.DBPE_4_FRC_Rep4

description: lane1-s014-indexRPI40-CTCAGA-68_S14_L001

value: 4 uM


title: OPSCC230


title: TBBPA.DBPE_3_FRC_Rep3

description: lane3-s043-indexRPI39-CTATAC-67_S43_L003


title: OPSCC229


title: OPSCC228


title: RWPE1 - NKX3.1(T164A) - Paraquat (CAD97)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

data_processing:
RNA-seq pipeline description:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq package in R-studio Version 0.99.484
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: Tab-delimited text or xls files include DESeq normalized values for each Sample

source_name: Human RWPE1 cells

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

tag: genotype


title: IPP_2_FRC_Rep2

description: lane2-s025-indexRPI30-CACCGG-54_S25_L002


title: TBBPA.DBPE_2_FRC_Rep2

description: lane2-s028-indexRPI38-CTAGCT-66_S28_L002


title: OPSCC236


title: OPSCC227


title: OPSCC235


title: OPSCC234


title: TiBP_3_FRC_Rep3

description: lane3-s039-indexRPI27-ATTCCT-51_S39_L003


title: TCDD_4_TCDD_Rep4

description: lane2-s014-indexRPI12-CTTGTA-WT-TCDD-rep4_S14_L002

extract_protocol:
Following exposure, 48-hpf whole embryos were homogenized using RNAzol (Molecular Research Center, Inc).  RNA was purified using the Direct-zol MiniPrep kit (Zymo Research)
150 bp sequencing was conducted using an Illumina HiSeq 3000 sequencer
mRNAs were enriched by polyA selection. Libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems)

value: TCDD

value: 1 ng/mL


title: T47D CAPER KD Input B [18301X4]


title: BRN2_HOM_TUM_1

source_name: Primary tumor

value: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 F/F

tag: Sex

value: male

tag: rin

tag: category

tag: mouseid


title: OPSCC226

tag: hpv status

value: HPV+

value: WashU cohort


title: OPSCC233

value: FFPE


title: TiBP_2_FRC_Rep2

description: lane2-s024-indexRPI26-ATGAGC-50_S24_L002

value: 48 hour post fertilization embryo


title: PME MLL1 A [18301X25]

tag: cell line

value: Adherent Epithelial from Breast

value: Epithelial

value: 4th passage


title: OPSCC232


title: TCDD_2_TCDD_Rep2

description: lane1-s006-indexRPI10-TAGCTT-WT-TCDD-rep2_S6_L001


title: T47D Control KD Input B [18301X2]

source_name: T47D Control KD Input

tag: tissue source


title: TCDD_1_TCDD_Rep1

description: lane1-s005-indexRPI9-GATCAG-WT-TCDD-rep1_S5_L001


title: TiBP_1_FRC_Rep1

value: Triisobutyl phosphate


title: OPSCC231


title: OPSCC225


title: OPSCC223


title: T47D Control KD Input A [18301X1]

tag: tissue type


title: RWPE1 - NKX3.1(T164A) - Paraquat (CAD98)


title: IPP_1_FRC_Rep1

description: lane1-s011-indexRPI29-CAACTA-53_S11_L001

value: Triisopropylated phenyl phosphate


title: TBBPA.DBPE_1_FRC_Rep1

description: lane1-s013-indexRPI37-CGGAAT-65_S13_L001


title: T47D WT SiRNA A

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat v2.1.1 with parameters --library-type fr-firststrand
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks v2.2.1
Differetially expressed genes were detected using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for wt and mutant

source_name: mammary gland; derived from metastatic site: pleural effusion

growth_protocol: T47D cells were maintained in RPMI medium as per the procedure mentioned on ATCC website.

extract_protocol:
RNA was isolated by using Qiagen RNA purification kit. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mammary gland

value: wild type


title: Retene_4_16PAH_Rep4

description: lane4-s043-indexRPI43-TACAGC-A8_S43_L004

extract_protocol:
Following exposure, 48-hpf whole embryos were homogenized using RNAzol (Molecular Research Center, Inc).  RNA was purified using the Direct-zol MiniPrep kit (Zymo Research)
100 bp sequencing was conducted using an Illumina HiSeq 3000 sequencer
mRNAs were enriched by polyA selection. Libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems)

value: Retene


title: RWPE1 - NKX3.1(T164A) - Paraquat (CAD96)


title: RWPE1 - NKX3.1(T164A) - Paraquat (CAD95)

tag: treatment

value: paraquat


title: OPSCC220

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were collected for pathologic analysis from biopsy or primary surgical resection.
Ribosomal RNA (rRNA) was removed with the RiboMinus kit (Life Technologies) and custom DNA oligonucleotide probes. The RNA was used to construct RNA-seq libraries with the NEBNext Ultra mRNA Library Prep kit (New England BioLabs). The resulting cDNA libraries were PCR amplified and subject to sequencing with Illumina HiSeq 3000 at Washington University Genome Technology Access Center.


title: Retene_2_16PAH_Rep2

description: lane2-s021-indexRPI21-GTTTCG-C4_S21_L002


title: MLL ChIP A

extract_protocol:
RBM39 and MLL1 bound DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

tag: cell type

tag: passages

value: 9th Passage


title: T47D RBM39 SiRNA B

tag: tissue

value: RBM39 KD


title: TCDD_3_TCDD_Rep3

description: lane2-s013-indexRPI11-GGCTAC-WT-TCDD-rep3_S13_L002

value: TCDD

value: 1 ng/mL


title: T47D RBM39 SiRNA A


title: OPSCC222

value: HPV+


title: T47D WT SiRNA B


title: OPSCC224

value: WashU cohort


title: RBM39 ChIP B

value: 8th Passage

tag: chip antibody


title: Retene_1_16PAH_Rep1

description: lane4-s045-indexRPI45-TCATTC-C8_S45_L004

value: 48 hour post fertilization embryo


title: MLL ChIP B

value: 10th Passage


title: Phenan_4_16PAH_Rep4

description: lane3-s029-indexRPI29-CAACTA-E5_S29_L003

value: Phenanthrene

value: 50 uM


title: OPSCC218

value: FFPE

tag: cohort


title: RBM39 ChIP A

value: Epithelial

value: 7th Passage


title: OPSCC219


title: OPSCC221


title: Phenan_2_16PAH_Rep2

description: lane2-s015-indexRPI15-ATGTCA-C3_S15_L002

tag: chemical


title: Phenan_3_16PAH_Rep3

description: lane6-s063-indexRPI15-ATGTCA-C11_S63_L006

tag: concentration


title: T47D Input A

value: 5th Passage


title: OPSCC216


title: T47D Input B

value: 6th Passage


title: Phenan_1_16PAH_Rep1

description: lane5-s058-indexRPI10-TAGCTT-D10_S58_L005


title: OPSCC217


title: Retene_3_16PAH_Rep3

description: lane5-s057-indexRPI9-GATCAG-C10_S57_L005

value: Retene


title: RWPE1 - NKX3.1(R52C) - Paraquat (CAD34)

description: processed data file: matrix for human_ENS.txt

data_processing:
RNA-seq pipeline description:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq package in R-studio Version 0.99.484
Genome_build: Ensembl/GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes DESeq normalized values for each Sample

tag: genotype

value: paraquat


title: RWPE1 - NKX3.1(R52C) - Paraquat (CAD36)


title: OPSCC215

value: HPV-


title: RWPE1 - NKX3.1(R52C) - Paraquat (CAD35)


title: OPSCC213


title: Fluoran_4_16PAH_Rep4

description: lane5-s056-indexRPI8-ACTTGA-B10_S56_L005

value: Fluoranthene


title: OPSCC214


title: Fluoran_3_16PAH_Rep3


title: RWPE1 - NKX3.1(R52C) - Paraquat (CAD33)


title: OPSCC211


title: OPSCC210


title: DMSO_4_TCDD_Rep4

description: lane2-s010-indexRPI4-TGACCA-WT-DMSO-rep4_S10_L002

value: DMSO


title: OPSCC212

value: HPV+


title: Fluoran_2_16PAH_Rep2

description: lane4-s040-indexRPI40-CTCAGA-D7_S40_L004


title: Fluoran_1_16PAH_Rep1


title: RWPE1 - NKX3.1(R52C) - Paraquat (CAD31)


title: RWPE1 - NKX3.1(R52C) - Paraquat (CAD32)


title: OPSCC209

value: WashU cohort


title: DMSO_2_TCDD_Rep2

description: lane1-s002-indexRPI2-CGATGT-WT-DMSO-rep2_S2_L001


title: OPSCC208


title: DMSO_1_TCDD_Rep1

description: lane1-s001-indexRPI1-ATCACG-WT-DMSO-rep1_S1_L001


title: OPSCC207


title: OPSCC204


title: OPSCC205


title: RWPE1 - NKX3.1 - Paraquat (CAD26)


title: RWPE1 - NKX3.1 - Paraquat (CAD25)


title: RWPE1 - NKX3.1 - Paraquat (CAD27)


title: RWPE1 - NKX3.1 - Paraquat (CAD28)


title: DMSO_A_4_16PAH_Rep4


title: OPSCC206


title: OPSCC203


title: RWPE1 - Control Vector - Paraquat (CAD12)

value: Control Vector


title: DMSO_B_1_16PAH_Rep1

description: lane4-s038-indexRPI38-CTAGCT-B7_S38_L004

value: 48 hour post fertilization embryo


title: OPSCC200


title: DMSO_B_3_16PAH_Rep3

description: lane3-s031-indexRPI31-CACGAT-A6_S31_L003


title: RWPE1 - Control Vector - Paraquat (CAD11)


title: OPSCC202


title: DMSO_A_3_16PAH_Rep3


title: RWPE1 - NKX3.1 - Paraquat (CAD30)


title: DMSO_3_TCDD_Rep3

description: lane2-s009-indexRPI3-TTAGGC-WT-DMSO-rep3_S9_L002


title: OPSCC197


title: RWPE1 - Control Vector - Paraquat (CAD10)


title: CHANGE-seq  mus musculus

source_name: mus musculus gDNA

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation

value: in situ gDNA digest

value: Cas9 digest with sgRNA-mP01

value: CHANGE-seq

value: Cas9-KO PCSK9


title: OPSCC196

value: FFPE


title: CIRCLE-seq  mus musculus target

value: CIRCLE-seq


title: OPSCC195


title: DMSO_B_2_16PAH_Rep2

description: lane6-s072-indexRPI24-GGTAGC-F12_S72_L006


title: RWPE1 - NKX3.1 - Paraquat (CAD29)


title: OPSCC201


title: RWPE1 - Control Vector - Paraquat (CAD9)


title: DMSO_4_FRC_Rep4


title: RWPE1 - Control Vector - Paraquat (CAD8)


title: OPSCC199


title: DBaiP_2_16PAH_Rep2

description: lane6-s065-indexRPI17-GTAGAG-E11_S65_L006

value: Dibenzo[a,i]pyrene

value: 5 uM


title: DMSO_A_2_16PAH_Rep2

description: lane3-s036-indexRPI36-CCAACA-F6_S36_L003


title: DMSO_3_FRC_Rep3


title: DMSO_B_4_16PAH_Rep4

description: lane6-s071-indexRPI23-GAGTGG-E12_S71_L006


title: OPSCC192


title: OPSCC198


title: DMSO_2_FRC_Rep2


title: DMSO_1_FRC_Rep1


title: DBahP_4_16PAH_Rep4

description: lane1-s012-indexRPI12-CTTGTA-F2_S12_L001

value: Dibenzo[a,h]pyrene

value: 10 uM


title: p53_long-term_Rep14

source_name: whole liver lysate

value: on-target, AAV delivery

value: tail vein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: DBaiP_3_16PAH_Rep3

description: lane2-s013-indexRPI13-AGTCAA-A3_S13_L002


title: OPSCC191

value: HPV+

value: WashU cohort


title: DBahP_3_16PAH_Rep3

value: 48 hour post fertilization embryo