title: Bovine,Hic,8c,rep3

data_processing:
For Hi-C libraries, paired-end raw reads underwent alignment, processing, and iterative correction via HiCPro (version 2.11.1b) (Servant, N. et al.,2015). Initially, sequencing reads were aligned to the reference genome using the "-s mapping" parameter. Post-mapping, removal of singleton, multi-mapped, dumped, dangling, self-circle paired-end reads, and PCR duplication occurred through HiC- Pro using the parameter “-s proc_hic”. Following this, files with “.bwt2pairs” and “.validPairs” suffixes from different libraries were combined. The raw inter- and intra- chromosomal contact maps were constructed, and ICE normalization was applied to these contact maps using HiC-Pro. The sequential execution of parameters included "-s merge_persample" for merging, "-s build_contact_maps" for map construction, and "-s ice_norm" for ICE normalization. Visualized contact matrices were generated at resolutions of 5-kb, 10-kb, 40-kb, and 100-kb using juicer tools v1.8.9102. To assess the correlation between biological condition replicates, Hi-C Stratum-adjusted Correlation Coefficients (SCC) were calculated using HiCRep software.
Assembly: bosTau9
Supplementary files format and content: validPairs files of each stage

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon).   Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), and 168-180 hpi (blastocyst). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
Small-scale in situ Hi-C (sis-Hi-C) libraries were generated with minor adjustments as outlined in previous protocols (Du, Z. et al. ,2017;Chen, X. et al.,2019). Oocytes or embryos were fixed with 1% formaldehyde at room temperature (RT) for 10 minutes, followed by quenching with glycine for an additional 10 minutes at RT. Fixed oocytes or embryos were incubated in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, and proteinase inhibitor) on ice for 15 minutes. Subsequently, samples were centrifuged at 3,000 rpm at 4°C for 5 minutes, and pelleted nuclei were resuspended in 15 μl molecular biology-grade water and 2.5 μl 10×NEB buffer 2, thoroughly mixed. Chromatin was solubilized in 2 μl 1% sodium dodecyl sulfate (SDS) and incubated at 62°C for 5 minutes. SDS was neutralized with 2.2 μl 10% Triton X-100 at 37°C for 30 minutes. Nuclei were then digested with 20 U MboI at 37°C for 5 hours, followed by incubation at 62°C for 20 minutes to inactivate MboI. Subsequently, the addition of fill-in mix (1 μl of 10 mM dCTP, 1 μl of 10 mM dGTP, 1 μl of 10 mM dTTP, 8 μl of 0.4 mM biotin-14-dATP, and 10U Klenow) facilitated the biotinylation of DNA, with samples incubated at 37°C for 30 minutes. Ligation mix (49.8 μl of water, 10 μl of 10×NEB T4 DNA ligase buffer, 0.5 μl 20 mg/mL BSA, 1 μl of 400 U/μl T4 DNA ligase) was added, and the fragments were ligated at 16°C for 16 hours with rotation. After the reversal of crosslinking, DNA purification was performed using phenol-chloroform extraction and ethanol precipitation. To fragment DNA ligation products, samples were treated with 1 U AluI at 37°C for 4 hours, followed by DNA purification. The fragments were then subjected to Illumina library preparation. The fragmented DNA was treated with the End Repair/dA-Tailing Module and Ligation Module following the KAPA hyper kit (Roche, KR0961) operation manual. The biotin-labeled DNA was captured using Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65001). The Hi-C library underwent 12- 16 cycles of PCR amplification with KAPA HiFi HotStart ReadyMix. Finally, size selection was achieved using AMPure XP beads, with fragments ranging from 200 bp to 1,000 bp being selected. All libraries were sequenced on Illumina Novaseq6000, following the manufacturer's instructions.


title: TRANSATRA Patient 05-001 day 20

status: Public on May 01 2025

type: SRA

city: Freiburg im Breisgau

first: Michael

last: Kruszewski

state: Baden-Württemberg

address: Hugstetter Str. 55

country: Germany

institute: Universitätsklinikum Freiburg

library_source: transcriptomic

data_processing:
Read quality was checked with FastQC (≥95% >Q30), alignment to the reference genome GRCh38/hg38 was performed with STAR aligner and read-counting was performed with featureCounts.
Each sample counts file was then fed to DESeq2 (16) to obtain the results file for treated samples vs screening timepoint. Differentially expressed genes (DEG)s were found by filtering genes with adjusted p value <0.05 and Log2 fold change >abs (0.6).
The result file is ranked using sign[log2fold]*Log10[p-adj] as suggested by Galaxy FGSEA tutorial before using them as input for FGSEA on the MSigDB Hallmark pathways database.
All analysis steps till here are calculated on the European Galaxy instance (https://usegalaxy.eu/) (17). The results files were further sorted, filtered, and plotted (Heatmap and Volcano plot) using Pandas, scikit, Matplotlib and the Seaborn library of Python.
Assembly: reference genome GRCh38/hg38
Supplementary files format and content: text file contianing raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
enrichment of blasts: aMACS sort for CD34 and CD117 positive cells, (Miltenyi: CD34 MicroBead Kit, human, #130-046-702, CD117 MicroBead Kit, human, # 130-091-332)total RNA isolation: Machery&Nagel Kit, NucleoSpin RNA, #740955.250
Library prep: Illumina, TruSeq Stranded Total RNA Library Prep Gold, Read: length 2x75, Depth 100 M

tag: tissue

value: peripheral blood

tag: cell type

value: non-M3 acute myeloid leukemia blasts


title: Y-Ctrl, Hip, snRNAseq

city: Shanghai

first: Kai

last: Zhang

address: No. 600 Yishan Road

country: China

institute: Shanghai Jiao Tong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Hippocampus (brain)

extract_protocol:
The hippocampus and neocortex were separately dissected from the Y-Ctrl, O-Ctrl, and O-Ex mice. In brief, fresh frozen hippocampus and neocortex were separately homogenized in about 1 mL of homogenization buffer using a freezing multi-sample tissue grinding system. Homogenization buffer contained 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 1 mM DTT (dithiothreitol), 1x protease inhibitor, 0.4 U/µL RNaseIn, 0.2 U/µl SUPERaseIn, 0.1% Triton X-100 in nuclease-free water (v/v), and 10 ng/mL Hoechst 33342 (Thermo Fisher Scientific). After being filtered through a 40-µm filter, nuclei were centrifuged at the speed of 500 ´ g for 5 min at 4℃, and resuspended in 0.1x PBS supplemented with 4% BSA and 0.2 U/µl protector RNaseIn. Nuclei positive for Hoechst 33342 were sorted by FACSAria (BD Biosciences) and counted by a dual fluorescence cell counter (Luna-FLTM. Logo Biosystems). The extracted nuclei were subjected to single-nuclei capture using the 10X Genomics Single Cell 3’ system. Approximately 15,000 nuclei per sample were captured according to the 10x capture and library preparation protocol (10x Genomics) and sequenced in a NovaSed 6000 Sequencing system according to the manufacturer’s instructions (Illumina).
Approximately 15,000 nuclei per sample were captured according to the 10x capture and library preparation protocol (10x Genomics) and sequenced in a NovaSed 6000 Sequencing system according to the manufacturer’s instructions (Illumina).

value: Hippocampus (brain)

value: Brain cells

tag: genotype

tag: treatment

value: Control


title: Exp-V6K_7A_Cell-HaCaT_Power-10_Frequency-40.5_Time-48_Treatment-sham

type: genomic

city: Bremen

first: Jyoti

last: Jyoti

state: Bremen

address: Campus Ring 6

department: School of Science

institute: Constructor University

description:
S69
P10_HaCat_Beta_detP.txt-S69
P10_HaCat_Beta_detP.txt

hyb_protocol: The microarray hybridization was performed according to the Infinium HD Assay Methylation Protocol Guide (Illumina, Inc.). The bisulfite-converted DNA samples were hybridized at 48°C for 16 hrs on separate Illumina Infinium MethylationEPIC Arrays. DNA fragments anneal to locus-specific 50 mers which are covalently linked to different bead types. After hybridization and washing of the microarrays, the primers on the BeadChips were extended complementary to the binding DNA sample. This reaction incorporates labelled nucleotides. Incorporation of a G corresponds to the methylated state, A to the unmethylated state on the complementary strand. Allele-specific single base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labelled nucleotide (C and G nucleotides are biotin labelled; A and T nucleotides are dinitrophenyl labelled.). Hybridized DNA was then removed and the labelled extended primers were stained and dried.

scan_protocol: Fluorescent signal intensities of the labelled and stained nucleotides on the BeadChips were detected with a dual color channel approach and the Illumina iScan™ System.

data_processing:
The software tool GenomeStudio V2011.1 (Illumina, Inc.) including the Methylation Module Version 1.9.0 was used for quality control and visualization of the performance of microarray analysis as well as for methylation analysis. Raw microarray data were imported into GenomeStudio V2011.1 and analyzed without normalization.
Beta Values with depection P values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: HaCaT

label_protocol: Illumina protocol

growth_protocol: Cells were cultured in DMEM, high glucose, supplemented with 10% FBS and 1% penicillin streptomycin in an incubator with 37°C, 5% CO2 and saturated humidity.

extract_protocol:
To keep the homogeneity of the transmitting power flux density or SAR as high as possible, the cells outside a defined area were excluded during harvesting. After exposure, the medium of the cell dishes was discarded and a template made with a 3D printer (at 27 GHz an ellipse with a radius of 24 mm/23 mm; at 40.5 GHz a capped circle with a radius of 24 mm and a distance of the capped area to the center of 19 mm) was applied to the outside of the bottom of the dish and the areas to be omitted were marked. The cells were removed according to the marking with a cell scraper and the cell monolayer was then rinsed twice with PBS.
Cells were harvested by washing the remaining cell monolayer once with PBS and transferring 350 ul lysis buffer to each of the dishes. The cell lysates were collected using a cell scraper and transferring them into reaction tubes. The lysates were frozen at -80C until further processing. DNA and RNA extraction was done using the DNA/RNA Allprep Mini Kit (Qiagen) or the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol:
For each exposure experiment 120,000 HDF or 200,000 HaCaT cells were seeded onto a 60 mm cell culture dish. Cells were used in passages 6-7 (HDF) and 35 (HaCaT). One day (48h experiments) or three days (2h experiments) after seeding, the dishes were transferred to the exposure incubators and cells were exposed or sham-exposed for 2h or 48h, with a frequency of 27 GHz or 40.5 GHz, and a power flux density of 1 mW/cm2 or 10 mW/cm2. In all experiments, the temperature was measured continuously using a fiber optic sensor. The internal temperature of the incubator in which the exposure takes place was reduced in the 10 mW/cm2 experiments manually, so that an average temperature of 37C could be maintained in the petri dishes and a lid heater was used to prevent condensation in the exposed petri dish and maintain blinding conditions.
Temperature controls: Cells were exposed or sham exposed at 40.5 GHz and 10 mW/cm2 for 48h without compensating for the temperature increase. The starting temperature of the medium was 37.0C in these experiments and increased to an average of 38.3C in the exposed samples. No lid heaters were used, so that the heating of the medium in the exposed samples led to medium condensation.
UV controls: Three replicates each of HaCaT and HDF cells were exposed or sham-exposed at a wavelength of 254 nm and an illuminance of 1 mW/cm2. The medium was removed and collected, rinsed twice with PBS and the cells were thinly coated with 600 ul PBS per dish. Exposure was performed without the dish lid for 20 sec, for sham exposure the dishes were stored in the dark at room temperature. The PBS was then aspirated, the cells were layered with the previously collected medium, and incubated for 2h at 37C and 5%CO2.

tag: cell line

value: HaCaT

value: sham

tag: column header in matrix processed file

tag: date

tag: trial

tag: incubator

value: A

tag: frequency [ghz]

tag: power [mw/cm2]

tag: exposuretime [hr]

tag: batch

tag: aliquot

tag: passage

value: b

value: a


title: TRANSATRA Patient 05-001 screening


title: Exp-V6K_7B_Cell-HaCaT_Power-10_Frequency-40.5_Time-48_Treatment-exposed

description:
S70
P10_HaCat_Beta_detP.txt-S70
P10_HaCat_Beta_detP.txt

value: exposed

value: B


title: Y-Ctrl, Ctx, snRNAseq

description: 10x Genomics

source_name: Neocortex (brain)

value: Neocortex (brain)


title: Exp-V5K_4B_Cell-HaCaT_Power-10_Frequency-27_Time-48_Treatment-exposed

description:
S68
P10_HaCat_Beta_detP.txt-S68
P10_HaCat_Beta_detP.txt


title: Bovine,Hic,8c,rep2

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

library_source: genomic

organism: Bos taurus


title: Bovine,Hic,8c,rep1


title: TRANSATRA Patient 03-001 screening


title: TRANSATRA Patient 01-002 EOT


title: Exp-V5K_4A_Cell-HaCaT_Power-10_Frequency-27_Time-48_Treatment-sham

description:
S67
P10_HaCat_Beta_detP.txt-S67
P10_HaCat_Beta_detP.txt


title: Exp-V5K_3B_Cell-HaCaT_Power-10_Frequency-27_Time-48_Treatment-exposed

description:
S66
P10_HaCat_Beta_detP.txt-S66
P10_HaCat_Beta_detP.txt

value: c


title: TRANSATRA Patient 05-001 day 56


title: Bovine,Hic,Ama4c,rep2

value: alpha-Amanitin


title: Bovine,Hic,Ama4c,rep1


title: Cd24a+ 10X Genomics scRNAseq

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

description: 10x Genomics

data_processing:
Raw data was processed using the Cell Ranger pipeline (cellranger-7.1.0) to generate gene-barcode matrices. Quality control was performed using Seurat (version 5.1.0) to filter out cells with low gene counts, high mitochondrial gene content, and potential doublets.
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz,features tsv.gz,matrix.mtx.gz

source_name: Cells isolated from primary tissues

extract_protocol:
Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.
Cell counting and viability confirmation were performed using the Countess II Automated Cell Counter (Thermo Fisher, AMQAX1000). Samples were then utilized for single-cell RNA sequencing with the 10x Genomics system

value: dental mesenchymal stem cells

value: Cells isolated from primary tissues

tag: strain

value: Cd24a-CreERT2; tdT mice

tag: age

value: 9days old


title: O-Ctrl, Ctx, snRNAseq

description: 10x Genomics

tag: tissue


title: Exp-V5K_3A_Cell-HaCaT_Power-10_Frequency-27_Time-48_Treatment-sham

description:
S65
P10_HaCat_Beta_detP.txt-S65
P10_HaCat_Beta_detP.txt


title: Bovine,Hic,Ama8c,rep2

tag: cell type


title: Bovine,RNA-seq,GV,rep1

data_processing:
We aligned all RNA-seq datasets to distinct genomes (bovine, bosTau9) utilizing Hisat2 v2.1.1. The quantification of gene expression was subsequently performed using StringTie 2.2.1.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

source_name: GV

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
For the generation of Smart-seq2 libraries, zona pellucida-free oocytes or embryos lysis in a 708 buffer containing RNase inhibitor, following the Smart-seq2 protocol as described (Picelli,2013). After completion of purification and fragmentation, the library was quantificatied and sequenced.

value: GV


title: TRANSATRA Patient 01-002 day 20

value: peripheral blood

value: non-M3 acute myeloid leukemia blasts


title: TRANSATRA Patient 01-002 day 28


title: O-Ex, Hip, snRNAseq

description: 10x Genomics

value: Hippocampus (brain)

value: Brain cells

tag: genotype

value: Exercise


title: O-Ex, Ctx, snRNAseq

description: 10x Genomics

tag: treatment


title: Bovine,Hic,Ama8c,rep1


title: LL_5

city: Groningen

first: Bart

middle: J L

last: Eggen

address: Antonius Deusinglaan 2

department: Biomedical Sciences

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Sequencing data were pre-processed using a GenomeScan RNA-seq pipeline, which includes library preparation and raw data quality control (FastQC v0.11.9) and in-house (FastQA v3.1.25) QC tools)
unique molecule identifier (UMI) processing, adapter trimming (cutadapt v2.10)
alignment of short reads to the reference mouse genome (GRCm39) (Tophat v2-2.1, samtools v1.10, Picard v2.13.2)
and feature counting (HTSeq v0.11.0).
Assembly: mouse genome (GRCm39)
Supplementary files format and content: comma separated values (csv) file with metadata table for samples
Supplementary files format and content: comma separated values (csv) file with gene raw count data for each sample

molecule: polyA RNA

source_name: brain

growth_protocol: Microglia were isolated as previously described (Galatro et al., 2017b). After transcardiac perfusion with PBS, brains were removed from the skull and kept in cold medium A (HBSS (Gibco, 14170-088) with 0.6% glucose (Sigma, G8769) and 7.5 mM HEPES (Lonza, BE17-737E)). The olfactory bulbs were removed prior to mechanical dissociation of the tissue. All subsequent steps were performed on ice, and centrifugation was at 4°C. Brains were dissociated using a glass Potter–Elvehjem tissue homogenizer until a single cell suspension was obtained and filtered through a 70 µm cell strainer (Corning, 21008-950), to obtain a total cell suspension of 15 mL in medium A. Cells were pelleted by centrifugation at 300 RCF for 10 minutes. Myelin was removed by 24% Percoll (Fisher Scientific, 17-0891-01) in medium A (1x final concentration) and PBS density gradient centrifugation for 20 minutes at 950 RCF with brakes off. The microglia enriched cell pellet was resuspended in medium A and incubated with CD11b-PE (1:166 dilution, clone M1/70, eBiosciences, 12-0112-82), CD45-FITC (1:200 dilution, clone 30-F11, eBiosciences, 11-0451-82), and Ly6c-APC (1:133 dilution, clone HK1.4, Biolegend, 128016) antibodies for 30 min on ice. The cells were then washed once in medium A without phenol red and passed through a 35-μm nylon mesh, collected in fluorescence-activated cell sorting (FACS) round bottom tubes (Corning, 352235). Immediately before sorting, 1 µL of DAPI (200 µg/mL stock solution) per 100 µL cell suspension was added to the samples (final concentration 0.2 µg/mL). Microglia were sorted by gating single DAPInegCD11bhighCD45intLy6cneg events (Sup Fig 3 A) using the Beckman Coulter MoFlo Astrios or MoFlo XDP FACS sorters. Sorted microglia were collected in siliconized polypropylene microcentrifuge tubes (Sigma, T3406-250EA) containing medium A for further RNA extraction or assay for transposase-accessible chromatin (ATAC).

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro kit (Qiagen, 74034) according to the manufacturer’s protocol. The integrity and concentration of RNA isolated from microglia were determined using Qubit™ RNA High Sensitivity assay (HS) (Invitrogen, Q32852) and High Sensitivity RNA ScreenTape assay on a 4200 TapeStation system (Agilent) at the Research Sequencing Facility (European Institute for the Biology of Ageing, ERIBA/UMCG).
Library preparation and sequencing services were outsourced to GenomeScan (Leiden, The Netherlands). Briefly, at GenomeScan, entry quality control (QC) was performed using a Fragment Analyzer, followed by library preparation using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420, New England BioLabs). cDNA libraries were sequenced on a NovaSeq6000 sequencer (Illumina).

treatment_protocol: C57BL/6J (Envigo) mice were used in the model for recurrent lipopolysaccharides (LPS)-induced peripheral inflammation and a cycle of enforced microglia repopulation (Fig 1 A, Fig 2 A). Animals were housed in standard macrolon cages with open tops, with ad libitum access to water and food, in a 12h dark/light cycle (lights on 8:00 am). All animal procedures were approved by the national authority for scientific procedures on animals (Centrale Commissie Dierproeven, CCD) and performed per ethical regulations (CCD license number AVD105002015360). Animals were group-housed throughout the experiment, with an acclimatization period of two weeks before the start of the experiment. 10-week-old male mice were challenged with 1 mg/kg intraperitoneal (i.p.) LPS from Escherichia coli O111:B4 (Sigma-Aldrich, L4391) and were housed in warming cabinets  (26 C) for the following two to three days until body weight returned to baseline. For unchallenged (PP, PBP) and naïve (PL, PBL) mice, sham injections consisted of the same volume/body mass of Dulbecco’s phosphate-buffered saline (DPBS) (Gibco, 14190-144). A week after the first challenge, microglia depletion was induced by colony-stimulating factor 1 receptor (CSF1R) inhibition for five days. Microglia depletion was established with daily administration via oral gavage of the CSF1R inhibitor (CSF1Ri) 4-((2-(((1R,2R)-2-hydroxycyclohexyl)amino)benzo[d]thiazol-6-yl)oxy)-N-methylpicolinamide (BLZ945 or Sotuletinib) (kindly provided by Novartis) at a dosage of 169 mg/kg per day (total cumulative dose of 845 mg/kg over the five days). Control (non-depleted) animals were treated with the same volume/body mass of vehicle containing 20% (w/v) 2-hydroxypropyl-beta-cyclodextrin (HPβCD). For the pilot experiment (Fig 1), mice were sacrificed on day 5 of BLZ945 treatment or 10 days after BLZ945 withdrawal (5 d + 10 d). For the main experiment (Fig 2 A), five weeks after the initial challenge, mice were similarly re-challenged with 1 mg/kg LPS (i.p.) and housed in warming cabinets for three hours before transcardiac perfusion under deep anesthesia (4% isoflurane with 7.5% O2) with cold saline (DPBS) and brain tissue collection. 100000 microglia cells were isolated via FACS and followed by RNA extraction for RNA-seq.

value: brain

tag: age (weeks)

tag: Sex

value: male

value: microglia

tag: challenge

value: vehicle

tag: facs sorter

value: XDP


title: Exp-V5K_2A_Cell-HaCaT_Power-10_Frequency-27_Time-48_Treatment-sham

description:
S63
P10_HaCat_Beta_detP.txt-S63
P10_HaCat_Beta_detP.txt

tag: cell line

value: HaCaT

value: sham

tag: column header in matrix processed file

tag: date

tag: trial

tag: incubator

value: A

value: b

value: a


title: TRANSATRA Patient 01-002 day 10


title: Bovine,Hic,GV,rep2


title: TRANSATRA Patient 03-001 day 28


title: TRANSATRA Patient 01-002 screening


title: Exp-V8K_6B_Cell-HaCaT_Power-10_Frequency-27_Time-2_Treatment-exposed

description:
S62
P10_HaCat_Beta_detP.txt-S62
P10_HaCat_Beta_detP.txt

value: exposed

value: B

tag: frequency [ghz]

tag: power [mw/cm2]

tag: exposuretime [hr]

tag: batch

tag: aliquot


title: O-Ctrl, Hip, snRNAseq

description: 10x Genomics

tag: tissue

tag: cell type

value: Control


title: Bovine,Hic,GV,rep1

value: GV


title: Exp-V8K_6A_Cell-HaCaT_Power-10_Frequency-27_Time-2_Treatment-sham

description:
S61
P10_HaCat_Beta_detP.txt-S61
P10_HaCat_Beta_detP.txt

tag: treatment

tag: passage


title: U937 cells, Ethacrynic acid, Day 3, rep 3

first: Xiaona

last: Wei

address: Shanghai Jiaotong University, Shanghai, China

institute: Shanghai Jiaotong University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: The mapped reads of each sample were assembled using StringTie (version:1.3.4d) with default parameters.
Supplementary files format and content: After the final transcriptome was generated, StringTie (version:1.3.4d) and was used to estimate the expression levels of all transcripts.

source_name: U937 cells

growth_protocol: U937 cells were maintained in RPMI 1640 medium supplemented with 10% fetal calf serum (FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37 ℃

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). 1μg total RNA was used for the consruction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: U937 cells were treated Ethacrynic acid for 2 days

value: U937 cells

value: AML

value: Ethacyrnic acid


title: LL_2

value: brain

tag: age (weeks)

tag: Sex


title: Bovine,Hic,4c,rep1


title: Exp-V8K_5A_Cell-HaCaT_Power-10_Frequency-27_Time-2_Treatment-sham

description:
S59
P10_HaCat_Beta_detP.txt-S59
P10_HaCat_Beta_detP.txt

value: ac


title: Bovine,Hic,4c,rep2


title: U937 cells, control, Day 3, rep 3

value: DMSO


title: U937 cells, Ethacrynic acid, Day 3, rep 2


title: Exp-V5K_2B_Cell-HaCaT_Power-10_Frequency-27_Time-48_Treatment-exposed

description:
S64
P10_HaCat_Beta_detP.txt-S64
P10_HaCat_Beta_detP.txt


title: LL_1

value: male

value: microglia

tag: challenge

value: vehicle

tag: facs sorter


title: Bovine,Hic,BL,rep4

source_name: Blastocyst

value: Blastocyst


title: LBL_5

value: XDP


title: U937 cells, control, Day 3, rep 2

tag: cell line


title: LBL_4


title: Exp-V8K_4B_Cell-HaCaT_Power-10_Frequency-27_Time-2_Treatment-exposed

description:
S58
P10_HaCat_Beta_detP.txt-S58
P10_HaCat_Beta_detP.txt

value: HaCaT

tag: column header in matrix processed file

tag: date

value: b


title: Exp-V8K_4A_Cell-HaCaT_Power-10_Frequency-27_Time-2_Treatment-sham

description:
S57
P10_HaCat_Beta_detP.txt-S57
P10_HaCat_Beta_detP.txt

value: sham

tag: trial

tag: incubator

value: A

value: a


title: LL_4


title: U937 cells, Ethacrynic acid, Day 3, rep 1


title: Bovine,Hic,BL,rep2


title: Exp-V8K_5B_Cell-HaCaT_Power-10_Frequency-27_Time-2_Treatment-exposed

description:
S60
P10_HaCat_Beta_detP.txt-S60
P10_HaCat_Beta_detP.txt

value: exposed

value: B

tag: frequency [ghz]

tag: power [mw/cm2]


title: LBL_3


title: Bovine,Hic,BL,rep3


title: U937 cells, control, Day 3, rep 1

value: U937 cells

value: AML


title: LBL_2

value: brain


title: LL_3


title: head and neck tumor after proton therapy human 4

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

data_processing:
nf-core/rnaseq
Assembly: hg38, mm39
Supplementary files format and content: comma delimeted text files include gene count values for each Sample

source_name: Squamous cell carcinoma

extract_protocol:
Processing of the biomaterial was carried out under aseptic conditions using sterile tools. Total RNA was isolated from snap-frozen tissue after removal after homogenization with Teflon beads in QIAZOL (Qiagen), followed by purification and concentration with RNA Clean & Concentrator kit (Zymo Research), quantity was estimated using Qubit 2.0 device (Invitrogen, Life Technologies).
After isolating total RNA from 1 μg, samples were prepared for sequencing on the Illumina platform. libraries using the TruSeq RNA kit Sample Prep Kit v2 with 10 cycle enrichment step in accordance with the manufacturer's recommendations. The quality of RNA and resulting libraries was checked using an Agilent 2100 Bioanalyzer capillary electrophoresis system (Agilent Tec. Inc., USA). The RIN parameter for RNA was at least 7. The concentration of the libraries was assessed using real-time polymerase chain reaction on the CFX96 Touch Real-Time PCR Detection System device (Bio-Rad, USA). The final libraries were pooled in equimolar proportions before sequencing on the Illumina HiSeq 2500 platform using 50-base paired-end reads.

value: Squamous cell carcinoma

value: head and neck tumor

value: proton therapy, total dose 10 Gy


title: Exp-V7K_7A_Cell-HaCaT_Power-10_Frequency-40.5_Time-2_Treatment-sham

description:
S55
P10_HaCat_Beta_detP.txt-S55
P10_HaCat_Beta_detP.txt

tag: exposuretime [hr]

tag: batch


title: Bovine,Hic,BL,rep1


title: LBL_1

tag: tissue

value: male

value: microglia


title: head and neck tumor before proton therapy human 4

tag: cell type


title: Exp-V7K_6B_Cell-HaCaT_Power-10_Frequency-40.5_Time-2_Treatment-exposed

description:
S54
P10_HaCat_Beta_detP.txt-S54
P10_HaCat_Beta_detP.txt

tag: treatment

tag: aliquot


title: bovine,H3K4me3,Sperm,rep2

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013)  was employed to map the filtered reads onto the genome (bovine, bosTau9). Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads. To mitigate batch and cell type variations in comparisons, RPKM values of CUT&RUN data underwent further normalization via z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

source_name: Sperm

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×107 bovine sperm were purified employing a Puresperm 40/80 gradient column (Nidacon).  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
CUT&RUN experiments were conducted following the established protocols with specific adaptations in cell permeabilization, DNA purification, and library construction steps, as previously described (Hainer, S. J., 2019;Patty, B. J. & Hainer, 2021).  In the ULI-NChIP-seq method, each reaction utilized 0.8 × 107 sperms. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021).For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.

value: Sperm


title: Exp-V7K_6A_Cell-HaCaT_Power-10_Frequency-40.5_Time-2_Treatment-sham

description:
S53
P10_HaCat_Beta_detP.txt-S53
P10_HaCat_Beta_detP.txt

tag: passage


title: bovine,H3K4me3,Sperm,rep1


title: PL_4

tag: age (weeks)

tag: Sex

value: vehicle

value: Astrios


title: Exp-V7K_5B_Cell-HaCaT_Power-10_Frequency-40.5_Time-2_Treatment-exposed

description:
S52
P10_HaCat_Beta_detP.txt-S52
P10_HaCat_Beta_detP.txt

value: HaCaT

value: b


title: PL_3

tag: challenge

tag: facs sorter


title: head and neck normal tissue before proton therapy human 4

source_name: normal tissue of peritumoral localization


title: bovine,H3K4me3,GV,rep1

value: GV


title: bovine,H3K4me3,GV,rep2


title: PL_2


title: head and neck normal tissue after proton therapy human 4

value: normal tissue of peritumoral localization


title: head and neck tumor after proton therapy human 3


title: Exp-V7K_5A_Cell-HaCaT_Power-10_Frequency-40.5_Time-2_Treatment-sham

description:
S51
P10_HaCat_Beta_detP.txt-S51
P10_HaCat_Beta_detP.txt

tag: cell line

value: sham

tag: column header in matrix processed file

value: A

value: a


title: bovine,H3K27me3,Sperm,rep2

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon). The sperm then underwent two washes with 2 ml of HEPES-TALP and subsequent lysis using GA buffer (TIANamp Genomic DNA Kit, DP304-03, up to 200 μL), supplemented with 20 μL of Proteinase K (20 mg/mL) and 20 μL of DTT (1M). The sperm genome was released at 56°C for 9-10 hours with shaking and following the extraction protocol of the TIANamp Genomic DNA Kit (Catalog No. DP304-03). The bovine sperm WGBS library was generated as described15. Briefly, purified DNA and unmethylated lambda DNA control were mixed and fragmented to 350 bp. End-repair, dA- tailing, and ligation were carried out using the NEBNext End Repair Module, dA-Tailing Module, and NEB T4 ligase. The adaptor-ligated DNA within the size range of 300-600 bp was selected through magnetic bead separation. Bisulfite conversion was then performed using the EZ DNA methylation-Gold Kit (Zymo Research, D5005), following the manufacturer’s instructions.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
CUT&RUN experiments were conducted following the established protocols with specific adaptations in cell permeabilization, DNA purification, and library construction steps, as previously described (Hainer, S. J., 2019;Patty, B. J. & Hainer, 2021).  In the ULI-NChIP-seq method, each reaction utilized 0.8 × 107 sperms. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021).For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.


title: Exp-V7K_7B_Cell-HaCaT_Power-10_Frequency-40.5_Time-2_Treatment-exposed

description:
S56
P10_HaCat_Beta_detP.txt-S56
P10_HaCat_Beta_detP.txt

value: exposed

tag: date

tag: trial

value: B


title: PL_1

value: brain


title: head and neck tumor before proton therapy human 3

value: Squamous cell carcinoma

value: head and neck tumor


title: bovine,H3K27me3,Sperm,rep1


title: Exp-V6K_5A_Cell-HaCaT_Power-10_Frequency-40.5_Time-48_Treatment-exposed

description:
S49
P10_HaCat_Beta_detP.txt-S49
P10_HaCat_Beta_detP.txt

tag: incubator

tag: frequency [ghz]


title: head and neck normal tissue after proton therapy human 3

value: proton therapy, total dose 10 Gy


title: Exp-V6K_5B_Cell-HaCaT_Power-10_Frequency-40.5_Time-48_Treatment-sham

description:
S50
P10_HaCat_Beta_detP.txt-S50
P10_HaCat_Beta_detP.txt

tag: power [mw/cm2]

tag: exposuretime [hr]


title: PBL_4

tag: tissue

value: male

value: microglia

value: XDP


title: Exp-V4F_3B_Cell-HDF_Power-1_Frequency-27_Time-48_Treatment-exposed

description:
S48
P1_HDF_Beta_detP.txt-S48
P1_HDF_Beta_detP.txt

source_name: HDF

tag: cell type

value: HDF

tag: batch

value: bc


title: head and neck normal tissue before proton therapy human 3


title: PBL_3

tag: treatment


title: bovine,H3K27me3,GV,rep1


title: bovine,H3K27me3,GV,rep2


title: head and neck tumor after proton therapy human 2


title: Exp-V4F_3A_Cell-HDF_Power-1_Frequency-27_Time-48_Treatment-sham

description:
S47
P1_HDF_Beta_detP.txt-S47
P1_HDF_Beta_detP.txt

tag: aliquot

tag: passage

value: b


title: bovine,H3K27ac,Sperm,rep2

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013)  was employed to map the filtered reads onto various genomes (bovine, bosTau9). Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads. To mitigate batch and cell type variations in comparisons, RPKM values underwent further normalization via z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

extract_protocol:
Approximately 0.8 ×107 bovine sperm were purified employing a Puresperm 40/80 gradient column (Nidacon).
In the ULI-NChIP-seq method, each reaction utilized 0.8 × 107 sperms. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021). For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.

value: Sperm


title: Exp-V4F_2B_Cell-HDF_Power-1_Frequency-27_Time-48_Treatment-exposed

description:
S46
P1_HDF_Beta_detP.txt-S46
P1_HDF_Beta_detP.txt


title: Exp-V4F_2A_Cell-HDF_Power-1_Frequency-27_Time-48_Treatment-sham

description:
S45
P1_HDF_Beta_detP.txt-S45
P1_HDF_Beta_detP.txt


title: PBL_1

tag: age (weeks)

tag: Sex


title: head and neck normal tissue before proton therapy human 2

value: normal tissue of peritumoral localization


title: bovine,DNAme,MII,rep2

data_processing:
Initial treatment of all PBAT and WGBS datasets involved the use of cutadapt v1.11, whereby low- quality reads and adapters were removed prior to mapping. Bismark (v0.24.1; bowtie2 2.3.5.1) was then employed to align the filtered reads to genomes (bovine, bosTau9). Removal of multi-mapped reads and PCR duplicates was achieved using Bismark. CpG methylation calling was executed with bismark methylation extractor.
Assembly: bosTau9
Supplementary files format and content: bigwig files of each stage

source_name: MII

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.  Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon). The sperm then underwent two washes with 2 ml of HEPES-TALP and subsequent lysis using GA buffer (TIANamp Genomic DNA Kit, DP304-03, up to 200 μL), supplemented with 20 μL of Proteinase K (20 mg/mL) and 20 μL of DTT (1M). The sperm genome was released at 56°C for 9-10 hours with shaking and following the extraction protocol of the TIANamp Genomic DNA Kit (Catalog No. DP304-03). The bovine sperm WGBS library was generated as described15. Briefly, purified DNA and unmethylated lambda DNA control were mixed and fragmented to 350 bp. End-repair, dA- tailing, and ligation were carried out using the NEBNext End Repair Module, dA-Tailing Module, and NEB T4 ligase. The adaptor-ligated DNA within the size range of 300-600 bp was selected through magnetic bead separation. Bisulfite conversion was then performed using the EZ DNA methylation-Gold Kit (Zymo Research, D5005), following the manufacturer’s instructions.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), 132 hpi (morula), and 168-180 hpi (blastocyst). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon). The sperm then underwent two washes with 2 ml of HEPES-TALP and subsequent lysis using GA buffer (TIANamp Genomic DNA Kit, DP304-03, up to 200 μL), supplemented with 20 μL of Proteinase K (20 mg/mL) and 20 μL of DTT (1M). The sperm genome was released at 56°C for 9-10 hours with shaking and following the extraction protocol of the TIANamp Genomic DNA Kit (Catalog No. DP304-03). The bovine sperm WGBS library was generated as described15. Briefly, purified DNA and unmethylated lambda DNA control were mixed and fragmented to 350 bp. End-repair, dA- tailing, and ligation were carried out using the NEBNext End Repair Module, dA-Tailing Module, and NEB T4 ligase. The adaptor-ligated DNA within the size range of 300-600 bp was selected through magnetic bead separation. Bisulfite conversion was then performed using the EZ DNA methylation-Gold Kit (Zymo Research, D5005), following the manufacturer’s instructions.  To produce the PBAT library, zona pellucida-free oocytes and embryos underwent rigorous washing in DPBS-0.001% BSA. Subsequently, lysis in a buffer with 20 mg/mL proteinase K (QIAGEN, 19131) at 37°C for 1 hour. The mixture was then combined with spike-in λ-DNA (Promega, D150A) at a mass ratio of 1:200 and subjected to the EpiTect Fast Bisulfite Conversion Kit (Zymo Research, D5006), following the manufacturer’s protocol.

value: MII


title: head and neck normal tissue after proton therapy human 2


title: PP_5

tag: challenge

value: vehicle

tag: facs sorter

value: Astrios


title: Exp-V4F_1B_Cell-HDF_Power-1_Frequency-27_Time-48_Treatment-exposed

description:
S44
P1_HDF_Beta_detP.txt-S44
P1_HDF_Beta_detP.txt

value: exposed

tag: column header in matrix processed file

value: c


title: head and neck tumor after proton therapy human 1


title: PP_4

value: brain


title: bovine,DNAme,MII,rep1


title: PBL_5


title: head and neck tumor before proton therapy human 1

value: Squamous cell carcinoma


title: PP_3


title: Exp-V1F_4B_Cell-HDF_Power-1_Frequency-40.5_Time-48_Treatment-sham

description:
S42
P1_HDF_Beta_detP.txt-S42
P1_HDF_Beta_detP.txt

value: sham

tag: date

value: B


title: Exp-V4F_1A_Cell-HDF_Power-1_Frequency-27_Time-48_Treatment-sham

description:
S43
P1_HDF_Beta_detP.txt-S43
P1_HDF_Beta_detP.txt

tag: trial

value: A


title: bovine,DNAme,GV,rep2

value: GV


title: bovine,DNAme,GV,rep1


title: PP_2

value: male

value: microglia


title: head and neck normal tissue after proton therapy human 1

value: head and neck tumor

value: proton therapy, total dose 10 Gy


title: PP_1


title: head and neck normal tissue before proton therapy human 1


title: PBL_2

value: XDP


title: bovine,H3K27ac,Sperm,rep1

value: Sperm


title: PBP_5


title: bovine,ATAC-seq,GV,rep1

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013)  was employed to map the filtered reads onto the genome (bovine, bosTau9). Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads. To mitigate batch and cell type variations in comparisons, RPKM values underwent further normalization via z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon).  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of zygotes and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant.  The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
We prepared libraries of oocytes and early embryos utilizing the TruePrep DNA Library Prep Kit V2 from Illumina (Vazyme Biotech, TD502), with slight modifications (Wu, J. et al. ,2018). Briefly, oocytes or embryos without zona pellucida were transferred into a 0.2-mL conventional, low-binding tube (Axygen, PCR-02D-L-C) with a small volume of DPBS-0.001% BSA. After incubation with 6 μL lysis buffer (10 mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL CA-630) on ice for 10-30 min, 4 μL ddH2O, 4 μL 5 × TTBL, and 5 μL TTE mix V5 were added to the sample. The mixture was incubated at 37°C for 30 min, followed by mixing with 5 μL of 5 × TS stop buffer and further incubation at room temperature for 5 min. The sample was then mixed with 103 μL nuclease-free water and 2 μL of 20 ng/μL carrier RNA (Qiagen, 1068337) and transferred to a phase-lock tube (Qiagen,129056), containing 130 μL of phenol: chloroform: isoamyl alcohol (25:24:1). After centrifugation, the supernatant was transferred to a new low-binding 1.5-mL tube containing 1 μL glycogen, 13 μL of 3 M sodium acetate, and 130 μL isopropanol for DNA precipitation at -20°C overnight. Following centrifugation, the precipitated DNA was washed twice with 500 μL ice-cold 80% ethanol and dissolved in 20 μL of nuclease-free H2O. PCR was performed to amplify the libraries, which were then purified with 1.3 × AMPure beads (Beckman, A63882). Subsequently, all miniATAC-seq libraries were sequenced using Illumina Novaseq-6000 with paired-ended 150-bp reads.


title: Exp-V1F_3B_Cell-HDF_Power-1_Frequency-40.5_Time-48_Treatment-sham

description:
S40
P1_HDF_Beta_detP.txt-S40
P1_HDF_Beta_detP.txt

value: HDF

tag: incubator

value: bc


title: Exp-V1F_3A_Cell-HDF_Power-1_Frequency-40.5_Time-48_Treatment-exposed

description:
S39
P1_HDF_Beta_detP.txt-S39
P1_HDF_Beta_detP.txt

tag: frequency [ghz]


title: Bovine,pol2,Sperm,rep2

data_processing:
For paired-end data, alignment to genomes was executed with Bowtie2 v.2.3.4. Aligned reads underwent filtering with a minimum mapping quality of 20, and PCR duplicates were subsequently removed. Estimation of read coverage across the genome was performed utilizing bamCoverage from deepTools v.3.3.1, with parameters -binSize 100, and normalization using RPKM. Visualization was accomplished using UCSC Browser or IGV (2.16.1). To mitigate batch and cell type variations in comparisons, RPKM values were additionally normalized through z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

extract_protocol:
Approximately 0.8 ×107 bovine sperm were purified employing a Puresperm 40/80 gradient column (Nidacon).
In the ULI-NChIP-seq method, each reaction utilized 0.8 × 107 sperms. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021).For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.


title: head and neck tumor before proton therapy cell 3

source_name: laryngeal tumor

value: laryngeal tumor

tag: cell line

value: continuous cell culture obtained from a patient with a laryngeal tumor, passage 4, in the form of tumoroids, before neutron therapy

value: Phenotype:CD44+, KRT17+


title: PBP_4

value: brain

value: Astrios


title: Exp-V1F_2B_Cell-HDF_Power-1_Frequency-40.5_Time-48_Treatment-sham

description:
S38
P1_HDF_Beta_detP.txt-S38
P1_HDF_Beta_detP.txt

value: sham

tag: power [mw/cm2]

tag: exposuretime [hr]

value: b

value: a

value: c


title: PBP_3

tag: tissue

value: male

tag: cell type


title: head and neck tumor after proton therapy cell 2

value: continuous cell culture obtained from a patient with a laryngeal tumor, passage 4, in the form of tumoroids, after neutron therapy

tag: treatment

value: neutron therapy (10 Gy)


title: Bovine,pol2,Sperm,rep1


title: head and neck tumor before proton therapy cell 2


title: Bovine,pol2,Zygote,rep2

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), and 168-180 hpi (blastocyst). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
For Stacc-seq library preparation, the method described previously was followed (Liu, B. et al. ,2020). Briefly, a mixture of 7 μL buffer 1 (10 mM Tris-HCl pH =7.4, 150 mM NaCl, 0.5 mM spermidine, and 1 × EDTA-free Roche complete protease inhibitor) with 0.05% digitonin (Sigma D141), 0.5 μL pG-Tn5(Vazyme, TD901), and 0.5 μg antibody was prepared in a 200-μL low-binding tube (Axygen, PCR-02D-L-C) and incubated at 4°C for 30 min. Oocytes or embryos without zona pellucida were then transferred into a 0.2-mL low-binding tube with a small volume of DPBS-0.001% BSA and incubated with 6 μL buffer 1 containing 0.05% digitonin on ice for 10 min. Subsequently, samples were mixed with 35 μL of buffer 1 with 0.05% digitonin and 12.5 μL of prewarmed 5 × TTBL and incubated with the antibody-pG-Tn5 complex at 37°C for 30 min on a thermomixer at 400 rpm (10s on and 10s off). The reaction was stopped by adding 65 μL of 1 × TE, and DNA was purified using phenol-chloroform with 40 ng carrier RNA, followed by isopropanol precipitation for 30 min at −80°C or overnight at −20°C. For the sample with spiked-in DNA, 0.2 pg spike in DNA (prepared from Drosophila genomic DNA) was added before the DNA extraction step (Liu, B. etal. ,2020). PCR was performed to amplify the libraries (Vazyme, TD601) with the following conditions after two wash steps with freshly-prepared, ice-cold 80% ethanol: 72°C for 3 min; 98°C for 30 s; thermocycling with 16 cycles at 98°C for 15 s, 60°C for 30 s, and 72°C for 3 min; followed by 72°C for 5 min. Post-PCR,libraries were purified with 1.7 × AMPure beads (Beckman, A63882) and subjected to next-generation sequencing.


title: Exp-V1F_2A_Cell-HDF_Power-1_Frequency-40.5_Time-48_Treatment-exposed

description:
37S
P1_HDF_Beta_detP.txt-37S
P1_HDF_Beta_detP.txt

value: exposed

value: A

tag: batch

tag: aliquot


title: PBP_2

tag: age (weeks)

value: microglia


title: head and neck tumor after proton therapy cell 1


title: Exp-V3F_3B_Cell-HDF_Power-1_Frequency-27_Time-2_Treatment-sham

description:
S36
P1_HDF_Beta_detP.txt-S36
P1_HDF_Beta_detP.txt

value: HDF

value: B

tag: passage

value: ac


title: PBP_1

tag: Sex

tag: challenge


title: Bovine,pol2,Zygote,rep1


title: head and neck tumor before proton therapy cell 1

value: laryngeal tumor

value: continuous cell culture obtained from a patient with a laryngeal tumor, passage 4, in the form of tumoroids, before neutron therapy


title: Exp-V1F_4A_Cell-HDF_Power-1_Frequency-40.5_Time-48_Treatment-exposed

description:
S41
P1_HDF_Beta_detP.txt-S41
P1_HDF_Beta_detP.txt

tag: column header in matrix processed file

value: bc


title: bovine,ATAC-seq,GV,rep2

value: GV


title: head and neck tumor after proton therapy cell 3

value: Phenotype:CD44+, KRT17+


title: Bovine,pol2,GV,rep4


title: Exp-V3F_2B_Cell-HDF_Power-1_Frequency-27_Time-2_Treatment-sham

description:
S34
P1_HDF_Beta_detP.txt-S34
P1_HDF_Beta_detP.txt

value: sham

tag: date

value: b


title: Exp-V3F_3A_Cell-HDF_Power-1_Frequency-27_Time-2_Treatment-exposed

description:
S35
P1_HDF_Beta_detP.txt-S35
P1_HDF_Beta_detP.txt

tag: trial

value: a


title: C57BL/6 Chek2 p.161T wt3,sorted CD34+ Bone Marrow

city: Chicago

first: Lucy

last: Godley

state: Illinois

address: 303 E Superior Street

department: Medicine

country: USA

institute: Northwestern University

data_processing:
Salmon
Assembly: GRCm38
Supplementary files format and content: Salmon quantification file

source_name: C57BL/6 chek2 p.I161T FACS sorted CD34+ ,Bone Marrow

extract_protocol:
Bone marrow from C57BL/6 mice was stained for CD34 and FACS sorted directly in RLT+ lysis buffer followed by column based RNA purification (Qiagen)
Oligo-dT mRNA directional libraries were prepared and sequenced on a the NovaSeq 6000 with a S1 flowcell, paired end 100bp reads with ~60M clusters/sample and ~120M PE reads/sample

value: Hematopoietic Cell

tag: genotype

value: wt


title: Bovine,pol2,GV,rep3


title: Exp-V3F_2A_Cell-HDF_Power-1_Frequency-27_Time-2_Treatment-exposed

description:
S33
P1_HDF_Beta_detP.txt-S33
P1_HDF_Beta_detP.txt

tag: incubator

tag: frequency [ghz]

value: c


title: ChIPseq_501mel H3K27ac

city: New York

first: Elissa

middle: WP

last: Wong

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were aligned to hg19 using BWA (v0.7.17-r1188). Unmapped and low MAPQ reads (< 30) were filtered out using SAMtools (v1.9) and PCR duplicates were removed using Picard tools (v2.18.16). Depth normalized bigWig tracks were generated using deepTools (v3.1.1) bamCoverage with `bamCoverage -b ${input_bam} -o ${output_bigwig} --normalizeUsing RPGC --ignoreForNormalization chrX chrM -bl hg19-blacklist.v2.bed`.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: skin

growth_protocol: All cells lines were cultured in media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. All cells were cultured at 37 ºC in 5% CO2.

extract_protocol:
20 x 106 cells were harvested and fixed in 1% formaldehyde for 10 min with gentle shaking. Glycine was added to final concentration of 125 mM and incubated for 5 min. Cells were washed once with PBS, resuspended in LB1 [50mM HEPES (pH 7.5), 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× complete EDTA-free protease inhibitor] and incubated with rotation at 4 °C for 10min. Samples were pelleted, resuspended in LB2 [10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA and 1× complete protease inhibitor] and incubated rotating at 4 °C for 10min. Nuclei were pelleted, resuspended in LB3 with 0.5% SDS [0.5% SDS, 20mM Tris-HCl (pH 8.0), 150mM NaCl, 2mM EDTA, 1% Triton X-100 and 1× complete protease inhibitor] and sonicated using Covaris E220 focused ultrasonicator (peak power = 150 W, duty factor = 2%, cycle per burst = 200) for 12 min. Soluble chromatin extracts were cleared by centrifugation and 1% was kept as input DNA. Sheared chromatin was diluted to contain 0.16% SDS for antibody binding and incubated overnight at 4 °C with 2 ug anti-H3K27Ac (Abcam, ab4729) and anti-SMC1A (Bethyl lab, A300-055A). 20 ul Pierce ChIP-grade magnetic beads were used for precipitation at 4 °C for 6 hr. Beads were washed 3x LiCl buffer [250 mM LiCl, 10 mM Tris-HCl (pH 8.0), 1% sodium deoxycholate, 1% NP-40 and 1 mM EDTA], 1x RIPA wash buffer [500 mM LiCl, 50 mM HEPES-KOH (pH 7.6), 0.7% sodium deoxycholate, 1% NP-40 and 1 mM EDTA] and 1x TE [10 mM Tris-HCl (pH 8.0) and 1 mM EDTA] + 50 mM NaCl. Chromatin was eluted in elution buffer [1% SDS, 50 mM Tris-HCl (pH 8.0) and 10 mM EDTA] and incubated at 65 °C for 30 min. Eluate was reverse cross-linked at 65 °C overnight, treated with RNaseA (Roche) at 37 °C for 1 hr and Proteinase K (Roche) at 55 °C for 2 hr before recovered using a miniElute PCR purification kit from Qiagen.
Library was prepared using KAPA HTP library kit (KAPA biosystems).
ChIP libraries were sequenced to obtain 30-40 M reads for each sample on HiSeq 2500 or 4000 with either SR50 or PE50.

treatment_protocol: Cells that were transduced with lentivirus carrying puromycin-resistant shRNA plasmids were treated with 2 µg/ml puromycin.

value: skin

tag: cell line

value: melanoma

value: no treatment

tag: antibody

value: H3K27ac antibody


title: C57BL/6 Chek2 p.161T wt2,sorted CD34+ Bone Marrow

tag: tissue

value: C57BL/6 chek2 p.I161T FACS sorted CD34+ ,Bone Marrow


title: Exp-V3F_1B_Cell-HDF_Power-1_Frequency-27_Time-2_Treatment-sham

description:
S32
P1_HDF_Beta_detP.txt-S32
P1_HDF_Beta_detP.txt

tag: cell type

value: HDF

value: B

tag: power [mw/cm2]

tag: exposuretime [hr]


title: ChIPseq_SKMEL-23 H3K27ac

tag: treatment


title: Bovine,pol2,GV,rep2


title: C57BL/6 Chek2 p.161T wt1,sorted CD34+ Bone Marrow


title: Exp-V3F_1A_Cell-HDF_Power-1_Frequency-27_Time-2_Treatment-exposed

description:
S31
P1_HDF_Beta_detP.txt-S31
P1_HDF_Beta_detP.txt

value: exposed

value: A

tag: batch

tag: aliquot


title: Bovine,pol2,D7_TE,rep2


title: diabetic_EVs_3

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

data_processing:
miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: adipose tissue derived extracellular vesicles

extract_protocol:
EVs were extracted from adipose tissues of nondiabetic and diabetic subjects and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by Novogene (Tianjin, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: diabetes


title: Exp-V2F_3B_Cell-HDF_Power-1_Frequency-40.5_Time-2_Treatment-exposed

description:
S30
P1_HDF_Beta_detP.txt-S30
P1_HDF_Beta_detP.txt

tag: passage


title: C57BL/6 Chek2 p.161T het1,sorted CD34+ Bone Marrow

value: het


title: Bovine,pol2,D7_TE,rep1


title: C57BL/6 Chek2 p.161T hom3,sorted CD34+ Bone Marrow

value: hom


title: nondiabetic_EVs_3

value: adipose tissue derived extracellular vesicles

value: nondiabetes


title: Exp-V2F_3A_Cell-HDF_Power-1_Frequency-40.5_Time-2_Treatment-sham

description:
S29
P1_HDF_Beta_detP.txt-S29
P1_HDF_Beta_detP.txt

value: sham

tag: column header in matrix processed file

value: b

value: a


title: C57BL/6 Chek2 p.161T het2,sorted CD34+ Bone Marrow

value: Hematopoietic Cell


title: ChIPseq_COLO800 H3K27ac

value: skin

value: melanoma


title: Bovine,pol2,D7_ICM,rep3


title: Exp-V2F_2B_Cell-HDF_Power-1_Frequency-40.5_Time-2_Treatment-exposed

description:
S28
P1_HDF_Beta_detP.txt-S28
P1_HDF_Beta_detP.txt

tag: date


title: Bovine,pol2,D7_ICM,rep2


title: diabetic_EVs_1


title: C57BL/6 Chek2 p.161T hom2,sorted CD34+ Bone Marrow


title: nondiabetic_EVs_2


title: Exp-V2F_2A_Cell-HDF_Power-1_Frequency-40.5_Time-2_Treatment-sham

description:
S27
P1_HDF_Beta_detP.txt-S27
P1_HDF_Beta_detP.txt

tag: trial


title: C57BL/6 Chek2 p.161T hom1,sorted CD34+ Bone Marrow

tag: genotype


title: Bovine,pol2,D7_ICM,rep1


title: nondiabetic_EVs_1


title: Exp-V2H_1B_Cell-HDF_Power-1_Frequency-40.5_Time-2_Treatment-exposed

description:
S26
P1_HDF_Beta_detP.txt-S26
P1_HDF_Beta_detP.txt

tag: incubator

value: ac


title: Bovine,pol2,GV,rep1

value: GV


title: Bovine,pol2,8cell,rep2


title: C57BL/6 Chek2 p.161T het3,sorted CD34+ Bone Marrow

value: C57BL/6 chek2 p.I161T FACS sorted CD34+ ,Bone Marrow


title: Exp-V2H_1A_Cell-HDF_Power-1_Frequency-40.5_Time-2_Treatment-sham

description:
S25
P1_HDF_Beta_detP.txt-S25
P1_HDF_Beta_detP.txt

value: HDF

tag: frequency [ghz]


title: Blood_2_WGBS

city: Sendai

first: Hiroaki

last: Okae

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Informative Genetics

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
After trimming the first 8 bases, the single-end reads were aligned to the reference genome (UCSC bosTau6) using Bismark (v.0.9.0) with default parameters. The methylation levels of cytosines were calculated using the Bismark methylation extractor.Reads from both strands were combined to calculate the methylation levels of CpGs.
Genome_build: bosTau6
Supplementary_files_format_and_content: The processed data files contain the methylation status of individual CpG sites. The colum names are: chromosome, start_position, end_position, methylation level (%), count_methylated, count_unmethylated.

source_name: Blood cells

extract_protocol:
Genomic DNA was purified with phenol/chloroform extraction and ethanol precipitation.
WGBS was performed using the post-bisulfite adapter-tagging (PBAT) method. Briefly, purified genomic DNA was spiked with unmethylated lambda DNA (Promega, Madison, WI) and treated with EZ DNA Methylation-Lightning Kit (Zymo Research, Orange, CA). The first-strand DNA was synthesized with the Bio-PEA2-W4N4 primer(5’- ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT WWW WNN NN-3’). The second-strand DNA was synthesized with the PE-reverse-W4N4 primer (5’-CAA GCA GAA GAC GGC ATA CGA GAT WWW WNN NN-3’). After removing the first-strand DNA, the second strand was double stranded with the Primer-3 primer (5’-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3’). The PBAT libraries were sequenced on the HiSeq 2500 platform (Illumina, CA, USA) with 101-bp single-end reads.

value: Blood cells


title: CON Single-cell sequencing

city: beijing

first: Xuejia

last: He

address: 2 yabao road

institute: Capital Institute of Pediatrics

description: one sample from murine embryonic brain tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

growth_protocol: Constructing a low-folate cell line. Mouse embryonic stem cells (mESCs) Sv/129 were maintained in Dulbecco’s modifed Eagle’s medium (DMEM, Gibco, USA) supplemented with 0.1  mM β-mercaptoethanol (Invitrogen, Carlsbad, USA), 0.1  mM non-essential amino acids (Invitrogen, Carls_x0002_bad, USA), 0.1  mM glutamate (Invitrogen, Carlsbad, USA), 15% fetal bovine serum (Gibco, USA), and 1000 U/ml mouse leukemia inhibitory factor (Millipore, Bill_x0002_erica, USA), cultured in culture dishes coated with 0.2% gelatin (Invitrogen, Carlsbad, USA). Constructing a low-folate cell line.After resuscitating normal mESCs, Sv129 cells were randomly split into FA4 and FA0. The FA0 group uses folate-free mESCs culture medium.Folate (Sigma) was added to the medium of FA0 as medium of the FA4 group(final concentration: 4 mg/L).  Next, two groups were added correspond medium and were cultured at 37°C with 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily.

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

treatment_protocol: 1.Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group.

value: brain

tag: cell line

value: Brain tissue

tag: type

value: con group

value: normal saline


title: diabetic_EVs_2

tag: tissue

value: adipose tissue derived extracellular vesicles

value: diabetes


title: Exp-V4K_4B_Cell-HaCaT_Power-1_Frequency-40.5_Time-48_Treatment-exposed

description:
S24
P1_HaCat_Beta_detP.txt-S24
P1_HaCat_Beta_detP.txt

source_name: HaCaT

extract_protocol:
To keep the homogeneity of the transmitting power flux density or SAR as high as possible, the cells outside a defined area were excluded during harvesting. After exposure, the medium of the cell dishes was discarded and a template made with a 3D printer (at 27 GHz an ellipse with a radius of 24 mm/23 mm; at 40.5 GHz a capped circle with a radius of 24 mm and a distance of the capped area to the center of 19 mm) was applied to the outside of the bottom of the dish and the areas to be omitted were marked. The cells were removed according to the marking with a cell scraper and the cell monolayer was then rinsed twice with PBS.
Cells were harvested by washing the remaining cell monolayer once with PBS and transferring 350 ul lysis buffer to each of the dishes. The cell lysates were collected using a cell scraper and transferring them into reaction tubes. The lysates were frozen at -80C until further processing. DNA and RNA extraction was done using the DNA/RNA Allprep Mini Kit (Qiagen) or the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

value: HaCaT

value: exposed

value: B


title: NTD Single-cell sequencing

tag: cell type

value: case group

value: MTX


title: Blood_1_WGBS


title: FA4

description:
RNA-seq
mESCs Gene Expression Profiling.xlsx

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: mouse genome (mm10)
Supplementary files format and content: HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Supplementary files format and content: related genes can be confirmed. Besides, the distribution of peak on different genome regions, such as intergenic, introns, downstream2k, upstream2k and exons) was performed.

extract_protocol:
Total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.
Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

value: Mouse embryonic stem cells (mESCs)

tag: group

value: normal folic acid(FA=4）


title: Bovine,pol2,4cell,rep2


title: Exp-V4K_4A_Cell-HaCaT_Power-1_Frequency-40.5_Time-48_Treatment-sham

description:
S23
P1_HaCat_Beta_detP.txt-S23
P1_HaCat_Beta_detP.txt

data_processing:
The software tool GenomeStudio V2011.1 (Illumina, Inc.) including the Methylation Module Version 1.9.0 was used for quality control and visualization of the performance of microarray analysis as well as for methylation analysis. Raw microarray data were imported into GenomeStudio V2011.1 and analyzed without normalization.
Beta Values with depection P values

value: sham

value: A

tag: power [mw/cm2]

tag: exposuretime [hr]

value: b

value: a


title: Bovine,pol2,4cell,rep1


title: Exp-V4K_3B_Cell-HaCaT_Power-1_Frequency-40.5_Time-48_Treatment-sham

description:
S22
P1_HaCat_Beta_detP.txt-S22
P1_HaCat_Beta_detP.txt

tag: treatment

tag: batch


title: FA0

value: low folic acid(FA=0）


title: Sperm_2_WGBS

value: Sperm


title: Exp-V4K_3A_Cell-HaCaT_Power-1_Frequency-40.5_Time-48_Treatment-exposed

description:
S21
P1_HaCat_Beta_detP.txt-S21
P1_HaCat_Beta_detP.txt

tag: aliquot


title: Bovine,pol2,16cell,rep1


title: Sperm_1_WGBS


title: Bovine,pol2,16cell,rep2


title: CON-3

description:
RNA-seq
mouse brain tissue Gene Expression Profiling.xlsx
Control3

value: brain

value: con group


title: CON-2

description:
RNA-seq
mouse brain tissue Gene Expression Profiling.xlsx
Control2

value: normal saline


title: Exp-V4K_1B_Cell-HaCaT_Power-1_Frequency-40.5_Time-48_Treatment-sham

description:
S20
P1_HaCat_Beta_detP.txt-S20
P1_HaCat_Beta_detP.txt

tag: passage

value: ba


title: KRV_Day11, bio rep 3

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: 10x Genomics

data_processing:
Samples were sequenced on an Illumina NextSeq 550 to a depth of 20-25k raw paired-end reads per cell, with an average of 12.2k transcripts/cell and 1.4k non-zero genes/cell
The 16-base cell barcode and 10-base UMI from the R1 read were first appended to the corresponding R2 read name as a colon-delimited pair. For all further processing, the reads were treated as single-ended.
Reads with cell barcodes that were not in the 10X barcode dictionary, or had UMIs containing 'N', or had cell barcodes that were observed fewer than 500 times were discarded.
mRNA sequences (R2) were aligned to the rat genome (rn6) using tophat2 (v2.0.12) with default settings and RefSeq transcript annotations.
Gene transcripts were quantified using ESAT (https://github.com/garber-lab/ESAT), again using RefSeq transcript annotations. ESAT ignores reads that result from PCR duplication during the library preparation process using the UMI. If reads from the same cell barcode map to the same gene and have the same UMI, they are considered PCR duplicates, and only one is counted.
The output of ESAT is an array containing the observed transcript countsfor each gene for each cell. Each row of the counts matrix corresponds to one gene and each column corresponds to one cell from the sample.
Assembly: rn6
Supplementary files format and content: Processed data files are in tab-separated value (*.tsv) text file format, compressed with gzip (*.tsv.gz)
Supplementary files format and content: Each file contains one matrix for the sample containing the transcript counts for each gene for each cell, with each row corresponding to a gene and each colum corresponding to a cell, labeled by its 16-base cell barcode.

organism: Rattus norvegicus

source_name: pancreas

extract_protocol:
Pancreatic islets were isolated from euthanized Ifnar1-KO animals on day 11 following pIC+KRV treatment (KRV) or day 11 following PBS control (PBS). n=2 animals per group
10X Genomics 3' single-cell RNA-Seq library construction.

value: pancreas

value: islet cells

value: LEW.1WR1, Ifnar1-KO

value: poly I:C x3 + KRV

tag: post-treatment day


title: CON-1

description:
RNA-seq
mouse brain tissue Gene Expression Profiling.xlsx
Control1


title: Bovine,pol2,8cell,rep1


title: S3

city: Hangzhou

first: qiang

last: zhao

address: 866 Yuhangtang Rd, Hangzhou

institute: Zhejiang University

data_processing:
Immunoprecipitated DNA was subjected to next generation sequencing using the Epicenter Nextera DNA Sample Preparation Kit or to real-time PCR. Library construction was performed using the High Molecular Weight tagmentation buffer, and tagmented DNA was amplified using 14 cycles of PCR. The libraries were then sequenced on a Novaseq according to manufacturer’s standard protocols.
Assembly: dm6
Supplementary files format and content: Bigwig

organism: Drosophila melanogaster

source_name: trachea of L3

extract_protocol:
The third larvae trachea were dissected in cold PBS and were fixed in 1% formaldehyde at room temperature for 20 min.The cross-linked chromatin was resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate). The extracts were sonicated to produce DNA fragments with an average size of 600 bp. Anti-FLAG M2 Magnetic Beads (Millipore, #8823) were used for enriched DNA binding to transcription factor Stat92E.Three biological replicates were performed for each genotype or treatment.
Immunoprecipitated DNA was subjected to next generation sequencing using the Epicenter Nextera DNA Sample Preparation Kit or to real-time PCR. Library construction was performed using the High Molecular Weight tagmentation buffer, and tagmented DNA was amplified using 14 cycles of PCR. The libraries were then sequenced on a Novaseq according to manufacturer’s standard protocols.

value: trachea of L3

value: normal food


title: Exp-V3K_4B_Cell-HaCaT_Power-1_Frequency-40.5_Time-2_Treatment-sham

description:
S18
P1_HaCat_Beta_detP.txt-S18
P1_HaCat_Beta_detP.txt

value: HaCaT

tag: column header in matrix processed file

tag: date

value: B

value: c


title: Exp-V4K_1A_Cell-HaCaT_Power-1_Frequency-40.5_Time-48_Treatment-exposed

description:
S19
P1_HaCat_Beta_detP.txt-S19
P1_HaCat_Beta_detP.txt

value: exposed

tag: trial

value: A

value: b


title: NTD-3

description:
RNA-seq
mouse brain tissue Gene Expression Profiling.xlsx
Case3

value: case group

value: MTX


title: Oocyte_WGBS

source_name: Oocytes

value: Oocytes


title: NTD-2

description:
RNA-seq
mouse brain tissue Gene Expression Profiling.xlsx
Case2

source_name: brain

value: brain


title: S1

tag: genotype


title: S2


title: KRV_Day11, bio rep 1

description: 10x Genomics


title: Exp-V3K_4A_Cell-HaCaT_Power-1_Frequency-40.5_Time-2_Treatment-exposed

description:
S17
P1_HaCat_Beta_detP.txt-S17
P1_HaCat_Beta_detP.txt

tag: incubator

tag: frequency [ghz]

value: a


title: Input3


title: NTD-1

description:
RNA-seq
mouse brain tissue Gene Expression Profiling.xlsx
Case1


title: PBS_Day11, bio rep 1

description: 10x Genomics

value: pancreas

value: PBS only


title: Exp-V3K_3B_Cell-HaCaT_Power-1_Frequency-40.5_Time-2_Treatment-exposed

description:
S16
P1_HaCat_Beta_detP.txt-S16
P1_HaCat_Beta_detP.txt

tag: cell line

value: ac


title: Input2

tag: tissue


title: FA4-6mA  INPUT

first: shan

address: 2yabao road

description:
6mA MeDIP seq
mESCs Peak_Annotations.xlsx

data_processing:
After sequencing on the Illumina NovaSeq6000 sequencer, image analysis, base calling, and quality control were performed, resulting in the generation of raw reads (Raw Data). Quality control was initially conducted using Q30. Then, the cutadapt software (v1.9.2) was employed to trim adapters and remove low-quality reads, obtaining high-quality reads. Subsequently, the bowtie2 software (v2.2.4) was used to align the adapter-trimmed reads to the mouse reference genome (mm10) with default parameters. The MACS software (v1.4.2) was utilized for the identification of methylated regions (enrichment peaks) through Peak Calling. The diffReps software (1.55.4) was then applied for the identification of differentially methylated regions. Annotation of methylated regions with gene information was performed using the UCSC RefSeq database. The methylated regions were linked with gene information. Visualization of enrichment peaks was conducted using the UCSC Genome Browser.
Assembly: mouse genome (mm10)
Supplementary files format and content: Annotation of methylated regions with gene information was performed using the UCSC RefSeq database. The methylated regions were linked with gene information. Visualization of enrichment peaks was conducted using the UCSC Genome Browser.
Supplementary files format and content: related genes can be confirmed. Besides, the distribution of peak on different genome regions, such as intergenic, introns, downstream2k, upstream2k and exons) was performed.
Library strategy: 6mA MeDIP-Seq

extract_protocol:
The process of 6mA MeDIP-Seq is briefly described as follows: Genomic DNA is extracted using the DNeasy kit (QIAGEN Inc.) and then sonicated to fragment sizes of 100-300bp. Subsequently, the fragmented DNA undergoes end repair, dA-tailing, and adapter ligation using the GenSeq® Universal DNA Library Prep Kit (GenSeq, Inc.). A portion of the adapter-ligated DNA, around 10%, is labeled as "Input" and kept aside, while the remainder is subjected to immunoprecipitation using the GenSeq® 6mA MeDIP kit (GenSeq Inc.). The DNA that underwent immunoprecipitation and the Input DNA are then subjected to library amplification using Illumina PCR primers and GenSeq® 2× HiFi PCR Mix (GenSeq Inc.). The purified DNA library is quantified using the Qubit fluorescence method (ThermoFisher) and sequenced on Illumina's NovaSeq sequencing platform.
The DNA that underwent immunoprecipitation and the Input DNA that did not undergo immunoprecipitation were amplified into libraries using Illumina PCR primers and GenSeq® 2× HiFi PCR Mix (GenSeq Inc.).

tag: cell type

value: Mouse embryonic stem cells (mESCs)

tag: medip kit

value: GenSeq 6mA MeDIP KIT(GenSeq Inc.)

value: normal folic acid(FA=4）


title: Exp-V3K_3A_Cell-HaCaT_Power-1_Frequency-40.5_Time-2_Treatment-sham

description:
S15
P1_HaCat_Beta_detP.txt-S15
P1_HaCat_Beta_detP.txt

value: HaCaT

value: sham

tag: power [mw/cm2]


title: Exp-V3K_1B_Cell-HaCaT_Power-1_Frequency-40.5_Time-2_Treatment-exposed

description:
S14
P1_HaCat_Beta_detP.txt-S14
P1_HaCat_Beta_detP.txt

value: B

tag: exposuretime [hr]


title: NL_M125_4

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

institute: University of North Dakota

data_processing:
Sequence reads were trimmed for adaptor sequences and low-quality using trimmomatic v0.39.
Reads were aligned to the rat assembly (rn7) using Hisat2 v2.2.1, and sorted/indexed by Samtools v1.13.
Annotation/Counts was performed by featureCounts (Subread v2.0.1).
Normalization and differential gene expression analysis was performed by DESeq2 v1.34.0
Assembly: rn7
Supplementary files format and content: Comma-separated values (csv) file, containing normalized counts for each sample

source_name: Neurohypophysis (Neural Lobe)

extract_protocol:
Rats were anesthetized with isoflurane and euthanized via transcardial perfusion with PBS. Brains were removed from the skull to gain access to the pituitary gland. The neurohypophysis was removed and immediately flash frozen by liquid nitrogen.
Frozen tissue was ground under liquid nitrogen. RNA was collected via phenol-chloroform extraction and Rneasy Mini Kit (Qiagen). Approximately 1.5 ug  of total RNA was used for QC and library construction.
RNA libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and NEBNext Ultra II RNA-seq library kit for Illumina (NEB).

treatment_protocol: Rats were grown to the ages of 35 days old or 125 days old prior to tissue collection.

value: Neurohypophysis (Neural Lobe)

tag: Sex

value: Male

tag: strain

value: Sprague Dawley

tag: treatment

value: Age - 125 days old


title: FA0-6mA  INPUT

value: low folic acid(FA=0）


title: NL_M125_3


title: Input1

value: trachea of L3

value: normal food


title: KRV_Day11, bio rep 2

description: 10x Genomics

value: islet cells

value: LEW.1WR1, Ifnar1-KO

value: poly I:C x3 + KRV


title: NL_M125_2


title: FA4-6mA  IP


title: FA0-6mA  IP


title: Exp-V3K_1A_Cell-HaCaT_Power-1_Frequency-40.5_Time-2_Treatment-sham

description:
S13
P1_HaCat_Beta_detP.txt-S13
P1_HaCat_Beta_detP.txt

value: A

tag: batch

tag: aliquot

tag: passage

value: b

value: a


title: Exp-V2K_6B_Cell-HaCaT_Power-1_Frequency-27_Time-2_Treatment-sham

description:
S12
P1_HaCat_Beta_detP.txt-S12
P1_HaCat_Beta_detP.txt

tag: column header in matrix processed file

tag: date


title: CON-6mA INPUT

description:
6mA MeDIP seq
Mouse tissue Peak_Annotations.xlsx

value: brain

value: GenSeq 6mA MeDIP KIT(GenSeq Inc.)

value: normal saline


title: NL_M35_4

value: Age - 35 days old (Control)


title: Exp-V2K_6A_Cell-HaCaT_Power-1_Frequency-27_Time-2_Treatment-exposed

description:
S11
P1_HaCat_Beta_detP.txt-S11
P1_HaCat_Beta_detP.txt

value: HaCaT

value: exposed

tag: trial


title: PBS_Day11, bio rep 2

description: 10x Genomics

value: pancreas

tag: genotype

value: PBS only

tag: post-treatment day


title: NTD-6mA INPUT

value: MTX


title: Exp-V2K_5B_Cell-HaCaT_Power-1_Frequency-27_Time-2_Treatment-exposed

description:
S10
P1_HaCat_Beta_detP.txt-S10
P1_HaCat_Beta_detP.txt

tag: cell line

tag: incubator

value: B

tag: frequency [ghz]


title: NL_M35_2

tag: tissue

value: Neurohypophysis (Neural Lobe)

value: Male

value: Sprague Dawley


title: CON-6mA IP

tag: medip kit


title: Exp-V2K_5A_Cell-HaCaT_Power-1_Frequency-27_Time-2_Treatment-sham

description:
S9
P1_HaCat_Beta_detP.txt-S9
P1_HaCat_Beta_detP.txt

value: sham

tag: power [mw/cm2]

tag: exposuretime [hr]


title: NL_M35_1

tag: Sex

tag: strain


title: NTD-6mA IP

tag: treatment


title: Exp-V2K_4B_Cell-HaCaT_Power-1_Frequency-27_Time-2_Treatment-sham

description:
S8
P1_HaCat_Beta_detP.txt-S8
P1_HaCat_Beta_detP.txt

tag: batch

tag: aliquot


title: DrpoZ_1h_rep2

type: RNA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

description: Gene expression after 1h at 3% CO2

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: liquid culture

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: All strains were maintained in BG-11 medium supplemented with 20 mM Hepes pH 7.5, continuous illumination at photosynthetic photon flux density 40 µmol m-2 s-1, 32 °C. Liquid cultures were shaken at 90 rpm. For the experiments, liquid cultures were grown without antibiotics in ambient air or in high CO2 by supplementing growth chamber air with 3% CO2.

extract_protocol: Cells were collected by centrifugation at 7000 g for 5 min at 4°C and the pellet was frozen in liquid nitrogen. Total RNA was prepared using the hot-phenol method.

treatment_protocol: Cells were shifted to 3% CO2 at an OD750 of 0.8-1. Cell samples were collected immediately before and 3 h and 24 h after the shift.

value: strain GT-T

value: drpoZ mutant

tag: condition

value: after 1h at 3% CO2


title: DrpoZ_24h_rep2

description: Gene expression after 24h at 3% CO2

value: after 24h at 3% CO2


title: IPRN3

city: Ji'nan

first: Kai

last: Cheng

address: Qingdao Road,6699

institute: Shandong First Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform. Using the Illuminapaired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-endreads. Reads obtained from the sequencing machines includes raw reads containing adapters or lowqualitybaseswhich will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/
Supplementary files format and content: Reads obtained from the sequencing machines includes raw reads containing adapters or lowqualitybaseswhich will affect the following assembly and analysis.

source_name: Embryo

extract_protocol:
After extracting total RNA from the samples, enrich eukaryotic mRNA using magnetic beads with Oligo(dT) (for prokaryotes, remove rRNA with a kit before proceeding to the next step).
Add fragmentation buffer to break the mRNA into short fragments. Using mRNA as a template, synthesize the first cDNA strand with random hexamers (six-nucleotide random primers). Add buffer, dNTPs, RNase H, and DNA polymerase I to synthesize the second cDNA strand. After purification with a QiaQuick PCR kit and elution with EB buffer, perform end repair and ligate sequencing adapters. Use agarose gel electrophoresis for fragment size selection, followed by PCR amplification. Finally, sequence the constructed library.

value: Embryo

tag: cell type

value: Fibroblast

value: WT

value: IPRN


title: Exp-V2K_4A_Cell-HaCaT_Power-1_Frequency-27_Time-2_Treatment-exposed

first: Jyoti

address: Campus Ring 6

description:
S7
P1_HaCat_Beta_detP.txt-S7
P1_HaCat_Beta_detP.txt

value: HaCaT

value: exposed

tag: column header in matrix processed file

tag: date

tag: trial

value: A

tag: passage

value: b

value: a


title: IPRN2

tag: cell line

tag: genotype