title: S6

description:
snRNA-seq 10x
s6

value: skin

value: frozen tissue

value: nucleus

value: single nucleus


title: VTA_Female_Water_1

status: Public on May 08 2023

type: SRA

city: Baltimore

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

country: USA

institute: Institute for Genome Sciences

library_source: transcriptomic

data_processing:
Samples were sequenced on an Illumina HiSeq 4000 with a 75 bp paired-end read.
An averageof 64–100million reads were obtained for each sample.
Reads were aligned to the mousegenome (Mus_musculus.GRCm38) usingTopHat(version 2.0.8; maximum number ofmismatches = 2; segment length = 30; maximum multi-hits per read = 25; maximum intronlength = 50,000).
The number of reads that aligned to the predicted coding regions wasdetermined using HTSeq.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Raw counts file (without normalization)
Supplementary files format and content: File is in text format with first column as gene ensemble IDs and second its counts.

molecule: total RNA

organism: Mus musculus

source_name: Ventral tegmental area

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and the MicroElute Total RNA kit (Omega) with a Dnase step (Qiagen, Germantown, MD)
Librarieswere prepared from10ng of RNAusing theSmart-Seq v4 kit(Takara).

tag: tissue

value: Ventral tegmental area

tag: Sex

value: Female

tag: genotype

value: Wildtype

tag: treatment

value: Water


title: Patient 70

type: RNA

city: Seong-nam

first: Yu Ho

last: Lee

address: 59 Yatap-ro, Bundang-gu

country: South Korea

institute: CHA

hyb_protocol: For analysing of miRNA expression, the digital multiplexed nanoString nCounter human miRNA expression assay (nanoString Technologies) was performed with Human miRNA Panel Kit according to the manufacturer’s protocol.

scan_protocol: Abundances of specific target molecules were quantified on the nCounter Digital Analyzer by counting the individual fluorescent barcodes and assessing the target molecules. For each assay, a high-density scan encompassing 555 fields of view was performed. The data was collected using the nCounter Digital Analyzer after taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera.

data_processing:
To analysis the miRNA data, we used the nSolver(version 4.0) software analysis, freely available from nanoString Technologies.
The miRNA data was normalized using Top100 genes.

label: biotin

organism: Homo sapiens

source_name: Urinary exosome

label_protocol: NanoString’s nCounter CodeSet chemistry utilizes target-specific Reporter and Capture Probes, collectively referred to as a CodeSet, that directly hybridize to a target of interest. Each probe pair consists of a color-coded Reporter and a Capture Probe to which a  target-specific sequence has been covalently attached.

extract_protocol: Mid-stream, second morning void urine samples were collected, centrifuged at 2,000× g for 20 minutes at room temperature, and the supernatant was transferred into RNA later solution and stored at -80 °C. Urinary exosomal RNA was isolated from 1 mL of urinary supernatant using spin column-based exoRNeasy serum/plasma midi kits (QIAGEN GmbH, Hilden, Germany), as described previously.

tag: urinary exosome

value: urinary exosome

tag: diagnosis

value: LTGS


title: LLC OVA, OT1 (day16), rep2

city: Beijing

first: Lijian

last: Wu

state: Beijing

address: 30 Shuangqing Rd, Haidian District, Beijing

department: School of Medicine

country: China

institute: 清华大学

data_processing:
STAR v2.6.1d, Salmon v0.13.1, tximport v1.22.0, DESeq2 v1.34.0
RNA-seq reads were aligned to mm10 genome vM25 using STAR v2.6.1d.
Read alignments were quantified by Salmon v0.13.1 in its alignment-based mode.
Gene-level raw counts as well as transcript per million (TPM) from quantification files were prepared with tximport v1.22.0.
Normalization of raw counts and differential expression analysis were performed by DESeq2 v1.34.0 with default parameters.
Assembly: mm10
Supplementary files format and content: comma-delimited csv files include TPM (Transcripts Per Million) values for each Sample
Supplementary files format and content: comma-delimited csv files include DESeq2 results for comparisons

source_name: LLC

growth_protocol: LLC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. T cell were maintained in RPMI 1640  supplemented with 10% fetal bovine serum (FBS), glutamine, sodium pyruvate, NEAA, HEPES and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LLC cells were either pretreated or left untreated for 200nM BAY-876 for 24 hours, followed by treatment with 20ng/ml TNF or left untreated for 32 hours; 10^6 of LLC-OVA-NGFR cells were subcutaneously injected to Rag1 ko mice. On 9 day, 2*10^6 activated OT1 T cells were transferred by tail vein injection. On day 16, tumors were harvested and tumor and OT1 T cell were sorted.

tag: time

tag: cell line

value: LLC

tag: cell type

value: T cell

value: Adoptive cell transfer


title: LLC OVA, OT1 (day16), rep3


title: RCAS-nTva-derived Cell Line, ATRX Negative Line 1, sample 2

city: Houston

first: Benjamin

last: Whitfield

state: TX

address: 5918 Belrose Dr

institute: MD Anderson/UT Health GSBS

data_processing:
The raw fastq files were subjected to FASTQC analysis for quality control analysis
Alignment to mouse mm9 genome was performed using RNASTAR (version 2.7.8a).
Raw transcript counts were generated using HTseq-count tool (version 0.9.1)
Assembly: mm9
Supplementary files format and content: Tab-delimited count file containing counts for all samples

source_name: Brain Tumor

extract_protocol:
Extraction was performed using the Qiagen Rneasy Plus kit according to manufacturer's instructions.
Libraries were generated using Truseq library preparation kits (Illumina)

value: Brain Tumor

value: Tumor

value: ATRX KO


title: LLC OVA, OT1 (day16), rep1


title: Patient 68


title: RCAS-nTva-derived Cell Line, ATRX Negative Line 1, sample 1


title: Ggcx flox/flox; Pdx1-Cre_replicate2

city: Montréal

first: Mathieu

last: Ferron

state: Quebec

address: 110 Ave des Pins O

country: Canada

institute: IRCM

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the reference mouse genome version GRCm38 using STAR version 2.5.1b
Raw counts for each feature from GRCm38 ENSEMBL v101 annotation file were extracted using FeatureCounts v1.6.0
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between conditions
Assembly: GRCm38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Mouse pancreatic islets

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit from Qiagen. Poly(A)+ transcrits were enriched before librairies preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated pancreatic islets were used.

tag: strain

value: pancreatic islets

tag: age

value: Ggcx flox/flox; Pdx1-Cre


title: Patient 69


title: LLC cells, BAY-876+TNF (32h), rep3

value: lung cancer

value: WT


title: Patient 67


title: Ggcx flox/flox; Pdx1-Cre_replicate1


title: Patient 74

value: TCMR


title: Ggcx flox/flox_replicate2

value: Ggcx flox/flox


title: Patient 66


title: LLC cells, BAY-876+TNF (32h), rep2


title: LLC cells, BAY-876+TNF (32h), rep1


title: Patient 64


title: Ggcx flox/flox_replicate1


title: Patient 65


title: LLC cells, TNF (32h), rep1

value: TNF


title: Patient 63


title: LLC cells, TNF (32h), rep3


title: LLC cells, BAY-876 (32h), rep3


title: LLC cells, TNF (32h), rep2


title: LLC cells, BAY-876 (32h), rep2


title: Patient 62


title: Patient 60


title: Patient 59


title: Patient 61


title: Patient 58


title: LLC cells, control (32h), rep3

value: Vehicle


title: Colon-28

city: Kobe

first: Hijiri

last: Fujioka

address: 6-7-5, Minatojimaminamimachi, Chuouku,

country: Japan

institute: NBI

description:
re-analysis of GSM4731850
TMG126_50_S36_L006

data_processing:
Illumina Real-Time Analysis (RTA) v2.7.7 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using STAR aligner.
After filtering out duplicate reads, RNA quantification and normarization with Trimmed mean of M-values (TMM) or Transcripts per million (TPM)  were done by using Strand NGS 3.4 (Strand Life Sciences).
blank
blank
Assembly: GRCh38
Supplementary files format and content: Matrix table with TMM or TPM-normalized gene counts for every gene and every sample

source_name: IBD

extract_protocol:
RNA was harvested using QIAzol reagent.Illumina TruSeq stranded totalRNA (#20020596) was used total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted and purified by using an RNeasy Mini kit (QIAGEN) according to manufacturer’s standard protocol. RNA quality was evaluated in the same way as the biopsy samples using the BioAnalyzer (Agilent Technologies).

value: IBD

tag: sampling region

value: non-inflammatory area

value: female

tag: race

value: Japanese


title: LLC cells, control (32h), rep2

value: LLC


title: Patient 57

value: urinary exosome

value: LTGS


title: Ileum-15

description:
re-analysis of GSM4731840
TMG126_49_S35_L006


title: LLC cells, control (32h), rep1


title: Colon-05

description:
re-analysis of GSM4731849
TMG126_48_S34_L006

value: male


title: Patient 56


title: Ileum-03

description:
re-analysis of GSM4731839
TMG126_47_S33_L006


title: Colon-04

description:
re-analysis of GSM4731848
TMG126_46_S30_L005


title: Patient 54

value: NP


title: Patient 55

value: aABMR


title: Ileum-02

description:
re-analysis of GSM4731838
TMG126_45_S29_L005


title: Patient 53


title: control ILC2-rep1

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
A total of 1,000 lung ILC2s(Abx group and Control group) were sorted and lysed in 5 μL lysis buffer (n=3)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 pregnant mice were randomly supplemented with a broad-spectrum antibiotics cocktail, termed Abx, in their drinking water from gestation day 10 to day 14 to eliminate gut commensal microflora.

value: Lung

value: primary cell

value: Lung group 2 innate lymphoid cell

value: wild type

value: Control group


title: Patient 52


title: control ILC2-rep2


title: control ILC2-rep3


title: prenatal Abx exposed ILC2-rep2

value: Abx treated pregnant mice


title: LLC cells, BAY-876 (32h), rep1

value: lung cancer

value: WT


title: Colon-03

description:
re-analysis of GSM4731847
TMG126_44_S47_L008

value: IBD

value: non-inflammatory area


title: prenatal Abx exposed ILC2-rep1


title: Rectum-01

description:
re-analysis of GSM4731852
TMG126_42_S45_L008

value: Japanese


title: Patient 49


title: Patient 50


title: Colon-02

description:
re-analysis of GSM4731846
TMG126_41_S32_L006


title: Ileum-14

description:
re-analysis of GSM4731837
TMG126_40_S31_L006


title: Rectum-02

description:
re-analysis of GSM4731851
TMG126_39_S44_L008


title: Patient 48


title: Patient 47

value: TCMR


title: microglia BV2, Trem2WT, nonfoamy, sample3

city: Minneapolis

first: Jesse

middle: W

last: Williams

state: MN

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

institute: University of Minnesota

data_processing:
Alignment, mapping and counting were performed using the CHURP pipeline
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing read count

extract_protocol:
BV2 cells harvested directly from plates were lysed using Trizol. RNA isolation was performed by the University of Minnesota Genomic Core using the Qiagen RNeasy kit.
Library was constructed by the University of Minnesota Genomic Core using the TruSeq RNA Library Prep Kit.

value: microglia


title: microglia BV2, Trem2WT, nonfoamy, sample4


title: Patient 45

value: urinary exosome


title: microglia BV2, Trem2WT, foamy, sample4

value: Cholesterol


title: microglia BV2, Trem2WT, nonfoamy, sample2


title: Colon-27

description:
re-analysis of GSM4731845
TMG126_38_S28_L005

value: female


title: Patient 51

value: aABMR


title: Patient 46

value: NP


title: microglia BV2, Trem2WT, nonfoamy, sample1


title: Duodenum-01

description:
re-analysis of GSM4731833
TMG126_43_S46_L008

value: male


title: Ileum-13

description:
re-analysis of GSM4731836
TMG126_37_S27_L005


title: Duodenum-03

description:
re-analysis of GSM4731831
TMG126_35_S41_L007


title: Colon-26

description:
re-analysis of GSM4731844
TMG126_34_S40_L007


title: Patient 43


title: Patient 41


title: Duodenum-02

description:
re-analysis of GSM4731832
TMG126_36_S42_L007


title: microglia BV2, Trem2WT, foamy, sample3


title: Patient 44


title: Colon-25

description:
re-analysis of GSM4731843
TMG126_33_S43_L008


title: microglia BV2, Trem2KO, nonfoamy, sample3


title: microglia BV2, Trem2WT, foamy, sample1


title: Colon-24

description:
re-analysis of GSM4731842
TMG126_32_S39_L007


title: microglia BV2, Trem2WT, foamy, sample2


title: microglia BV2, Trem2KO, nonfoamy, sample2


title: Patient 42


title: prenatal Abx exposed ILC2-rep3

value: Lung

value: primary cell

value: Lung group 2 innate lymphoid cell


title: Ileum-12

description:
re-analysis of GSM4731835
TMG126_31_S38_L007


title: microglia BV2, Trem2KO, nonfoamy, sample1


title: microglia BV2, Trem2KO, foamy, sample4


title: microglia BV2, Trem2KO, foamy, sample1


title: Patient 37


title: Patient 39


title: Patient 38


title: Duodenum-04

description:
re-analysis of GSM4731830
TMG126_30_S37_L007


title: Patient 34


title: Patient 33


title: Patient 30


title: Patient 36


title: Patient 32


title: Ileum-04

description:
re-analysis of GSM4731834
TMG126_28_S25_L005


title: PDAC_BM2

first: Emily

last: Lo

address: 733 N Broadway

institute: Johns Hopkins

library_source: genomic

data_processing:
Adapter sequences were computationally trimmed with Trim Galore using default parameters for libraries prepared with NEBNext. For libraries prepared with Accel-NGS, an additional 10 bp were trimmed from the 3’ end of R1 and 10 bp from the 5’ end of R2 to account for the low complexity polynucleotide tail added by the Adaptase enzyme.
Bisulfite-aware alignment of the trimmed reads to the hg19 genome was performed using Bismark with default parameters. Samtools was used to merge individual bam files corresponding to fastq file pairs and to name sort the merged bam file. Methylation bias (mbias) plots were generated using Bismark’s methylation extractor in --mbias_only mode. Bismark was then used to deduplicate merged, name-sorted bam files. Position-sorted and indexed bam files were then created using samtools.
Bismark methylation_extractor was used to create CpG_report files. CpG report files were read into R using Bioconductor package bsseq, smoothed using default parameters, and coverage-filtered with a cutoff of 2X for each biological replicate. Smoothed, coverage-filtered bsseq object was saved as a .rda (RData) file.
Assembly: hg19
Supplementary files format and content: lcm_wbgs_bsseq_smoothed_coverage_filtered_geo.rda: Rdata file containing smoothed and coverage-filtered bsseq object (with CpG reports from all samples)

molecule: genomic DNA

source_name: Pancreas

extract_protocol:
Frozen tissue samples were cryo-sectioned at 5 - 9 uM thick onto PEN membrane slides and stored at -80°C. Slides were fixed briefly in 70% ethanol, then stained with cresyl violet acetate or hematoxylin and eosin. Immediately following staining, laser-capture microdissection for the appropriate cell compartment targeted was performed using Zeiss PALM Microbeam on 10X or 20X magnification. The number of pooled cuts per cell type needed to reach a desired input of 20-50 ng DNA for WGBS varied for each sample. Genomic DNA was extracted using QIAamp DNA Micro Kit (Qiagen cat. #56304) according to manufacturer’s instructions for the “Isolation of Genomic DNA from Laser-Microdissected Tissues” protocol, with carrier RNA inclusion. To increase final DNA yield, samples were eluted twice, using the eluate from the first elution for the second, incubating for 5 min each before centrifugation.
Genomic DNA samples were quantified by Qubit dsDNA HS assay (ThermoFisher Scientific, cat# Q32851). 1% unmethylated Lambda DNA (Promega cat. #D1521) was spiked into genomic DNA to monitor bisulfite conversion efficiency. For WGBS library preparation, either NEBNext Ultra DNA Library Prep Kit (New England BioLabs, cat. #E7370L) or Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences cat. #30024, now xGen Methyl-Seq, IDT cat. #10009860) were used.  For the modified NEBNext Ultra DNA Library Prep Kit, genomic DNA (39–119 ng) was fragmented to a target peak of 300-400 bp using the Covaris S2 Focused-ultrasonicator in a 50 μl volume according to the manufacturer’s instructions. The fragmented DNA was converted to end-repaired, adenylated DNA using NEBNext Ultra End Repair/dA-Tailing Module (New England BioLabs, cat. #7442L). Methylated adaptors (NEBNext Multiplex Oligos for Illumina; New England BioLabs, cat. #E7535L) were ligated to the product from the preceding step using  NEBNext Ultra Ligation Module (New England BioLabs, cat. #7445L). The resulting product was size-selected as described in the manufacturer’s protocol by employing modified AMPure XP bead ratios of 0.4X and 0.2X to select for an insert size of 300–400 bp. After size-selection, the samples were bisulfite converted and purified using the EZ DNAm-Lightning Kit (Zymo Research, cat. #D5030). Bisulfite converted libraries were PCR amplified and indexed using primers from the NEBNext Multiplex Oligos for Illumina module (New England BioLabs, cat. #E7535L) and the Kapa HiFi Uracil+ PCR system (Kapa Biosystems, cat. #KK2801). PCR enrichment was performed with the following cycling parameters: 98°C for 45 sec followed by 10 - 11 cycles at 98°C for 15 sec, 65°C for 30 sec, 72°C for 30 sec and a final extension at 72°C for 1 min. The PCR enriched product was cleaned up using 0.9X AMPure XP beads (Beckman Coulter, cat. #A63881).   For the Accel-NGS Methyl-Seq DNA Library Kit, genomic DNA (11–25 ng) was fragmented to a target peak of 300-400 bp using the Covaris S2 Focused-ultrasonicator in a 50 μl volume according to the manufacturer’s instructions. The fragmented genomic DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research, cat# D5005) following the manufacturer’s instructions. Methyl-seq libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, cat# 30024) according to the manufacturer’s instructions and the resulting libraries were amplified for 7 PCR cycles using unique dual indexing primers (Swift Bioscience, cat# X9096-PLATE).
The resulting WGBS libraries were evaluated on a 2100 Bioanalyzer using the Agilent High-Sensitivity DNA Kit (Agilent Technologies, cat. #5067-4626) and quantified via qPCR using the KAPA Library Quantification Kit (KAPA Biosystems, cat. #KK4824). NEBNext Ultra DNA libraries were sequenced on the Illumina HiSeq 4000 system at a 2 × 151 bp read length with 8% PhiX spike-in. Accel-NGS Methyl-Seq DNA libraries were pooled and sequenced on an Illumina NovaSeq 6000 system at a 2 × 150 bp read length with 7% spike-in of a balanced library.

value: Pancreas

value: PDAC lesion

tag: disease state

value: Malignant neoplasia


title: microglia BV2, Trem2KO, foamy, sample2


title: Patient 35


title: microglia BV2, Trem2KO, foamy, sample3


title: PDAC_BM3


title: PDAC_BF2


title: PDAC_BF3


title: PDAC_BF1


title: Colon-06

description:
re-analysis of GSM4731841
TMG126_29_S26_L005

value: IBD


title: PanIN_BM3

value: PanIN lesion

value: Non-invasive neoplasia


title: Patient 31

value: TCMR


title: Patient 29


title: MEF IFNAR-KO, 4sU, IFNbeta, biol rep 4

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

data_processing:
Reads were first mapped against databases containing murine rRNA and mycoplasma sequences using bowtie2 2.3.0.
All remaining reads were then mapped against the mouse genome (Ensembl v90) using STAR 2.5.3a using the parameters --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH.
All mapped reads were then processed using GRAND-SLAM 2.0.7 using the parameters -trim5p 15 -modelall
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts and new-to-total RNA ratios

molecule: polyA RNA

source_name: MEF

growth_protocol: Primary MEF cells were maintained in MEM supplemented with 10% foetal calf serum and 1% penicilin/streptomycin in humified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Samples were lysed in TRIzol and total RNA was extracted using the DirectZOL Microprep kit (Zymo Research). For SLAM conversion, RNA was mixed with 20 mM Iodacetamide (Thermo Fisher Scientific) and incubated at 50°C shaking for 30 min in the dark. The reaction was stopped by mixing with 100 µM dithiothreitol, and converted RNA was purified using the RNA Clean&Concentrator-5 (Zymo Research). 200 ng of converted RNA was used for constructing the libraries.
RNA libraries for SLAM-seq were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) with oligo-dT beads for capture of poly-A-mRNA following manufacturer's protocols.

treatment_protocol:
Metabolic labeling of nascent transcripts was performed by adding 200 µM 4sU into the conditioned medium for 2 hours before harvest.
IRF3 was stimulated by mixing 5 µg/mL ISD (45bp) with Lipofectamin2000 (1:1), incubation for 20  min and adding the transfection mix into the conditioned medium. Transfection of Lipofectamin2000 only served as mock treatment.
ISGF3 was stimulated by adding 100 U/ml of murine IFNbeta into the conditioned medium. Untreated cells served as control.

value: MEF

value: primary fibroblast

value: IFNAR-knockout

tag: time-point

value: 3h IFNbeta/ with 2h 4sU

value: IFNbeta / 4sU

tag: assay

value: SLAM-seq


title: Patient 28

value: urinary exosome


title: PanIN_BM1


title: PanIN_BF3


title: Patient 40


title: PDAC_BM1


title: MEF IRF3-KO, 4sU, IFNbeta, biol rep 4


title: Patient 25

value: aABMR


title: Patient 22


title: PanIN_BF1


title: Patient 26


title: H1975 cells, 342-shtip60-c input

city: Boston

first: Daisuke

middle: Jefferson

last: Shibahara

state: Massachusetts

address: 330 Brookline Avenue, E/CLS-0417

department: Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
Sequenced reads were aligned to hg19 with Bowtie2 and peaks were called with MACS (v1.4.2).
wig files are scaled by wigmath. Scale of java-genomics-toolkit
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: H1975 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were crosslinked for 10 min with 1% formaldehyde. After quenching and cell lysis, chromatin was sonicated to obtain chromatin fragment lengths of 100-to-1,000 bp.
Indexed libraries were prepared using NEB Next DNA Library Prep (Illumina) and then sequenced using paired-end reads (75 bp) on the NextSeq500 platform (Illumina).

treatment_protocol: Tet-inducible conditional shRNA knockdown were induced by 2-day treatment with 0.5 ug/ml doxycycline.

value: Non-small cell lung cancer

tag: chip antibody

value: none (input)


title: Duct_B4

tag: tissue

value: Pancreas

value: Ducts

value: Normal


title: Duct_B3


title: MEF IRF3-KO, 4sU, ISD, biol rep 4

value: 4h transfection / with 2h 4sU

value: ISD-transfection / 4sU


title: MEF IFNAR-KO, 4sU, mock, biol rep 4

value: mock-tranfection / 4sU


title: MEF WT, 4sU, IFNbeta, biol rep 4

value: WT


title: MEF WT, 4sU, ISD, biol rep 4

value: MEF


title: MEF IRF3-KO, 4sU, mock, biol rep 4

value: primary fibroblast


title: Patient 20

value: LTGS


title: H1975 cells, 331-shtip60-b input


title: MEF WT, 4sU, mock, biol rep 4


title: Duct_B2


title: Patient 19


title: Duct_B1


title: Patient 23

value: TCMR


title: Acinar_BM3

value: Acini


title: H1975 cells, 328-shControl input


title: Acinar_BF3


title: PanIN_BF2

value: PanIN lesion

value: Non-invasive neoplasia


title: Patient 27

value: urinary exosome

value: NP


title: MEF IFNAR-KO, 4sU, ISD, biol rep 4

value: IFNAR-knockout

value: SLAM-seq


title: Patient 24


title: Patient 18

value: aABMR


title: Patient 21


title: H1975 cells, 342-shtip60-c H4ac

value: Non-small cell lung cancer

value: H4ac (EMD Millipore, #06-866)


title: H1975 cells, 331-shtip60-b H4ac


title: MEF WT, 4sU, untreated, biol rep 4

value: 2h 4sU


title: Acinar_BF1

value: Pancreas

value: Normal


title: Acinar_BF2


title: H1975 cells, 328-shControl H4ac


title: MEF IFNAR-KO, 4sU, untreated, biol rep 4

value: MEF


title: Acinar_BM1


title: MEF IFNAR-KO, no4sU, untreated, biol rep 4

value: primary fibroblast


title: Patient 17


title: Patient 15


title: Patient 16


title: MEF IFNAR-KO, 4sU, IFNbeta, biol rep 3

value: 3h IFNbeta/ with 2h 4sU

value: IFNbeta / 4sU


title: MEF WT, no4sU, untreated, biol rep 4

value: WT


title: Col0_rep3_g2_RNAseq

first: Zejia

last: Wang

address: Yanyuan Street

institute: Peking University

data_processing:
For data analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1 . The resulting trimmed reads were aligned to TAIR10 reference genome using HISAT2 v2.2.1  under default settings. Alignments of Phred score (Q) less than 30 were removed using samtools. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2 with default parameters. Differentially expressed genes were defined by DESeq2  using |log2FC|>1 and Padj<0.01 as cut off.
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol: For RNA-seq, total RNA was extracted from 10-day-old seedlings using the Direct-zol RNA MiniPrep kit (Promega, LS1040) and sent to Novogene (Tianjin, China) for library preparation and deep sequencing.

value: seedling

value: DAY 10


title: Col0_rep2_g2_RNAseq


title: MEF IRF3-KO, 4sU, untreated, biol rep 4


title: Patient 13

value: urinary exosome

value: TCMR


title: ZF-DDR4_rep4_g2_RNAseq


title: Patient 11

value: NP


title: MEF IRF3-KO, 4sU, IFNbeta, biol rep 3

value: SLAM-seq


title: Patient 12


title: ZF-DDR4_rep2_g2_RNAseq


title: MEF WT, 4sU, IFNbeta, biol rep 3


title: ZF-DDR4_rep3_g2_RNAseq


title: MEF IRF3-KO, no4sU, untreated, biol rep 4


title: Patient 10

value: aABMR


title: Col0_rep1_g2_RNAseq


title: MEF IFNAR-KO, 4sU, ISD, biol rep 3

value: IFNAR-knockout

value: 4h transfection / with 2h 4sU

value: ISD-transfection / 4sU


title: ZF-DDR4_rep1_g2_RNAseq


title: Patient 14


title: Patient 9


title: Col0_rep3_g3_RNAseq


title: MEF IRF3-KO, 4sU, ISD, biol rep 3


title: MEF WT, 4sU, ISD, biol rep 3


title: post-exposed to PM2.5-6

first: Rui

last: Chen

address: No.10 Xitoutiao, You An Men

institute: Capital medical university

description: circRNA expression of human plasma

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 6 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 2 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: plasma,post-exposed to PM2.5

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: gender

value: female


title: post-exposed to PM2.5-8

description: circRNA expression of human plasma


title: post-exposed to PM2.5-5

description: circRNA expression of human plasma


title: post-exposed to PM2.5-7

description: circRNA expression of human plasma


title: MEF IFNAR-KO, 4sU, mock, biol rep 3

tag: genotype

value: mock-tranfection / 4sU


title: Col0_rep1_g3_RNAseq


title: Patient 7


title: MEF WT, 4sU, mock, biol rep 3

value: MEF

tag: treatment


title: Patient 6

tag: urinary exosome


title: MEF IRF3-KO, 4sU, mock, biol rep 3

value: primary fibroblast


title: ZF-DDR5_rep3_g3_RNAseq


title: Patient 5

tag: diagnosis

value: LTGS


title: pre-exposed to PM2.5-8

description: circRNA expression of human plasma


title: MEF IFNAR-KO, 4sU, untreated, biol rep 3

value: 2h 4sU


title: MEF IRF3-KO, 4sU, untreated, biol rep 3


title: ZF-DDR5_rep2_g3_RNAseq

tag: time


title: post-exposed to PM2.5-1

description: circRNA expression of human plasma

value: male


title: Patient 4


title: ZF-DDR5_rep1_g3_RNAseq

value: seedling


title: Patient 8


title: Col0_rep2_g3_RNAseq

value: DAY 10


title: Patient 3

value: urinary exosome


title: post-exposed to PM2.5-4

description: circRNA expression of human plasma


title: post-exposed to PM2.5-3

description: circRNA expression of human plasma


title: post-exposed to PM2.5-2

description: circRNA expression of human plasma


title: MEF WT, 4sU, untreated, biol rep 3

tag: cell line

value: WT


title: pre-exposed to PM2.5-7

description: circRNA expression of human plasma

source_name: plasma,pre-exposed to PM2.5


title: Patient 2


title: Patient 1


title: pre-exposed to PM2.5-5

description: circRNA expression of human plasma


title: pre-exposed to PM2.5-6

description: circRNA expression of human plasma


title: MEF IFNAR-KO, no4sU, untreated, biol rep 3

tag: cell type


title: Col0_rep3_g4_RNAseq


title: Col0_rep2_g4_RNAseq


title: MEF WT, no4sU, untreated, biol rep 3


title: MEF IRF3-KO, no4sU, untreated, biol rep 3


title: GRC353-D5-8I_S16

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

data_processing:
Fastq files were aligned to Danio rerio GRCz11 using STAR (v.2.5.3a) with default settings in Partek Flow (v.8.0.19.0428; St. Louis, MO).
Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation
Gene features were offset to 0.0001 and those with geometric means across all samples ≤ 1 were filtered
Sample gene counts were quantile normalized and log2 transformed
Genome_build: GRCz11 Ensembl version 93 gene annotation build
Supplementary_files_format_and_content: tab delimited, raw gene count matrix, normalized gene count matrix

organism: Danio rerio

source_name: pooled heads collected anterior to swim bladder

growth_protocol: All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency (EPA) National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild-type (WT) adult zebrafish line (Danio rerio) that was generated and maintained as previously described (Phelps et al. 2017). Briefly, to maintain genetic diversity, a minimum of one WT line (AB and/or Tupfel long fin WT strains) was added one time per year. Zebrafish adults were housed in 6-L tanks at an approximate density of 8 fish/L. Adults were fed Gemma Micro 300 (Skretting) once daily and shell free E-Z Egg (Brine Shrimp Direct) twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5°C and bred every 2–3 weeks. For embryo collection, 60–100 adults were placed in 10- or 20-L angled static breeding tanks overnight. The following morning, adults were transferred to new angled bottom tanks containing fish facility water, and embryos were collected 30–40 min later.

extract_protocol:
Each pooled sample underwent RNA extraction using Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit.
The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA (500 ng per sample) selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size (bp) was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library (volume x concentration) was pooled from 16 randomized libraries to make the sequencing library pools (total 3 pools of 16 libraries each) and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFOS, the final concentrations for sequencing were 2.5 pM + 2% Phix, and they were run for 75 cycles single read.

treatment_protocol: At 0 dpf, zebrafish embryos were bleached as previously described (Tal et al. 2017). A single embryo at the dome-to-epiboly stages (Kimmel et al. 1995) was placed into each individual well of a 96-well plate containing a 40-μm nylon mesh filter (Millipore, Catalog No. MANMN4010) with 400μL of 10% Hanks’ balanced salt solution (HBSS) per well. Filter inserts containing zebrafish embryos were transferred to 96-well culture trays (Millipore, Catalog No. MAMCS9610) containing 250μL of 10% HBSS (Westerfield 2007) and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily, from 1–4 or 1-5 dpf, plates underwent 100% media changes to refresh chemical dosing solutions by blotting (Brandel; Catalog No. FPXLR-196) and transferring mesh inserts containing zebrafish to new bottom plates (Millipore; Catalog No. MAMCS9610). To minimize evaporation, plates were sealed (Biorad; Catalog No. MSA5001) and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0°C and scored daily for death, malformations, hatching, and swim bladder inflation. Zebrafish embryos were exposed to 0.88-2.8 μM PFOS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.

value: head anterior to swim bladder

value: 0.4% DMSO

tag: concentration (microm)

value: 5 days post fertilization

tag: Stage

value: larvae

tag: strain

value: mixed wildtype


title: chr11chr17ddr4_rep2_g4_RNAseq


title: chr11chr17_rep3_g4_RNAseq


title: MEF IRF3-KO, 4sU, IFNbeta, biol rep 2

value: 3h IFNbeta/ with 2h 4sU

value: IFNbeta / 4sU

value: SLAM-seq


title: chr11chr17ddr4_rep3_g4_RNAseq


title: MEF IFNAR-KO, 4sU, IFNbeta, biol rep 2

value: MEF

value: IFNAR-knockout


title: GRC353-D5-8G_S8

tag: age


title: GRC353-D5-8E_S4


title: GRC353-D5-8H_S9


title: chr11chr17ddr4_rep1_g4_RNAseq


title: MEF WT, 4sU, IFNbeta, biol rep 2

value: primary fibroblast


title: MEF IFNAR-KO, 4sU, ISD, biol rep 2

value: 4h transfection / with 2h 4sU

value: ISD-transfection / 4sU


title: chr11chr17_rep2_g4_RNAseq

value: seedling


title: HFC-14

type: genomic

city: Gliwice

first: Joanna

last: Tobiasz

address: Akademicka 2A

department: Department of Data Science and Engineering

country: Poland

institute: Silesian University of Technology

description:
Copy number variation data from patient id131.
id131

hyb_protocol: PCR producte were purified using magnetic beads (Agencourt AMPure, Beckman Coulter, Beverly, MA) and subsequently endlabeled with biotin and hybridized to the array. Arrays were washed and stained using a GeneChip Fluidics Station 450.

scan_protocol: Scanning used the Affymetrix GeneChip Scanner 3000 7G. Scanned data files were generated using Affymetrix GeneChip Command Console Software (version 1.2) and analyzed with the Chromosome Analysis Suite.

data_processing:
The data were processed with Chromosome Analysis Suite 3.1 tool.
Log2 Ratios

source_name: Cell culture, no specific treatment

label_protocol: 250ng of genomic DNA was digested with the restriction enzyme NspI and then ligated to an adapter, followed by polymerase chain reaction (PCR) amplification using a single pair of primers that recognized the adapter sequence.

growth_protocol: Contact-inhibited (about 90% in G0-G1) fibroblast cell cultures.

extract_protocol: DNA was extracted from non-irradiated fibroblast cell cultures using Puregene DNA Purification Kit (Gentra System, Qiagen, Minneapolis, MN, USA) according to the manufacturer’s instruction.

treatment_protocol: No particulat treatment was applied prior to genomic DNA extraction. For clonogenic survival curves, X-Ray 320 kv (dose range 0-4 Gy) was used to generate survival curves.

value: non-irradiated fibroblasts

tag: surviving fraction after 2 gy

tag: Sex

value: F


title: HFC-21

description:
Copy number variation data from patient id130.
id130

value: M


title: pre-exposed to PM2.5-1

description: circRNA expression of human plasma

value: male


title: CCF-04

description:
Copy number variation data from patient id132.
id132


title: CCB-101

description:
Copy number variation data from patient id133.
id133


title: CCT-39

description:
Copy number variation data from patient id134.
id134


title: pre-exposed to PM2.5-3

description: circRNA expression of human plasma


title: pre-exposed to PM2.5-4

description: circRNA expression of human plasma


title: CCB-31

description:
Copy number variation data from patient id129.
id129


title: GRC353-D5-8C_S15

value: head anterior to swim bladder

value: 0.4% DMSO


title: pre-exposed to PM2.5-2

description: circRNA expression of human plasma


title: MEF IRF3-KO, 4sU, ISD, biol rep 2

tag: time-point

tag: assay


title: CCF-45

description:
Copy number variation data from patient id128.
id128

tag: tissue


title: GRC353-D5-8B_S13

value: 5 days post fertilization

value: larvae


title: CCF-05

description:
Copy number variation data from patient id127.
id127


title: Col0_rep3_g1_RNAseq

value: DAY 10


title: GRC353-D5-7I_S12

value: perfluorooctane sulfonic acid

value: mixed wildtype


title: MEF WT, 4sU, ISD, biol rep 2

value: MEF

value: WT

value: SLAM-seq


title: CCF-33

description:
Copy number variation data from patient id126.
id126


title: Col0_rep2_g1_RNAseq


title: MEF IFNAR-KO, 4sU, mock, biol rep 2

value: primary fibroblast

value: IFNAR-knockout

value: 4h transfection / with 2h 4sU

value: mock-tranfection / 4sU


title: ddr4_rep3_g1_RNAseq

value: seedling


title: CCT-08

description:
Copy number variation data from patient id125.
id125

value: non-irradiated fibroblasts

value: F


title: MEF IRF3-KO, 4sU, mock, biol rep 2


title: chr11chr17_rep1_g4_RNAseq


title: GRC353-D5-7G_S14

value: head anterior to swim bladder


title: GRC353-D5-7D_S9


title: GRC353-D5-7F_S2


title: HF-70

description:
Copy number variation data from patient id123.
id123

value: M


title: ddr4_rep2_g1_RNAseq


title: HFC-10

description:
Copy number variation data from patient id122.
id122


title: MEF WT, 4sU, mock, biol rep 2


title: MEF IFNAR-KO, 4sU, untreated, biol rep 2

value: 2h 4sU


title: MEF IRF3-KO, 4sU, untreated, biol rep 2


title: ddr4_rep1_g1_RNAseq


title: Col_g3_MNase-seq

data_processing:
For MNase-seq data analysis, the upstream analysis was performed using the same methods as for ChIP-seq. To normalize the data across different samples, we used DANPOS3 software  with the "wiq" option. The "dpos" option of the DANPOS3 software was used to identify changes in nucleosome occupancy. To describe changes in nucleosome occupancy between the ddr4 mutant and wild-type, we used the "bigwigCompare" option of the DeepTools v3.5.1.
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol: 1.5g samples of 12-day-old seedlings were ground into powder in liquid nitrogen and homogenizated in 20 ml Honda Buffer (0.44 M Sucrose, 1.25 % Ficoll, 2.5 % Dextran T40, 20 mM HEPES-KOH pH 7.4, 10 mM MgCl2, 0.5 % Triton X-100, 5 mM DTT, EDTA-free cOmplete). After filtration with two layers of Miracloth (Merck Millipore, 475855), the nuclei were centrifuged and washed twice with 10 ml Honda Buffer, and were eventually resuspended with 900 ul of MNase digestion buffer (20 mM Tris-Cl pH 8, 5 mM NaCl, 2.5 mM CaCl2). The isolated chromatin was digested with gradient concentration of Micrococcal Nuclease (Takara, 2910 A) for 10 min at 37 °C to obtain mostly mono-nucleosomes. The digestion was stopped with 10 mM EDTA and treated with lysis solution (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA) and 20 mg/ml Proteinase K at 37 °C overnight. DNA was purified with phenol-chloroform-isoamyl alcohol, and was precipitated with salts and ethanol followed by treatment with 10 mg/ml RNase A. The digestion efficiency of different enzyme gradient was examined on a 2 % agarose gel through electrophoresis. The reaction generating 80% of mono-nucleosome was chosen, where the DNA band corresponding to ~150 bp was cut from gel and purified with a the QIAquick gel extraction kit (Qiagen, 28115). The purified DNA band corresponding to ~150 bp were sent to Novogene (Tianjin, China) for library preparation and deep sequencing.

value: DAY 12


title: GRC353-D5-7A_S5

value: 5 days post fertilization

value: larvae


title: MEF IFNAR-KO, no4sU, untreated, biol rep 2


title: MEF WT, 4sU, untreated, biol rep 2


title: CCT-10

description:
Copy number variation data from patient id121.
id121


title: HFC-05

description:
Copy number variation data from patient id124.
id124


title: HFC-12

description:
Copy number variation data from patient id120.
id120


title: GRC353-D5-7H_S1

value: perfluorooctane sulfonic acid

value: mixed wildtype


title: MEF IRF3-KO, no4sU, untreated, biol rep 2

value: MEF


title: Col0_rep2_g2_MNase-seq


title: Col0_rep1_g1_RNAseq

value: DAY 10


title: HF-08

description:
Copy number variation data from patient id119.
id119


title: Col_g1_MNase-seq


title: MEF WT, no4sU, untreated, biol rep 2

value: primary fibroblast

value: WT

value: SLAM-seq


title: Col0_rep1_g2_MNase-seq


title: GRC353-D5-6F_S15


title: GRC353-D5-6E_S3


title: CCB-111

description:
Copy number variation data from patient id118.
id118


title: MEF IFNAR-KO, 4sU, IFNbeta, biol rep 1

value: IFNAR-knockout

value: 3h IFNbeta/ with 2h 4sU

value: IFNbeta / 4sU


title: CCT-07

description:
Copy number variation data from patient id116.
id116

value: non-irradiated fibroblasts

value: F


title: GRC353-D5-6C_S16

value: head anterior to swim bladder


title: GRC353-D5-6H_S2


title: GRC353-D5-6D_S11


title: CCF-32

description:
Copy number variation data from patient id117.
id117


title: MEF WT, 4sU, IFNbeta, biol rep 1


title: MEF IRF3-KO, 4sU, IFNbeta, biol rep 1


title: ZF-DDR4_rep1_g2_MNase-seq

value: seedling


title: GRC353-D5-5H_S14


title: ZF-DDR5_rep1_g3_MNase-seq

value: DAY 12


title: GRC353-D5-5G_S8

value: 5 days post fertilization


title: ddr4_rep2_g1_MNase-seq


title: GRC353-D5-5I_S13

value: larvae


title: CCF-03

description:
Copy number variation data from patient id112.
id112


title: ddr4_rep1_g1_MNase-seq


title: MEF WT, 4sU, ISD, biol rep 1

value: 4h transfection / with 2h 4sU

value: ISD-transfection / 4sU


title: HF-75

description:
Copy number variation data from patient id115.
id115

value: M


title: MEF IFNAR-KO, 4sU, ISD, biol rep 1

value: MEF


title: HF-58

description:
Copy number variation data from patient id114.
id114


title: Col0_g3_ChIPseq

data_processing:
For ChIP-seq data analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. Trimmed reads were aligned to TAIR10 reference using bowtie2 v2.4.2  using the default settings. Alignments of Phred score (Q) less than 30 were removed using samtools. A java program MarkDuplicates.jar from the Picard Toolkit V2.25.6 was used to remove the PCR duplicates. The enrichments of DDR4-ZF over the FWA promoter were normalized to the sequencing depth of each sample using deeptools v3.5.1, and directly visualized using IGV genome browser.
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol: 2g of 12-14 days       post germination seedlings from untransformed Col-0 and two independent T3 homozygous transgenic lines expressing DDR4-ZF were harvested and ground in liquid nitrogen. After 20 minutes cross-linking with the Nuclei Isolation buffer (1 M Sucrose, 50 mM HEPES-KOH pH 8.0, 5 mM KCl, 5 mM MgCl2, 0.6 % Triton X-100, 0.4 mM PMSF, 5mM Benzamidine, EDTA-free cOmplete) containing 1% formaldehyde, chromatin was extracted and sonicated to a range of sizes from 200 bp to 500 bp using Bioruptor Plus (Diagenode, Belgium). 5 ul Anti-FLAG monoclonal (Sigma, F1804) was used to immunoprecipitate the protein-DNA complex. After overnight incubation, chromatin-bound proteins were isolated with Protein A and Protein G Dynabeads (Invitrogen, 10001D, 10003D) mixture for 3 h at 4 °C. The magnetic beads were sequentially washed with low salt buffer, high salt buffer, LiCl buffer, and TE buffer for 10 min each at 4 °C, and immunocomplexes were eluted with elution buffer (2×) by incubating at 65 °C for 20 min. The DNA-protein complexes were reverse-crosslinked at 65 °C overnight and treated with proteinase K at 45 °C for 5 h. DNA was purified by a standard phenol/chloroform/isoamyl alcohol extraction


title: MEF IFNAR-KO, 4sU, mock, biol rep 1

value: primary fibroblast

value: mock-tranfection / 4sU


title: ZF-DDR4_rep2_g2_MNase-seq


title: MEF IRF3-KO, 4sU, ISD, biol rep 1

value: SLAM-seq


title: CCT-56

description:
Copy number variation data from patient id113.
id113


title: ZF-DDR5_rep2_g3_ChIPseq


title: GRC353-D5-5E_S7

value: perfluorooctane sulfonic acid

value: mixed wildtype


title: GRC353-D5-5C_S10


title: GRC353-D5-5F_S13


title: MEF WT, 4sU, mock, biol rep 1

value: WT


title: HF-26

description:
Copy number variation data from patient id109.
id109

value: non-irradiated fibroblasts


title: HF-39

description:
Copy number variation data from patient id111.
id111


title: MEF IRF3-KO, 4sU, mock, biol rep 1


title: GRC353-D5-6I_S1


title: ZF-DDR5_rep1_g3_ChIPseq


title: ZF-DDR5_rep2_g3_MNase-seq


title: GRC353-D4-4I_S7

value: 0.4% DMSO

value: 4 days post fertilization


title: HF-77

description:
Copy number variation data from patient id108.
id108

value: F


title: Col0_rep2_WGBS

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to TAIR10 reference genome using BSMAP v2.90  under default settings (-v 2, allowing up to 2 mismatches; -w 1, report the best hit; -n 1, aligning to both strands). Reads with more than three consecutive methylated CHH were removed as described previously. The methratio.py script from the BSMAP package was used to extract the number of methylated cytosine at single base pair resolution.
Assembly: TAIR10
Supplementary files format and content: The processed data is generated  by the BSMAP methratio.py script.

extract_protocol: 10-day-old seedlings were collected for DNA extraction using a CTAB-based method. 400 ng DNA was used for bisulfite conversion with the EZ DNA methylation-lighting kit

value: seedling

value: DAY 10


title: GRC353-D4-4H_S1

value: head anterior to swim bladder

value: larvae


title: MEF IRF3-KO, 4sU, untreated, biol rep 1

value: 2h 4sU


title: HF-44

description:
Copy number variation data from patient id107.
id107

value: M


title: MEF IFNAR-KO, 4sU, untreated, biol rep 1

value: MEF

value: IFNAR-knockout


title: Col0_rep1_WGBS


title: ddr4_rep2_WGBS


title: GRC353-D4-4G_S10


title: MEF WT, 4sU, untreated, biol rep 1

value: primary fibroblast


title: GRC353-D4-4F_S15


title: ddr4_rep1_WGBS


title: CCF-10

description:
Copy number variation data from patient id106.
id106


title: CCT-06

description:
Copy number variation data from patient id110.
id110


title: MEF IFNAR-KO, no4sU, untreated, biol rep 1

value: SLAM-seq


title: HFC-11

description:
Copy number variation data from patient id105.
id105


title: HF-65

description:
Copy number variation data from patient id104.
id104


title: GRC353-D4-4D_S16


title: GFP-morc1/ddr4, rep3, RNAseq

value: morc1/ddr4 mutant


title: GFP-morc1/ddr4, rep2, RNAseq


title: GRC353-D4-4A_S3

value: mixed wildtype


title: CCF-30

description:
Copy number variation data from patient id103.
id103


title: MEF IRF3-KO, no4sU, untreated, biol rep 1


title: MEF WT, no4sU, untreated, biol rep 1

value: WT


title: GFP-morc1/ddr4, rep1, RNAseq


title: GRC353-D4-3I_S6

value: perfluorooctane sulfonic acid


title: CCF-22

description:
Copy number variation data from patient id102.
id102

value: non-irradiated fibroblasts


title: CCF-01

description:
Copy number variation data from patient id101.
id101


title: GRC353-D4-3H_S4

value: 4 days post fertilization


title: GFP-morc1, rep3, RNAseq

value: morc1 mutant


title: iMEF M35, 4sU, mock, 6h, biol repl 3

source_name: iMEF

growth_protocol: iMEF were maintained in DMEM supplemented with 10% foetal calf serum, 1x non-essential amino acids, 10 µg/ml puromyin for selection, and 1% penicilin/streptomycin in a humidified incubator at 7.5% CO2 and 37°C. The selection antibiotic was not added during experiments.

extract_protocol:
Samples were lysed in TRIzol and total RNA was extracted using the DirectZOL Miniprep kit (Zymo Research). For SLAM conversion, 2 µg of total RNA was mixed with 20 mM Iodacetamide (Thermo Fisher Scientific) and incubated at 50°C shaking for 30 min in the dark. The reaction was stopped by mixing with 100 µM dithiothreitol, and converted RNA was purified using the RNeasy Micro Kit (Qiagen). 100 ng of converted RNA was used for constructing the libraries.
RNA libraries for SLAM-seq were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext PolyA mRNA magnetic isolation module (both New Englang Biolabs) and SPRIselect beads (Beckman Coulter) according to the manufacturer's protocols.

treatment_protocol:
PRR signalling was stimulated by mixing 5 µg/mL Alexa488-coupled ISD (45bp) with Lipofectamin2000 (1:1), incubation for 20  min and adding the transfection mix into the conditioned medium. Transfection of Lipofectamin2000 alone served as mock treatment.
Metabolic labeling of nascent transcripts was performed by adding 200 µM 4sU into the conditioned medium for 90 min before harvest.

value: iMEF

value: immortalised fibroblast

tag: virus (protein)

value: MCMV M35

value: 6h tranfection / with 90min 4sU

value: mock-transfection / 4sU


title: GFP-morc1, rep2, RNAseq

value: seedling

tag: genotype

value: DAY 10


title: GFP-morc1, rep1, RNAseq


title: iMEF EV, 4sU, ISD, 6h, biol repl 3

tag: treatment

value: ISD transfection / 4sU


title: HF-69

description:
Copy number variation data from patient id100.
id100

value: M


title: CCF-83

description:
Copy number variation data from patient id99.
id99

value: F


title: GRC353-D4-3F_S7

value: head anterior to swim bladder

value: larvae


title: GRC353-D4-3G_S10

value: mixed wildtype


title: iMEF EV, 4sU, mock, 6h, biol repl 3

value: SLAM-seq


title: GFP-wt, rep3, RNAseq

value: wt


title: iMEF M35, 4sU, ISD, 4h, biol repl 3

value: 4h tranfection / with 90min 4sU


title: GRC353-D4-3D_S11

value: perfluorooctane sulfonic acid

value: 4 days post fertilization


title: GRC353-D4-3B_S4


title: GRC353-D4-2H_S5


title: iMEF M35, 4sU, mock, 4h, biol repl 3

value: iMEF

value: immortalised fibroblast


title: iMEF EV, 4sU, ISD, 4h, biol repl 3


title: CCT-75

description:
Copy number variation data from patient id98.
id98

value: non-irradiated fibroblasts


title: GFP-wt, rep1, RNAseq


title: GRC353-D4-2E_S6


title: iMEF EV, 4sU, mock, 4h, biol repl 3

value: mock-transfection / 4sU


title: HF-64

description:
Copy number variation data from patient id97.
id97


title: GFP-wt, rep2, RNAseq

value: seedling


title: iMEF M35, 4sU, ISD, 6h, biol repl 3

value: MCMV M35

value: 6h tranfection / with 90min 4sU


title: GRC353-D4-2D_S9


title: HF-38

description:
Copy number variation data from patient id96.
id96

value: M


title: Col0, rep2, ChIPseq

data_processing:
For ChIP-seq data analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. Trimmed reads were aligned to TAIR10 reference using bowtie2 v2.4.2 using the default settings. Alignments of Phred score (Q) less than 30 were removed using samtools. A java program MarkDuplicates.jar from the Picard Toolkit V2.25.6 was used to remove the PCR duplicates. The enrichments of DDR4-ZF over the FWA promoter were normalized to the sequencing depth of each sample using deeptools v3.5.1, and directly visualized using IGV genome browser.
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol: 2g of 12-14 days post germination seedlings from untransformed Col-0 and two independent T3 homozygous transgenic lines expressing DDR4-ZF were harvested and ground in liquid nitrogen. After 20 minutes cross-linking with the Nuclei Isolation buffer (1 M Sucrose, 50 mM HEPES-KOH pH 8.0, 5 mM KCl, 5 mM MgCl2, 0.6 % Triton X-100, 0.4 mM PMSF, 5mM Benzamidine, EDTA-free cOmplete) containing 1% formaldehyde, chromatin was extracted and sonicated to a range of sizes from 200 bp to 500 bp using Bioruptor Plus (Diagenode, Belgium). 5 ul Anti-FLAG monoclonal (Sigma, F1804) was used to immunoprecipitate the protein-DNA complex. After overnight incubation, chromatin-bound proteins were isolated with Protein A and Protein G Dynabeads (Invitrogen, 10001D, 10003D) mixture for 3 h at 4 °C. The magnetic beads were sequentially washed with low salt buffer, high salt buffer, LiCl buffer, and TE buffer for 10 min each at 4 °C, and immunocomplexes were eluted with elution buffer (2×) by incubating at 65 °C for 20 min. The DNA-protein complexes were reverse-crosslinked at 65 °C overnight and treated with proteinase K at 45 °C for 5 h. DNA was purified by a standard phenol/chloroform/isoamyl alcohol extraction

tag: expressing

value: control

value: DAY 12

tag: chip antibody

value: anti-FLAG monoclonal (Sigma, F1804)


title: HF-57

description:
Copy number variation data from patient id94.
id94


title: CCT-05

description:
Copy number variation data from patient id95.
id95

value: F


title: Col0, rep1, ChIPseq

tag: time


title: GRC353-D4-2C_S5

value: head anterior to swim bladder

value: larvae

value: mixed wildtype


title: GRC353-D4-2B_S12

value: perfluorooctane sulfonic acid


title: iMEF M35, 4sU, ISD, 2h, biol repl 3

tag: cell line

value: 2h tranfection / with 90min 4sU

value: ISD transfection / 4sU

value: SLAM-seq


title: iMEF EV, 4sU, mock, 2h, biol repl 3

value: iMEF

tag: cell type

value: immortalised fibroblast


title: iMEF EV, 4sU, ISD, 2h, biol repl 3


title: GRC353-D4-2A_S14

tag: concentration (microm)

value: 4 days post fertilization


title: CCT-01

description:
Copy number variation data from patient id92.
id92

value: non-irradiated fibroblasts


title: HFC-17

description:
Copy number variation data from patient id93.
id93


title: HFC-13

description:
Copy number variation data from patient id91.
id91


title: Col0_rep1_g4_RNAseq

value: seedling

value: DAY 10


title: Shell-Female-2

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

institute: Douglas Mental Health University Institute

library_source: transcriptomic single cell

data_processing:
Data processed with Cell Ranger (10X Genomics)
rn6 pre-mRNA reference made with cellranger mkref
Reads aligned and counted with cellranger count
Assembly: Rattus norvegicus rn6
Supplementary files format and content: Feature-barcode matrix, consisting of barcodes and features in TSV format and matrix in MTX format

organism: Rattus norvegicus

source_name: Nucleus accumbens shell

growth_protocol: Long-Evans rats were bred and offspring were weaned on postnatal day 22. Animals were pair housed in groups of the same sex until 90 to 100 days old.

extract_protocol:
Adult rat's brain were rapidly removed, flash frozen using cold isopentane, stored at -80°C. Brain was sliced coronally at 200 µm thickness. Nucleus accumbens shell and core was punched. 50 mg frozen tissue of NAc shell or NAc core from 4 animals of the same sex were pooled.
Tissues were homogenized and nuclei were obtained as reported by Nagy etl., 2020.Gel beads in emulsion was made by using 10 X Genomics chromium controller and barcoding using chromium NEXT GEM single cell 3' reagent kits v3.1 and chromium Next GEM Chip G single cell kit.
GEMs were incubated at 53 ° C to break emulsions, cDNA was then bulk amplified for 11 cycles and standard illumina libraries were prepared.

value: Nucleus accumbens shell

value: Female


title: iMEF M35, 4sU, untreated, biol repl 3

value: MCMV M35

value: 90min 4sU


title: Shell-Male-3

value: Male


title: Shell-Female-1


title: GRC353-D4-1I_S11

value: head anterior to swim bladder

tag: Stage

value: larvae


title: iMEF EV, 4sU, untreated, biol repl 3


title: HF-51

description:
Copy number variation data from patient id90.
id90

value: F


title: CCF-15

description:
Copy number variation data from patient id89.
id89


title: HFC-18

description:
Copy number variation data from patient id88.
id88

value: M


title: iMEF M35, 4sU, mock, 2h, biol repl 3

value: 2h tranfection / with 90min 4sU

value: mock-transfection / 4sU


title: iMEF M35, no 4sU, untreated, biol repl 3

value: iMEF

value: SLAM-seq


title: ZF-DDR4, rep2, ChIPseq

value: DDR4-FLAG-ZF fusion protein

value: DAY 12

value: anti-FLAG monoclonal (Sigma, F1804)


title: GRC353-D4-1G_S6

value: perfluorooctane sulfonic acid

value: 4 days post fertilization

tag: strain

value: mixed wildtype


title: GRC353-D4-1H_S12

tag: age


title: Shell-Male-2

value: Nucleus accumbens shell


title: iMEF EV, no 4sU, untreated, biol repl 3

value: immortalised fibroblast


title: GRC353-D4-1E_S8


title: GRC353-D4-1A_S3


title: ZF-DDR4, rep1, ChIPseq

value: seedling


title: iMEF M35, 4sU, mock, 6h, biol repl 2

value: MCMV M35

value: 6h tranfection / with 90min 4sU


title: GRC350-D5-4I_S13

extract_protocol:
Each pooled sample underwent RNA extraction using Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit.
The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA (500 ng per sample) selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size (bp) was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library (volume x concentration) was pooled from 16 randomized libraries to make the sequencing library pools (total 3 pools of 16 libraries each) and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS, the final concentrations for sequencing were 2.8-3.0 pM + 2% Phix, and they were run for 75 cycles single read.

treatment_protocol: At 0 dpf, zebrafish embryos were bleached as previously described (Tal et al. 2017). A single embryo at the dome-to-epiboly stages (Kimmel et al. 1995) was placed into each individual well of a 96-well plate containing a 40-μm nylon mesh filter (Millipore, Catalog No. MANMN4010) with 400μL of 10% Hanks’ balanced salt solution (HBSS) per well. Filter inserts containing zebrafish embryos were transferred to 96-well culture trays (Millipore, Catalog No. MAMCS9610) containing 250μL of 10% HBSS (Westerfield 2007) and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily, from 1–4 or 1-5 dpf, plates underwent 100% media changes to refresh chemical dosing solutions by blotting (Brandel; Catalog No. FPXLR-196) and transferring mesh inserts containing zebrafish to new bottom plates (Millipore; Catalog No. MAMCS9610). To minimize evaporation, plates were sealed (Biorad; Catalog No. MSA5001) and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0°C and scored daily for death, malformations, hatching, and swim bladder inflation. Zebrafish embryos were exposed to 7.87-25.1 μM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.

value: 0.4percent DMSO

tag: concentration (µm)

value: 5 days post fertilization

tag: developmental stage

value: larvae


title: HF-37

description:
Copy number variation data from patient id87.
id87

value: non-irradiated fibroblasts

tag: surviving fraction after 2 gy

tag: Sex

value: F


title: HF-72

description:
Copy number variation data from patient id85.
id85

tag: tissue

value: M


title: GRC353-D4-1D_S2

value: head anterior to swim bladder


title: NF1Fbr10

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

description: PS fibroblasts

data_processing:
Raw reads were trimmed of sequencing adapters with Trim_Galore
Trimmed reads were mapped to Rnor 6.0 assembly with STAR v2.5.2b using options ‘--twopassMode Basic’ and ‘--quantMode GeneCounts’ to directly output counts for all features from the ensemble annotation 6.0.90
Assembly: Rnor 6.0
Supplementary files format and content: raw_counts.tsv has the raw counts output from STAR mapping for features in the ensemble 6.0.90 annotation.

source_name: fibroblasts

extract_protocol:
For RNA extraction of whole fat pads and tumors, fresh harvested samples were cut up and added to MPbio lysing matrix E tube. Cells were homogenized for 20 seconds in an MPbio homogenizer, then RNA was isolated from the supernatant using the Trizol-chloroform-isopropanol RNA extraction method. For RNA extraction of mature adipocytes, RNA was isolated using the Trizol-chloroform-isopropanol RNA extraction method. For RNA extraction of cultured epithelial cells and fibroblast, 1.2105 cells were plated into one well of a six-well plate. At 90-100% confluency, RNA was isolated using QIAGEN QIAshredder and RNeasy Kit manufacturer’s instructions.
Libraries were prepared by the Van Andel Institute Genomics Core from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).Individually indexed libraries were pooled and 50 bp, paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2 sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 45M reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: fibroblasts

value: PS


title: iMEF M35, 4sU, ISD, 6h, biol repl 2

value: iMEF

tag: virus (protein)

tag: time-point

value: ISD transfection / 4sU

tag: assay

value: SLAM-seq


title: NF1Fbr12

description: PS fibroblasts

tag: genotype


title: NF1Fbr11

description: PS fibroblasts


title: CCF-43

description:
Copy number variation data from patient id86.
id86


title: GRC350-D5-4H_S12

tag: treatment

value: mixed wildtype


title: iMEF EV, 4sU, ISD, 6h, biol repl 2

value: immortalised fibroblast


title: CCT-58

description:
Copy number variation data from patient id82.
id82


title: NF1Fbr9

description: IF fibroblasts

value: IF


title: GRC350-D5-4F_S2


title: NF1Fbr7

description: IF fibroblasts


title: GRC350-D5-4E_S14


title: CCF-31

description:
Copy number variation data from patient id84.
id84


title: iMEF EV, 4sU, mock, 6h, biol repl 2

value: mock-transfection / 4sU


title: CCF-97

description:
Copy number variation data from patient id80.
id80


title: CCB-40

description:
Copy number variation data from patient id81.
id81


title: HF-24

description:
Copy number variation data from patient id83.
id83


title: NF1Fbr8

description: IF fibroblasts


title: iMEF M35, 4sU, mock, 4h, biol repl 2

value: MCMV M35

value: 4h tranfection / with 90min 4sU


title: NF1Fbr4

description: IFPS fibroblasts

value: IFPS


title: iMEF EV, 4sU, mock, 4h, biol repl 2


title: GRC350-D5-4G_S1

value: 0.4percent DMSO

value: 5 days post fertilization

value: larvae


title: iMEF M35, 4sU, ISD, 4h, biol repl 2


title: NF1Fbr3

description: wildtype fibroblasts

value: wildtype


title: NF1Fbr6

description: IFPS fibroblasts


title: GRC350-D5-3I_S4

value: potassium perfluorohexane-1-sulfonate


title: iMEF EV, 4sU, ISD, 4h, biol repl 2


title: HF-14

description:
Copy number variation data from patient id77.
id77

value: non-irradiated fibroblasts

value: M


title: NF1Fbr1

description: wildtype fibroblasts

value: fibroblasts


title: GRC350-D5-4C_S14


title: HF-49

description:
Copy number variation data from patient id79.
id79


title: CCT-60

description:
Copy number variation data from patient id78.
id78

value: F


title: iMEF EV, 4sU, mock, 2h, biol repl 2

value: iMEF

value: 2h tranfection / with 90min 4sU

value: SLAM-seq


title: iMEF M35, 4sU, mock, 2h, biol repl 2

value: immortalised fibroblast


title: GRC350-D5-3F_S10

value: mixed wildtype


title: GRC350-D5-3H_S2


title: GRC350-D5-3G_S14


title: GRC350-D5-3D_S11


title: iMEF M35, 4sU, ISD, 2h, biol repl 2

value: MCMV M35

value: ISD transfection / 4sU


title: HFC-19

description:
Copy number variation data from patient id73.
id73


title: GRC350-D5-3C_S8


title: iMEF EV, 4sU, ISD, 2h, biol repl 2


title: NF1Fbr5

description: IFPS fibroblasts

value: IFPS


title: NF1MAd9

description: IF adipocytes

source_name: adipocytes

value: adipocytes

value: IF


title: iMEF EV, 4sU, untreated, biol repl 2

value: 90min 4sU


title: NF1MAd12

description: PS adipocytes

value: PS


title: HF-73

description:
Copy number variation data from patient id75.
id75


title: NF1MAd11

description: PS adipocytes


title: HF-63

description:
Copy number variation data from patient id76.
id76


title: iMEF M35, 4sU, untreated, biol repl 2


title: CCF-20

description:
Copy number variation data from patient id71.
id71


title: NF1Fbr2

description: wildtype fibroblasts

value: wildtype


title: iMEF M35, no 4sU, untreated, biol repl 2


title: CCT-59

description:
Copy number variation data from patient id74.
id74

value: non-irradiated fibroblasts


title: HF-71

description:
Copy number variation data from patient id72.
id72

value: M


title: GRC350-D5-2E_S2

value: potassium perfluorohexane-1-sulfonate

value: 5 days post fertilization

value: larvae


title: GRC350-D5-2H_S16


title: GRC350-D5-2I_S11


title: GRC350-D5-2D_S8


title: iMEF EV, no 4sU, untreated, biol repl 2

value: iMEF


title: NF1MAd7

description: IF adipocytes


title: NF1MAd8

description: IF adipocytes


title: NF1MAd4

description: IFPS adipocytes


title: GRC350-D5-2A_S4


title: CCF-89

description:
Copy number variation data from patient id67.
id67

value: F


title: GRC350-D5-1I_S7


title: iMEF M35, 4sU, ISD, 6h, biol repl 1

value: immortalised fibroblast

value: 6h tranfection / with 90min 4sU

value: SLAM-seq


title: GRC350-D5-2G_S9

value: mixed wildtype


title: iMEF EV, 4sU, mock, 6h, biol repl 1

value: mock-transfection / 4sU


title: CCB-94

description:
Copy number variation data from patient id70.
id70


title: NF1MAd3

description: wildtype adipocytes

value: adipocytes


title: iMEF M35, 4sU, ISD, 4h, biol repl 1

value: MCMV M35

value: 4h tranfection / with 90min 4sU

value: ISD transfection / 4sU


title: HF-41

description:
Copy number variation data from patient id66.
id66


title: iMEF M35, 4sU, mock, 6h, biol repl 1


title: NF1MAd6

description: IFPS adipocytes

value: IFPS


title: iMEF M35, 4sU, mock, 4h, biol repl 1


title: CCF-76

description:
Copy number variation data from patient id69.
id69

value: non-irradiated fibroblasts


title: NF1MAd10

description: PS adipocytes

value: PS


title: HF-78

description:
Copy number variation data from patient id65.
id65

value: M


title: HF-12

description:
Copy number variation data from patient id64.
id64


title: iMEF EV, 4sU, ISD, 4h, biol repl 1


title: CCB-114

description:
Copy number variation data from patient id68.
id68


title: NF1MAd5

description: IFPS adipocytes


title: iMEF EV, 4sU, ISD, 6h, biol repl 1


title: GRC350-D5-1F_S16

value: potassium perfluorohexane-1-sulfonate

value: 5 days post fertilization


title: GRC350-D5-1D_S15

value: larvae


title: GRC350-D5-1G_S7


title: GRC350-D5-1H_S15


title: iMEF M35, 4sU, ISD, 2h, biol repl 1

value: iMEF

value: 2h tranfection / with 90min 4sU


title: NF1MAd2

description: wildtype adipocytes

value: wildtype


title: NF1MEC10

description: PS MECs

source_name: MECs

value: MECs


title: GRC350-D4-4I_S13

value: 0.4percent DMSO

value: 4 days post fertilization

value: mixed wildtype


title: iMEF M35, 4sU, mock, 2h, biol repl 1

value: immortalised fibroblast

value: MCMV M35

value: mock-transfection / 4sU

value: SLAM-seq


title: HFC-04

description:
Copy number variation data from patient id63.
id63

value: non-irradiated fibroblasts


title: GRC350-D5-1C_S3


title: NF1MEC11

description: PS MECs

value: PS


title: iMEF EV, 4sU, mock, 2h, biol repl 1


title: NF1MEC9

description: IF MECs

value: IF


title: CCF-62

description:
Copy number variation data from patient id60.
id60

value: F


title: iMEF M35, 4sU, untreated, biol repl 1

value: 90min 4sU


title: HFC-15

description:
Copy number variation data from patient id59.
id59

value: M


title: NF1MAd1

description: wildtype adipocytes

value: adipocytes


title: NF1MEC7

description: IF MECs


title: NF1MEC8

description: IF MECs


title: GRC350-D4-4H_S4

value: larvae


title: CCB-35

description:
Copy number variation data from patient id61.
id61


title: GRC350-D4-4G_S1


title: NF1MEC12

description: PS MECs


title: iMEF EV, 4sU, mock, 4h, biol repl 1

value: iMEF

value: 4h tranfection / with 90min 4sU


title: iMEF M35, no 4sU, untreated, biol repl 1


title: iMEF EV, 4sU, untreated, biol repl 1


title: NF1MEC4

description: IFPS MECs

value: MECs

value: IFPS


title: GRC350-D4-4B_S9

value: 0.4percent DMSO

value: 4 days post fertilization

value: mixed wildtype


title: GRC350-D4-4E_S12


title: NF1MEC5

description: IFPS MECs


title: HF-60

description:
Copy number variation data from patient id56.
id56


title: NF1MEC3

description: wildtype MECs

value: wildtype


title: GRC350-D4-4F_S1


title: iMEF EV, no 4sU, untreated, biol repl 1

value: immortalised fibroblast

value: SLAM-seq


title: experiment 3: TVA stimulated 2 hr, biol rep2

city: Chicago

first: Matthew

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

institute: University of Chicago

description: Column "O" is catenated, columns "P" and "Q" are individual component files

data_processing:
Sequence reads from two separate Illumina sequencing runs were catenated
First, the fastqc (0.11.9) and trim-galore (0.6.7) packages were used for (i) quality control and (ii) to remove low-qualified bases and adapter-containing reads from raw KAS-seq data, respectively. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome using bowtie2 (2.4.4) under default parameters.
Bed files were converted to bedGraph files using bedtools (2.30.0). Bedgraph files were then normalized to total read counts using the normalize_KAS-seq script (KAS-pipe) and normalized bedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Differential analysis was then performed using the diff_KAS-seq script (KAS-pipe: which applies DESeq2 (1.26.0) differential analysis)
Assembly: hg19/mm10
Supplementary files format and content: bigWig, read density

source_name: CD8+ T cells

growth_protocol: Mouse and human CD8+ T cells were maintained in Click's medium supplemented with 10% fetal bovine serum (FBS), 1% glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
After labeling, genomic DNA was isolated using a PureLink Genomic DNA mini kit. 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin. The mixture was shaken at 37 °C for 1.5 h, after which 5 µL RNase A was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. 5% of the sonicated DNA was set aside and saved, and the rest was used for enrichment with 10 µL Dynabeads MyOne Streptavidin C1. The beads were washed with three times with 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. The binding was performed at room temperature for 15 min. The beads were then washed five times in 1× B&W buffer and then were resuspended in 15 uL H2O. Beads were then heated at 95 °C for 10 min to elute DNA; DNA eluate solution was then moved onto ice for library construction.
Sonicated/sheared enriched DNA libraries were constructed using a Accel-NGS Methyl-Seq DNA library kit

treatment_protocol:
After activation with anti-CD3/28, CD8+ T cells were treated with 20 μM TVA for various timepoints, or were untreated as indicated above
To detect ssDNA levels, following TVA stimulation (or no stimulation for unstimulated cells), cells were treated with 5 mM N3-kethoxal in DMSO supplemented into the growth media

value: CD8+ T cells

value: Primary T cell

value: WT

value: 20 uM TVA

tag: time

value: 2 hours


title: GRC350-D4-3I_S6

value: potassium perfluorohexane-1-sulfonate


title: GRC350-D4-3H_S3

value: larvae


title: iMEF EV, 4sU, ISD, 2h, biol repl 1

tag: cell line

value: iMEF

value: 2h tranfection / with 90min 4sU

value: ISD transfection / 4sU


title: HFC-03

description:
Copy number variation data from patient id55.
id55

value: non-irradiated fibroblasts

value: M


title: HF-67

description:
Copy number variation data from patient id52.
id52

value: F


title: experiment 3: TVA stimulated 40 min, biol rep2

tag: cell type

value: 40 min


title: experiment 3: TVA stimulated 2 hr, biol rep1


title: GRC350-D4-3G_S5

value: 4 days post fertilization

value: mixed wildtype


title: GRC350-D4-3E_S8


title: CCB-98

description:
Copy number variation data from patient id54.
id54


title: CCB-121

description:
Copy number variation data from patient id58.
id58


title: CCF-14

description:
Copy number variation data from patient id57.
id57


title: GRC350-D4-3B_S9


title: NF1MEC6

description: IFPS MECs

value: MECs

value: IFPS


title: HF-42

description:
Copy number variation data from patient id50.
id50


title: CCF-102

description:
Copy number variation data from patient id53.
id53


title: NF1MEC2

description: wildtype MECs

value: wildtype


title: experiment 3: TVA stimulated 20 min, biol rep2

value: CD8+ T cells

value: Primary T cell

value: WT

value: 20 min


title: GRC350-D4-2I_S10

value: potassium perfluorohexane-1-sulfonate

value: larvae


title: GRC350-D4-2H_S3


title: NF1MEC1

description: wildtype MECs


title: experiment 3: TVA stimulated 40 min, biol rep1

value: 20 uM TVA


title: GRC350-D4-3A_S16


title: MSR592

description: IFPS tumor

source_name: tumor

value: tumor


title: HF-29

description:
Copy number variation data from patient id51.
id51

value: non-irradiated fibroblasts


title: CCB-88

description:
Copy number variation data from patient id48.
id48


title: MSR770

description: IFPS tumor


title: experiment 3: unstimulated, biol rep1


title: MSR687

description: IFPS tumor


title: experiment 3: TVA stimulated 20 min, biol rep1


title: MSR2R4

description: IFPS tumor


title: GRC350-D4-2D_S10


title: MSR536

description: PS tumor

value: PS


title: MSR673

description: PS tumor


title: CCF-96

description:
Copy number variation data from patient id47.
id47

value: F


title: MSR2R2

description: IFPS tumor


title: experiment 3: unstimulated, biol rep2


title: GRC350-D4-2C_S7


title: CCF-18

description:
Copy number variation data from patient id42.
id42


title: HF-52

description:
Copy number variation data from patient id46.
id46

value: M


title: MSR3

description: PS tumor


title: HF-30

description:
Copy number variation data from patient id45.
id45


title: HF-36

description:
Copy number variation data from patient id41.
id41


title: D3_iHAFoxk1_EB_ND_rep2

first: Daniel

last: Garry

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

data_processing:
Sequenced reads were mapped to mm10 whole genome using Kallisto v0.46.2 with default parameters.
Assembly: mm10
Supplementary files format and content: Counts matrix

source_name: EB

growth_protocol: iHA-Foxk1 and Foxk1 KO ESCs were cultured in media containing 15% fetal bovine serum (FBS), 2 mM Glutamax, 1X penicillin/streptomycin, 0.1 mM β-mercaptoethanol, and 1,000 U/mL LIF, at 37°C in 5% CO2 together with irradiated mouse embryonic fibroblasts as a feeder layer. We differentiated iHA-Foxk1 and Foxk1 KO ESCs into embryoid bodies (EBs) using mesodermal differentiation conditions. Briefly, ESCs were separated into single cells using 0.25% trypsin and plated for 50 minutes to remove fibroblast cells from the feeder layer (de-MEF step). Following de-MEF, ESCs were differentiated in mesodermal media using the shaking method in media containing 15% FBS (Foundation GeminiBio), 1X penicillin / streptomycin, 1X GlutaMAX, 50 μg/ml Fe-saturated transferrin, 450 mM monothioglycerol, 50 μg/ml ascorbic acid in IMDM media (Thermo).

extract_protocol:
Total RNA was isolated from D3, D5 and D10 Control (iHA-Foxk1) and Foxk1 KO EBs using the RNeasy kit (Qiagen, Cat# 74104) following the manufacturer’s protocol. Briefly, EBs were lysed in RLT-lysis buffer, followed by a column-based purification process and on-column DNA digestion. Libraries for bulk RNAseq were generated by the University of Minnesota Genome Center.
Sample Quality Assessment: Total eukaryotic RNA isolates are quantified using a fluorimetric RiboGreen assay.  Total RNA integrity is assessed using capillary electrophoresis (e.g. Agilent BioAnalyzer 2100), generating an RNA Integrity Number (RIN).  For samples to pass the initial QC step, they need to quantify higher than 500 ng and have a RIN of 8 or greater.  Total RNA samples are then converted to Illumina sequencing libraries.    Library Creation: Total RNA samples are converted to Illumina sequencing libraries using Illumina’s TruSeq RNA Sample Preparation Kit (Cat. # RS-122-2001 or RS-122-2002) or Stranded mRNA Sample Preparation Kit (Cat. # RS-122-2101).  (Please see www.illumina.com for a detailed list of kit contents and methods). In summary, the mRNA from a normalized input mass of total RNA is isolated using oligo-dT coated magnetic beads, fragmented and then reverse transcribed into cDNA. The cDNA is blunt-ended, A-tailed and indexed by ligating molecularly barcoded adaptors.  Libraries are amplified using 15 cycles of PCR. Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen) and via Q-PCR.  Indexed libraries are then normalized, pooled and size-selected to 320 bp (tight) using the PippinHT instrument.
Cluster generation and sequencing:  Pooled libraries are denatured and diluted to the appropriate clustering concentration. The libraries are then loaded onto the NovaSeq paired end flow cell and clustering occurs on board the instrument.  Once clustering is complete, the sequencing reaction immediately begins using Illumina’s 2-color SBS chemistry.  Upon completion of read 1, a 7 base pair index read is performed in the case of single indexed libraries.  If dual indexing was used during library preparation, 2 separate 8 or 10 base pair index reads are performed.  Finally, the clustered library fragments are re-synthesized in the reverse direction thus producing the template for paired end read 2.    Primary analysis and de-multiplexing:  Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software.  The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute.  Primary analysis and de-multiplexing are performed using Illumina’s bcl2fastq v2.20.  The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released to client accounts for subsequent analysis by the mapping software and aligner of their own choosing.

value: Day 3

tag: paired-end or single

value: paired-end


title: HF-48

description:
Copy number variation data from patient id44.
id44


title: D5_iHAFoxk1_EB_ND_rep2

value: Day 5


title: D5_Foxk1KO_EB_rep2


title: GRC350-D4-1F_S15

value: 4 days post fertilization

value: mixed wildtype


title: D5_iHAFoxk1_EB_ND_rep1


title: GRC350-D4-2A_S5


title: GRC350-D4-1H_S6


title: MSR1269

description: PS tumor


title: GRC350-D4-2B_S5


title: CCF-86

description:
Copy number variation data from patient id38.
id38


title: D3_Foxk1KO_EB_rep2


title: D5_Foxk1KO_EB_rep1


title: MSR354

description: PS tumor


title: CCT-54

description:
Copy number variation data from patient id36.
id36


title: D3_Foxk1KO_EB_rep1


title: CCF-90

description:
Copy number variation data from patient id40.
id40


title: D10_Foxk1KO_IWR1_EBs_rep2

value: Day 10


title: MSR359

description: PS tumor


title: CCF-54

description:
Copy number variation data from patient id35.
id35


title: CCB-34

description:
Copy number variation data from patient id39.
id39


title: MSR526

description: PS tumor


title: GRC350-D4-1E_S13


title: D10_Foxk1KO_IWR1_EBs_rep1


title: D3_iHAFoxk1_EB_ND_rep1


title: HF-50

description:
Copy number variation data from patient id37.
id37


title: GRC350-D4-1D_S6


title: GRC350-D4-1C_S11


title: D10_Control_EBs_rep2


title: GRC350-D4-1B_S12


title: MSR420

description: IF tumor

value: IF


title: MSR295

description: PS tumor


title: HF-43

description:
Copy number variation data from patient id34.
id34


title: D10_Foxk1KO_EBs_rep2


title: MSR208

description: PS tumor


title: CCF-92

description:
Copy number variation data from patient id33.
id33


title: HF-53

description:
Copy number variation data from patient id30.
id30


title: CCF-88

description:
Copy number variation data from patient id29.
id29


title: MSR353

description: IF tumor


title: CCB-13

description:
Copy number variation data from patient id32.
id32


title: D10_Foxk1KO_EBs_rep1


title: MSR352

description: IF tumor


title: MSR291

description: IF tumor


title: IVC_Old-LP

city: CHANDIGARH

first: Rashmi

last: Kumar

state: Punjab

address: CSIR-Institute of microbial technology,sector 39A chandigarh, IMTECH, housing, Type 1 A6, IMTECH, housing, Type 1 A6

country: India

institute: CSIR-Institute of microbial technology

description: Gene expression after 24hrs of LPS treatment in different groups as mentioned

hyb_protocol: Cy3-labelled mRNA samples were hybridized onto a mouse 8x60K Gene Expression V2 Array kit, G4858A (Agilent Technologies, Palo Alto, CA, USA) for 16 h at 55°C in a rotator oven and subsequently washed.

scan_protocol: The array slides were scanned using a DNA microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Hybridization signals were extracted using the Agilent Feature Extraction software 10.5 (Agilent Technologies, Palo Alto, CA, USA). Thereafter, quantitative microarray data were normalized by using the quantile normalization method from the limma R package. Estimation of differential features was performed with limma R package by using lmFit (function to fit a linear model to expression data of each feature) and eBayes (empirical Bayes function used to determine adj.P.value and logFC. Significant differential features were obtained by using thresholds adj.P.value<=0.05 and abs(logFC)>=0.5. Enrichment of functional annotation was performed with R package gprofiler2. Gene ontology summarization and treemap plot were generated with R package rrvgo.

source_name: Bone marrow derived dendritic cells

label_protocol: 500 ng of total RNA were labelled with a (Cy3 fluorochrome) one-colour  Low-Input Quick Amp labelling kit, 5190-2305 (Agilent Technologies, Palo Alto, CA, USA).

growth_protocol: Bone marrow cells were flushed away with RPMI media from mice femurs and tibiae and after RBC lysis by ACK lysis buffer and counting, 2x106 cells were plated per well in a 6-well plate. Cells were grown in RPMI-1640 with 10% FCS supplemented with penicillin (100 U/ml), L-glutamine (100 mM), streptomycin (100 mg/ml), rmGM-CSF (recombinant murine granulocyte-macrophage colony-stimulating), 2ng/ml- 554586, Biosciences (San Diego, CA, USA) and rmIL-4 (recombinant murine interleukin-4), 4ng/ml-550067, Biosciences (San Diego, CA, USA), for DC cultures. The culture was supplemented with fresh complete RPMI media containing GM-CSF (2 ng/ml) and rIL-4 (4 ng/ml) at half of its initial volume on the third day of culture. On day 7, loosely adherent cells were harvested by gentle pipetting and counted for further experiments. The methodology was followed as per the already mentioned protocol (Lutz et al., 1999).

extract_protocol: TRIzol reagent was used to isolate total RNA from DCs after LPS stimulation (1μg/ml) according to the manufacturer's protocol (Invitrogen, Carisbad, CA, USA). DNA contamination if any, was removed by incubating RNA samples with amplification grade DNase1 enzyme. Taking 260/280 ratio of 1.9-2.0 as a standard ratio for RNA purity

treatment_protocol: Later, for maturation of BMDCs (2x106/well) were stimulated with LPS-1μg/ml, L2630- Sigma-Aldrich (St. Louis, MO, USA) in 6 well plate.

tag: gender

value: female

tag: agent

value: LP


title: IVB_Old-LP

tag: age


title: CCF-93

description:
Copy number variation data from patient id27.
id27


title: D10_Control_EBs_rep1

value: Control


title: IIIB_Old


title: MSR304

description: IFPS tumor

value: IFPS


title: D10_Control_rep2

description: NoDox

data_processing:
Illumina used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ATAC-seq peaks were called by MACS2
Assembly: mm10
Supplementary files format and content: peak files
Supplementary files format and content: bigwig files

extract_protocol:
iHA-Foxk1 and Foxk1 KO EBs were collected at different time periods during differentiation and disaggregated in 0.25% trypsin at 37C for 3 min incubation with gentle agitation followed by inactivation with culture medium containing 10% FBS. Cells were collected by centrifugation at 500g for 5 minutes at 4 degrees celcius and washed once with ice-cold PBS. ATAC reaction was performed with 50,000 cells as previously described38 using the Tn5 transposase (Illumina) and libraries were created at the University of Minnesota Genome Center. Libraries were then sequenced on a NextSeq Illumina platform (2x50 bp) aiming for 25 million reads per sample.
Library Creation:   ATAC-Seq library prep was performed in accordance with the ATAC-Seq protocol as described by Buenrostro, et al. In brief, transposed DNA was amplified for 5 cycles using Nextera-compatible indexed sequencing adapters. 5 ul from the PCR reaction was ran on qPCR to assess the number of additional PCR cycles required without reducing library diversity. All samples underwent additional PCR cycling as determined by their qPCR amplification curve. Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Libraries are normalized, pooled, and subjected to a double-sided AmPure to deplete un-tagmented material. Pools are QC’ed via Picogreen, Agilent BioAnalyzer High-Sensitivity, and KAPA qPCR (to assess library functionality) before normalization for sequencing.
Cluster generation and sequencing:  Pooled libraries are denatured and diluted to the appropriate clustering concentration. The libraries are then loaded onto the NovaSeq paired end flow cell and clustering occurs on board the instrument.  Once clustering is complete, the sequencing reaction immediately begins using Illumina’s 2-color SBS chemistry.  Upon completion of read 1, 2 separate 8 or 10 base pair index reads are performed.  Finally, the clustered library fragments are re-synthesized in the reverse direction thus producing the template for paired end read 2.    Primary analysis and de-multiplexing:  Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software.  The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute.  Primary analysis and de-multiplexing are performed using Illumina’s bcl2fastq v2.20.  The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released to client accounts for subsequent analysis by the mapping software and aligner of their own choosing.


title: D10_Control_rep1

description: NoDox


title: IVA_Old-LP


title: MSR362

description: IFPS tumor


title: D10_Foxk1_KO_rep2

description: NoDox


title: MSR224

description: IFPS tumor


title: NF1Mam19

description: PS whole_mammary_pad


title: HF-61

description:
Copy number variation data from patient id23.
id23


title: IIIC_Old


title: HF-34

description:
Copy number variation data from patient id22.
id22


title: IIA_Young-Abx

value: antibiotic cocktail


title: IIIA_Old


title: IIB_Young-Abx


title: IC_Young


title: MSR415

description: IF tumor

value: tumor


title: D10_Foxk1_KO_rep1

description: NoDox


title: Th17TOFA+LPE_3_ATAC

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
ATAC-seq reads were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)  using Bowtie2.
Normalization was performed using RPGC method with Bamcoverage of Deeptools.
Assembly: mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Supplementary files format and content: Excel files include TPM values for each Sample
Supplementary files format and content: wig files were generated using "Deep tools".

source_name: Spleen

growth_protocol: See method in article

extract_protocol: QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN) and ATAC-Seq (ACTIVE MOTIF) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: See method in article

value: Spleen

value: CD4 T cell

value: Wild type

value: TOFA + LPE


title: HF-68

description:
Copy number variation data from patient id28.
id28

value: non-irradiated fibroblasts

value: M


title: FoxK1_KO_D5_rep2

description: NoDox

value: Day 5


title: CCF-68

description:
Copy number variation data from patient id31.
id31

value: F


title: MSR366

description: IFPS tumor


title: FoxK1_KO_D5_rep1

description: NoDox


title: IIC_Young-Abx


title: NF1Mam15

description: wildtype whole_mammary_pad

value: wildtype


title: IB_Young


title: Th17TOFA_3_ATAC

value: TOFA


title: HF-54

description:
Copy number variation data from patient id20.
id20


title: HF-74

description:
Copy number variation data from patient id19.
id19


title: FoxK1_KO_D3_rep1

description: NoDox

value: Day 3


title: Th17TOFA_2_ATAC


title: HF-18

description:
Copy number variation data from patient id26.
id26


title: NF1Mam21

description: PS whole_mammary_pad

value: PS


title: NF1Mam13

description: wildtype whole_mammary_pad


title: iFoxk1_ND_D5_rep2

description: NoDox


title: Th17Control_3_ATAC

value: Vehicle


title: NF1Mam11

description: PS whole_mammary_pad


title: HF-47

description:
Copy number variation data from patient id25.
id25


title: Meljuso_RDA763_RDA988_RepB

city: Cambridge

first: John

last: Doench

state: MA

address: 75 Ames St

department: Genetic Perturbation Platform

institute: Broad Institute

description: MelJuSo cells expressing 5x-tag-dCas12a and without the cassette containing three CD4-targeting guides

data_processing:
Sequencing reads from Genewiz were aligned to the human Genome Reference Consortium Human Build 38 (hg38) using the STAR aligner.
Transcript abundances were quantified using RNA-Seq by Expectation Maximization (RSEM).
Assembly: human Genome Reference Consortium Human Build 38 (hg38)
Supplementary files format and content: compressed tab-delimited text files include raw count values for each Sample

source_name: MelJuSo

extract_protocol:
Cells were cultivated as normal in preparation for RNA sequencing. When cells reached confluency, they were scraped from their flasks using cell scrapers, with existing media still present. 10 mL serological pipettes were used to break up cell clumps and cell-containing media was transferred to conicals. Cell mixtures were counted using a Coulter Counter to ensure that each pellet contained >1e6 cells. Cells were then pelleted by centrifugation at 321 x g for 5 minutes. Media was aspirated, pellets were resuspended in PBS, and the PBS-cell mixture was aliquoted into Eppendorf tubes. Cells were pelleted once more by centrifugation in a table-top centrifuge at maximum speed for 2 minutes. The supernatant was aspirated and pellets were flash frozen on dry ice, then frozen at -80 C, and submitted to Genewiz from Azenta Life Sciences for RNA extraction and sequencing.
RNA libraries for RNA-seq were prepared by Genewiz from Azenta Life Sciences

value: MelJuSo

tag: tag vector

tag: nanobody vector

value: nanobody

tag: group

value: CD4 guides -  FALSE