title: ilc-17.1_rescue_replicate _4

data_processing:
The quality of the RNA sequences was assessed with FastQC
Adapters sequences and reads with a quality lower than Q25 were trimmed by using Trimgalore version 0.67.
Ribosomal RNA (rRNA) contamination was filtered with sortmeRNA, version 4.3.41.
Sequencing reads were aligned to the C. elegans genome WBcel235  using the Star aligner v2.7.9a2
Aligned reads were quantified with FeatureCounts v2.0.1 from the package Rsubread3 .
Differential expression analysis was performed using DESeq2
Assembly: WBcel235
Supplementary files format and content: Excel file include DESeq2 normalized counts for all Samples
Supplementary files format and content: Excel file include CPM values for all Samples
Supplementary files format and content: Excel File Raw normalized counts include raw values for all  Samples

growth_protocol: Day-1 adult worms were bleach-hatched and ~3200 eggs/genotype (~800 eggs/plate and 4 plates/genotype) were seeded on fresh OP50 plates and allowed to grow for 30-34 hrs. at 25°C.

extract_protocol:
Worms were washed with sterile water and total RNA was extracted from biological triplicates using the Direct-zol RNA Miniprep Kits Worms were washed with sterile water and total RNA was extracted from biological triplicates using the Direct-zol RNA Miniprep Kits
Libraries were prepared using the Illumina Stranded Total RNA Prep   with Ribo-Zero Plus, for rRNA depletion


title: Mid thoracic spinal cord, drug_meth_5 (rnaseq)

status: Public on Jan 30 2024

type: SRA

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

country: Switzerland

institute: EPFL

description: 10x v3

library_source: transcriptomic single cell

data_processing:
For the snRNA-seq, reads were aligned using Cellranger v 4.0.0 and the final data matrix is generated as per Cellranger pipeline. For the spatial transcriptomics, reads were aligned with SpaceRanger v 1.0.0 and the final data matrix is generated as per Spaceranger pipeline
Data were analyzed using Seurat v3
Assembly: mm10-1.2.0 (GRCm38.101)
Supplementary files format and content: tab-delimited text files include UMI values for each cell with tab delimeters

molecule: total RNA

organism: Mus musculus

source_name: Mid thoracic spinal cord

extract_protocol:
For snRNA-seq experiment, single-nucleus dissociation of the mouse lumbar spinal cord was performed according to our established procedures. Following euthanasia by isoflurane inhalation and cervical dislocation, the spinal cord injury site was immediately dissected and frozen on dry ice. Spinal cords were doused in 500 µL sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was then added and filtered through a 40 µm cell strainer. The lysate was centrifuged at 3200 g for 10 min at 4°C. The supernatant was then decanted, and 3 mL of sucrose buffer was added to the pellet for 1 min. We homogenized the pellet using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant poured off. Nuclei on the bottom half of the tube wall were collected with 100 µL PBS with 0.04% BSA and 0.2 U/µL RNase inhibitor. Finally, nuclei were resuspended through a 30 µm strainer, and adjusted to 1000 nuclei/µL. snRNA-seq library preparation was carried out using the 10x Genomics Chromium Multiome ATAC + Gene Expression Kit Version 3. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 10,000 nuclei. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed. For spatial transcriptomics, we carried out two separate experiments to study the cytoarchitecture of the lesion microenvironment after SCI. First, we prepared sections from uninjured mice, 7 days and 2 months after crush SCI. For each experimental condition, we prepared sections from the lesion epicenter of three independent biological replicates. Second, to prepare our four-dimensional spatiotemporal atlas, we collected sections throughout the entire spinal cord of mice from each of the three experimental conditions. The spinal cord injury sites of mice were embedded in OCT and cryosections were generated at 10 µm at −20 °C. For the four-dimensional atlas, every fifth section was collected throughout the entire dorsoventral axis of each spinal cord. Sections were immediately placed on chilled Visium Tissue Optimization Slides or Visium Spatial Gene Expression Slides.
We used 10x Genomics Chromium Single Cell Gene Expression Kit Version 3.1 kit to profile the snRNA sequencing and Visium Spatial Gene Expression to profile the spatial transcriptomics.

tag: strain

tag: tissue

value: spinal cord

tag: condition

value: Methylprednisolone treatment

tag: genotype

value: wild type


title: ilc-17.1_rescue_replicate _3

city: Buffalo

first: Johnny

last: Cruz Corchado

state: NY

address: Elm & Carlton Streets Buffalo,L3-L125

department: Cell Stress

country: USA

institute: Roswell Park Comprehensive Cancer Institue

library_source: transcriptomic

organism: Caenorhabditis elegans

source_name: Whole Animal

value: Whole Animal


title: Mid thoracic spinal cord, drug_meth_4 (rnaseq)

description: 10x v3


title: FMN_14h_50J_0m 1

city: Rehovot

first: Shay

last: Covo

state: Central District

address: POB 12

department: Plant Pathology and Microbiology

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Raw data quality was assessed using FASTQC (Babraham Bioinformatics)
Raw reads were mapped against the F. mangiferae [GCA_900044065.1] reference genome using STAR version 2.5 (Dobin et al., 2013).
Reads were counted with with HTSeq (Anders et al., 2014).
Reads were assembled, normalized and gene-expression level was quantified using the DESeq2 R package (version 1.3.4) data-normalization method
Assembly: GCA_900044065.1
Supplementary files format and content: Excel file contaning normalized reads of all samples. file includes two sheets, each sheet contains samples for one of two time points; 8 h post innoculation (fmn_uv_8h_norm_counts) and 14 h post innoculation (fmn_uv_14h_norm_counts)

organism: Fusarium mangiferae

source_name: Germinating conidia

growth_protocol: Spores of F. mangiferae strain MRC7560 were incubated in KNO3-based medium on an orbital shaker (250 rpm) at 25 °C for 5 days. Microconidia were obtained by filtering the culture through a nylon cell strainer (mesh size 40 µm, Corning, USA) and resuspended in sterile water. Conidia were then inoculated into potato dextrose broth (PDB; BD Sparks, USA) at 1 x 108 conidia/ml. The cultures were incubated on an orbital shaker at 25 °C for either 8 or 14 h and then harvested immediately or treated as specified.

extract_protocol:
Germinating conidia / filaments were disrupted in a Minilys bead beater (Bertin Instruments, France) for 30 s at medium speed. Total RNA was extracted with the Qiagen (USA) RNeasy micro kit and was treated on-column with RQ1 RNase-free DNase (Promega, USA) to remove additional residues of genomic DNA. RNA quality was quantified by Agilent 2200 TapeStation machine using an RNA kit (Agilent Technologies, USA). For quantification, 1 µl RNA was quantified with a Qubit 2.0 Fluorometer and RNA BR kit (Life Technologies, USA).
cDNA libraries were prepared using 0.5 µg RNA with a QuantSeq 3ʹ mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, Austria) and were sequenced using the NextSeq 500 system (Illumina, USA) at the Center for Genomic Technologies of the Hebrew University of Jerusalem.

treatment_protocol: Spores or germlings of F. mangiferae (8 and 14 h post-inoculation) were obtained by filtering 10 ml of the cultures, and suspensions with 2 x 107 conidia/ml were irradiated with either 50 -200 J/m2 UV light (254 nm, 15 W lamp, Osram, Germany); the incident fluence was measured with a radiometer (YK-35UV, Digital Instruments, USA).

value: Germinating conidia

tag: cell type

value: Fungal asexual spore

value: WT

tag: treatment

value: 50J UVC + 0 m recovery at 14 hpi


title: TMD8_WIPI2_24hr_DMSO

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
36_TMD8_WIPI2_24hr_DMSO_S71

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 hg19 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
Assembly: hg19
Supplementary files format and content: Tab-delimited text files of median-shift normalized count of each gene and each sample

organism: Homo sapiens

source_name: cell line

growth_protocol: TMD8 cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
RNA wass extracted using the Qiagen AllPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The DLBCL cell line TMD8 was grown at 0.5 x 10^6 cells/ml and either treated  with vehicle (DMSO) or 25 nM acalabrutinib  for  24 hours. 2 x 10^6 cells were collected for each sample.

value: cell line

tag: cell line

value: human DLBCL cell line

value: Cas9 engineered, WIPI2 KO


title: FMN_14h_50J_60m 1

value: 50J UVC + 60 m recovery at 14 hpi


title: TMD8_ULK1_then2_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
30_TMD8_ULK1_then2_24hr_DMSO_S65

value: Cas9 engineered, ULK1 and ULK2 KO


title: Mid thoracic spinal cord, drug_gfp_9 (rnaseq)

description: 10x v3

value: GFP control


title: TMD8_ATG101_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
28_TMD8_ATG101_24hr_DMSO_S63

value: Cas9 engineered, ATG101 KO


title: ilc-17.1_deletion_replicate_4


title: FMN_14h_50J_30m 1

value: 50J UVC + 30 m recovery at 14 hpi


title: Mid thoracic spinal cord, drug_gfp_6 (rnaseq)

description: 10x v3


title: Mid thoracic spinal cord, drug_gfp_2 (rnaseq)

description: 10x v3


title: ilc-17.1_deletion_replicate_3


title: ilc-17.1_deletion_replicate_2


title: FMN_8h_200J_30m 2

value: 200J UVC + 30 m recovery at 8 hpi


title: TMD8_A20_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
26_TMD8_A20_24hr_DMSO_S61

value: Cas9 engineered, TNFAIP3 KO


title: TMD8_ULK2_then1_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
31_TMD8_ULK2_then1_24hr_DMSO_S66


title: ilc-17.1_rescue_replicate _2


title: Mid thoracic spinal cord, drug_chabc_8 (rnaseq)

description: 10x v3

value: spinal cord

value: ChABC treatment


title: N2_WT_replicate_4

value: Whole Animal


title: TMD8_ATG9A_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
29_TMD8_ATG9A_24hr_DMSO_S64

value: Cas9 engineered, ATG9A KO


title: FMN_8h_200J_30m 1

value: Germinating conidia

value: Fungal asexual spore


title: FMN_8h_200J_30m 3

value: WT


title: N2_WT_replicate_3


title: Mid thoracic spinal cord, drug_chabc_10 (rnaseq)

description: 10x v3

value: wild type


title: FMN_8h_50J_30m 3

value: 50J UVC + 30 m recovery at 8 hpi


title: N2_WT_replicate_2


title: FMN_8h_50J_30m 2


title: FMN_8h_50J_30m 1


title: 5885_23: Primary MEFs DM-2 B

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

description: Primary dm mef, clone2, replicate 2, passage 2

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (grcm38_snp_tran) using Hisat2
Hisat2 was run with default parameters but strandedness of the reads was taken into account.
Genecounts were generated using Itreecount that outputs the number of reads per gene for all samples.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: TP53-proficient MEFs

growth_protocol: MEFs were cultured in IMDM medium supplemented with 8% of Fetal Bovine Serum (FBS), 100 U/ml Penicillin, 100 µg/ml Streptomycin, 50 µM 2-Mercaptoethanol.

extract_protocol:
MEFs were trypsinised and collected in medium, washed once in PBS and lysed in RLT buffer supplemented with 10% 2-Mercaptoethanol. RNA was stored at -80C.
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: MEFs were plated in 10cm dishes in triplicates and RNA was isolated when cells reach 70% confluency.

value: Mouse embryonic fibroblasts

value: PCNAK164R/K164R;FancG-/- (DM)


title: HepG2_IP_Flag_3B-1

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

description:
Ribozero RNA
MX_Su21

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RIP-seq reads were aligned to the GRCh38 genome assembly using STAR
peaks were called using exomePeak.
the RIP peaks were annotated using an ad hoc perl script.
Assembly: GRCh38
Supplementary files format and content: peak files were generated using exomePeak

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA Clean & Concentrator-5 Kit (R1015, Zymo Research). 1.5 ug of input RNA and 0.25-1ug IP RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit following manufacturer's protocols.

treatment_protocol: HepG2 cells were infect with pmiRNA1-3XFlag-METTL16, pSIN4-3XFlag-eIF3a and pSIN4-3XFlag-eIF3b to obtain stable cell lines.

value: liver cancer cells

tag: rip antibody

value: Flag(F3165, Sigma-Aldrich)


title: FMN_8h_CTRL 2

value: Untreated at 8 hpi


title: HepG2_IP_3A_3A-2

description:
Ribozero RNA
MX_Su18

value: eIF3a(ab86146, Abcam)


title: 6056_21: Primary MEFS DM-1 C

description: Primary dm mef, clone1, replicate 3, passage 2


title: FMN_8h_CTRL 3


title: 5885_22: Primary MEFs DM-2 A

description: Primary dm mef, clone2, replicate 1, passage 2


title: Rabbit ear hypertrophic scar, 5-Fu injection, rep3

city: Wuhan

first: Huinan

last: Suo

state: Hubei Province

address: 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China

department: Dermatology

country: China

institute: Huazhong University of Science and Technology

description: Sample 12

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to OryCun3.0 using CLC genomic benchmork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fracion: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: OryCun3.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Oryctolagus cuniculus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and used for the construction of sequencing libraries.
RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The three rabbits without treatment were taken as the control group (NS). The other  rabbits with HS lesions were randomly divided into 3 groups (three rabbits in each group): HS, drug-loaded MNs, and 5-Fu injection. Administration started from the 22nd day after skin resection, once a week for 3 consecutive weeks (on the 22nd, 29th and 36th day). For NS and HS, no treatment was given. For drug-loaded MNs, one patch of drug-loaded MNs was used in each HS lesion. For 5-Fu injection, 0.1 mL of 5-Fu solution (120 μg) was injected in each HS lesion.

value: Rabbit ear hypertrophic scar

value: 5-Fu injection


title: 5885_24: Primary MEFs DM-2 C

description: Primary dm mef, clone2, replicate 3, passage 2


title: Rabbit ear hypertrophic scar, 5-Fu injection, rep2

description: Sample 11


title: Rabbit ear hypertrophic scar, 5-Fu injection, rep1

description: Sample 10


title: Mid thoracic spinal cord, drug_chabc_7 (rnaseq)

description: 10x v3

value: spinal cord


title: FMN_8h_CTRL 1


title: Rabbit ear hypertrophic scar, drug-loaded MNs, rep3

description: Sample 9

value: drug-loaded MNs


title: TMD8_NT_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
25_TMD8_NT_24hr_DMSO_S60

value: cell line

value: human DLBCL cell line

value: Cas9 engineered, control KO


title: HepG2_IP_3A_3A-1

description:
Ribozero RNA
MX_Su17


title: 6056_20: Primary MEFS DM-1 B

description: Primary dm mef, clone1, replicate 2, passage 2


title: Rabbit ear hypertrophic scar, drug-loaded MNs, rep2

description: Sample 8


title: HepG2_IP_Flag_3B-2

description:
Ribozero RNA
MX_Su22


title: nanoPARE Col0_Rec3

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
NanoPARE libraries were analyzed using the pipeline provided by the authors (http:/www.github.com/Gregor-Mendel-Institute/nanoPARE)
Assembly: Arabidopsis TAiR 10
Supplementary files format and content: tsv files with cleavage results

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized using ethanol and plated on MS agar (MES-buffered MS salts medium [Duchefa, Murashige & Skoog medium inc. vitamins/MES- MO255)], 1% sucrose, and 0.8% agar, pH 5.7). The seeds were then stratified for 2 days at 4°C in the dark and then transferred in 16h light/8h dark (20,5/17°C,70% humidity) growth chamber, under fluorescent light (Osram Biolux 58W/965)

extract_protocol:
Total RNA was extracted using Tri-Reagent according to the manufacturer’s instruction
We constructed the libraries using the nanoPARE protocol by Schon et al., 2018

treatment_protocol: 7-day old Col-0 seedling +/- 1hour treatment at 37°C (HS) and after an additional 2H period back at 22°C (Recovery)

value: Seedlings

value: Col 0

tag: developmental stage

value: Recovery


title: HepG2_Input 3A-2

description:
Ribozero RNA
MX_Su14


title: 6056_19: Primary MEFS DM-1 A

description: Primary dm mef, clone1, replicate 1, passage 2


title: Rabbit ear hypertrophic scar, drug-loaded MNs, rep1

description: Sample 7

value: WT


title: nanoPARE Col0_Rec2


title: HepG2_Input 3A-1

description:
Ribozero RNA
MX_Su13


title: HepG2_Input 3B-1

description:
Ribozero RNA
MX_Su19


title: HepG2_Input 3B-2

description:
Ribozero RNA
MX_Su20


title: 5885_18: Primary MEFs WT-2 C

description: Primary wt mef, clone2, replicate 3, passage 2

value: Mouse embryonic fibroblasts

value: PCNAWT/WT;FancG+/+ (WT)


title: nanoPARE Col0_Rec1


title: 5885_17: Primary MEFs WT-2 B

description: Primary wt mef, clone2, replicate 2, passage 2


title: Rabbit ear hypertrophic scar, without treatment, rep2

description: Sample 5

value: without treatment


title: HepG2_IP_Flag_ M16-2

description:
Ribozero RNA
MX_Su12

value: liver cancer cells

value: Flag(F3165, Sigma-Aldrich)


title: nanoPARE Col0_HS3

value: Heat shock


title: HepG2_IP_Flag_ M16-1

description:
Ribozero RNA
MX_Su11


title: Rabbit ear hypertrophic scar, without treatment, rep1

description: Sample 4

value: Rabbit ear hypertrophic scar


title: nanoPARE Col0_HS2


title: 6056_15: Primary MEFS WT-1 C

description: Primary wt mef, clone1, replicate 3, passage 2


title: HepG2_Input M16-2

description:
Ribozero RNA
MX_Su10


title: nanoPARE Col0_HS1


title: Rabbit ear normal skin, without treatment, rep3

description: Sample 3

value: Rabbit ear normal skin


title: HepG2_Input M16-1

description:
Ribozero RNA
MX_Su9


title: Rabbit ear normal skin, without treatment, rep2

description: Sample 2


title: sPCL13

city: Nantes

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq files into a single-end fastq file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: CD138 positive plasma cells

growth_protocol: Non applicable

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)
RNA-Seq (3'SRP)

treatment_protocol: Non applicable

value: untreated

value: CD138 positive plasma cells


title: 6056_14: Primary MEFS WT-1 B

description: Primary wt mef, clone1, replicate 2, passage 2


title: Rabbit ear normal skin, without treatment, rep1

description: Sample 1


title: nanoPARE Col0_C3

value: Control


title: nanoPARE Col0_C2


title: Rabbit ear hypertrophic scar, without treatment, rep3

description: Sample 6


title: 5885_12: p53KD MEFs DM-2 C

description: Immortalised dm mef, clone2, replicate 3, passage 2

source_name: TP53-deficient MEFs

value: PCNAK164R/K164R;FancG-/- (DM)


title: KJ10 Top2-AID Smc6-AID Nse4-AID Nse5-AID

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Assembly: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary files format and content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option . The total hic contact number of Hi-C samples was normalized  (see the manuscript for detail).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose, or 2 % galactose, as stated, and at 30°C if not stated otherwise.

extract_protocol:
Hi-C was performed as detailed in Jeppsson et al., 2022. Briefly, S. cerevisiae cells were crosslinked with 3 % formaldehyde for 20 minutes at room temperature. Following spheroplasting and gentle lysis, restriction digestion of crosslinked chromatin by DpnII (NEB, R0543M) was performed overnight at 37°C, after which the restriction enzyme was inactivated by incubation at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps were confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy. Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification were then performed as in Jeppsson et al., 2022.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014).

treatment_protocol: For synchronization in G1-phase, 3 μg ml-1 α-factor mating pheromone (Merck, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically. For G2/M cell cycle arrest, benomyl (Merck, 381586) was added to the YEPD media for a final concentration 80 µg ml-1. A complete G2/M-arrest of logarithmically growing cells was achieved after 90 minutes at 30°C, or 120 minutes at 23°C. For G2/M-arrest following synchronization in G1-phase, cells were released into benomyl-containing YEPD for 60 minutes. For depletion of Scc2, Wpl1, Top1, Smc6, Nse4, Nse5 and Top2 in Figures 1A, 1D, 4A, S10C, auxin (3-indoleacetic acid, 1 mM final concentration, Merck, I2886) and doxycycline (5 μg ml-1 final concentration, Merck, D9891) were added to simultaneously degrade the proteins and inhibit their transcription, respectively. For degradation of Smc5 and Smc6 in Figure S9C, auxin (3-indoleacetic acid, Merck, I2886) was added at a final concentration of 1 mM. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

value: Top2-AID Smc6-AID Nse4-AID Nse5-AID

value: Auxin+doxycycline


title: nanoPARE Col0_C1

value: Seedlings

value: Col 0


title: sPCL11


title: 5885_11: p53KD MEFs DM-2 B

description: Immortalised dm mef, clone2, replicate 2, passage 2


title: 5885_16: Primary MEFs WT-2 A

description: Primary wt mef, clone2, replicate 1, passage 2


title: sPCL10


title: RNA Col0_Rec3

data_processing:
RNAseq libraries were analyzed unsing the HISAT2 and StringTie pipeline (Pertea et al., 2016).
Assembly: Arabidopsis TAiR 10
Supplementary files format and content: Count file

extract_protocol:
Total RNA was extracted using Tri-Reagent according to the manufacturer’s instruction
We ocnstructed the libraries using the Samrt-Seq2 protocol as described in Picelli et al

value: Recovery


title: 5885_10: p53KD MEFs DM-2 A

description: Immortalised dm mef, clone2, replicate 1, passage 2

value: Mouse embryonic fibroblasts


title: KJ8 Smc6-AID Nse4-AID Nse5-AID

value: Smc6-AID Nse4-AID Nse5-AID


title: RNA Col0_Rec2


title: 6056_9: p53KD MEFS DM-1 C

description: Immortalised dm mef, clone1, replicate 3, passage 2


title: KJ6 WT

value: WT


title: sPCL9


title: RNA Col0_Rec1


title: 6056_8: p53KD MEFS DM-1 B

description: Immortalised dm mef, clone1, replicate 2, passage 2


title: 6056_13: Primary MEFS WT-1 A

description: Primary wt mef, clone1, replicate 1, passage 2

value: PCNAWT/WT;FancG+/+ (WT)


title: sPCL8


title: KJ61 top2-4 -b

value: G2/M-arrest following an S-phase at 35°C


title: 6056_7: p53KD MEFS DM-1 A

description: Immortalised dm mef, clone1, replicate 1, passage 2


title: RNA Col0_HS3

value: Heat shock


title: sPCL7


title: RNA Col0_HS2


title: KJ60 top2-4 -a


title: sPCL6


title: sPCL12


title: 5885_6: p53KD MEFs WT-2 C

description: Immortalised wt mef, clone2, replicate 3, passage 2


title: sPCL5


title: RNA Col0_HS1


title: KJ56 WT-a


title: sPCL4


title: KJ57 WT-b


title: 5885_5: p53KD MEFs WT-2 B

description: Immortalised wt mef, clone2, replicate 2, passage 2


title: KJ51 Smc5-AID Smc6-AID b

value: Smc5-AID Smc6-AID

value: Auxin


title: KJ7 Top2-AID


title: RNA Col0_C1


title: sPCL2

value: untreated


title: sPCL3

value: CD138 positive plasma cells


title: 6056_3: p53KD MEFS WT-1 C

description: Immortalised wt mef, clone1, replicate 3, passage 2


title: KJ49 WT b


title: sPCL1


title: 6056_1: p53KD MEFS WT-1 A

description: Immortalised wt mef, clone1, replicate 1, passage 2


title: WFS1 KO, scRNA-seq

city: Shanghai

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

description: DNBelab C4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBelab_C4_scRNA_v2.3
Assembly: GRCH38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: hES-derived islet organoid

extract_protocol:
SC-islets were dissociated into single cells with TrypLE and resuspended with DPBS with 0.5% fat-acid -free BSA. Added DNase I to eliminate the DNA released form the dead cells to prevent cell caking and placed the tubes containing cells on ice for preservation.
DNBelab C Series High-throughput Single-Cell RNA Library (MGI, #940-000047-00) was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 250-400 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the MGISEQ-2000RS with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.

value: hES-derived islet organoid


title: WT, scRNA-seq

description: DNBelab C4


title: KJ48 WT a


title: sample38_UOT5_24h

status: Public on Jan 29 2024

city: Hannover

first: Reinhold

last: Förster

address: Carl-Neuberg-Str. 1

department: Institute of Immunology

country: Germany

institute: Hannover Medical School

data_processing:
Raw fastq data was quality.controlled and filtered by BGI using the in-house software SOAPnuke with the following parameters: -n 0.01 -I 20 -q 0.4 -- adaMR 0.25 -- ada_trim -- polyX 50 -- minReadLen 150 to obtain cleaned data. Cleaned files were saved as fastq files.
Cleaned transcripts were mapped to the human genome using the pseudo-alignment software kallisto (0.46.1).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: comma separated values (csv) file with raw counts for each sample

source_name: Whole blood

extract_protocol:
RNA was isolated from PAXgene blood RNA tubes using Qiagen's BloodRNA Kit following manufacturer's protocol.
Samples were sent to BGI Genomics (Danmark branch) for library construction and sequencing. mRNA was enriched using oligo dT beads, and then fragemented. Fragmented RNA was reverse transcribed to double-strand cDNA using random primers.Synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these fragements before PCR amplification and purification. After quality control and library circulization, the library was amplified to make DNA nanoball (DNB). Finally, sequencing was conducted using the DNBSEQ platform.

value: Whole blood

tag: participant id

tag: response group

value: High-responder

tag: time point


title: sample36_SNX_14d

value: SNX

value: Low-responder


title: sample39_UOT5_48h


title: 5885_4: p53KD MEFs WT-2 A

description: Immortalised wt mef, clone2, replicate 1, passage 2


title: sample33_SNX_pre

value: pre


title: sample35_SNX_48h


title: RNA Col0_C3

value: Seedlings

value: Col 0

value: Control


title: sample32_4UE_14d


title: sample31_4UE_48h


title: sample30_4UE_24h


title: sample27_GV8A_48h


title: RNA Col0_C2


title: sample24_RRRS_14d

value: RRRS


title: sample21_RRRS_pre


title: sample29_4UE_pre


title: sample28_GV8A_14d


title: 6056_2: p53KD MEFS WT-1 B

description: Immortalised wt mef, clone1, replicate 2, passage 2

value: Mouse embryonic fibroblasts

value: PCNAWT/WT;FancG+/+ (WT)


title: sample26_GV8A_24h


title: sample15_54Z_48h


title: sample23_RRRS_48h


title: sample22_RRRS_24h


title: sample13_54Z_pre


title: sample19_RQSI_48h

value: RQSI


title: sample12_U9GI_14d


title: sample5_KSE3_pre


title: sample18_RQSI_24h


title: sample16_54Z_14d


title: sample20_RQSI_14d


title: sample10_U9GI_24h


title: sample11_U9GI_48h


title: sample4_QHMH_14d

value: QHMH


title: sample14_54Z_24h


title: sample9_U9GI_pre


title: sample1_QHMH_pre


title: sample7_KSE3_48h


title: sample6_KSE3_24h


title: Capture-MNase-seq_Probe2_231_DOX_12h_BRG1_shRNA-rep3

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

description: run1 MiSeq, run2 NextSeq 500

data_processing:
Adapter sequences were removed with cutadapt v1.2.1.
Reads were mapped to the hg19 genome using Bowtie 1.2 with paramters -m 1 -X 2000 --chunkmbs 1024.
Mapped hits were filtered to retain only those with fragment size 120-170bp.
Signal tracks were generated after collapsing mononucleosome-sized fragments to their midpoint coordinate, with conversion to bedGraph via Bedtools v2.17.0 genomeCoverageBed followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format

growth_protocol: DMEM High glucose + 10% FBS

extract_protocol:
MNase digested DNAs were purified by Phenol-chloroform extraction with ethanol precipitation
MNase-seq libraries were prepared by NEXTFLEX Rapid DNA-Seq kit (PerkinElmer).

treatment_protocol: For transient GATA3 expression, DOX (1 µg/ml at final) was added to medium. For CHD4 knockdown, MDA-MB-231 cells were infected with lentiviruses encoding CHD4 shRNA. After overnight incubation, the meidum was replaced with fresh medium and the cells were further incubated for 2 days until DOX induction.

tag: passages


title: Capture-MNase-seq_Probe2_231_DOX_12h_BRG1_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: sample8_KSE3_14d


title: Capture-MNase-seq_Probe2_231_DOX_12h_CHD4_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: sample3_QHMH_48h


title: sample2_QHMH_24h


title: Capture-MNase-seq_Probe2_231_DOX_12h_BRG1_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_12h_CHD4_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_12h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_6h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_12h_control_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: sample17_RQSI_pre


title: Capture-MNase-seq_Probe2_231_DOX_12h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_6h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_12h_CHD4_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_0h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_3h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_0h_control_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_3h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe2_231_DOX_0h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_BRG1_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_BRG1_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_CHD4_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_BRG1_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_CHD4_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_CHD4_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_control_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_12h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_6h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_3h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_6h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_0h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_0h_control_shRNA-rep3

description: run1 MiSeq, run2 NextSeq 500


title: Capture-MNase-seq_Probe1_231_DOX_0h_control_shRNA-rep1

description: run1 MiSeq, run2 NextSeq 500


title: KJ50 Smc5-AID Smc6-AID a

value: Smc5-AID Smc6-AID

value: Auxin


title: wildtype 25°C 0min Replicate3

city: Garching

first: Johannes

last: Buchner

state: Bavaria

address: Ernst-Otto-Fischer Strasse 8

department: Center for Protein Assemblies and Department of Chemistry

institute: Technische Universität München

data_processing:
Conversion to fastq: bcl2fastq (v.1.8.4) Reads were converted to Fastq using the bcl2fastq converter from Illumina.
Alignment (no processed files) : Contextmap2 (v.2.8.0) The quality controlled sequencing reads were aligned to the yeast reference genome (yeast genome 2011; R64-1-1 (Ensembl version 75)) (Howe et al., 2020) using the mapping tool Contextmap2 (v.2.8.0) (Bonfert et al., 2015).
Quantification: featureCounts (v.2.0.0) Gene quantification was performed using featureCounts (Liao et al., 2014) at the gene level to the corresponding yeast gene transfer format. A minimum fraction of 0.5 of overlapping bases were required for assigning a read to a feature and only primary alignments were considered.
DE analysis: DESeq2 (v.1.28.1)  These gene counts were normalized and further analysed by DESeq2 (v.1.28.1) (Anders and Huber, 2010) for pairwise differential expression. msn2Δ/msn4Δ, -Hsf1, -Hsf1/ msn2Δ/msn4Δ, and wild-type strains were always compared to the 25°C reference of the same strain, thereby eliminating/reducing strain bias. These pairwise fold changes are the basis for subsequent analysis of the dataset.  These gene counts were normalized and further analysed by DESeq2 (v.1.28.1) (Anders and Huber, 2010) for pairwise differential expression. msn2Δ/msn4Δ, -Hsf1, -Hsf1/ msn2Δ/msn4Δ, and wild-type strains were always compared to the 25°C reference of the same strain, thereby eliminating/reducing strain bias. These pairwise fold changes are the basis for subsequent analysis of the dataset.
Genome_build: yeast genome 2011
Genome_build: R64-1-1 (Ensembl version 75)
Supplementary_files_format_and_content: tsv / combined deseq results
Supplementary_files_format_and_content: Tab separated file; DESEQ fdr & log2fc of the used comparisons listed colwise
Supplementary_files_format_and_content: tsv / count file
Supplementary_files_format_and_content: Tab separated file; Rowise genes listed with information and featureCounts read counts

source_name: yeast heatshock

growth_protocol: W303 yeast cells were grown in YPD-A at 25 °C from an OD595 of 0.3 to an OD of 0.8 while shaking.

extract_protocol:
Total RNA was extracted using a modified protocol based on Collart and Oliviero, 1993. Briefly, shock frozen cells were suspended in TES buffer and acidic phenol was added.  The suspension was vigorously shaken for 30 min at 65°C. The total RNA was extracted by phase separation with the classic phenol-chloroform procedure.
Libraries were prepared with the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Cat. No. 001.96) according to the manufacturers instructions. Briefly, total RNA was denatured for 2 min at 60 °C and polyA RNA was captured. After reverse transcription and second strand synthesis libraries were amplified and quality assessment was performed. The finished libraries were sequenced on a Illumina HiSeq1500 as 50 bp single reads with an average sequencing depth of 15 million reads per sample.

treatment_protocol: Mid logarithmic W303 Hsf1-anchor away yeast cells and W303 Hsf1-anchor away msn2Δ/msn4Δ cells were cultivated for 45 min at 25°C after addition of DMSO or Rapamycin/DMSO for Hsf1 depletion (-Hsf1). Thereafter heat shock was performed both at 37°C and 42°C for 10 min or 30 min and 42°C, respectively. Immediately after treatment, cells were collected by centrifugation, briefly washed with PBS and shock frozen.

value: wildtype

tag: temperature

tag: time


title: -hsf1 25°C 0min Replicate3


title: -hsf1 37°C 30min Replicate3


title: wildtype 42°C 10min Replicate3


title: -hsf1 42°C 30min Replicate2


title: wildtype 37°C 30min Replicate2


title: -hsf1 37°C 10min Replicate3


title: -hsf1 37°C 30min Replicate2


title: -hsf1 42°C 30min Replicate1


title: Capture-MNase-seq_Probe1_231_DOX_3h_control_shRNA-rep2

description: run1 MiSeq, run2 NextSeq 500


title: -hsf1 37°C 10min Replicate2


title: -hsf1 25°C 0min Replicate1


title: wildtype 37°C 10min Replicate2


title: -hsf1 42°C 10min Replicate1


title: wildtype 37°C 10min Replicate1


title: wildtype 42°C 30min Replicate3


title: wildtype 42°C 30min Replicate1


title: -hsf1 42°C 30min Replicate3


title: wildtype 37°C 30min Replicate3


title: -hsf1 42°C 10min Replicate3


title: wildtype 42°C 30min Replicate2


title: -hsf1 42°C 10min Replicate2


title: -hsf1 37°C 10min Replicate1


title: wildtype 42°C 10min Replicate1


title: wildtype 42°C 10min Replicate2


title: wildtype 25°C 0min Replicate1


title: wildtype 25°C 0min Replicate2


title: -hsf1/msn2Δ/msn4Δ 25°C 0min Replicate3


title: wildtype 37°C 30min Replicate1


title: msn2Δ/msn4Δ 42°C 30min Replicate2


title: wildtype 37°C 10min Replicate3


title: msn2Δ/msn4Δ 37°C 10min Replicate2


title: -hsf1/msn2Δ/msn4Δ 42°C 30min Replicate2


title: msn2Δ/msn4Δ 42°C 10min Replicate1


title: -hsf1/msn2Δ/msn4Δ 42°C 10min Replicate2


title: -hsf1/msn2Δ/msn4Δ 37°C 10min Replicate3


title: msn2Δ/msn4Δ 42°C 30min Replicate1


title: msn2Δ/msn4Δ 25°C 0min Replicate2


title: msn2Δ/msn4Δ 25°C 0min Replicate3


title: -hsf1 37°C 30min Replicate1


title: -hsf1/msn2Δ/msn4Δ 42°C 30min Replicate3


title: msn2Δ/msn4Δ 42°C 10min Replicate3


title: -hsf1/msn2Δ/msn4Δ 37°C 30min Replicate3


title: msn2Δ/msn4Δ 37°C 30min Replicate2


title: -hsf1/msn2Δ/msn4Δ 37°C 10min Replicate2


title: msn2Δ/msn4Δ 37°C 30min Replicate3


title: msn2Δ/msn4Δ 42°C 30min Replicate3


title: -hsf1/msn2Δ/msn4Δ 25°C 0min Replicate1


title: -hsf1/msn2Δ/msn4Δ 42°C 10min Replicate3


title: msn2Δ/msn4Δ 42°C 10min Replicate2


title: msn2Δ/msn4Δ 37°C 10min Replicate3


title: msn2Δ/msn4Δ 37°C 10min Replicate1


title: -hsf1/msn2Δ/msn4Δ 37°C 30min Replicate2


title: -hsf1/msn2Δ/msn4Δ 42°C 10min Replicate1


title: -hsf1/msn2Δ/msn4Δ 25°C 0min Replicate2


title: -hsf1/msn2Δ/msn4Δ 42°C 30min Replicate1


title: -hsf1/msn2Δ/msn4Δ 37°C 10min Replicate1


title: msn2Δ/msn4Δ 25°C 0min Replicate1


title: H3 profile, normalization for whole worm HDA-1 binding profile in hcf-1(pk924) mutants, L4440, rep1

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

address: 520 Campus road

institute: Cornell University

description:
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_L4440_H3antibody_rep1

data_processing:
Adaptor sequences were trimmed and low quality reads were filtered out from sequencing files using Trim Galore! (v0.6.5) with the settings –paired –q 20 –fastqc.
Trimmed paired-end sequencing files were then aligned to the ce11/WBcel235 C. elegans reference genome using bowtie2 (v2.4.3) with the options –very-sensitive-local –no-unal –no-mixed –no-discordant –phred33 -p 4 -I 10 -X 700.
The individual bam files corresponding to two biological replicates were merged using the ‘samtools merge’ command in SAMTools.
Indexed bam files combined from both replicates were used for narrow peak calling with MACS2 (v2.1.4) using the settings -f BAM - g ce –call-summits –keep-dup all -q 0.01 -m 5 50 –nomodel. Peaks were called against a control track, representing a bam file with combined replicates of CUT&RUN experiments targeting either the tagged factor of interest in untagged control worms or H3 CUT&RUN in the same genotype run in parallel for normalization.
To generate bigwig files for visualization, combined bam files from both biological replicates were put through the ‘bamCompare’ command in deepTools (v3.3) with the settings –binSize 20 –operation log2 –scaleFactors Method None –normalizeUsing CPM –numberOfProcessors 8 –outFileFormat bigwig –smoothLength 60 –extendReads –centerReads, and with –bamfile2 representing a bam file with combined replicates of CUT&RUN experiments targeting either the tagged factor of interest in untagged control worms or H3 for normalization.
Assembly: WBcel235/ce11
Supplementary files format and content: bigWig and narrowPeakfiles (normalized to either antibody or H3 control files)
Library strategy: CUT&RUN

source_name: somatic and germline cells

growth_protocol: Worms were grown for ~48h at 25C until they reached the young adult/day 1 adult stage.

extract_protocol:
Worms were exposed to an SDS-DTT buffer to weaken their cuticle, then dounced in CUT&RUN wash buffer and the resulting worm/cell mixture was used for standard CUT&RUN protocol (See Emerson & Lee, 2022, Current Protocols, DOI: 10.1002/cpz1.445)
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina with 14 PCR cycles for amplification, as previously described (See Emerson & Lee, 2022, Current Protocols, DOI: 10.1002/cpz1.445)

value: somatic and germline cells

tag: diet

tag: antibody

value: H3 (abcam #ab1791)


title: msn2Δ/msn4Δ 37°C 30min Replicate1

tag: strain


title: H3 profile, normalization for whole worm HDA-1 binding profile in set-26(tm2467) mutants, L4440, rep1

description:
set-26mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_L4440_H3antibody_rep1


title: -hsf1/msn2Δ/msn4Δ 37°C 30min Replicate1


title: Whole worm HDA-1 binding profile in hcf-1(pk924) mutants, L4440, rep2

description:
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_L4440_HAantibody_rep2

value: HA (Cell Signaling #3724)


title: Whole worm HDA-1 binding profile in set-26(tm2467) mutants, L4440, rep2

description:
set-26mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_L4440_HAantibody_rep2


title: H3 profile, normalization for whole worm HDA-1 binding profile in hcf-1(pk924) mutants, L4440, rep2

description:
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_L4440_H3antibody_rep2


title: H3 profile, normalization for whole worm HDA-1 binding profile in set-26(tm2467) mutants, L4440, rep2

description:
set-26mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_L4440_H3antibody_rep2


title: Whole worm HDA-1 binding profile, L4440, rep1

description:
HDA-1.vs.H3_L4440_mergedreps.bigwig
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_L4440_HAantibody_rep1


title: H3 profile, normalization for whole worm HDA-1 binding profile, L4440, rep2

description:
HDA-1.vs.H3_L4440_mergedreps.bigwig
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_L4440_H3antibody_rep2


title: Whole worm HDA-1 binding profile in set-26(tm2467) mutants, L4440, rep1

description:
set-26mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_L4440_HAantibody_rep1


title: H3 profile, normalization for somatic HDA-1 binding in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep2

description:
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_glp-1RNAi_H3antibody_rep2

source_name: somatic cells

value: somatic cells

value: glp-1 RNAi


title: H3 profile, normalization for whole worm HDA-1 binding profile, L4440, rep1

description:
HDA-1.vs.H3_L4440_mergedreps.bigwig
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_L4440_H3antibody_rep1


title: Somatic HDA-1 binding profile in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep2

description:
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_glp-1RNAi_HAantibody_rep2


title: H3 profile, normalization for somatic HDA-1 binding, germline-less glp-1 RNAi, rep2

description:
HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_glp-1RNAi_H3antibody_rep2


title: Somatic HDA-1 binding profile in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep1

description:
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_glp-1RNAi_HAantibody_rep1


title: H3 profile, normalization for somatic HDA-1 binding in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep1

description:
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_glp-1RNAi_H3antibody_rep1


title: Somatic HDA-1 binding profile in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep2

description:
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_glp-1RNAi_HAantibody_rep2


title: H3 profile, normalization for somatic HDA-1 binding in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep2

description:
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
set-26HDA-1GFP_glp-1RNAi_H3antibody_rep2


title: H3 profile, normalization for somatic HDA-1 binding, germline-less glp-1 RNAi, rep1

description:
HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_glp-1RNAi_H3antibody_rep1


title: Whole worm HDA-1 binding profile in hcf-1(pk924) mutants, L4440, rep1

description:
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_L4440_HAantibody_rep1


title: Whole worm HDA-1 binding profile, L4440, rep2

description:
HDA-1.vs.H3_L4440_mergedreps.bigwig
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_L4440_HAantibody_rep2


title: Whole worm SET-26 binding profile in hcf-1(pk924) mutant, L4440, rep2

description:
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_L4440_HAantibody_rep2


title: H3 profile, normalization for whole worm SET-26 binding in hcf-1(pk924) mutant, L4440, rep1

description:
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_L4440_H3antibody_rep1


title: Somatic HDA-1 binding profile, germline-less glp-1 RNAi, rep1

description:
HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_glp-1RNAi_HAantibody_rep1


title: Somatic HDA-1 binding profile in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep1

description:
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_glp-1RNAi_HAantibody_rep1


title: Whole worm SET-26 binding profile in hcf-1(pk924) mutant, L4440, rep1

description:
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_L4440_HAantibody_rep1


title: H3 profile, normalization for whole worm SET-26 binding, L4440, rep1

description:
SET-26.vs.H3_L4440_MergedReps.bigwig
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
SET-26HA_L4440_H3antibody_rep1


title: H3 profile, normalization for whole worm SET-26 binding in hcf-1(pk924) mutant, L4440, rep2

description:
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_L4440_H3antibody_rep2


title: sample34_SNX_24h

tag: tissue

value: Whole blood

value: SNX

value: Low-responder


title: Whole worm SET-26 binding profile, L4440, rep1

description:
SET-26.vs.H3_L4440_MergedReps.bigwig
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
SET-26HA_L4440_HAantibody_rep1


title: H3 profile, normalization for somatic HDA-1 binding in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep1

description:
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
hcf-1HDA-1GFP_glp-1RNAi_H3antibody_rep1


title: Whole worm SET-26 binding profile, L4440, rep2

description:
SET-26.vs.H3_L4440_MergedReps.bigwig
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
SET-26HA_L4440_HAantibody_rep2


title: Somatic SET-26 binding profile in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep2

description:
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_glp-1RNAi_HAantibody_rep2


title: H3 profile, normalization for whole worm SET-26 binding, L4440, rep2

description:
SET-26.vs.H3_L4440_MergedReps.bigwig
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
SET-26HA_L4440_H3antibody_rep2


title: Somatic SET-26 binding profile in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep1

description:
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_glp-1RNAi_HAantibody_rep1


title: H3 profile, normalization for somatic SET-26 binding in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep2

description:
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_glp-1RNAi_H3antibody_rep2


title: H3 profile, normalization for somatic SET-26 binding, germline-less glp-1 RNAi, rep2

description:
SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
SET-26HA_glp-1RNAi_H3antibody_rep2


title: H3 profile, normalization for somatic SET-26 binding, germline-less glp-1 RNAi, rep1

description:
SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
SET-26HA_glp-1RNAi_H3antibody_rep1


title: Somatic SET-26 binding profile, germline-less glp-1 RNAi, rep2

description:
SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
SET-26HA_glp-1RNAi_HAantibody_rep2


title: Whole worm HCF-1 binding profile in set-26(tm2467) mutant, L4440, rep2

description:
set-26mutant_HCF-1.vs.H3_L4440_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_L4440_FLAGantibody_rep2

value: FLAG (ThermoFisher #MA1-91878) primary; Mouse IgG (Abcam #ab46540) secondary


title: Whole worm HCF-1 binding profile in set-26(tm2467) mutant, L4440, rep1

description:
set-26mutant_HCF-1.vs.H3_L4440_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_L4440_FLAGantibody_rep1


title: H3 profile, normalization for somatic SET-26 binding in hcf-1(pk924) mutant, germline-less glp-1 RNAi, rep1

description:
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
hcf-1SET-26HA_glp-1RNAi_H3antibody_rep1


title: H3 profile, normalization for whole worm HCF-1 binding profile, L4440, rep2

description:
HCF-1.vs.H3_L4440_MergedReps.bigwig
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_L4440_H3antibody_rep2


title: Somatic SET-26 binding profile, germline-less glp-1 RNAi, rep1

description:
SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
SET-26HA_glp-1RNAi_HAantibody_rep1


title: H3 profile, normalization for whole worm HCF-1 binding profile in set-26(tm2467) mutant, L4440, rep2

description:
set-26mutant_HCF-1.vs.H3_L4440_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_L4440_H3antibody_rep2


title: H3 profile, normalization for whole worm HCF-1 binding profile, L4440, rep1

description:
HCF-1.vs.H3_L4440_MergedReps.bigwig
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_L4440_H3antibody_rep1


title: Somatic HCF-1 binding profile in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep2

description:
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_glp1RNAi_FLAGantibody_rep2


title: Somatic HCF-1 binding profile in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep1

description:
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_glp-1RNAi_FLAGantibody_rep1


title: Whole worm HCF-1 binding profile, L4440, rep2

description:
HCF-1.vs.H3_L4440_MergedReps.bigwig
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_L4440_FLAGantibody_rep2


title: H3 profile, normalization for somatic HCF-1 binding in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep1

description:
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_glp-1RNAi_H3antibody_rep1


title: H3 profile, normalization for somatic HCF-1 binding in set-26(tm2467) mutant, germline-less glp-1 RNAi, rep2

description:
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_glp1RNAi_H3antibody_rep2


title: Whole worm HCF-1 binding profile, L4440, rep1

description:
HCF-1.vs.H3_L4440_MergedReps.bigwig
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_L4440_FLAGantibody_rep1


title: Somatic HCF-1 binding profile, germline-less glp-1 RNAi, rep 2

description:
HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_glp1RNAi_FLAGab_rep2


title: Antibody background, FLAG, whole worm background, rep 2

description:
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
N2_FLAGantibody_rep2


title: Somatic HCF-1 binding profile, germline-less glp-1 RNAi, rep 1

description:
HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_glp-1RNAi_FLAGantibody_rep1


title: H3 profile, normalization for somatic HCF-1 binding, germline-less glp-1 RNAi, rep1

description:
HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_glp-1RNAi_H3antibody_rep1


title: Antibody background, FLAG, whole worm background, rep 1

description:
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
N2_FLAGantibody_rep1


title: Antibody background, HA, whole worm background, rep 1 for SET-26 profile

description:
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
N2_HAantibody_rep1forSET26


title: H3 profile, normalization for somatic HCF-1 binding, germline-less glp-1 RNAi, rep2

description:
HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_glp1RNAi_H3antibody_rep2


title: Antibody background, HA, whole worm background, rep 1 for HDA-1 profile

description:
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
N2_HAantibody_rep1forHDA1


title: Antibody background, HA, whole worm background, rep 2

description:
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
N2_HAantibody_rep2


title: Whole worm HDA-1 binding profile, rep 2

description:
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1GFP_HAantibody_rep2


title: Whole worm HCF-1 binding profile, rep 2

description:
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_FLAGantibody_rep2


title: Whole worm HCF-1 binding profile, rep 1

description:
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1GFP_FLAGantibody_rep1


title: Whole worm HDA-1 binding profile, rep 1

description:
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1GFP_HAantibody_rep1


title: Antibody background, HA, germline-less glp-1(e2141) background, rep 2

description:
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HA background in glp-1 rep 2


title: Whole worm SET-26 binding profile, rep 1

description:
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
SET-26HA_HAantibody_rep1


title: Somatic HDA-1 binding profile, germline-less glp-1(e2141) background, rep 1

description:
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1GFPglp-1_HAantibody_rep1


title: H3 profile, normalization for somatic HCF-1 profile in set-26(tm2467) mutant, germline-less glp-1(e2141) backgrnd, rep1

description:
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFPglp-1_H3antibody_rep1


title: Somatic HCF-1 binding profile in set-26(tm2467) mutant, germline-less glp-1(e2141) background, rep2

description:
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFPglp-1_FLAGantibody_rep2


title: glp-1;hcf-1, hda-1 RNAi, day12, rep2

data_processing:
Adaptor sequences were trimmed and low quality reads were filtered out from sequencing files using Trim Galore! (v0.6.5) with the settings –q 20 –fastqc.
Trimmed sequencing files were then aligned to the ce11/WBcel235 C. elegans reference genome using STAR (v2.7.9a) with the options –runThreadN 2 –quantMode GeneCounts —-outFilterMultiMapNmax 1 –outFilterMismatchNmax 2 –outSAMtype BAM SortedByCoordinate.
The resulting tab delimited text files containing read count per gene, with column 3 (the middle column of counts) representing the correct counts for 3’ RNA-seq data, were used to create a matrix of gene expression to compare multiple samples.
Assembly: WBcel235/ce11
Supplementary files format and content: tab-delimited text files include read count per gene

growth_protocol: All worms were grown on empty vector L4440 bacteria for ~48h at 25C until they reached the young adult/day 1 adult stage. Then, worms were split between L4440 and hda-1 RNAi bacteria for aging. Samples were collected at day 1, day 3, and day 12 of adulthood. All worms were germline-less, representing somatic-only samples.

extract_protocol:
Worms were frozen in Tri Reagent, and RNA was isolated with chloroform and isopropanol. RNA was treated with Dnase (TURBO Dnase kit, Invitrogen, AM1907), and cleaned with ethanol precipitation before library preparation.
315ng RNA from each sample was used for QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) following the manufacturer’s instructions and using 13 PCR cycles.
3' mRNA-seq

value: hda-1 RNAi

value: day 12


title: Somatic HDA-1 binding profile, germline-less glp-1 RNAi, rep2

description:
HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak
HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt
HDA-1GFP_glp-1RNAi_HAantibody_rep2


title: Antibody background , FLAG, germline-less glp-1(e2141) background, rep 2

description:
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps.bigwig
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
FLAG background in glp-1 rep 2


title: Somatic HCF-1 binding profile, germline-less glp-1(e2141) background, rep 2

description:
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps.bigwig
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1GFPglp-1_FLAGantibody_rep2


title: Somatic SET-26 binding profile, germline-less glp-1(e2141) background, rep 2

description:
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
SET-26HAglp-1_Haantibody_rep2


title: Somatic HDA-1 binding profile, germline-less glp-1(e2141) background, rep 2

description:
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1GFPglp-1_HAantibody_rep2


title: Antibody background, FLAG, germline-less glp-1(e2141) background, rep 1

description:
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps.bigwig
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
FLAG background in glp-1 rep 1


title: glp-1, hda-1 RNAi, day 12, rep1


title: Whole worm SET-26 binding profile, rep 2

description:
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt
SET-26HA_HAantibody_rep2


title: glp-1;hcf-1, L4440, day12, rep2


title: H3 profile, normalization for whole worm HCF-1 binding profile in set-26(tm2467) mutant, L4440, rep1

description:
set-26mutant_HCF-1.vs.H3_L4440_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_L4440_H3antibody_rep1


title: glp-1;set-26, L4440, day12, rep2


title: Antibody background, HA, germline-less glp-1(e2141) background, rep 1

description:
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HA background in glp-1 rep 1


title: glp-1;set-26, L4440, day12, rep1


title: Somatic HCF-1 binding profile in set-26(tm2467) mutant, germline-less glp-1(e2141) background, rep1

description:
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFPglp-1_FLAGantibody_rep1


title: H3 profile, normalization for somatic HCF-1 binding, germline-less glp-1(e2141) background, rep1

description:
HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1GFPglp-1_H3antibody_rep1


title: glp-1;set-26, hda-1 RNAi, day12, rep1


title: glp-1;hcf-1, hda-1 RNAi, day3, rep2

value: day 3


title: Somatic HCF-1 binding profile, germline-less glp-1(e2141) background, rep 1

description:
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps.bigwig
HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1GFPglp-1_FLAGantibody_rep1


title: Somatic SET-26 binding profile, germline-less glp-1(e2141) background, rep 1

description:
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt
SET-26HAglp-1_Haantibody_rep1


title: glp-1;set-26, L4440, day3, rep2


title: glp-1, hda-1 RNAi, day 3, rep1


title: glp-1;hcf-1, L4440, day3, rep2


title: glp-1;hcf-1, L4440, day1, rep2

value: day 1


title: glp-1;hcf-1, L4440, day3, rep1


title: sample37_UOT5_pre

value: High-responder

value: pre


title: glp-1, hda-1 RNAi, day 12, rep2


title: glp-1;hcf-1, hda-1 RNAi, day12, rep1


title: glp-1, L4440, day 3, rep2


title: glp-1;hcf-1, L4440, day12, rep1


title: H3 profile, normalization for somatic HCF-1 profile, germline-less glp-1(e2141) background, rep2

description:
HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
HCF-1GFPglp-1_H3antibody_rep2


title: -hsf1 25°C 0min Replicate2


title: H3 profile, normalization for somatic HCF-1 profile in set-26(tm2467) mutant, germline-less glp-1(e2141) backgrnd, rep2

description:
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFPglp-1_H3antibody_rep2


title: glp-1;set-26, hda-1 RNAi, day12, rep2


title: glp-1, L4440, day 12, rep2


title: glp-1, L4440, day 12, rep1


title: glp-1;set-26, hda-1 RNAi, day3, rep2


title: glp-1;set-26, hda-1 RNAi, day3, rep1


title: glp-1, hda-1 RNAi, day 3, rep2


title: glp-1, L4440, day 3, rep1


title: glp-1;set-26, L4440, day3, rep1


title: glp-1;set-26, L4440, day1, rep2


title: glp-1;hcf-1, L4440, day1, rep1


title: glp-1;set-26, L4440, day1, rep1


title: glp-1, L4440, day 1, rep1


title: glp-1;hcf-1, hda-1 RNAi, day3, rep1


title: glp-1, L4440, day 1, rep2


title: Cal33_ALDH_plus_rep3

type: genomic

city: Dresden

first: Claudia

last: Peitzsch

address: Fetscherstr. 105

institute: Center for Regenerative Therapies Dresden (CRTD)

description: ALDH positive Cal33 cell subpopulation, replicate 3

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC V1 Beadchip using standard Illumina protocol.

scan_protocol: Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol.

data_processing: The data were normalised for red and green channel separately using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore.

label: Cy3 and Cy5

source_name: ALDH positive Cal33 cell subpopulation

label_protocol: Genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Orange, US) according to the manufacturer recommendations. Each sample was whole genome amplified and enzymatically fragmented following the instructions in the Illumina Infinium HD Assay Methylation Protocol Guide.

growth_protocol: The cell lines were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% L-Glutamine, 1% 2-(4-(2-Hydroxyethyl)-1-piperazinyl)-ethansulfonacid (HEPES), 1% minimum essential medium (MEM), 1% non-essential amino acid (NEAA), and 1% sodium pyruvate. All cell lines were used for experiments until passage 15, tested for mycoplasma infection and SNP-based cell authentication on a regular basis.

extract_protocol: Genomic DNA was isolated from each cell population with the Qiamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations.

treatment_protocol: Generation of radioresistant (RR) cells: Radioresistant sublines were generated from indicated parental cell lines via selection with at least 15 fractions of 4 Gy and analyzed together with age-matched controls.  Isolation of ALDH positive cell population: Cells were harvested with Accutase (Sigma-Aldrich) and stained with the Aldefluor assay (Stem cell technologies) according to the manufacture’s recommendatio. To exclude dead cells from the analysis, cells were additionally stained with the viability dye 7-Aminoactionomycin D (1:1000, Thermo Fisher). The samples were acquired with the BD FACSCelesta and analyzed with FlowJo software (version 10.9.0). The ALDH+ population was gated based on background fluorescence from the negative control, the diethylaminobenzaldehyde (DEAB) treated cells.

tag: gender

value: male

value: head and neck squamous cell carcinoma


title: Cal33_ALDH_plus_rep2

description: ALDH positive Cal33 cell subpopulation, replicate 2


title: FaDu_radioresistant_rep2

description: FaDu cell line, irradiated at least 15 times with 4 Gy, replicate 2


title: Cal33_ALDH_plus_rep1

description: ALDH positive Cal33 cell subpopulation, replicate 1


title: FaDu_ALDH_minus_rep1

description: ALDH negative FaDu cell subpopulation, replicate 1

source_name: ALDH negative FaDu cell subpopulation


title: FaDu_radioresistant_rep1

description: FaDu cell line, irradiated at least 15 times with 4 Gy, replicate 1


title: Cal33_ALDH_minus_rep2

description: ALDH negative Cal33 cell subpopulation, replicate 2

source_name: ALDH negative Cal33 cell subpopulation


title: FaDu_ALDH_minus_rep2

description: ALDH negative FaDu cell subpopulation, replicate 2


title: FaDu_ALDH_plus_rep1

description: ALDH positive FaDu cell subpopulation, replicate 1

source_name: ALDH positive FaDu cell subpopulation


title: Cal33_ALDH_minus_rep1

description: ALDH negative Cal33 cell subpopulation, replicate 1


title: Cal33_radioresistant_rep2

description: Cal33 cell line, irradiated at least 15 times with 4 Gy, replicate 2


title: Cal33_ALDH_minus_rep3

description: ALDH negative Cal33 cell subpopulation, replicate 3


title: FaDu_radioresistant_rep3

description: FaDu cell line, irradiated at least 15 times with 4 Gy, replicate 3


title: FaDu_ALDH_minus_rep3

description: ALDH negative FaDu cell subpopulation, replicate 3


title: genomic DNA from High-grade undifferentiated sarcoma/cellular mesoblastic neprhoma; case 38

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: Final integrated diagnosis of Mesenchimal EML4-NTRK3 rearranged neoplasia (high-grade)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from FFPE samples using Resnova MagPurix FFPE DNA Extraction Kit according to standard instructions

value: M

tag: sample type

value: DNA extracted from FFPE tissue

tag: study group


title: Cal33_parental_rep1

description: Cal33 cell line replicate 1

source_name: Cal33 cell line


title: Cal33_radioresistant_rep1

description: Cal33 cell line, irradiated at least 15 times with 4 Gy, replicate 1


title: Cal33_radioresistant_rep3

description: Cal33 cell line, irradiated at least 15 times with 4 Gy, replicate 3


title: FaDu_parental_rep2

description: FaDu cell line replicate 2

source_name: FaDu cell line


title: genomic DNA from High-grade infantile TRK-rearranged mesenchymal tumor; case 43

description: Final integrated diagnosis of Pediatric NTRK-rearranged spindle cell neoplasm


title: Cal33_parental_rep2

description: Cal33 cell line replicate 2


title: FaDu_parental_rep3

description: FaDu cell line replicate 3


title: FaDu_ALDH_plus_rep2

description: ALDH positive FaDu cell subpopulation, replicate 2


title: FaDu_parental_rep1

description: FaDu cell line replicate 1


title: genomic DNA from High-grade undifferentiated sarcoma; case 35

description: Final integrated diagnosis of High-grade undifferentiated spindle cell sarcoma

value: F


title: genomic DNA from Infantile Fibrosarcoma; case 37

description: Final integrated diagnosis of Mesenchimal low-grade myofibroblastic neoplasia

source_name: Infantile Fibrosarcoma; case 37


title: genomic DNA from TRK-rearranged mesenchymal tumor; case 42

description: Final integrated diagnosis of TRK-rearranged mesenchymal tumor


title: Cal33_parental_rep3

description: Cal33 cell line replicate 3


title: genomic DNA from Infantile Fibrosarcoma; case 39

description: Final integrated diagnosis of Mesenchimal CLIP-RAF rearranged neoplasia (low-grade)

source_name: Infantile Fibrosarcoma; case 39


title: genomic DNA from Infantile TRK-rearranged mesenchymal tumor; case 40

description: Final integrated diagnosis of Spindle cell mesenchimal RPBMS-NTRK3 rearranged neoplasia


title: genomic DNA from High-grade undifferentiated sarcoma; case 41

description: Final integrated diagnosis of High-grade undifferentiated pleomorphic sarcoma


title: genomic DNA from Infantile Fibrosarcoma; case 36

description: Final integrated diagnosis of Mesenchimal TPM3-NTRK rearranged neoplasia (low-grade)

source_name: Infantile Fibrosarcoma; case 36


title: genomic DNA from High-grade undifferentiated sarcoma; case 34


title: genomic DNA from MPNST; case 25

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 25


title: genomic DNA from MPNST; case 22

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 22


title: genomic DNA from Atypical Neurofibroma; case 30

description: Final integrated diagnosis of Atypical neurofibroma

source_name: Atypical Neurofibroma; case 30


title: genomic DNA from MPNST; case 23

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 23


title: genomic DNA from Malignant Triton Tumor/Rhabdomyosarcoma; case 27

description: Final integrated diagnosis of Rhabdomyosarcoma in NF1


title: genomic DNA from Atypical Neurofibroma; case 32

source_name: Atypical Neurofibroma; case 32


title: genomic DNA from MPNST; case 29

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 29


title: 5637_PAI1rs1050813_2

type: RNA

city: Los Angeles

first: Hideki

last: Furuya

address: 110 N. George Burns Road, Davis 2025

department: Surgery

institute: Cedars Sinai Medical Center

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: biotin

source_name: Human bladder cancer cell

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: UROtsa and 5637 were cultured in low glucose DMEM or RPMI1640 containing 10% FBS, 1% Penicillin-Streptomycin and incubated at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: PAI1-WT-pDEST26, PAI1- rs7242-pDEST26, or PAI1-rs1050813-pDEST26 were used as plasmid DNA. C125E01 in pDONR223 (Kind gift from Dr. Dominic Esposito, NIH/NCI) was also subcloned into pDEST26 (C125E01-pDEST26) and this plasmid was used as a negative control. Two µg of plasmid DNA was used for plasmid transfection using jetPRIME.

tag: cell type

value: Human bladder cancer cell

tag: transfection plasmid

value: PAI1 rs1050813 mutant


title: genomic DNA from MPNST; case 20

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 20


title: 5637_PAI1rs7242_2

tag: cell line

value: PAI1 rs7242 mutant


title: genomic DNA from MPNST; case 16

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 16


title: 5637_PAI1rs1050813_1


title: genomic DNA from Atypical Neurofibroma; case 28

source_name: Atypical Neurofibroma; case 28


title: genomic DNA from Atypical Neurofibroma; case 31

source_name: Atypical Neurofibroma; case 31


title: genomic DNA from MPNST; case 21

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 21


title: genomic DNA from MPNST; case 24

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 24


title: genomic DNA from MPNST; case 15

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 15


title: genomic DNA from Malignant Triton Tumor; case 12

description: Final integrated diagnosis of Spindle cell rhabdomyosarcoma, MYOD1-mutated

source_name: Malignant Triton Tumor; case 12


title: 5637_PAI1WT_2

value: PAI1 wild type


title: genomic DNA from MPNST; case 13

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 13


title: genomic DNA from MPNST; case 19

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 19


title: 5637_Mock_2

value: Mock


title: genomic DNA from MPNST; case 10

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 10


title: 5637_PAI1rs7242_1


title: genomic DNA from MPNST; case 5

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 5


title: genomic DNA from MPNST; case 7

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 7


title: genomic DNA from Atypical Neurofibroma; case 6

source_name: Atypical Neurofibroma; case 6


title: Papain_Br_CD11b_replicate3

city: Seattle

first: Michael

last: Gerner

state: WA

address: 750 Republican St

department: Immunology

institute: University of Washington

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.  The FASTQs were aligned to the GRCm38 mouse reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count.  QC and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCm38
Supplementary files format and content: 210408-P408-1_RawGeneCounts
Supplementary files format and content: 210408-P408-1_NormGeneCounts

source_name: Br

extract_protocol:
Cells were sorted on an Aria III (BD Biosciences) directly into reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA/
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: Mice were injected with 50µg papain and 10µg EaGFP in the ear or forepaw and draining LNs were harvested 48 hours later.

value: Br

value: MHC2-hi CD11c-int CD11b+ CD301b-

tag: mouse genotype

tag: treatment

value: Papain 48h


title: 5637_PAI1WT_1


title: Papain_Br_TN_replicate3

value: MHC2-hi CD11c-int CD11b- CD301b-


title: Papain_Br_CD301b_replicate3

value: MHC2-hi CD11c-int CD11b+ CD301b+


title: UROtsa_Mock_2

source_name: Human benign urothelial cell

value: UROtsa

value: Human benign urothelial cell


title: UROtsa_Mock_1


title: genomic DNA from MPNST; case 11

description: Final integrated diagnosis of BCOR-ITD sarcoma

source_name: MPNST; case 11


title: UROtsa_PAI1WT_1


title: Papain_Au_TN_replicate3

source_name: Au

value: Au


title: 5637_Mock_1

source_name: Human bladder cancer cell


title: Papain_Au_CD301b_replicate3


title: Papain_Au_CD11b_replicate3


title: UROtsa_PAI1rs1050813_2


title: Papain_Br_CD11b_replicate2


title: UROtsa_PAI1rs7242_2


title: Papain_Br_TN_replicate2


title: genomic DNA from MPNST; case 17

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 17


title: genomic DNA from MPNST; case 8

source_name: MPNST; case 8


title: genomic DNA from MPNST; case 14

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 14


title: Papain_Br_CD301b_replicate2


title: genomic DNA from Malignant Triton Tumor; case 3

description: Final integrated diagnosis of Malignant Triton Tumor in NF1

source_name: Malignant Triton Tumor; case 3


title: Papain_Au_CD11b_replicate2


title: UROtsa_PAI1rs7242_1


title: UROtsa_PAI1rs1050813_1


title: Papain_Au_CD301b_replicate2


title: Papain_Br_CD11b_replicate1


title: Papain_Br_TN_replicate1


title: Papain_Br_CD301b_replicate1


title: Papain_Au_CD11b_replicate1


title: Papain_Au_TN_replicate1


title: genomic DNA from MPNST; case 18

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 18


title: Papain_Au_CD301b_replicate1


title: Naïve_Br_TN_replicate3

value: Naive


title: Naïve_Br_CD11b_replicate3


title: Naïve_Br_CD301b_replicate3


title: Naïve_Au_CD11b_replicate3


title: Naïve_Au_CD301b_replicate3


title: Naïve_Br_TN_replicate2


title: Naïve_Au_CD11b_replicate2


title: Naïve_Au_TN_replicate2


title: Naïve_Au_CD301b_replicate2


title: Naïve_Br_TN_replicate1


title: Naïve_Au_TN_replicate1


title: Naïve_Au_CD11b_replicate1


title: Naïve_Au_CD301b_replicate1


title: HF-1 [RNA-seq]

city: Bronx

first: Deyou

last: Zheng

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm39) using STAR aligner (v2.7.9a). Expression levels of individual genes (from the GENCODE annotation v105, both coding and non-coding) were quantified using the RSEM software (v1.3.3) to estimate counts and TPMs (transcript per million). Differential expression analysis was performed using DESeq2 (v1.38.2) after genes with TPM < 1 in all samples were excluded. Genes reaching multiple test adjusted p-value < 0.05 and absolute fold change > 1.5 were considered to be significantly differentially expressed.
Assembly: mm39
Supplementary files format and content: text file for counts and TPMs

source_name: Skin epidermis

extract_protocol:
P60 TNC-CREER; tdTomato back skins were collected and subjected to 0.25% trypsin digestion for 60 minutes at 37ºC with 50 rpm shaking. 1:100 SCA1-Cy7 (Biolegend), 1:100 α6-integrin -FITC (Biolegend) and 1:500 EPCAM-APC (Biolegend) for 30 minutes on ice and washed twice with 1x DPBS before cell sorting. Touch dome cells (TD) was sorted as EPCAM (+), SCA1 (+), integrin α6 (+) and TOMATO (+). IFE were sorted as EPCAM (+), integrin α6 (+), SCA1 ( +) and TOMATO (-). Hair follicle cells were sorted as EPCAM (+), integrin α6 (+), SCA1(-) and TOMATO (-). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
To generate RNA-seq libraries, 50ng of total RNA was subjected to Poly(A) selection using Universal Plus mRNA-Seq with NuQuant (TECAN). Following elution, mRNA was subjected to fragmentation at 94ºC for 8min. First strand, second strand cDNA synthesis, end repair, adapter ligation and amplification were carried out using Universal Plus mRNA-Seq with NuQuant (TECAN) and by following manufacturer’s instructions.  The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced at GENEWIZ on the Illumina HiSeq platform, obtaining 150 nucleotide paired-end reads.

treatment_protocol: Mice were injected by Tamoxifen at 100ug/g body weight 2 times in 2 consecutive days at P51 and P52.

value: Epidermal cells

value: Skin epidermis

tag: age

value: Postnatal day 60

tag: strain background

tag: genotype

value: TNC-CREER; tdTomato

tag: cell subtype

value: HF


title: HF-2 [RNA-seq]


title: HF-3 [RNA-seq]


title: Naïve_Br_CD11b_replicate1


title: Touchdome-2 [RNA-seq]

value: Touchdome


title: Touchdome-3 [RNA-seq]


title: IFE-2 [RNA-seq]

value: IFE


title: Touchdome-1 [RNA-seq]


title: HF-2

description: tagmented DNA

data_processing:
Paired-end ATAC-seq reads were trimmed with trim_galore (v0.6.7; https://github.com/FelixKrueger/TrimGalore) and then mapped to the mouse genome (mm10) using the Bowtie2 (v2.4.5; option -X 2000 –no-mixed –no-discordant). Read pairs of mapping score >20 were kept for analysis and duplicated reads due to PCR amplification were removed by SAMtools (v1.9). MACS2 (v 2.2.7.1) were used to call peaks in paired-end mode and default options.
Assembly: mm10
Supplementary files format and content: peaks in bed format

extract_protocol:
P60 TNC-CREER; tdTomato back skins were collected and subjected to 0.25% trypsin digestion for 60 minutes at 37ºC with 50 rpm shaking. 1:100 SCA1-Cy7 (Biolegend), 1:100 α6-integrin -FITC (Biolegend) and 1:500 EPCAM-APC (Biolegend) for 30 minutes on ice and washed twice with 1x DPBS before cell sorting. Touch dome cells (TD) was sorted as EPCAM (+), SCA1 (+), integrin α6 (+) and TOMATO (+). IFE were sorted as EPCAM (+), integrin α6 (+), SCA1 ( +) and TOMATO (-). Hair follicle cells were sorted as EPCAM (+), integrin α6 (+), SCA1(-) and TOMATO (-). FACS-purified cells were collected directly into E-media, and cells sample preparation, tagmentation and PCR amplification of tagmented DNA was done using the ATAC-seq kit (Active Motif) .
50,000 FACS-purified cells were collected directly into E-media. Cells sample preparation, tagmentation and PCR amplification of tagmented DNA was done using the ATAC-seq kit (Active Motif).

treatment_protocol: TNC-CREER;tdTomato mice were injected by Tamoxifen at 100ug/g body weight 2 times in 2 consecutive days at P51 and P52.


title: IFE-1 [RNA-seq]


title: UROtsa_PAI1WT_2

value: PAI1 wild type


title: IFE-2

description: tagmented DNA


title: IFE-3 [RNA-seq]


title: genomic DNA from MPNST; case 26

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 26

value: M

value: DNA extracted from FFPE tissue


title: IFE-1

description: tagmented DNA


title: Naïve_Br_CD301b_replicate1

value: Br


title: Touchdome-2

description: tagmented DNA


title: Touchdome-1

description: tagmented DNA


title: HF-1

description: tagmented DNA


title: genomic DNA from MPNST; case 4

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 4


title: genomic DNA from Malignant Triton Tumor; case 2

description: Final integrated diagnosis of DICER1 syndrome-associated sarcoma

source_name: Malignant Triton Tumor; case 2


title: genomic DNA from MPNST; case 9

description: Final integrated diagnosis of MPNST

source_name: MPNST; case 9

value: F