title: iBAT_cdna_cold_15

city: Odense

first: Jan-Wilhelm

last: Kornfeld

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

data_processing:
basecalling using Guppy
Quality trimming using NanoFilt (-q 7)
mapping to the transcriptome (GENCODE M22) using minimap2 (-ax map-ont –secondary=no)
quantification using GenomicAlignments
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw transcript counts for every transcript

source_name: interscapular brown adipose tissue

growth_protocol: Mice were kept at 22°C to 24°C on a regular 12 h light cycle with ad libitum access to food (Altromin 1324) and water.

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Whole frozen eWAT samples were homogenised in 1 ml TRIsure (Bioline) per animal using a tabletop homogeniser (FastPrep-24 5G, MP Biomedicals). RNA was isolated by phenol chloroform extraction and alcohol precipitation. RNA was poly-A selected in two consecutive rounds using oligo(dT) beads (GenElute mRNA Miniprep Kit, Sigma MRN10) following the manufacturer’s recommendations and subsequently alcohol precipitated.
Libraries were prepared from 100 ng poly-A+ RNA using the SQK-DCS109 direct cDNA sequencing kit and the EXP-NBD104 barcoding kit according to the manufacturer’s protocol.

treatment_protocol: 20 weeks old male wild type C57BL/6N mice were singly housed at 4 °C for a period of 24 h prior to harvesting adipose tissues.

value: interscapular brown adipose tissue

value: cold

tag: mouse id


title: iBAT_cdna_ctrl_14

status: Public on Sep 18 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: treatment

value: ctrl


title: WT_1

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Sequencing data were processed with RTA v1.18.66.3.
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
Sequencing adapter contaminations were removed using Cutadapt.
Reads were mapped on transcriptome and gene expression quantified using RSEM.
RSEM-estimated raw gene counts were normalized with Limma-Voom.
Genome_build: GRCm38 assembly, Ensembl genebuild 70.
Supplementary_files_format_and_content: Matrix table contains raw expected_counts as obtained from RSEM aligner.

source_name: Embryo

extract_protocol:
RNA was isolated at E15.5 from ventricles of Control (Mib1flox/+; Tnnt2-Cre/+) and Mib1R530X/flox; Tnnt2-Cre/+, and WT and Mib1R530X/+ Asxl3M1361V/+ Apcdd1V150I/+ embryos. Samples were distributed in three pools of four pairs of ventricles per genotype. Tissue was homogenized with a pestle mechanical homogenizer and RNA was extracted using RNEasy Mini Kit (Qiagen, 74104).
cDNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit
Libraries were sequenced on a HiSeq 2500 system (Illumina) to generate 60 base single reads.

tag: genotype

value: WT


title: WC55

city: Bethesda

first: Francis

last: Collins

state: MD

address: 50 South Dr

department: NHGRI

country: USA

institute: NIH

data_processing:
Aligned the processed reads to the GRCm38 genome assembly using STAR v2.73a with default parameters
Quantified expression levels of gencode.vM24 genes using QoRTs (v1.3.6).
Generated a raw read count matrix of gene by library
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include read counts per gene per sample

molecule: total RNA

source_name: 8-week femoral diaphysis

extract_protocol:
total RNA extracted using Trizol, then treated with 1U/ul Dnase I
Strand-specific
Poly-A enrichment, 80M clusters PE150 each

value: 8-week femoral diaphysis

value: Lmna+/+

tag: gender

value: male


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_8

type: RNA

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H10_6

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the oligo package. We used an alternative CDF probset description file from Brainarray (version 22) at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): pd.hgu133plus2.hs.entrezg_22.0.0.tar.gz

label: biotin

organism: Homo sapiens

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: paired samples

value: patient 8

tag: timepoint

value: lung


title: Biopsy_end.of.cold.ischemia_patient_9

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H11_0

value: patient 9

value: cit


title: Mib1_R530X_3

value: Mib1_R530X/Mib1_flox; Tnnt2-Cre/+

tag: developmental stage


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_9

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H11_6


title: iBAT_cdna_cold_11


title: Biopsy_end.of.cold.ischemia_patient_11

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H13_0

value: patient 11


title: WC54


title: Mib1_R530X_2


title: PrEC cells MeRIP-seq m6A IP (replicate 1)

city: Boston

first: Xinlei

last: Gao

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
RNA-Seq reads were mapped to human reference genome version hg19 using TopHat (version v2.0.12)  with default parameters. Next, Cuffdiff (version 2.2.1) was used to generate read count matrix. Normalized gene expression values in FPKM (fragments per kilobases per million mapped reads) was further calculated using UCSC knownGene as the reference genes. Genes with FPKM value larger than one were retained for further analysis. Differential expression test was performed using edgeR.
MeRIP-Seq data was filtered by Trimmomatic to remove low-quality bases and then mapped to human genome (version hg19) by Tophat (version v2.0.12) using default parameters. The read coverage calculation and normalization were conducted by deepTools. The distribution of m6A signal across gene body (5’UTR, CDS and 3’UTR) was measured by FPKM values in bins by deepTools. The normalized IP signal per bin was subtracted by normalized input signal to generate m6A signal coverage plot. Enrichment peaks of m6A signal were called by MACS2 and exomePeak2 using default parameters (parameter and p-value). M6A peaks called by MACS2 required q-value less than 0.05, and by exomePeak2 q-value less than 0.1. Differential methylation sites were identified by exomePeak2.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized gene expression (FPKM values) for all the RNA-seq samples.
bigWig for all the MeRIP-seq samples.

source_name: human prostate primary epithelial cells

extract_protocol:
MeRIP-seq was conducted in duplicates using Magna MeRIP™ m6A Kit (Millipore) with the procedure provided by the manufacturer. In brief, the total RNA from C4-2 and PrEC cells was extracted using RNeasy Plus Mini Kit (Qiagen), followed by mRNA isolation using PolyATtract mRNA Isolation System (Promega). The obtained mRNA was fragmented into ~100 nt in length and purified by miRNeasy Mini Kit (Qiagen). After incubation with anti-m6A antibody-magnetic beads mixture at 4 °C overnight, the m6A-modified mRNA fragments bound to beads were eluted and shipped to BGI for library preparation and sequencing using the DNBseq platform.
Samples were sent to BGI for library preparation and follow-up sequencing
MeRIP-seq

tag: cell type

value: prostate primary epithelial cells (PrEC)

value: control

tag: rip antibody

value: anti-m6A antibody


title: WC53

value: female


title: iBAT_cdna_cold_4

value: interscapular brown adipose tissue


title: Mib1_R530X_1


title: WC52


title: Triple_Het_3


title: WC51


title: Triple_Het_2


title: WC50


title: iBAT_telo_cold_15

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Whole frozen eWAT samples were homogenised in 1 ml TRIsure (Bioline) per animal using a tabletop homogeniser (FastPrep-24 5G, MP Biomedicals). RNA was isolated by phenol chloroform extraction and alcohol precipitation. RNA was poly-A selected in two consecutive rounds using oligo(dT) beads (GenElute mRNA Miniprep Kit, Sigma MRN10) following the manufacturer’s recommendations and subsequently alcohol precipitated.
The TeloPrime Full-Length cDNA Amplification Kit (Lexogen, Austria) was used to select for full length mRNAs (27 PCR cycles). 400 ng of the cDNA were processed with the SQK-LSK109 ligation sequencing kit (ONT) and the EXP-NBD104 barcoding kit (ONT) following manufacturer’s instructions.

value: cold


title: Biopsy_end.of.cold.ischemia_patient_7

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H7_0

value: patient 7


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_7

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H7_6


title: Triple_Het_1


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_6

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H6_6

value: patient 6


title: Biopsy_end.of.cold.ischemia_patient_6

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H6_0


title: Biopsy_end.of.cold.ischemia_patient_8

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H10_0


title: WC49

value: 8-week femoral diaphysis


title: WC48


title: iBAT_cdna_ctrl_9

value: ctrl


title: iBAT_telo_cold_11


title: iBAT_telo_ctrl_9


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_5

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H5_6

value: patient 5


title: WC46

value: Lmna+/+


title: iBAT_cdna_ctrl_2


title: iBAT_telo_cold_4


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_4

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H4_6

value: patient 4

value: lung


title: WC45


title: Monocytes from  healthy donor RTD317

city: Waltham

first: Ming

last: Tang

state: Massachusetts

address: 21 Hickory Drive, 1

department: Computational biology

institute: Immunitas Therapeutics

data_processing:
The preprocessing steps were carried out using a Snakemake pipeline.
Briefly, the raw FASTQ files were aligned using STAR (v2.7.10b)  to genome GRCh38.primary_assembly.genome.fa using annotation file gencode.v40.annotation.gtf
and the count matrix was generated by FeatureCounts (v2.0.1). The raw counts were imported into DESeq2 41 (v1.36.0) in R (v4.2.1) and differential expression analysis was carried out following the standard procedure
Assembly: GRCh38
Supplementary files format and content: tab delimited files for the raw counts

source_name: blood

growth_protocol:
Healthy Donors PBMNC were acquired to isolate human M0 (CD16 negativemonoctye) and applied to Miltenyi biotec kit, (#130-117-337) following the manufacture instruction manual.
Monocytes were seeded on 100mm culture dishes with X-Vivo15 media supplied with 5% human serum.

extract_protocol:
Total RNA was isolated from cell lysates using the RNeasy Mini Kit (Qiagen) per the “Purification of Total RNA from Animal Cells using Spin Technology” section of the kit manual. An optional DNase I treatment was included and performed using the RNase-Free DNase Set (Qiagen)
Bulk libraries were prepared using the NEBNext Ultra ii Directional RNA Library Prep for Illumina Kit (New England BioLabs) per Section 1 of the manufacturer’s protocol. 500ng of total RNA was used as input for each sample, and an rRNA depletion was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). SPRIselect beads (Beckman Coulter) were used in place of NEB Sample Purification Beads for all purification steps. For the final enrichment PCR, bulk libraries were barcoded using the NEBNext Multiplex Oligos for Illumina – 96 Index Primers Kit (New England BioLabs) and amplified for 10 PCR cycles.

treatment_protocol: To generate M1 macrophages, cells were cultured for 5 days under GM-CSF stimulation and then for 2 days with IFNg and a final 18h touch of LPS treatments. M2-like macrophages were developed through 5 days of culture with M-CSF and further 48h treatment of IL-4 stimulation. TAM development was accomplished through continues 7-days of cell culture, under influence of M-CSF+IL4 and IL10. The medium was enriched with 20% TCM media as the required supplement. Through the last 48h of culture, TGF-b stimulation was added to the culture medium as well.Medium change for the culture systems, administrated once during the 7 days of culture

value: blood

value: monocyte


title: M2-like macrophage differentiated from healthy donor RTD317

value: macrophage


title: iBAT_telo_ctrl_2


title: Monocytes from  healthy donor RTD230


title: Biopsy_end.of.cold.ischemia_patient_4

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H4_0

value: cit


title: iBAT_telo_ctrl_14


title: WC43

value: male


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_3

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H3_6

value: patient 3


title: iBAT_rna_ctrl

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Whole frozen eWAT samples were homogenised in 1 ml TRIsure (Bioline) per animal using a tabletop homogeniser (FastPrep-24 5G, MP Biomedicals). RNA was isolated by phenol chloroform extraction and alcohol precipitation. RNA was poly-A selected in two consecutive rounds using oligo(dT) beads (GenElute mRNA Miniprep Kit, Sigma MRN10) following the manufacturer’s recommendations and subsequently alcohol precipitated.
Libraries were prepared from 500 ng poly-A+ RNA using the SQK-RNA002 direct RNA sequencing kit according to manufaturer’s protocol (ONT).


title: M1-like macrophage differentiated from healthy donor RTD230


title: WC44


title: Biopsy_end.of.cold.ischemia_patient_5

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H5_0


title: iBAT_rna_cold


title: TAM differentiated from healthy donor RTD230


title: M2-like macrophage differentiated from healthy donor RTD230


title: Eed-Het mice pooled

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 203 Research Dr

department: Head and Neck Surgery & Communication Sciences

institute: Duke University

library_source: transcriptomic single cell

data_processing:
Raw base call files were analyzed using Cell Ranger v.4.0.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
CellRanger v.4.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to mouse genome GRCm38 with tdTomato sequence appended
Assembly: GRCm38 mouse assembly + tdTomato
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mx (filtered_feature_bc_matrix.tar.gz)

source_name: Olfactory epithelium

extract_protocol:
Specimens were collected in either HBSS + 10% FBS, spun down, then digested using Accutase, 1 mM EDTA, DNAse I, and papain. Cells were filtered through a 70 μm strainer, pelleted and washed, and then treated with an erythrocyte lysis buffer and washed again. The cells were then resuspended in PBS with 0.1% bovine serum albumin and 0.2% anti-clumping agent (Invitrogen) and immediately processed for scRNA-seq. Note that cells from three Eed-Het animals were pooled for a single 10x Chromium run.
Samples were processed for scRNA-seq using Chromium Single Cell 3′ Paired-End, Dual-Index Library & Gel Bead Kit v3.1 (10X Genomics) targeting 10000 cells, then sequenced using NovaSeq 50bp (Illumina) flow cells.

value: Olfactory epithelium

value: K5-creER;Ai9;Eed fl/wt

value: Tamoxifen & methimazole


title: TAM differentiated from healthy donor RTD317


title: Biopsy_end.of.cold.ischemia_patient_3

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H3_0


title: M1-like macrophage differentiated from healthy donor RTD317


title: Eed-KO mouse 2

value: K5-creER;Ai9;Eed fl/fl


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_2

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H2_6

value: patient 2


title: Eed-KO mouse 3


title: Biopsy_6.hours.of.ex.vivo.lung perfusion_patient_1

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H1_6

value: patient 1


title: cDNA-Bleo3

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Examine reads base-pair quality with fastqc
Map reads with bwa-mem
Examine gene-feature content
Quantify read counts with featureCounts from Subread
Assembly: GRCh37 GENCODE v29
Supplementary files format and content: Gene counts in csv format
Library strategy: Nascent RNASeq

source_name: fibrosarcoma cell line

growth_protocol: standard tissue culture conditions

extract_protocol:
RNA was isolated using the Monarch Total RNA Miniprep Kit (New England BioLabs, cat #T2010) following the manufacturer's protocol.
After cDNA synthesis, samples were sheared with Covaris and libraries were constructed using KAPA HyperPrep kit following manufacture instructions.

treatment_protocol: 400ug/ml bleomycin or 0.5uM CBL0137 24 hours

value: fibrosarcoma cell line

tag: cell line

value: GSE56 (p53 mutant)

value: Bleo

tag: replicate


title: Biopsy_end.of.cold.ischemia_patient_2

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H2_0


title: cDNA-Bleo2


title: D728,48h,rep5

city: Miaoli County

first: Ya-Hui

last: Chi

address: 35 Keyan Road, Zhunan Town

department: Institute of Biotechnology and Pharmaceutical Research

country: Taiwan

institute: National Health Research Institutes

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1).
The raw data, generated by high-throughput sequencing (Illumina NovaSeq 6000 platform), were initially converted into raw sequenced reads using CASAVA base calling and were stored in FASTQ format. To ensure data quality, FastQC and MultiQC were used to perform quality checks on the fastq files. Subsequently, Trimmomatic was employed to filter out low-quality reads, trim adapter sequences, and eliminate poor-quality bases from the obtained raw paired-end reads. The resulting high-quality data, referred to as "clean reads", was used for downstream analysis. The read pairs from each sample were then mapped to the corresponding reference genome (e.g., H. sapiens, GRCh38) using HISAT2, and the number of reads mapped to individual genes was counted using featureCounts. To normalize gene expression, we performed two types of normalization depending on the presence of biological replicates. For experiments with biological replicates, we used the "Relative Log Expression" (RLE) normalization, which was performed using DESeq2. Principal component analysis (PCA) was used to visualize correlation in gene expression profiles between each dataset. Due to the extrinsic nature of the experimental design, the dataset that is deviated from the others under same experimental condition was excluded for p value calculation. To detect differentially expressed genes (DEGs) under two conditions, we used DESeq2 (for experiments with biological replicates), which are R packages based on the negative binomial distribution and Poisson distribution model, respectively. We performed various enrichment analyses and network analyses to gain insights into the differentially expressed genes (DEGs). First, the p-values obtained from DEG detection were adjusted using the Benjamini and Hochberg's approach to control the false discovery rate (FDR). We then conducted Gene Ontology (GO) and KEGG pathway enrichment analysis of DEGs using clusterProfiler, while Disease Ontology (DO) enrichment analysis was conducted using the DOSE package against DO, DisGeNET and NCG databases.
Assembly: CanFam3.1
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: Original_read_count.txt and TPM.txt

source_name: tumor xenograft

growth_protocol: NCI-H446 cancer cells were prepared in cold medium RPMI, mixed with an equal volume of Matrigel® Basement Membrane Matrix (Corning), and transplanted subcutaneously (at densities 1 × 106 in 100 ul medium/Matrigel® mixture) into the left flank of NU/NU or SCID mice.

extract_protocol:
Total RNAs were extracted from the tumor xenografts using the TRIzolTM Reagent (ThermoFisher Scientific).
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol
A total amount of 1 μg total RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using magnetic oligo-dT beads. Captured mRNA was fragmented by incubating at a high temperature in the presence of magnesium in KAPA Fragment, Prime and Elute Buffer (1x). First strand cDNA was synthesized using random hexamer priming. Combined 2nd strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporated dUTP into the second cDNA strand, and added dAMP to the 3’ ends of the resulting dscDNA. dsDNA adapter with 3’dTMP overhangs were ligated to library insert fragments to generate the library fragments carrying the adapters. In order to select cDNA fragments of preferentially 300~400bp in length, the library fragments were purified with KAPA Pure Beads system (KAPA Biosystems, Roche, Basel, Switzerland). The library carrying appropriate adapter sequences at both ends was amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Roche, Basel, Switzerland) along with library amplification primers. The strand marked with dUTP in not amplified, allowing strand-specific sequencing. At last, PCR products were purified using KAPA Pure Beads system and the library quality was assessed on the Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). The library quality was assessed on the Qubit® 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina NovaSeq6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Male NU/NU (Bltw:NU-Foxn1nu, BIOLASCO, Taiwan) mice bearing with NCI-H446 tumors at about 700 mm3 were treated with one 300 mg/kg oral dose of DBPR728.Tumors were harvested at 0 (Mock), 24 hours and 48 hours after drug administration.

value: tumor xenograft

value: small cell lung cancer

value: DBPR728 48h


title: Injury LD 14D, snATAC-seq

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description:
Injury_LD_14D_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
The multi-omic sequencing files were processed for demultiplexing and analyzed using Cell Ranger ARC v2.0. The genes were mapped and referenced using the zebrafish reference genome DanRer11.
To address potential ambient RNA contamination in the cell-by-gene expression matrix, we employed scAR module from scvi-tools with default parameters for further ambient RNA cleaning for each sample.
Assembly: DanRer11
Supplementary files format and content: Tab separated and matrix files

molecule: genomic DNA

organism: Danio rerio

source_name: Retina

growth_protocol: All the zebrafish used in this study were adults between 6 and 12 months old. Prior to any experiments, the fish were anesthetized or euthanized using 1:1000 or 1:500 2-phenoxyethanol (Sigma), respectively.

extract_protocol:
Zebrafish retinas (4-6 retinas from 4-6 fish) were collected at different timepoints after NMDA and LD treatments, and flash-frozen in dry ice for ~15min before being transferred to a -80C freezer for storage.
Nuclei were extracted from frozen retinal tissues according to 10x Multiome ATAC + Gene Expression (GEX) protocol (CGOOO338). Briefly, frozen retinal tissues were lysed in ice-cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged, washed 3 times and resuspended in 10x Multiome nuclei buffer at a concentration of ~3000-5000 nuclei/ml. Nuclei (~15k) then were loaded onto 10x Genomic Chromium Controller, with a target number of ~10K nuclei per sample. RNA and ATAC libraries were prepared according to the 10x Multiome ATAC + Gene Expression protocol and subjected for Illumina NovaSeq sequencing at ~500 million reads per library.

treatment_protocol:
Phototoxic treatment that causes photoreceptor ablation was used to initiate a regenerative response in the zebrafish retina 2,53. All fish subjected to light damage were dark-adapted for two weeks and then placed adjacent to intense fluorescent lights for 96 hours. The temperature of the fish tanks was regularly monitored and maintained at 34ºC. After 96 hours, the fish were returned to the animal facility with a normal light/dark cycle and maintained for 7, 14, or 21 days recovery (DR).
N-methyl-D-aspartate (NMDA, Sigma M3262) was administered to normal light/dark cycled fish via an intravitreal injection of 0.3µL 100mM NMDA solution in sterile PBS with a Hamilton syringe (Hamilton, 2.5µL Model 62 RN SYR, 87942), followed by placing the tanks in a dark incubator at 33ºC for 96 hours, after which the tanks were moved back into a normal light/dark cycle for 7 or 14 days recovery.
EdU (5-Ethynyl-2′-deoxyuridine, Life Technologies A10044) was administered as previously described 53. Fish were anesthetized using 1:1000 2-phenoxyethanol and immobilized under a paper towel in a petri dish. Then, using an insulin syringe equipped with a 30-gauge needle, approximately 20 µL 1mg/mL EdU in water was injected intraperitoneally into each zebrafish at 60, 72, 84, 96 and 108 hours after damage. The retinal tissues were harvested at either 3, 7, 14, or 21 days recovery.

value: Retina

value: LD

tag: time point


title: Eed-KO mouse 1


title: Biopsy_end.of.cold.ischemia_patient_1

description:
This sample is previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.
H1_0

value: cit

value: lung


title: WC42

value: 8-week femoral diaphysis

value: Lmna+/+

value: male


title: cDNA-Bleo1


title: D728,48h,rep3


title: D728,48h,rep2


title: LiverNlrp3△Hep-TAA_rep3 [C954]

city: chengdu

first: yang

last: xiao

address: NO. 1, 4th Keyuan Road

country: China

institute: Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University

data_processing:
Raw data were firstly processed through custom perl and python scripts, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.2.1).
For each sample, read counts for each gene were obtained with featureCounts (v1.5.0-p3) and were standardized as fragments per kilobase million (FPKM).
Assembly: mm10
Supplementary files format and content: Matrix table with mRNA FPKM for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from liver samples using TRIzol reagent (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver

value: Hepatocyte-specific Nlrp3 deletion

value: 8-week thioacetamide i.p.


title: Injury LD 96hr, snATAC-seq

description:
Injury_LD_96hr_ATAC
10x Genomics


title: Injury LD 72hr, snATAC-seq

description:
Injury_LD_72hr_ATAC
10x Genomics


title: Injury LD 7D, snATAC-seq

description:
Injury_LD_7D_ATAC
10x Genomics


title: cDNA-CBL137-3


title: cDNA-CBL137-2


title: Liver_ Nlrp3△Hep-TAA_rep1 [C924]


title: D728,48h,rep1


title: D728,24h,rep5

value: DBPR728 24h


title: cDNA-CBL137-1

value: fibrosarcoma cell line


title: Injury LD 54hr, snATAC-seq

description:
Injury_LD_54hr_ATAC
10x Genomics


title: Liver_TAA_rep3 [BA4]

value: Wild type


title: D728,48h,rep4


title: D728,24h,rep4


title: Injury LD 14D, snRNA-seq

description:
Injury_LD_14D
10x Genomics

molecule: nuclear RNA


title: cDNA-CTR3

value: GSE56 (p53 mutant)

value: CTR


title: Liver_TAA_rep2 [BA2]


title: Liver_TAA_rep1 [BA1]


title: Injury LD 7D, snRNA-seq

description:
Injury_LD_7D
10x Genomics


title: cDNA-CTR2


title: D728,24h,rep3

value: tumor xenograft

value: small cell lung cancer


title: D728,24h,rep2


title: Liver_STING KO-CCl4_rep3 [SWT5]

value: Sting knock out

value: 6-week CCl4 i.p.


title: cDNA-CTR1


title: Liver_Nlrp3△Hep-TAA_rep2 [C935]


title: Injury LD 72hr, snRNA-seq

description:
Injury_LD_72hr
10x Genomics

value: Retina

value: LD


title: Injury LD 96hr, snRNA-seq

description:
Injury_LD_96hr
10x Genomics


title: D728,24h,rep1


title: HT1080-Bleo-3

value: wild type TP53

value: Bleo


title: Injury LD 54hr, snRNA-seq

description:
Injury_LD_54hr
10x Genomics


title: HT1080-Bleo-2


title: Liver_STING KO-CCl4_rep2 [SWT4]


title: Mock,rep5

value: mock


title: Mock,rep4


title: Liver_ STING KO-CCl4_rep1 [SWT3]

value: Liver


title: HT1080-Bleo-1


title: Injury NMDA 14D, snATAC-seq

description:
Injury_NMDA_14D_ATAC
10x Genomics

value: NMDA


title: Liver_CCl4_rep3 [S1861]


title: Injury NMDA 7D, snATAC-seq

description:
Injury_NMDA_7D_ATAC
10x Genomics


title: Mock,rep3


title: HT1080-CBL137-3


title: Injury NMDA 96hr, snATAC-seq

description:
Injury_NMDA_96hr_ATAC
10x Genomics


title: Liver_CCl4_rep2 [S1859]


title: HT1080-CBL137-2


title: Liver_CCl4_rep1 [C4]


title: HT1080-CBL137-1


title: Mock,rep2


title: Mock,rep1


title: Liver_Oil_rep3 [O2032]

value: 6-week oil i.p.


title: HT1080-CTR3


title: CtIP PC, plus 4-OHT, input

city: Austin

first: Tanya

middle: T.

last: Paull

state: TX

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

description:
CtIP pellet-ChIP, plus 4-OHT, - antibody, rep1
hg19

library_source: genomic

data_processing:
DNA-PKcs and CtIP GLASS-ChIP and pellet-ChIP: Raw data was pre-processed with BedTools fastp, mapped with BWA-MEM, duplicates were removed with SAMTools RmDup, and peaks called with MACS2. AsiSI-associated data was processed using genome build Hg19; Cas9-associated data was processed using genome build Hg38. Mre11 ChIP data:
For Glass-ChIP, no-antibody sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls. body sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls.
Bedgraph output files from MACS2 were converted to bigwig files using ucsc-wigtobigwig (Version 357)
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
GLASS-ChIP assay  Human U2OS cells with inducible AsiSI15 were grown to 50-60% confluency in 150 mm dishes and treated with 600 nM 4-OHT for 4 h at 37°C. When used, 10 µM NU7441 was added 30 min. prior to 4-OHT addition. After 4-OHT treatment, cells were fixed with 1% formaldehyde for 7 min at RT with gentle rotation. Crosslinking was stopped by addition of 125 mM glycine for 5 min, washed twice with cold PBS, harvested, flash frozen in liquid nitrogen and stored at -80°C.  For the GLASS-ChIP assay, we modified a standard protocol (Abcam) with a gentle lysis procedure and minimal, low-level sonication to rupture cells without extensive DNA damage as previously described16. The formaldehyde fixed cells were thawed at RT for 5 min, resuspended in RIPA buffer (50 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA pH8.0, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) with 1x protease inhibitors (Pierce #A32955) and sonicated using a Cell Ruptor at low power, for 10 sec followed by 10 pulses after a 20 sec interval. Cell lysates were then centrifuged at 3000 rpm for 3 min at RT to remove the bulk of chromatin. The supernatant was then incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. Beads were then washed sequentially once in low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), once in high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), once in LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0). Beads were then resuspended in TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA) and transferred to a fresh tube and finally eluted with 100 µl elution buffer (1% SDS, 100mM NaHCO3). Crosslinks were reverted for the elutions (65°C for 24 h) and DNA was purified with a Qiagen Nucleotide Clean up kit. DNA fragments <300 bp from ChIP elutions were separated by pulling down larger fragments using paramagnetic Ampure XP beads: 65 µl of Ampure XP beads were added to the uncrosslinked ChIP elution and mixed thoroughly. After 10 min incubation at RT, beads were isolated using a magnet. The supernatant was collected and 25 µl of fresh Ampure XP beads were added and mixed thoroughly. After 10 min at RT, beads were separated and the supernatant was purified using Qiagen Nucleotide Clean up kit. At the final step DNA was eluted in 60 µl of elution buffer (TE). To monitor the Mre11 nuclease dependence, we treated the human U2OS cells expressing inducible AsiSI with 10 µM NU7441, 100 µM PFM01 or PFM39 and 600 nM 4-OHT simultaneously for 1 hour at 37°C before harvesting cells.  Pellet ChIP For DNA-PKcs pellet ChIP, the protocol for GLASS-ChIP was followed through the step where chromatin is isolated. The chromatin fraction was then resuspended in 2.2 ml RIPA buffer and was fragmented using a Diagenode Bioruptor on high setting for 30 min. with 10 sec on, 10 sec off. After removal of debris by centrifuging at 800 g for 3 min., the supernatant was incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. The rest of the procedure was identical to GLASS-ChIP above except that the AMPure bead size selection was not performed.
For GLASS-ChIP and pellet-ChIP sequencing libraries, the eluted DNA was used to make sequencing libraries using the NEBNext Ultra or Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext Multiplex dual index primers.
DNA-PKcs and CtIP GLASS-ChIP and pellet-ChIP: NovaSeq SP platform with PE150.

value: osteosarcoma

tag: chip antibody

value: plus 4-OHT, input


title: Injury NMDA 54hr, snATAC-seq

description:
Injury_NMDA_54hr_ATAC
10x Genomics


title: Liver_Oil_rep2 [O1124]

value: Wild type


title: CtIP PC, plus 4-OHT, +antibody, rep2

description:
CtIP pellet-ChIP, plus 4-OHT, + antibody, rep2
hg19

value: CtIP (Active Motif 61141)

value: plus 4-OHT, +antibody


title: Injury NMDA 14D, snRNA-seq

description:
Injury_NMDA_14D
10x Genomics


title: HT1080-CTR2

value: fibrosarcoma cell line

value: CTR


title: CtIP PC, plus 4-OHT, +antibody, rep1

description:
CtIP pellet-ChIP, plus 4-OHT, + antibody, rep1
hg19


title: Liver_Oil_rep1 [N3]


title: HT1080-CTR1


title: Injury NMDA 7D, snRNA-seq

description:
Injury_NMDA_7D
10x Genomics


title: Hepatocyte_LPS+Nigericin+MCC950_rep3 [LNM3]

source_name: primary murine hepatocyte

value: primary murine hepatocyte

value: 6h LPS, 30min Nigericin after MCC950 2h


title: CtIP PC, no 4-OHT, input

description:
CtIP pellet-ChIP, no 4-OHT, - antibody, rep1
hg19

value: no 4-OHT, input


title: Total T cells inhibited by actinomycin D for 2 hour (replicate 3)

source_name: human total T cells

extract_protocol:
Human primary total T cells were isolated from the blood sample of three donors from Gulf Coast Regional Blood Center using Ficoll density gradient method. The cells were collected and washed with PBS + 0.5% FBS and taken into culture. After isolation, the cells were activated with anti-CD3/CD28 microbeads (Thermo Fisher) for 24 hours. For transcription inhibition, the cultured cells were treated with ActD (10 μg/ml), for four time points, 0 hour (immediately after ActD treatment), 15 minutes, 1 hour and 2 hours. After treatment, RNA was isolated by RNeasy kit (Qiagen).
Samples were sent to BGI for library preparation and follow-up sequencing

value: total T cells

value: control

value: actinomycin D

value: 2 hours


title: Hepatocyte_LPS+Nigericin+MCC950_rep2 [LNM2]


title: Injury NMDA 72hr, snRNA-seq

description:
Injury_NMDA_72hr
10x Genomics

value: Retina


title: Injury NMDA 72hr, snATAC-seq

description:
Injury_NMDA_72hr_ATAC
10x Genomics

value: NMDA


title: Hepatocyte_LPS+Nigericin+MCC950_rep1 [LNM1]


title: Total T cells inhibited by actinomycin D for 2 hour (replicate 2)


title: CtIP PC, no 4-OHT, +antibody, rep1

description:
CtIP pellet-ChIP, no 4-OHT, + antibody, rep1
hg19

value: no 4-OHT, +antibody


title: Injury NMDA 54hr, snRNA-seq

description:
Injury_NMDA_54hr
10x Genomics


title: Total T cells inhibited by actinomycin D for 2 hour (replicate 1)


title: Injury Control, snATAC-seq

description:
Injury_Control_ATAC
10x Genomics

value: Control


title: CtIP GC, plus 4-OHT, -antibody

description:
CtIP GLASS-ChIP, plus 4-OHT, - antibody, rep1
released genomic DNA
hg19

value: osteosarcoma

value: plus 4-OHT, -antibody


title: Total T cells inhibited by actinomycin D for 1 hour (replicate 3)

value: 1 hour


title: Hepatocyte_LPS+Nigericin_rep2 [LN2]

value: Wild type

value: 6h LPS and 30min Nigericin


title: Total T cells inhibited by actinomycin D for 1 hour (replicate 2)


title: Igrov1 0 hours post infection, replicate 3

city: Singapore

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke-NUS Medical School

data_processing:
STAR Aligner 2.7.10
featureCounts
Assembly: Hg38
Supplementary files format and content: tab separated

extract_protocol:
RNEasy Mini
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: 0 hours post infection


title: Hepatocyte_LPS+Nigericin_rep1 [LN1]

value: primary murine hepatocyte


title: Igrov1 0 hours post infection, replicate 2


title: Injury NMDA 96hr, snRNA-seq

description:
Injury_NMDA_96hr
10x Genomics


title: CtIP GC, plus 4-OHT, +antibody, rep1

description:
CtIP GLASS-ChIP, plus 4-OHT, + antibody, rep1
released genomic DNA
hg19

value: CtIP (Active Motif 61141)

value: plus 4-OHT, +antibody


title: eWAT_illu_cold_16

data_processing:
barcode and adapter removal using bcl2fastq2
quality trimming using cutadapt
quantification of transcripts by salmon (GENCODE M22)
Assembly: GRCm38
Supplementary files format and content: Matrix table with length, effective length, TPM and number of reads mapping to each transcript

source_name: epididymal white adipose tissue

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Whole frozen eWAT samples were homogenised in 1 ml TRIsure (Bioline) per animal using a tabletop homogeniser (FastPrep-24 5G, MP Biomedicals). Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250)
The NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) was used to prepare 50 nt paired-end, strand specific libraries following the manufacturer’s protocol.

value: epididymal white adipose tissue

value: cold


title: eWAT_illu_cold_12


title: Igrov1 72 hours post infection, replicate 3

value: 72 hours post infection


title: CtIP GC, plus 4-OHT, +antibody, rep2

description:
CtIP GLASS-ChIP, plus 4-OHT, + antibody, rep2
released genomic DNA
hg19


title: Total T cells inhibited by actinomycin D for 15 minutes (replicate 2)

value: total T cells

value: control

value: actinomycin D

value: 15 minutes


title: CtIP GC, no 4-OHT, +antibody, rep2

description:
CtIP GLASS-ChIP, no 4-OHT, + antibody, rep2
released genomic DNA
hg19

value: no 4-OHT, +antibody


title: CtIP PC, no 4-OHT, +antibody, rep2

description:
CtIP pellet-ChIP, no 4-OHT, + antibody, rep2
hg19

value: osteosarcoma


title: CtIP GC, no 4-OHT, -antibody

description:
CtIP GLASS-ChIP, no 4-OHT, - antibody, rep1
released genomic DNA
hg19

value: no 4-OHT, -antibody


title: eWAT_illu_ctrl_10

value: ctrl


title: Igrov1 72 hours post infection, replicate 2


title: CtIP GC, no 4-OHT, +antibody, rep1

description:
CtIP GLASS-ChIP, no 4-OHT, + antibody, rep1
released genomic DNA
hg19


title: Total T cells inhibited by actinomycin D for 15 minutes (replicate 1)


title: Hepatocyte_LPS+Nigericin_rep3 [LN3]

value: Wild type


title: Total T cells inhibited by actinomycin D for 15 minutes (replicate 3)


title: eWAT_illu_cold_7


title: Igrov1 72 hours post infection, replicate 1


title: Total T cells inhibited by actinomycin D for 0 hour (replicate 3)

value: 0 hour


title: GSC-040815-97-48h-3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: GSCs treated with CIDD-0149897 in neurobasal medium

data_processing:
Illumina bcl2fastq v2.20.0.422 used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC hg19) using HiSAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FatureCounts to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName

source_name: Patient derived Glioma stem cells (GSC)- 040815

growth_protocol: GSC-040815  were cultured  as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL).

extract_protocol:
Total RNA from  vehicle (0.1% DMSO v/v) and  CIDD-0149897 treated cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: GSC-040815  were treated with vehicle (0.1% DMSO v/v) or  ERβ agonist (CIDD-0149897-20 µM) syntesized by Center for Innovative Drug Discovery-UTSA. GSCs were cultured as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL) for 48 hrs. After 48 hrs of treatment cell pellet were collected and used for RNA isolation.


title: Igrov1 48 hours post infection, replicate 3

value: 48 hours post infection


title: eWAT_illu_ctrl_6


title: Total T cells inhibited by actinomycin D for 0 hour (replicate 2)


title: GSC-040815-97-48h-2


title: Igrov1 0 hours post infection, replicate 1

value: 0 hours post infection


title: Total T cells inhibited by actinomycin D for 1 hour (replicate 1)

value: 1 hour


title: GSC-040815-97-48h-1


title: Total T cells inhibited by actinomycin D for 0 hour (replicate 1)


title: iBAT_illu_cold_16

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Whole frozen eWAT samples were homogenised in 1 ml TRIsure (Bioline) per animal using a tabletop homogeniser (FastPrep-24 5G, MP Biomedicals). RNA was isolated by phenol chloroform extraction and alcohol precipitation.
The NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) was used to prepare 50 nt paired-end, strand specific libraries following the manufacturer’s protocol.

value: interscapular brown adipose tissue


title: Igrov1 48 hours post infection, replicate 1


title: iBAT_illu_cold_15


title: Igrov1 24 hours post infection, replicate 3

value: 24 hours post infection


title: Igrov1 24 hours post infection, replicate 2


title: iBAT_illu_ctrl_14


title: Igrov1 24 hours post infection, replicate 1


title: GSC-040815-C1

description: GSCs cultures in neurobasal medium

value: Control


title: iBAT_illu_cold_12

value: cold


title: Igrov1 48 hours post infection, replicate 2


title: eWAT_illu_ctrl_5

value: epididymal white adipose tissue


title: GC, plus 4-OHT, +NU-7441, + PFM39, 1 hr only, -antibody

description:
All processed data files are Hg19 except files with 'light' in the name which are Hg38
GC +DNAPKi plus 4H 1 hr only +PFM39 +antibody.bigwig

data_processing:
DNA-PKcs GLASS-ChIP and pellet-ChIP :Raw data was pre-processed with BedTools fastp, mapped with BWA-MEM, duplicates were removed with SAMTools RmDup, and peaks called with MACS2. AsiSI-associated data was processed using genome build Hg19; Cas9-associated data was processed using genome build Hg38. Mre11 ChIP data:
For Glass-ChIP, no-antibody sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls. body sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls.
Bedgraph output files from MACS2 were converted to bigwig files using ucsc-wigtobigwig (Version 357)

extract_protocol:
GLASS-ChIP assay   Human U2OS cells with inducible AsiSI15 were grown to 50-60% confluency in 150 mm dishes and treated with 600 nM 4-OHT for 4 h at 37°C. When used, 10 µM NU7441 was added 30 min. prior to 4-OHT addition. After 4-OHT treatment, cells were fixed with 1% formaldehyde for 7 min at RT with gentle rotation. Crosslinking was stopped by addition of 125 mM glycine for 5 min, washed twice with cold PBS, harvested, flash frozen in liquid nitrogen and stored at -80°C.   For the GLASS-ChIP assay, we modified a standard protocol (Abcam) with a gentle lysis procedure and minimal, low-level sonication to rupture cells without extensive DNA damage as previously described16. The formaldehyde fixed cells were thawed at RT for 5 min, resuspended in RIPA buffer (50 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA pH8.0, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) with 1x protease inhibitors (Pierce #A32955) and sonicated using a Cell Ruptor at low power, for 10 sec followed by 10 pulses after a 20 sec interval. Cell lysates were then centrifuged at 3000 rpm for 3 min at RT to remove the bulk of chromatin. The supernatant was then incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. Beads were then washed sequentially  once in low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), once in high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), once in LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0).  Beads were then resuspended in TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA) and transferred to a fresh tube and finally eluted with 100 µl elution buffer (1% SDS, 100mM NaHCO3). Crosslinks were reverted for the elutions (65°C for 24 h) and DNA was purified with a Qiagen Nucleotide Clean up kit. DNA fragments <300 bp from ChIP elutions were separated by pulling down larger fragments using paramagnetic Ampure XP beads: 65 µl of Ampure XP beads were added to the uncrosslinked ChIP elution and mixed thoroughly. After 10 min incubation at RT, beads were isolated using a magnet. The supernatant was collected and 25 µl of fresh Ampure XP beads were added and mixed thoroughly. After 10 min at RT, beads were separated and the supernatant was purified using Qiagen Nucleotide Clean up kit. At the final step DNA was eluted in 60 µl of elution buffer (TE). To monitor the Mre11 nuclease dependence, we treated the human U2OS cells expressing inducible AsiSI with 10 µM NU7441, 100 µM PFM01 or PFM39 and 600 nM 4-OHT simultaneously for 1 hour at 37°C before harvesting cells.   Pellet ChIP  For DNA-PKcs pellet ChIP, the protocol for GLASS-ChIP was followed through the step where chromatin is isolated. The chromatin fraction was then resuspended in 2.2 ml RIPA buffer and was fragmented using a Diagenode Bioruptor on high setting for 30 min. with 10 sec on, 10 sec off. After removal of debris by centrifuging at 800 g for 3 min., the supernatant was incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. The rest of the procedure was identical to GLASS-ChIP above except that the AMPure bead size selection was not performed.
For DNA-PKcs GLASS-ChIP and pellet-ChIP  sequencing libraries, the eluted DNA was used to make sequencing libraries using the NEBNext Ultra or Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext Multiplex dual index primers.

value: plus 4-OHT, + NU7441, + PFM39, 1 hr only, -antibody


title: iBAT_illu_ctrl_10


title: Huh7 0 hours post infection, replicate 2


title: GC, plus 4-OHT, +NU-7441, + PFM39, 1 hr only, +antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, + NU7441, + PFM39, 1 hr only, +antibody


title: PC346C, AR, -R1881

city: Rotterdam

first: Selçuk

last: Yavuz

state: South-Holland

address: wytemaweg 80

department: Department of pathology

country: Netherlands

institute: Erasmus MC

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 36bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using NARWHAL and Bowtie
Reads were filtered based on mapping quality (MAPQ ≥ 20) and duplicate reads were removed.
MACS 1.4.2 was used for generating wig files using default settings. Peak calling over mixed input controls was performed using MACS.
The .wig files from MACS were converted to .bw files using UCSC WigTBigWig
Assembly: hg19
Supplementary files format and content: .bw

growth_protocol: DMEM/F12, 10% DCC-treated FCS, 1% insulin-transferrin-selenium, 0,01% BSA, 10ng/ml Epidermal Growth Factor, 100U/ml penicillin, 100 μg/ml streptomycin, 100 ng/ml fibronectin, 20μg/ml fetuine, 50ng/ml cholera toxin, 0.1 mM phosphoethanolamine, 0.6 ng/ml triiodothyronine. Cells were cultured at 37C at 5% CO2.

extract_protocol:
PC346C cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde to cross-link chromatin. Chromatin was prepared for sonication with 20 mM Tris-HCl pH8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100. We used 15 cycles of 30 seconds ON, 30 seconds OFF on a Bioruptor Pico sonication device (Diagenode Cat# B01060001) to shear chromatin to 150-200bp fragments. The resulting chromatin extract was incubated overnight at 4°C with 100ul of Dynal Protein G magnetic beads that had been pre-incubated with approximately 10 μg of the appropriate antibody. Beads were washed 1X with the sonication buffer, 1X with 20 mM Tris-HCl pH8, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1%Triton X-100, 1X with 10 mM Tris-HCl pH8, 250 mM LiCl, 2 mM EDTA, 1% NP40 and 1X with TE containing 50 mM NaCl. Bound complexes were eluted from the beads (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) by heating at 65°C for 1 hr with occasional vortexing and crosslinking was reversed by overnight incubation at 65°C. Finally ,DNA was precipitated using phenol:chloroform:isoamyl alcohol (PCI).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex ChIP-seq kit from BioO Scientific. Libraries were prepared according to illumina's instructions accompanying the DNA sample kit.

treatment_protocol: R1881 treated cells were cultured in medium containing 100nM R1881 16 hours prior fixation. Untreated cells were grown with regular medium without R1881 in DMSO conditions

tag: disease

value: Human Prostate cancer

tag: chip-antibody

value: AR (santa cruz, SC-816)

value: With R1881


title: PC436C, AR, +R1881

value: Without R1881


title: GC, plus 4-OHT, +NU-7441, + PFM01, 1 hr only, -antibody

description:
All processed data files are Hg19 except files with 'light' in the name which are Hg38
GC +DNAPKi plus 4H 1 hr only +PFM01 +antibody.bigwig

value: osteosarcoma

value: plus 4-OHT, + NU7441, + PFM01, 1 hr only, -antibody


title: iBAT_illu_ctrl_9

value: ctrl

tag: mouse id


title: GC, plus 4-OHT, +NU-7441, + PFM01, 1 hr only, +antibody

value: plus 4-OHT, + NU7441, + PFM01, 1 hr only, +antibody


title: Hearts from non-transgenic FVB mice 2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Cardiac gene expression data of 8-month-old, male, non-transgenic FVB mice

hyb_protocol: For hybridization, 15 µg of fragmented, biotin-labeled cRNA were incubated with the chip (Affymetrix Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

source_name: Hearts from 8-month-old non-transgenic FVB mice

label_protocol: Biotin-labeled cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: The study was performed with 8-month-old male Tg-BBLN-low mice, and age-matched, male non-transgenic FVB control mice. Mice had free access to food and water, and were fed a standard rodent chow. At an age of 8 months, hearts were isolated from Tg-BBLN mice and from non-transgenic FVB control mice.

extract_protocol: Total cardiac RNA was isolated with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: The study used hearts from 8-month-old, male Tg-BBLN-low mice with myocardium-specific expression of BBLN. BBLN was expressed under control of the alpha-MHC promoter. Hearts from age- and sex-matched non-transgenic FVB mice served as controls.

tag: tissue

value: Heart

value: Male

tag: age

value: 8 months

tag: heart function

value: Normal left ventricular ejection fraction


title: Hearts from Tg-BBLN-low mice 2

description: Cardiac gene expression data of 8-month-old, male Tg-BBLN-low mice

source_name: Hearts from 8-month-old Tg-BBLN-low mice

value: Reduced left ventricular ejection fraction


title: Huh7 0 hours post infection, replicate 1

value: 0 hours post infection


title: GSC-040815-C3

description: GSCs cultures in neurobasal medium

tag: treatment

value: Control


title: Hearts from non-transgenic FVB mice 1

tag: gender


title: iBAT_illu_cold_7

value: interscapular brown adipose tissue

tag: strain

value: cold


title: Huh7 72 hours post infection, replicate 3

value: 72 hours post infection


title: Hearts from Tg-BBLN-low mice 1


title: GC, plus 4-OHT, +NU-7441, 1 hr only, -antibody

description:
All processed data files are Hg19 except files with 'light' in the name which are Hg38
GC +DNAPKi plus 4H 1 hr only +antibody.bigwig

value: plus 4-OHT, + NU7441, 1 hr only, -antibody


title: Huh7 72 hours post infection, replicate 2


title: iBAT_illu_cold_11


title: Huh7 0 hours post infection, replicate 3


title: MSAR_OEControl_rep1

city: Guangzhou

first: shuang

last: deng

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then  RNA-seq reads were mapped to hg38 using STAR.
RSEM was used for quantification.
bam file were transform into bigwig format using deepTools.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: PANC-1 cells

growth_protocol: PANC-1 cells were cultured in DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Sequencing libraries for RNA-sesq were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) and the library preparations were sequenced on an Illumina Hiseq platform.

treatment_protocol: We used the lentiviral vector expressing human MSAR to construct MSAR-overexpressing PDAC cells. Synthesized full-length of MSAR sequence was inserted into pHS-BVC-LW308-Puromycin lentiviral expression vector to construct the lentiviral vector expressing human MSAR. Stable MSAR-overexpressing PDAC cells were generated by lentiviral infection and corresponding antibiotics selection.

value: PANC-1 cells

tag: genotype

value: WT


title: GC, plus 4-OHT, +NU-7441, 1 hr only, +antibody

value: osteosarcoma

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: plus 4-OHT, + NU7441, 1 hr only, +antibody


title: iBAT_illu_ctrl_6

city: Odense

first: Jan-Wilhelm

last: Kornfeld

address: Campusvej 55

institute: University of Southern Denmark

source_name: interscapular brown adipose tissue

value: ctrl


title: iBAT_illu_ctrl_5


title: Huh7 72 hours post infection, replicate 1


title: Huh7 48 hours post infection, replicate 3

value: 48 hours post infection


title: iBAT_illu_cold_4


title: MSAR_OEControl_rep2


title: MSAR_OE1_rep1

value: MSAR-overexpression


title: Mre11, 60m post-light, +NU-7441, +antibody, rep1

data_processing:
DNA-PKcs GLASS-ChIP and pellet-ChIP :Raw data was pre-processed with BedTools fastp, mapped with BWA-MEM, duplicates were removed with SAMTools RmDup, and peaks called with MACS2. AsiSI-associated data was processed using genome build Hg19; Cas9-associated data was processed using genome build Hg38. Mre11 ChIP data:
For Glass-ChIP, no-antibody sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls. body sample libraries were used as controls whereas for pellet-ChIP, input DNA libraries were used as controls.
Bedgraph output files from MACS2 were converted to bigwig files using ucsc-wigtobigwig (Version 357)
Assembly: all processed data files are Hg19 except files with 'light' in the name which are Hg38

extract_protocol:
GLASS-ChIP assay   Human U2OS cells with inducible AsiSI15 were grown to 50-60% confluency in 150 mm dishes and treated with 600 nM 4-OHT for 4 h at 37°C. When used, 10 µM NU7441 was added 30 min. prior to 4-OHT addition. After 4-OHT treatment, cells were fixed with 1% formaldehyde for 7 min at RT with gentle rotation. Crosslinking was stopped by addition of 125 mM glycine for 5 min, washed twice with cold PBS, harvested, flash frozen in liquid nitrogen and stored at -80°C.   For the GLASS-ChIP assay, we modified a standard protocol (Abcam) with a gentle lysis procedure and minimal, low-level sonication to rupture cells without extensive DNA damage as previously described16. The formaldehyde fixed cells were thawed at RT for 5 min, resuspended in RIPA buffer (50 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA pH8.0, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) with 1x protease inhibitors (Pierce #A32955) and sonicated using a Cell Ruptor at low power, for 10 sec followed by 10 pulses after a 20 sec interval. Cell lysates were then centrifuged at 3000 rpm for 3 min at RT to remove the bulk of chromatin. The supernatant was then incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. Beads were then washed sequentially  once in low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), once in high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), once in LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0).  Beads were then resuspended in TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA) and transferred to a fresh tube and finally eluted with 100 µl elution buffer (1% SDS, 100mM NaHCO3). Crosslinks were reverted for the elutions (65°C for 24 h) and DNA was purified with a Qiagen Nucleotide Clean up kit. DNA fragments <300 bp from ChIP elutions were separated by pulling down larger fragments using paramagnetic Ampure XP beads: 65 µl of Ampure XP beads were added to the uncrosslinked ChIP elution and mixed thoroughly. After 10 min incubation at RT, beads were isolated using a magnet. The supernatant was collected and 25 µl of fresh Ampure XP beads were added and mixed thoroughly. After 10 min at RT, beads were separated and the supernatant was purified using Qiagen Nucleotide Clean up kit. At the final step DNA was eluted in 60 µl of elution buffer (TE). To monitor the Mre11 nuclease dependence, we treated the human U2OS cells expressing inducible AsiSI with 10 µM NU7441, 100 µM PFM01 or PFM39 and 600 nM 4-OHT simultaneously for 1 hour at 37°C before harvesting cells.   Pellet ChIP  For DNA-PKcs pellet ChIP, the protocol for GLASS-ChIP was followed through the step where chromatin is isolated. The chromatin fraction was then resuspended in 2.2 ml RIPA buffer and was fragmented using a Diagenode Bioruptor on high setting for 30 min. with 10 sec on, 10 sec off. After removal of debris by centrifuging at 800 g for 3 min., the supernatant was incubated with 1.6 µg of anti-DNA-PKcs pS2056 antibodies (abcam 124918) overnight at 4°C, followed by incubation with 25 µl Protein A/G magnetic beads (Pierce) at RT for 2 h. The rest of the procedure was identical to GLASS-ChIP above except that the AMPure bead size selection was not performed.
For DNA-PKcs GLASS-ChIP and pellet-ChIP  sequencing libraries, the eluted DNA was used to make sequencing libraries using the NEBNext Ultra or Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext Multiplex dual index primers.
DNA-PKcs GLASS-ChIP and pellet-ChIP: NovaSeq SP platform with PE150

value: embryonic kidney

value: 60m post-light, +antibody


title: Mre11, 60m post-light, +NU-7441, +antibody, rep2


title: Lm planktonic cells in TSB, biolog rep 3, technical rep 2

city: College Park

first: Jie

last: Zheng

address: 5001 Campus Drive

institute: FDA

data_processing:
FastQC was used to check the quality of the sequence reads.
Read counts were generated using Salmon v1.9.0.
Supplementary files format and content: tab-delimited .sf files including raw counts and tpm values for each sample

organism: Listeria monocytogenes

source_name: planktonic cell

growth_protocol: Listeria monocytogenes FS2025 (serotype 1/2b, ST5, CC5) was grown in cantaloupe juice or TSB at 24C statically.

extract_protocol:
RNA was harvested using Invitrogen RiboPure™ Bacteria Kit (ThermoFisher Scientific).
RNA libraries for RNA Seq were prepared using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus kit following manufacturer's instructions.

treatment_protocol: Planktonic cells were collected after 48h incubation and biofilm cells were harvested from stainless steel coupons after 3 days incubation via sonication.

tag: agent

value: TSB

value: planktonic cell


title: iBAT_illu_ctrl_2


title: Prj169-L3-48

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

description:
Adult male mouse dosed every 4 days for 28 days
48

data_processing:
Read quality was assessed using FastQC v0.11.7 and adapter trimming was performed using Trimmomatic v0.39.
Alignment was performed with STAR v2.7.3a. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
Gene counts were determined using STAR v2.7.3a.
Assembly: mm10 (build 39)
Supplementary files format and content: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Supplementary files format and content: Tab-delimited text files represent the number of aligned PE reads to each gene.

extract_protocol:
Frozen liver (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using a Ultra2 NEB RNA kit.

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 28 days at 28°C.

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: Lm planktonic cells in TSB, biolog rep 3, technical rep 1

tag: agent

value: TSB

tag: cell type

value: planktonic cell

tag: genotype

value: WT


title: Mre11, 15m post-light, +NU-7441, +antibody, rep2

tag: cell line

value: embryonic kidney

tag: chip antibody

tag: treatment

value: 15m post-light, +antibody


title: Huh7 48 hours post infection, replicate 1

tag: time point

value: 48 hours post infection


title: Lm planktonic cells in TSB, biolog rep 2, technical rep 2


title: Mre11, no light, +NU-7441, +antibody, rep2

value: no light, +antibody


title: Lm planktonic cells in TSB, biolog rep 2, technical rep 1


title: MSAR_OE1_rep2

value: PANC-1 cells

value: MSAR-overexpression


title: Lm planktonic cells in TSB, biolog rep 1, technical rep 2


title: Huh7 24 hours post infection, replicate 2

value: 24 hours post infection


title: Mre11, no light, +NU-7441, +antibody, rep1


title: Prj169-L3-45

description:
Adult male mouse dosed every 4 days for 28 days
45

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: Huh7 24 hours post infection, replicate 1

tag: cell line

tag: time point


title: Prj169-L3-46

description:
Adult male mouse dosed every 4 days for 28 days
46

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: PC, 60m post-light, +NU-7441, +antibody, rep2

tag: cell line

tag: cell type

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

tag: treatment

value: 60m post-light, +antibody


title: Huh7 48 hours post infection, replicate 2

tag: time point

value: 48 hours post infection


title: Lm planktonic cells in TSB, biolog rep 1, technical rep 1

tag: agent

value: TSB

value: planktonic cell

tag: genotype

value: WT


title: Prj169-L3-44

description:
Adult male mouse dosed every 4 days for 28 days
44

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: PC, 60m post-light, +NU-7441, +antibody, rep1

tag: cell line

tag: cell type

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

tag: treatment


title: Lm planktonic cells in cantaloupe juice, biolog rep 3, technical rep 2

tag: agent

value: cantaloupe juice

tag: genotype


title: Prj169-L3-43

description:
Adult male mouse dosed every 4 days for 28 days
43

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: SNIP1_CLIP

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then CLIP-seq reads were mapped to hg38 using Bowtie2, RNA-seq and RIP-seq reads using STAR.
Piranha was used for CLIP-seq peak calling,  RSEM was used for quantification.
bam file were transform into bigwig format using deepTools.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Sequencing libraries for RNA-sesq were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) and the library preparations were sequenced on an Illumina Hiseq platform. For c-Myc RIP-seq assays, the RNA from controls and RIPs was converted to cDNA for sequencing library construction and sequenced on Illumina NovaSeq 6000. SNIP1 CLIP-sequencing was performed on Illumina Hiseq4000.

treatment_protocol: We used the CRISPR interference system to construct MSAR-silencing PDAC cells named ‘MSAR-KD-1’ and ‘MSAR-KD-2’. For CRISPR interference, pLV-CMV-NLS-3× flag-dCas9-NLS-KRAB-T2A-Puro plasmid was used. Small guide RNA (sgRNA) targeting the transcription start site of MSAR or non-targeting control sgRNA was designed and subcloned into the pLV-hU6-sgRNA-hef1a-mNeongreen vector. Stable knockdown cells were generated by lentiviral infection and selection.

tag: cell line

tag: cell type

value: pancreas ductal adenocarcinoma cells

tag: treatment

value: SNIP1 CLIP


title: NAA38.T15C.br1

city: Toronto

first: Jason

last: Moffat

address: 686 Bay Street

department: Genetics and Genome Biology

institute: Hospital for Sick Children

description: gDNA amplicon

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary files format and content: tab-delimited read count matrix

source_name: haematopoeitic

growth_protocol: Cells were cultured in IMDM media supplemented with 10% FBS and 1% Penicillin/Streptomycin and serially passaged for up to 18 days (propagated in biological triplicates).  Aliquots were pelleted at indicated timepoints for gDNA extraction and quantification by next-generation sequencing.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.
CRISPRseq

tag: tissue

value: haematopoeitic

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA38 31bp deletion (HAP1) (KO3)

value: TKOv3 (lentiCRISPRv2)


title: PC, 15m post-light, +NU-7441, +antibody, rep2

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: 15m post-light, +antibody


title: Prj169-L3-47

description:
Adult male mouse dosed every 4 days for 28 days
47

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: Mre11, 15m post-light, +NU-7441, +antibody, rep1

tag: cell line

tag: cell type

tag: chip antibody

tag: treatment


title: Huh7 24 hours post infection, replicate 3

tag: time point

value: 24 hours post infection


title: PC, 15m post-light, +NU-7441, +antibody, rep1

value: embryonic kidney


title: Prj169-L3-41

description:
Adult male mouse dosed every 4 days for 28 days
41

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: Lm planktonic cells in cantaloupe juice, biolog rep 2, technical rep 2

tag: agent

value: cantaloupe juice

tag: cell type

value: planktonic cell

tag: genotype

value: WT


title: Prj169-L3-40

description:
Adult male mouse dosed every 4 days for 28 days
40

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: time point


title: NAA38.T15A.br1

description: gDNA amplicon

tag: tissue

value: haematopoeitic

tag: cell line

tag: cell type

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA38 31bp deletion (HAP1) (KO3)

tag: treatment

value: TKOv3 (lentiCRISPRv2)


title: Lm planktonic cells in cantaloupe juice, biolog rep 2, technical rep1

tag: agent


title: Prj169-L3-39

description:
Adult male mouse dosed every 4 days for 28 days
39

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: PC, no light, +NU-7441, +antibody, rep2

tag: cell line

tag: cell type

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

tag: treatment

value: no light, +antibody


title: NAA38.T0.br1

description: gDNA amplicon

tag: tissue

value: haematopoeitic

value: chronic myelogenous leukemia-derived

tag: genotype


title: PC, no light, +NU-7441, +antibody, rep1


title: Lm planktonic cells in cantaloupe juice, biolog rep 1, technical rep 2

tag: agent

value: cantaloupe juice

value: planktonic cell

value: WT


title: NAA30.T14C.br1

description: gDNA amplicon

value: NAA30 1bp ins (HAP1) (HZGHC006637c010)

value: TKOv3 (lentiCRISPRv2)


title: GC, 60m post-light, +NU-7441, +antibody, rep2

value: 60m post-light, +antibody


title: Prj169-L3-38

description:
Adult male mouse dosed every 4 days for 28 days
38

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: time point


title: Lm planktonic cells in cantaloupe juice, biolog rep 1, technical rep1

tag: agent

value: cantaloupe juice

tag: cell type

value: planktonic cell

tag: genotype

value: WT


title: Prj169-L3-36

description:
Adult male mouse dosed every 4 days for 28 days
36

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: NAA30.T14B.br1

description: gDNA amplicon

tag: tissue

value: haematopoeitic

tag: cell line

tag: cell type

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA30 1bp ins (HAP1) (HZGHC006637c010)

tag: treatment

value: TKOv3 (lentiCRISPRv2)


title: Lm planktonic cells in cantaloupe juice, biolog rep 3, technical rep 1

tag: agent


title: GC, 60m post-light, +NU-7441, +antibody, rep1

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: 60m post-light, +antibody


title: NAA38.T15B.br1

description: gDNA amplicon

value: NAA38 31bp deletion (HAP1) (KO3)


title: Prj169-L3-34

description:
Adult male mouse dosed every 4 days for 28 days
34

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: time point


title: NAA30.T0.br1

description: gDNA amplicon

tag: tissue

value: haematopoeitic

tag: cell line

tag: cell type

value: chronic myelogenous leukemia-derived

tag: genotype

value: NAA30 1bp ins (HAP1) (HZGHC006637c010)

tag: treatment

value: TKOv3 (lentiCRISPRv2)


title: Prj169-L3-33

description:
Adult male mouse dosed every 4 days for 28 days
33

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: milliliter

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: NAA30.T14A.br1

description: gDNA amplicon

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: GC, 15m post-light, +NU-7441, +antibody, rep2

value: embryonic kidney

tag: chip antibody

value: phospho-DNA-PKcs(S2056)(Abcam ab124918)

value: 15m post-light, +antibody


title: GC, 15m post-light, +NU-7441, +antibody, rep1