title: Primary Lung Cancer EML-ALK V1, sgSetd2 Sample4

city: Stanford

first: Stewart

last: Kim

address: 1291 Welch Rd

department: Genetics

institute: Stanford University

description: Library name: V1Setd2_Rep4

data_processing:
Sequencing reads were adapter-trimmed with Trim Galore!.
Reads were then aligned to the reference genome using BWA.
Duplicates were marked with Picard.
Reads were filtered to remove reads mapping to mitochondrial DNA and blacklisted regions using SAMtools and BEDTools.
Normalized bigWig files (scaled to 10^6 mapped reads) were generated using BEDTools
Assembly: mm10
Supplementary files format and content: Normalized BigWig files (scaled to 10^6 mapped reads) from each indicated sample.

source_name: Primary Lung

growth_protocol: R26LSL-Cas9-eGFP mice 8-14 weeks old were transduced with lentivirus and primary tumors were harvested.

extract_protocol:
Individuals tumors were microdissected and minced into <0.5 mm3 pieces and transferred into pre-warmed digestion media (Dispase (5 U/mL)), DNase I, Grade II (1 mg/mL), Y-27632 ROCK inhibitor (0.5 mM) in Advanced DMEM/F-12. The minced tumors were digested at 37°C for 40 minutes with gentle horizontal shaking. Tumors were vigorously disrupted by pipetting every 15 minutes.   The   digestion   media   was   then   neutralized   with   stop   media   (DMEM/F-12), FBS (10%), HEPES (0.01 M) with DNase I, Grade II (0.1 mg/mL), and ROCK inhibitor (0.05 mM)) and cell suspensions were passed through 40 μm cell strainers. The samples were centrifuged at 1,100 rpm for 7 minutes and pellets were resuspended in red blood cell lysis buffer (Sigma-Aldrich, R7757). Cells were washed with FACS buffer by spinning at 1,100 rpm for 7 minutes. Cell pellets were then resuspended in an appropriate volume of FACS buffer and sorted for Tdtomato-expressing cells
Between 6,000 and 25,000 cells were isolated by FACS and frozen in 500 μL Bambanker freezing media. Cells were thawed, washed once in 1 mL cold PBS, and resuspended in 50 μl cold lysis buffer (Buenrostro et al., 2015). Nuclei were centrifuged for 1 minute at 500 g at 4 °C and transposed with adaptor loadedTn5 transposase for 30 minutes. DNA was purified using a Zymo DNA Clean and Concentrator 5 kit (Zymo D4004). ATAC-Seq libraries were prepared using NEBNext High-Fidelity 2× PCR Master Mix (NEB M0541) as described (Buenrostro et al., 2015). Purified libraries were assessed using Agilent High Sensitivity DNA 1000 Tapestation Kit (Agilent). Paired-end 150 bp reads were sequenced with Novogene on the NovaSeq XPlus platform at approximately 5 x 107 paired-end reads per sample

treatment_protocol: Mouse primary lung cancer cells from R26LSL-Cas9-eGFP mice with lentiviral vectors containing sgRNAs generating either EML-ALK V1 or EML-ALK V3 and sgRNAs targeting either Neomycin or Setd2.

value: Primary Lung

tag: cell line

value: Primary Lung Cancer

value: Tumor Cell

value: R26LSL-Cas9-eGFP;EML-ALK V1, sgSedt2

value: Intratracheal injection of lentivirus

tag: batch


title: NOVA74_Blood_Phase_2_SD_-1_b

status: Public on Aug 06 2025

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description: Gene expression profiling of PBMC  from influenza infected humans

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from PBMCs in Paxgene tubes according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: PBMCs  collected from humans  and stored in Paxgene tubes  according to manufacturer's instructions.

tag: disease state

value: influenza

tag: tissue

value: PBMC

tag: study date

value: SD -1


title: NOVA80_Blood_Phase_2_SD_-1

tag: study group

value: Unvaccinated


title: Primary Lung Cancer EML-ALK V1, sgSetd2 Sample3

type: SRA

state: CA

description: Library name: V1Setd2_Rep3

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genotype

tag: treatment


title: NeuN+ ATAC-seq, Cat, rep2

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: ATAC_Cat2079-NEUN

data_processing:
Samples were processed using the standard ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline v.1.7.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: ATAC-seq peak calls, tagAlign alignment files

organism: Felis catus

source_name: Cortex

extract_protocol:
After centrifugation to remove sucrose gradient, nuclei were labeled by resuspending the pellet in 1 mL blocking buffer with NeuN-488 antibody (Millipore, cat. no. MAB377X) at 1:4,000 and 4,6-diamidino-2-phenylindole at 1:20,000 for at least 30 minutes at 4°C with rotation. Nuclei were then centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was removed the pellet was resuspended in 500 μL cold 1% BSA in PBS with RNase Inhibitor. Nuclei were then filtered through a 35 μm filter, washing the filter with an additional 100 μL 1% BSA in PBS. Nuclei were then sorted using a Sony MA900 device with a 70-μm nozzle and pressure not exceeding a pressure setting of 7. Gates were set to capture those populations that were positive for 488 signal (NeuN+). Both the NeuN+ and NeuN- populations were collected and held at 4°C . Purity of selected samples was typically >95% based on reanalysis of sorted samples.
Approximately 100,000 NeuN+ nuclei were isolated from cortex tissues and used for ATAC-seq library preparation as per standard protocols (PMID: 24097267, PMID: 25559105, PMID: 28846090) with the following modifications. Briefly, 50 μL of cold 5x lysis buffer was added to sorted nuclei to reach a final concentration of 1x (1- mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and incubated for 20 min on ice followed by centrifugation for 10 minutes. The transposition reaction was incubated for 30 minutes at 37°C with agitation at 1000 rpm (Illumina Tagment DNA Enzyme and Buffer kit, cat. no. 20034198). After column clean up via the QIAGEN MinElute Reaction Cleanup kit (QIAGEN, cat. no. 28204) and PCR amplification of libraries, an additional clean up with AMPure XP beads (0.8X ratio) was performed with two 80% ethanol washes before quantification using a DNA High-Sensitivity chip on a 2100 BioAnalyzer (Agilent). Libraries were sequenced paired-end with the Illumina dual indexes on a NovaSeq X Plus 10 B 300 cycle flowcell targeting 100 million reads per sample.

value: Cortex

value: Neurons


title: 20211022_control

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: ChIL-Seq with no first antibody

data_processing:
After sequencing, reads were cleaned by trim_galore (version0.6.10) and mapped to rn6 with Bowtie2(version 2.3.1).
bigwig files for visualization were generated by deeptools(version 3.5.4) with following command "bamCoverage --binSize 100 --normalizeUsing CPM".
Assembly: rn6
Supplementary files format and content: bigWig
Library strategy: ChIL-seq

organism: Rattus norvegicus

source_name: Schwann cells

extract_protocol:
Chromatin integration labelling (ChIL): ChIL-seq for Schwann cells was performed described previously (https://doi.org/10.1038/protex.2018.122).
Chromatin integration labelling (ChIL): ChIL-seq library for Schwann cells was performed described previously  (https://doi.org/10.1038/protex.2018.122). , except following. After library PCR, the  amplified DNA were purified and size selected using magnetic bead.

value: Schwann cells

value: primary cells

value: WT


title: Pancreas, Acini_Distal, 10

city: Edinburgh

first: Carla

last: Salomo Coll

address: Crewe Rd S

department: Institute of Genetics and Cancer - CRUK Scotland Centre

country: United Kingdom

institute: University of Edinburgh

description: NanoString GeoMx Digital Spatial Profiler(DSP)

library_source: transcriptomic

data_processing:
FastQ files were transformed into digital count conversion (DCC) files using Nanostring GeoMx NGS pipeline and uploaded to the GeoMX DSP for analysis following the GeoMx DSP Data Analysis User Manual. Outlier probes were removed from all segments when the limit of quantitation (LOQ) was higher than 2. Targets were filtered and only genes with an expression greater than the LOQ in at least 5% of the segments were used. Q3 normalisation was performed on the remaining genes.
Assembly: GeoMx Mouse WholeTranscriptome Atlas
Supplementary files format and content: GeoMX_Q3Norm_values.xlxs: Includes a matrix with Q3 normalised gene expression values for each sample
Supplementary files format and content: GeoMX_Segment_properties.xlx: List of segments and spatial information of each
Supplementary files format and content: .DCC files, digital count conversion files for the GeoMX Analysis
Library strategy: Spatial transcriptomics

source_name: Pancreas

extract_protocol:
Slides were prepared following NanoString GeoMx DSP Manual RNA Assay Slide Preparation. In the scan area of each slide, two 5-μm-thick FFPE tissue sections were placed, for a total of four mice. Slides were incubated with Whole Transcriptome Atlas Probe Mix overnight. For segmentation of the different cell populations, slides were incubated with the following morphology markers: Reg3a/g (B-10) (Santacruz biotechnologies, sc-377038), Amylase (D55H10) XP (CST, 3796), PanCK AlexaFluor 532 (Novus Biologicals, NBP2-33200AF532) and SYTO 13 (Invitrogen, S7575) for nuclear staining. Slides were then scanned with GeoMx Digital Spatial Profiler (Nanostring). Regions of interest (ROIs) were selected based the morphology markers and a total of 95 segments were collected for analysis.
After the GeoMx DSP system has completed collection, the DSP collection plate can be removed from the instrument. Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. 95 ROIs were dried down at 65C for 1 hour on a PCR block and resuspended in 10ul of Nuclease-Free water for 10 minutes. PCR was then performed with the matching primers from the primer plate Seq Code C. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. After the PCR step, 4ul of each library were pooled, size selected and clean-up using AMPure XP beads (Beckman Coulter, #A63881). 4ul of each library was pooled, creating a volume of 380ul. 456ul of Ampure was added to the first step of the size selection. The final elution volume was 48ul. The final library had an average peak size of 153bp. The library pool was quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Fragment size and quantity measurements were used to calculate molarity. The pool had a molarity of 29.7nM.

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: Pancreas, ADM, 5

value: ADM


title: Primary Lung Cancer EML-ALK V1, sgSetd2 Sample1

description: Library name: V1Setd2_Rep1

value: Primary Lung


title: Pancreas, Acini_REG3, 11


title: Primary Lung Cancer EML-ALK V1, sgSetd2 Sample2

description: Library name: V1Setd2_Rep2

value: Primary Lung Cancer


title: 20210608_Hif

description: ChIL-Seq with HIF1


title: Pancreas, Acini_Proximal, 8


title: NOVA73_Blood_Phase_2_SD_-1


title: 20210608_control

description: ChIL-Seq with no first antibody


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample6

description: Library name: V1Neo_Rep6

value: Tumor Cell

value: R26LSL-Cas9-eGFP;EML-ALK V1, sgNeomycin


title: NOVA77_Blood_Phase_2_SD_-1


title: NOVA82_Blood_Phase_2_SD_-1


title: NOVA45_Blood_Phase_2_SD_-1

value: Vaccinated


title: Primary Lung Cancer EML-ALK V1, sgSetd2 Sample5

description: Library name: V1Setd2_Rep5

value: R26LSL-Cas9-eGFP;EML-ALK V1, sgSedt2

value: Intratracheal injection of lentivirus


title: RA_3rd

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

description: Library name: Sample3

library_source: transcriptomic single cell

data_processing:
All resulting sequence libraries were preprocessed on an Illumina platform (Roket Genomics, Seoul, South Korea).
Assembly: GRCh38-1.2.0
Supplementary files format and content: tab-delimited file includes raw counts for each sample.

source_name: Blood

extract_protocol: Single-cell 3’ gene expression libraries were prepared by strictly following the protocols of a Chromium Single Cell 3’v2 Library kit (10× Genomics). All resulting libraries were sequenced on an Illumina platform (Roket Genomics, Seoul, South Korea).

value: Blood


title: NOVA78_Blood_Phase_2_SD_-1

value: influenza

value: PBMC

value: Unvaccinated

value: SD -1


title: NOVA76_Blood_Phase_2_SD_-1


title: Pancreas, Acini_REG3, 10


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample3

description: Library name: V1Neo_Rep3


title: Pancreas, Acini_Distal, 8


title: Pancreas, Acini_Distal, 7


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample2

description: Library name: V1Neo_Rep2


title: Pancreas, Acini_Proximal, 6


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample7

description: Library name: V1Neo_Rep7


title: Saline, Veh, scRNA

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

description:
Library name: Saline_Veh_RNA
10x Genomics

data_processing:
Cell Ranger ARC (cellranger-arc) v.2.0.2 from 10x Genomics was utilized to process Chromium Single Cell Multiome ATAC + Gene Expression (GEX) sequencing data. Initially, raw BCL files from the Illumina NovaSeq were demultiplexed into paired-end, gzip-compressed FASTQ files using the default parameters of cellranger-arc mkfastq. Subsequently, the cellranger-arc count function was employed for read alignment, filtering, barcode counting, peak calling, and the quantification of both ATAC and GEX molecules. The rat genome mRatBN7 and its annotated transcriptome served as the reference for alignment. Only confidently mapped reads with valid barcodes, unique molecular identifiers (UMIs), and non-PCR duplicates were retained
Assembly: mRatBN7
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each sample from filtered_feature_bc_matrix folder
Supplementary files format and content: CellRanger output files: fragments.tsv.gz for each sample

molecule: nuclear RNA

source_name: Brain, periaqueductal gray

extract_protocol:
After one hour, the rats were euthanized, and the periaqueductal gray (PAG) was dissected from their flash-frozen brains. To isolate cell nuclei from the midbrain PAG, the tissue was flash-frozen, dissected with a cryotome, minced into small pieces, homogenized, filtered through a 70 μm strainer, and centrifuged. ReadiDrop 7-AAD cell viability dye (Bio-Rad) was added, and live nuclei (7-AAD positive) were sorted using a BioRad Cell Sorter S3e in purity mode. Nuclei were counted with a Nexcelom automated Cellometer using acridine orange/propidium iodide (AOPI) staining, and the nuclei stock concentration was adjusted to target 10,000 nuclei per sample. The samples were bulk transposed, and approximately 16,100 nuclei were loaded into each channel of the microfluidic chip, with GEMs generated using the 10x Chromium controller and reagents from the Chromium Next GEM Single Cell ATAC Kit, 1,000,280 (10x Genomics), following the manufacturer’s instructions
After post-GEM cleanup with Dynabeads and SPRIselect (Beckman Coulter), samples underwent pre-amplification PCR and were then divided for constructing ATAC and GEX libraries. Quality control for the libraries was performed using an Agilent Bioanalyzer 2100 with High Sensitivity DNA chips. After verifying sample traces, each library was normalized based on the average fragment size, and concentration was determined using a Qubit 4.0 fluorometer (Thermo Fisher Scientific). The pooled libraries were subsequently sequenced using Illumina high output kits on a NovaSeq 6000 platform from Illumina

treatment_protocol: Sprague Dawley rats were injected with Complete Freund’s adjuvant (CFA) or Saline and later ApAP or SRP-001 were administered per os. The left hind paws of Sprague-Dawley rats were injected with 150 µl of 50% CFA, freshly diluted with sterile saline on the day of administration, to induce significant long-term inflammatory pain and mechanical hyperalgesia, assessed using eVF. Following this, the rats were administered either ApAP or SRP-001 at a dose of 100 mg/kg

value: Brain, periaqueductal gray

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: age

value: 2 months

value: Saline

tag: library type

value: mRNA


title: LM-V4

city: Rockville

first: Jie

last: Liu

state: MD

address: 5625 Fishers Lane

institute: National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism

description: Library name: LM-V4

data_processing:
The FASTQ files were quantified using Kallisto with an index file generated from the Ensembl mouse reference genome (release 105).
Assembly: GRCm39
Supplementary files format and content: Text files containing estimated raw counts and TPM values

molecule: polyA RNA

source_name: Liver

extract_protocol:
Total RNA from mouse liver was extracted using TRIzol (Sigma) and quality control-confirmed RNA samples were submitted to GENEWIZ/Azenta (South Plainfield, NJ) for Standard RNA-Seq using Next Generation Sequencing, or to quantify gene expression using nCounter Mouse Metabolic Pathways panel.
RNA quality control, library preparations, sequencing reactions and initial bioinformatic analysis were conducted at GENEWIZ, LLC (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). Only samples with integrity number ≥7 were used. RNA-sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 min at 94°C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on flow-cells.

value: Liver

value: WT + HFD


title: NOVA57_Blood_Phase_2_SD_-1


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample1

description: Library name: V1Neo_Rep1

value: Primary Lung

value: Primary Lung Cancer

value: Tumor Cell

value: R26LSL-Cas9-eGFP;EML-ALK V1, sgNeomycin


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample8

description: Library name: V3Setd2_Rep8

value: R26LSL-Cas9-eGFP;EML-ALK V3, sgSedt2

value: Intratracheal injection of lentivirus


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample4

description: Library name: V1Neo_Rep4


title: LM-V3

description: Library name: LM-V3


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample7

description: Library name: V3Setd2_Rep7


title: 20211022_Hif

description: ChIL-Seq with HIF1

value: Schwann cells

value: primary cells

value: WT


title: LM-V1

description: Library name: LM-V1


title: RA_4th

description: Library name: Sample4

value: Blood


title: Pancreas, Acini_Distal, 9

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: Pancreas, Acini_Distal, 6


title: LM-V5

description: Library name: LM-V5


title: Primary Lung Cancer EML-ALK V1, sgNeo Sample5

description: Library name: V1Neo_Rep5


title: Pancreas, Acini_Proximal, 5


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample6

description: Library name: V3Setd2_Rep6


title: Pancreas, Acini_Proximal, 7


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample5

description: Library name: V3Setd2_Rep5


title: NOVA23_Blood_Phase_2_SD_-1

value: influenza

value: PBMC

value: Vaccinated

value: SD -1


title: RA_2nd

description: Library name: Sample2


title: LM-RC2

description: Library name: LM-RC2

value: Liver

value: WT + STD


title: LM-V6

description: Library name: LM-V6

value: WT + HFD


title: NOVA16_Blood_Phase_2_SD_-1


title: NOVA46_Blood_Phase_2_SD_-1


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample4

description: Library name: V3Setd2_Rep4

value: Primary Lung

value: Primary Lung Cancer

value: Tumor Cell


title: LM-RC1

description: Library name: LM-RC1


title: NOVA30_Blood_Phase_2_SD_-1


title: Pancreas, Acini_Distal, 4


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample2

description: Library name: V3Setd2_Rep2

value: R26LSL-Cas9-eGFP;EML-ALK V3, sgSedt2

value: Intratracheal injection of lentivirus


title: Pancreas, Acini_Proximal, 4


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample3

description: Library name: V3Setd2_Rep3


title: LM-JD1

description: Library name: LM-JD1

value: WT + HFD + JD


title: NOVA02_Blood_Phase_2_SD_-1


title: Pancreas, Acini_REG3, 9


title: NOVA37_Blood_Phase_2_SD_-1

value: Unvaccinated


title: LCB1-V3

description: Library name: LCB1-V3

value: hCB1R knockout + HFD


title: Primary Lung Cancer, EML-ALK V3, sgNeo Sample3

description: Library name: V3Neo_Rep3

value: R26LSL-Cas9-eGFP;EML-ALK V3, sgNeomycin


title: LCB1-V2

description: Library name: LCB1-V2


title: Pancreas, Acini_REG3, 8

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: Pancreas, ADM, 4

value: ADM


title: NOVA39_Blood_Phase_2_SD_-1

value: influenza

value: PBMC

value: Vaccinated


title: Pancreas, Acini_Distal, 5


title: NOVA56_Blood_Phase_2_SD_-1

value: SD -1


title: LM-RC3

description: Library name: LM-RC3

value: Liver

value: WT + STD


title: LM-JD4

description: Library name: LM-JD4


title: Pancreas, Acini_Proximal, 3


title: Pancreas, Acini_Distal, 3


title: Primary Lung Cancer EML-ALK V3, sgSetd2 Sample1

description: Library name: V3Setd2_Rep1

value: Primary Lung

value: Primary Lung Cancer


title: LM-JD2

description: Library name: LM-JD2


title: Pancreas, Acini_REG3, 7


title: NOVA10_Blood_Phase_2_SD_-1


title: NOVA04_Blood_Phase_2_SD_-1


title: Primary Lung Cancer, EML-ALK V3, sgNeo Sample4

description: Library name: V3Neo_Rep4

value: Tumor Cell


title: Pancreas, Acini_REG3, 6


title: Pancreas, Acini_REG3, 5


title: LCB1-RC2

description: Library name: LCB1-RC2

value: hCB1R knockout + STD


title: LCB1-V1

description: Library name: LCB1-V1


title: Primary Lung Cancer, EML-ALK V3, sgNeo Sample2

description: Library name: V3Neo_Rep2

value: Intratracheal injection of lentivirus


title: NOVA64_Blood_Phase_2_SD_-1

value: Unvaccinated


title: Primary Lung Cancer, EML-ALK V3, sgNeo Sample1

description: Library name: V3Neo_Rep1


title: Pancreas, Acini_REG3, 4


title: C2C12 cells, Per1 transduction, 15

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

description: Library name: PER15

data_processing:
Libraries were demultiplexed, adapters trimmed, and trimmed reads were aligned to the mouse genome (UCSC mm10) using Illumina Dragen RNA v4.1.23, full pipeline mode with differential expression enabled by the core facility.
Assembly: UCSC mm10
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx). Contains normalized counts by Dragen RNA.

growth_protocol: C2C12 myoblasts were cultured subconfluently at 37°C in 5% CO2 in complete growth media consisting of high glucose DMEM containing 10% FBS and 1% PS. Experiments were conducted in 12-well plates that were pre-coated with a Type I rat tail collagen matrix. Coating consisted of diluting RatCol collagen solution (cat. #5056-20ML; Advanced Biomatrix, Carlsbad, CA) and acetic acid into sterile water to a final concentration of 100 µg/mL for rat collagen and 0.1% acetic acid. Five hundred µL of the final solution was added to each well of the plate and incubated under UV light for 2 h to allow collagen to polymerize. Prior to plating myoblasts, the collagen solution was aspirated, and wells were rinsed twice with sterile phosphate buffered saline (PBS). Myotube differentiation was initiated when cells reached ~95% confluency by changing to differentiation media consisting of high glucose DMEM containing 2% horse serum,  1% PS, and 1 µm insulin. Media changes occurred every 48 h.

extract_protocol:
RNA was isolated using Zymo RNA Miniprep kit . 300 nanoograms of total RNA was used for construction of sequencing libraries.
A cDNA library was prepared for each sample using the the NEBNext PolyA mRNA and Ultra II RNA library kit for Illumina. Libraries were barcoded for multiplexing with NEBNext Multiplex Oligos for Illumina unique dual index Primer Pairs. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Tapestation D1000 high sensitivity (Agilent Technologies). The pooled sample was sequenced, with paired-end, 150 base reads on an Illumina NovaSeq X Plus located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

treatment_protocol: C2C12 myocytes were differentiated for 3 days. On day 4 post differentiation, C2C12 myotubes were transfected using adenoviruses encoding Per2+Gfp, Per1 + Gfp, or Gfp only as a control. Virus-containing media was changed 24 h after transfection to fresh differentiation media.

value: Mouse Myoblasts

value: Per1 transduction


title: C2C12 cells, Per1 transduction, 14

description: Library name: PER14


title: LCB1-RC3

description: Library name: LCB1-RC3


title: NOVA03_Blood_Phase_2_SD_-1


title: LCB1-JD6

description: Library name: LCB1-JD6

value: hCB1R knockout + HFD + JD


title: NOVA07_Blood_Phase_2_SD_-1


title: P2, VisiumFFPE

city: Tokyo

first: Kotaro

last: Matsumoto

address: 35, Shinanomachi, Shinjuku-ku

department: Division of Rheumatology, Department of Internal Medicine

institute: Keio University School of Medicine

description: 10x Genomics

data_processing:
Libraries were sequenced on the MGI DNBSEQ sequencer to generate 150 bp paired end reads.
Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10x Cell Ranger software.
Assembly: hg38

source_name: Temporal artery from a patient with giant cell arteritis

extract_protocol:
Paraffin-embedded tissue sections from patients with giant cell arteritis and granulomatous with polyangiitis were used. The samples were mounted onto Visium Spatial Gene Expression Slides (10x Genomics), fixed in ice-cold methanol, and stained. Tissue permealization was then performed to extract mRNA according to the Visium Spatial Gene Expression user guide
The Visium Spatial Gene Expression Reagents Kit (10x Genetics) was used to generate spatially barcorded cDNA libraries following the manufacturer's instructions. Optimal experiment conditions were investigated using the Visium Spatial Tissue Optimization Kit (10x Genomics).


title: C2C12 cells, Per1 transduction, 13

description: Library name: PER13


title: Pancreas, ADM_REG3, 3

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: NOVA41_Blood_Phase_2_SD_-1

value: influenza


title: Pancreas, ADM, 3

value: ADM


title: C2C12 cells, Per1 transduction, 12

description: Library name: PER12


title: D. Flos-aquae, sonicated to collapse gas vesicles, B

city: HOUSTON

first: George

last: Lu

state: Texas

address: 6500 Main St

department: Bioengineering

institute: Rice University

description: Library name: D. Flos-aquae GV collapse B

data_processing:
Image analysis and base calling were conducted by the Illumina Control Software. Raw sequence data (.bcl files) generated were converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were then mapped to the Dolichospermum_flos-aquae reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within gene regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the control and treated samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: ASM1251639v1
Supplementary files format and content: .txt format text files, tab delimited, containing counts for each sample
Supplementary files format and content: .csv format file, containing the results of differential gene expression analysis based on the counts

organism: Dolichospermum flos-aquae

source_name: whole cell

growth_protocol: D. flos-aquae cultures were grown in BG11-media (Sigma-Aldrich, St. Louis, MO, USA) under 1% CO2 at 26 °C and approximately 50 µM photons / m2 / s-1 from a white LED light source.

extract_protocol:
All samples were then collected on Whatman filter membranes (Cytiva, Marlborough, USA) and resuspended in 5 ml phosphate-buffered saline before addition of 10 ml RNAProtect reagent (Qiagen, Hilden, Germany). After agitating the samples for 5 seconds, they were incubated for 5 minutes, collected by on Whatman filter membranes (Cytiva, Marlborough, USA) and flash frozen in liquid nitrogen for subsequent use. RNA extraction was performed with a Qiagen RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, with modifications to the lysis procedure as follows: Lysozyme was added to 2.5 mg / ml and supplemented with 40 µM Spermine as well as 0,2% of the detergent C7Bz0 and 2% of the detergent SB3-14, in addition to 50 mM dithiothreitol (Mehta et al., 2015). Cells were then subjected to homogenization in a Bead Mill Homogenizer (VWR, Radnor,PA, USA) for 2 cycles with 2.4 mm metal beads (VWR, Radnor,PA, USA) and 3 cycles with 0.5 mm glass beads (VWR, Radnor,PA, USA) for 45 seconds each while resting on ice in between steps. RNA samples were quantified using a Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with a 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
rRNA depletion sequencing library was prepared by using three probes from QIAGEN FastSelect rRNA 5S/16S/23S Kit (Qiagen, Hilden, Germany), respectively. RNA sequencing library preparation was performed using the NEBNext Ultra II RNA Library Preparation Kit for Illumina, following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). In brief, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at the 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto 1 lane of a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Three separate cultures of 50 ml cells each were collected at an OD600 of 2.0 and split into two samples of 25 ml each. Control samples were left at room temperature, GV collapse samples were subjected to waterbath sonication (intensity, device) three times for 10 seconds each.

value: whole cell

value: Bacteria

value: wild type

value: sonicated (gas vesicles collapsed)


title: Pancreas, Acini_Distal, 1


title: LCB1-JD4

description: Library name: LCB1-JD4

value: Liver


title: D. Flos-aquae, sonicated to collapse gas vesicles, C

description: Library name: D. Flos-aquae GV collapse C


title: NOVA62_Blood_Phase_2_SD_-1

value: PBMC

value: SD -1


title: NOVA34_Blood_Phase_2_SD_-1


title: LCB1-JD5

description: Library name: LCB1-JD5


title: C2C12 cells, Gfp transduction, 16

description: Library name: GFP16

value: Gfp transduction


title: P3, VisiumFFPE

description: 10x Genomics

source_name: Lung from a patient with granulomatous with polyangiitis


title: P1, VisiumFFPE

description: 10x Genomics

value: Temporal artery from a patient with giant cell arteritis


title: D. Flos-aquae, sonicated to collapse gas vesicles, A

description: Library name: D. Flos-aquae GV collapse A


title: LCB1-JD2

description: Library name: LCB1-JD2


title: Pancreas, Acini_Distal, 2


title: D. Flos-aquae, control C

description: Library name: D. Flos-aquae C

value: control


title: Pancreas, Acini_REG3, 3


title: D. Flos-aquae, control, A

description: Library name: D. Flos-aquae A


title: 7days,Rep6

city: San Francisco

first: Susanna

last: Rosi

address: 2200 Island Dr

institute: Altos labs

description: Library name: m-7dpi-3_S59_L007_R1_001_T1

data_processing:
RNA-seq FASTQ files were trimmed, aligned to the mouse reference genome (GRCm39, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0). Gene-level length-scaled counts were used for all downstream analyses.
Assembly: GRCm39
Supplementary files format and content: quant.sf files from salmon quantification.

source_name: Whole Brain

extract_protocol:
CD11b+ CD45+ tdTomato+ cells (MDMs) were sorted from whole brains of Ccr2-creERT2::Ai14D mice at 7 and 30 days after TBI.
cDNAs were generated using the SMART-Seq v4 Ultra Low input RNA kit for sequencing (Takara bio, 634891), according to the vendor protocol with 14 cycles of cDNA amplification. At the last step, the cDNA was eluted in 30ul of RNase/DNase free water. Subsequently 30ul of cDNA was used as a starting material with Illumina DNA Prep library kit (Illumina, 20018705) according to the vendor protocol, with final library PCR amplification of 10 cycles. After library completion, individual libraries were pooled equally by volume, and quantified on Fragment Analyzer (Agilent, DNF-474). Quantified library pool was diluted to 1nM and sequenced on MiniSeq (Illumina, FC-420-1001) to check for quality of reads. Finally, individual libraries were normalized according to MiniSeq output reads, specifically by % protein coding genes and were sequenced on two lanes of HiSeq4000 SE50 for a total of ~30M reads per sample.

value: Whole Brain

value: Monocyte-derived Macrophages

value: TBI

tag: time

tag: lane


title: C2C12 cells, Gfp transduction, 11

description: Library name: GFP11

value: Mouse Myoblasts


title: LCB1-JD1

description: Library name: LCB1-JD1

value: hCB1R knockout + HFD + JD


title: 7days,Rep5

description: Library name: m-7dpi-2_S61_L007_R1_001_T1


title: Pancreas, Acini_Proximal, 2

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: inputt AA112, PS9179, early stage mixed larvae

city: New York

first: Avrami

last: Aharonoff

state: NY

address: 29 Washington Place

department: Biology

institute: New York University

description: Library name: input_AA112_PS9179_mixed_early_larvae_ext810

data_processing:
Adapters were trimmed when necessary with trimmomatic (version 0.39). Reads were aligned with bowtie2 (version 2.4.2) using the default parameters. Sam files were converted to bam files, sorted and indexed using samtools (version 1.11). Bam files were used to generate bigwig files with the bamCoverage tool in deeptools (version 3.5.0) with the following parameters: --binsize 10 --minMappingQuality 20 --extendReads 200 --ignoreDuplicates --normalizeUsing CPM --exactScaling --ignoreForNormalization chrM.
Assembly: PRJNA982879 (S. hermaphroditum), this paper (P. pacificus), PRJNA644888 (O. tipulae)
Supplementary files format and content: bigwig

organism: Steinernema hermaphroditum

source_name: whole worm

growth_protocol: S. hermaphroditum early stage mixed larvae were isolated by filtering mixed stage worms through a 30 micron nylon mesh filter, and collecting the flow through. Pristionchus pacificus J2-J3 larvae were isolated by filtering mixed stage worms through a 20 micron nylon mesh, and collecting the flow through. Oscheius tipulae early stage synchronized larvae were isolated by bleaching mixed stage worms (0.5 M NaOH, 1% sodium hypochlorite for 2 minutes), hatching embryos in M9, and growing synchronized L1 larvae on NGM plates supplemented with agarose at 22˚C for 24 hours.

extract_protocol:
Around 100-150 µL of pelleted larvae was removed from -80 ˚C and washed in FA Buffer (final concentrations of 50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 150 mM NaCl, filter sterilized) with 0.1% sarkosyl, 1 mM PMSF, and 1X protease inhibitors (protease inhibitor cocktail set I – Calbiochem, catalog # 539131) added fresh. Larvae were then dounced 30 times in a glass dounce tissue grinder (VWR, catalog number 22877-280) with pestle type B. Sonication was performed in a Biopruptor ® Pico (catalog # B01060010) to obtain fragments between 200 and 800 bp in length (30 seconds on, 30 seconds off, 10-15 cycles). Protein concentration was determined using the Bradford assay (Bio-Rad, catalog # 500-0006). For chromatin immunoprecipitation, 1-2 mg of extract and 3-5 µg of antibody were used (see supplemental file 1), and allowed to rotate overnight at 4 ˚C. nProtein A Sepharose beads (Cytiva, catalog # 17528001) were added and incubation was allowed to continue for 2 hours. Beads were washed with FA buffer, FA buffer – 1 M NaCl, FA buffer – 500 mM NaCl, TEL buffer (final concentrations of 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0, filter sterilized), and TE, respectively. Immunocomplexes were eluted twice with ChIP elution buffer (final concentrations of 1% SDS, 250 mM NaCl, 10 mM Tris, pH 8.0, 1 mM EDTA) at 65 ˚C for 15 min at 1400 rpm. The eluate was then treated with 2 µL of 10 mg/mL proteinase K for 1 hour at 50 ˚C, and reverse crosslinked overnight in a 65 ˚C waterbath. DNA was purified the next morning with Qiagen MinElute PCR Purification Kit (catalog # 28006), and fragment size was checked by agarose gel electrophoresis or TapeStation. The remaining DNA was stored at -20 ˚C.
Library preparation was performed as follows. To perform end repair, we used half the ChIP DNA and 10-30 ng of input DNA, T4 DNA Ligase Reaction Buffer (NEB, catalog #  B0202S), 0.4 mM dNTPs, 20 U PNK (Fisher, catalog # FEREK0032), 0.7 U Large Klenow Fragment (NEB, catalog # M0210S), and 6 U T4 DNA Polymerase (Fisher, catalog # FEREP0062) (total volume 33 µL). The reaction was incubated at 20 ˚C for 30 minutes, and was cleaned with Qiagen MinElute PCR Purification Kit (eluted in 21 µL). To perform A-tailing, NEBuffer 2 (catalog # B7002S), 0.2 mM dATP, and 7.5 U of Klenow Fragment (3’ → 5’ exo-) (NEB, catalog # M0212L) were added to the cleaned DNA (total volume of 25 µL), and incubated for an hour in a 37 ˚C water bath. The reaction was cleaned with Qiagen MinElute PCR Purification Kit (eluted in 17 µL). To perform adapter ligation, Quick Ligation Buffer, Illumina Truseq Adapters (see supplemental file 1), and 2 µL of Quick Ligase (NEB, catalog # M2200L) were added to cleaned DNA (total volume of 40 µL), and incubated for 20 minutes at 23 ˚C. The reaction was size selected and cleaned with Ampure XP beads (Beckman Coulter, catalog # A63881). The eluate was amplified by PCR with Phusion HF Reaction Buffer, 0.5 µM TruSeq forward and reverse primers (see supplemental file 1), 0.2 mM dNTP, and 1 U Phusion High-Fidelity DNA Polymerase (Fisher, catalog F-530L) for a total reaction volume of 50 µL under the following parameters: 98 ˚C for 1 min, 98 ˚C for 30 seconds, 60 ˚C for 30 seconds, 72 ˚C for 30 seconds, repeat steps 2-4 14 times, 72 ˚C for 5 min, 8 ˚C forever. 10 µL of 3 M sodium acetate (pH 5.2) was added to reaction, and the reaction was cleaned with Qiagen MinElute PCR Purification Kit, (eluted in 11 µL). The eluate was gel purified (1.5% agarose gel) to obtain fragments between 250-600 bp using the Qiagen MinElute Gel Extraction Kit (catalog # 28606). Library concentration was determined with the KAPA Library Quantification Kit (catalog # KK4824). Single-end (75 bp) sequencing was performed at the Genomics Core at the Center for Systems and Genome Biology, New York University using the Illumina NextSeq 500 platform.

treatment_protocol: Larvae were treated with 2% formaldehyde for 30 minutes, washed with M9 (PBS was used for S. hermaphroditum), collected by centrifugation, flash frozen in liquid nitrogen, and stored at -80˚C until extract preparation

tag: source

value: whole worm

value: hermaphrodite

tag: developmental stage

value: early stage mixed larvae


title: LCB1-RC1

description: Library name: LCB1-RC1

value: hCB1R knockout + STD


title: C2C12 cells, Per2 transduction, 5

description: Library name: PER5

tag: cell line

value: Per2 transduction


title: C2C12 cells, Per1 transduction, 11

description: Library name: PER11

value: Per1 transduction


title: D. Flos-aquae, control B

description: Library name: D. Flos-aquae B

value: whole cell

value: Bacteria

value: wild type


title: Pancreas, ADM, 2

value: ADM


title: C2C12 cells, Gfp transduction, 13

description: Library name: GFP13

value: Gfp transduction


title: input AA103, PS9179, early stage mixed larvae

description: Library name: input_AA103_PS9179_mixed_early_larvae_ext804


title: Pancreas, ADM_REG3, 2


title: Pancreas, ADM, 1


title: C2C12 cells, Gfp transduction, 15

description: Library name: GFP15


title: C2C12 cells, Gfp transduction, 14

description: Library name: GFP14


title: C2C12 cells, Per2 transduction, 4

description: Library name: PER4


title: Pancreas, Acini_Proximal, 1


title: input AA104, PS9179, early stage mixed larvae

description: Library name: input_AA104_PS9179_mixed_early_larvae_ext805


title: 7days,Rep4

description: Library name: m-7dpi-1_S55_L006_R1_001_T1

value: Whole Brain

value: Monocyte-derived Macrophages


title: 30days,Rep6

description: Library name: m-30dpi-9_S54_L006_R1_001_T1

value: TBI


title: 30days,Rep5

description: Library name: m-30dpi-8_S53_L006_R1_001_T1


title: C2C12 cells, Per2 transduction, 3

description: Library name: PER3

value: Mouse Myoblasts


title: Pancreas, ADM_REG3, 1

value: Pancreas


title: IgG, ChIP, PS9179, early stage mixed larvae, rep 2

description: Library name: IgG_ab46540_PS9179_mixed_early_larvae_ext805_AA102_rep2

tag: antibody (target)

value: IgG

tag: antibody (vendor,_catalog_number)

value: Abcam, ab46540

tag: antibody (host,_clonality)

value: rabbit, polylconal

tag: matching input

value: input AA104, PS9179, early stage mixed larvae


title: Pancreas, Acini_REG3, 2

tag: tissue

value: LSL-KrasG12D; Pdx1-Cre


title: C2C12 cells, Per2 transduction, 2

description: Library name: PER2

tag: cell type

value: Per2 transduction


title: 30days,Rep4

description: Library name: m-30dpi-7_S58_L006_R1_001_T1

tag: genotype


title: C2C12 cells, Per2 transduction, 1

description: Library name: PER1

tag: treatment


title: Pancreas, Acini_REG3, 1


title: 7days,Rep3

description: Library name: f-7dpi-6_S62_L007_R1_001_T1


title: H3K4me3, ChIP, PS9179, early stage mixed larvae, rep 3

description: Library name: H3K4me3_ab8580_PS9179_mixed_early_larvae_ext810_AA109_rep3

value: whole worm

value: hermaphrodite

tag: strain

value: early stage mixed larvae

value: Abcam, ab8580

value: input AA112, PS9179, early stage mixed larvae


title: C2C12 cells, Gfp transduction, 5

description: Library name: GFP5

value: Gfp transduction


title: Mutant ZmNFYA1, replicate 3

city: Beijing

first: Qiang

last: Huo

address: Yuanmingyuan West Road

country: China

institute: China Agricultural University

data_processing:
Trimmomatic  (version 0.39) was used to trim the sequence reads and Hisat2 (version 2.2.1) was used to align them to the B73 v4 reference genome.
Supplementary files format and content: Zea mays ssp mays B73 v4
Supplementary files format and content: Matrix table with raw counts for every sample (column) and gene (rows)

organism: Zea mays

source_name: Endosperm

growth_protocol: Wild type and mutant plant kernels cultivated in the shangzhuang of Beijing, China

extract_protocol:
5-10 of 15 DAP endosperms of wild type and mutant were pooled for extracting total RNA with an RNAprep Pure Plant Kit (cat. no. DP441, TIANGEN)
MP3RNA-seq

value: Endosperm

tag: gene id

tag: cultivar

value: 15 DAP

value: mutant


title: Mutant ZmNFYA1, replicate 2

tag: age


title: H3K4me3, ChIP, PS9179, early stage mixed larvae, rep 2

description: Library name: H3K4me3_ab8580_PS9179_mixed_early_larvae_ext805_AA101_rep2

tag: Sex


title: C2C12 cells, Gfp transduction, 4

description: Library name: GFP4

value: Mouse Myoblasts


title: 7days,Rep1

description: Library name: f-7dpi-4_S64_L007_R1_001_T1

value: Whole Brain

value: Monocyte-derived Macrophages

value: TBI

tag: time

tag: lane


title: H3K4me3, ChIP, PS9179, early stage mixed larvae, rep 1

description: Library name: H3K4me3_ab8580_PS9179_mixed_early_larvae_ext804_AA98_rep1

tag: source

tag: developmental stage

value: rabbit, polylconal

value: input AA103, PS9179, early stage mixed larvae


title: LCB1-JD3

description: Library name: LCB1-JD3

value: Liver

value: hCB1R knockout + HFD + JD


title: Mutant ZmNFYA1, replicate 1


title: H4K20me1, ChIP, PS9179, early stage mixed larvae, rep 3

description: Library name: H4K20me1_ab9051_PS9179_mixed_early_larvae_ext810_AA108_rep3

value: whole worm

tag: antibody (target)

value: Abcam, ab9051


title: 30days,Rep3

description: Library name: f-30dpi-12_S56_L006_R1_001_T1


title: Wild type ZmNFYA1, replicate 3

value: wild type


title: C2C12 cells, Gfp transduction, 1

description: Library name: GFP1

tag: cell line


title: 30days,Rep1

description: Library name: f-30dpi-10_S60_L007_R1_001_T1


title: IgG, ChIP, PS9179, early stage mixed larvae, rep 1

description: Library name: IgG_ab46540_PS9179_mixed_early_larvae_ext804_AA99_rep1

value: hermaphrodite

value: early stage mixed larvae

value: IgG

tag: antibody (vendor,_catalog_number)

value: Abcam, ab46540

tag: antibody (host,_clonality)


title: 30days,Rep2

description: Library name: f-30dpi-11_S63_L007_R1_001_T1

tag: tissue


title: H4K20me1, ChIP, PS9179, early stage mixed larvae, rep 2

description: Library name: H4K20me1_ab9051_PS9179_mixed_early_larvae_ext805_AA100_rep2

tag: matching input

value: input AA104, PS9179, early stage mixed larvae


title: TdTomato+ cells collected from Ptbp1 fl/fl;Aldh1l1+;tdT+/- 9 weeks old mouse brain (Replicate 3)

city: Riverside

first: Sika

last: Zheng

address: University Ave 900

institute: University of California, Riverside

description: Library name: KO_M_4

data_processing:
For quality control and alignment of raw bulk RNA-seq reads from Ptbp1 knockout samples, we employed the Snakemake workflow "preprocessing_RNAseq.smk" from SnakeNgs (version 0.2.0) (https://github.com/NaotoKubota/SnakeNgs). In brief, low-quality reads were filtered using fastp (version 0.23.4), and the remaining reads were aligned to the mouse reference genome (mm10) using STAR (version 2.7.11a), with Ensembl transcript annotation (v102). Quality metrics were then collected with Picard (version 3.1.1) (http://broadinstitute.github.io/picard/) and summarized using MultiQC (version 1.25). We applied Shiba (version 0.4.0) to the mapped reads with the default parameters for differential gene expression and splicing analysis. Shiba internally employs DESeq2 for differential gene expression analysis. Genes with adjusted P < 0.05 and the absolute log2 fold change greater than 1 were considered differentially expressed genes (DEGs). For differential splicing analysis, events with adjusted Fisher’s exact test P < 0.05, difference in percent spliced in (ΔPSI) greater than 10, and Welch’s t-test P < 0.05 were considered differentially spliced events (DSEs).
Assembly: mm10
Supplementary files format and content: Gene expression and PSI values in excel format

extract_protocol:
Cortices were isolated at postnatal week 9 from animals injected with tamoxifen at postnatal week 5 and collected for single tdT+ cell sorting. Differently, the single cells were directly sorted into a 1.5 mL Eppendorf tube containing 750 μL of Trizol LS (Thermo Fisher Scientific #10296028). Cell sorting in each tube proceeded until volume reached 1mL and then a new tube with Trizol LS was replaced until the end of the sorting. Total RNA was extracted according to manufacturer’s instructions for Trizol reagent. The RNA quality was monitored by Agilent TapeStation 4150.
The libraries were prepared using ABClonal mRNA-seq Lib Prep Kit for Illumina by Novegene Corporation Inc.

value: Cortex

tag: genotype

value: Ptbp1 fl/fl;Aldh1l1+;tdT+/-


title: Wild type ZmNFYA1, replicate 1

value: Endosperm

value: 15 DAP


title: H4K20me1, ChIP, PS9179, early stage mixed larvae, rep 1

description: Library name: H4K20me1_ab9051_PS9179_mixed_early_larvae_ext804_AA97_rep1


title: Cow, snATAC

description:
Library name: Cow_snATAC
Cow_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Data was processed using cellranger-arc (v2.0.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: h5 files contain all snRNA and snATAC-seq counts for each sample. Fragment files included for snATAC-seq.

organism: Bos taurus

source_name: cortex

extract_protocol:
At least 10 – 20 mg of frozen tissue was obtained from each sample using a metallic block and hammer to take a portion of the dissected cortex tissue. The tissue was then sealed inside of a Covaris Tissue TUBE (Covaris, cat. Nos. 520021 and 520023) and thoroughly pulverized using the chilled hammer and metallic block, with intermittent submerging into liquid nitrogen to maintain cold temperature and brittleness. Using a clean, pre-chilled scoopula, pulverized tissue was then transferred to a pre-chilled 2 mL DNA LoBind tube. RNA was isolated using the miRNeasy Mini Kit according to manufacturer instructions (QIAGEN, cat. no. 217084). RIN scores were calculated by a 2100 BioAnalzyer (Agilent) using the RNA 6000 Nano Kit following manufacturer instructions (Agilent cat. no. 50671511) .
Transposition, nuclei isolation, barcoding, and library preparation were performed according to the 10X Genomics Chromium Next GEM Single Cell Multiome protocol CG000338 Rev E with the following alterations. Each sample was loaded on one lane of the Chromium Next GEM Chip J. Nuclei were loaded according to manufacturer’s recommendations to target recovery of 10,000 nuclei per lane.

value: cortex


title: TdTomato+ cells collected from Ptbp1 fl/fl;Aldh1l1+;tdT+/- 9 weeks old mouse brain (Replicate 2)

description: Library name: KO_M_3


title: Mutant ZmMYBR6, replicate 3

value: mutant


title: Cow, snRNA

description: Library name: Cow_snRNA


title: 7days,Rep2

description: Library name: f-7dpi-5_S57_L006_R1_001_T1

value: Whole Brain

tag: cell type

value: Monocyte-derived Macrophages

tag: treatment

value: TBI


title: BLZ_Jung_Tam_3

description: Library name: N126-14

data_processing:
Read1(10bp of UMI + 9bp of cell barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore.
Reads were aligned to GRCm38 reference using HISAT2.
Uniquely mapped reads were counted by featureCounts and UMI duplication was ramoved by using UMI tools.
Assembly: GRCm38
Supplementary files format and content: compressed tab separated files(.tsv.gz)

source_name: Brain

growth_protocol: Mice postnatal 8 days, 14 days, and 6-15 weeks old were bred under SPF conditions.

extract_protocol:
Brains were excised from mice transcardially perfused with PBS and 500 cells of CD11b+ CD45+ Ly6G- CD206- microglia were collected into 30uL of direct lysis buffer (TaKaRa #635013) by CytoFlex SRT(Beckman Coulter, Inc).
Libraries were prepared using 15uL out of 30uL lysate by CEL-Seq2(Hashimshony T et al.) method individually. 10nt of UMI followed by 9nt of cell barcode are in Read1 and 81nt of insert reads are in Read2.

treatment_protocol: Tamoxifen was dissolved in corn oil before injection. In 6- to 15-week-old mice, adult mice were induced by injecting 4 mg TAM per 200 µl oil intraperitoneally twice. In neonates, pups were intraperitoneally injected with 0.1 mg TAM per 10 µl oil at P1 and P3 or 0.2 mg TAM per 20 µl at P5 and P7. For functional inhibition of CDKN1A, postnatal mice were intraperitoneally injected with UC2288 (100 mg per kg body weight) in corn oil containing 2% DMSO. The BLZ945 was dissolved in 20% (2-hydroxypropyl)-β-cyclodextrin. A dose of 100 mg kg−1 bodyweight of BLZ945 was applied by oral gavage in adult mice for five consecutive days.

value: Brain

value: Microglia

value: Cx3cr1CreERT2(Jung) Hetero; Rosa26YFP Hetero

value: TAM


title: Mutant ZmMYBR6, replicate 2

tag: gene id


title: TdTomato+ cells collected from Ptbp1 fl/fl;Aldh1l1+;tdT+/- 9 weeks old mouse brain (Replicate 1)

description: Library name: KO_F_1


title: C2C12 cells, Gfp transduction, 3

description: Library name: GFP3

value: Mouse Myoblasts

value: Gfp transduction


title: C2C12 cells, Gfp transduction, 2

description: Library name: GFP2


title: BLZ_Jung_Tam_2

description: Library name: N126-13


title: Horse, NEUN sorted

description:
Library name: Horse-NEUN
NeuN+ RNA-seq from crotex

data_processing:
Reads were trimmed using cutadpat for adapter removal (AGATCGGAAGAGC) and quality trimming (-m 30).
Reads were then aligned to to corresponding reference genome with STAR [--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix alignment/${sample}/ --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD].
Duplicate reads were filtered using picard MarkDuplicates.
Counts were generated using  htseq-count using the intersection-nonempty method and non-stranded counting.
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: Raw counts tsv

extract_protocol:
At least 10 – 20 mg of frozen tissue was obtained from each sample using a metallic block and hammer to take a portion of the dissected cortex tissue. The tissue was then sealed inside of a Covaris Tissue TUBE (Covaris, cat. Nos. 520021 and 520023) and thoroughly pulverized using the chilled hammer and metallic block, with intermittent submerging into liquid nitrogen to maintain cold temperature and brittleness. Using a clean, pre-chilled scoopula, pulverized tissue was then transferred to a pre-chilled 2 mL DNA LoBind tube. RNA was isolated using the miRNeasy Mini Kit according to manufacturer instructions (QIAGEN, cat. no. 217084). Approximately 100,000 NeuN+ nuclei were sorted into 650 μL cold Trizol for RNA isolation. RNA isolation was performed using the Direct-zol RNA microprep kit  (Zymo Research. cat. no. R2060) per manufacturer instructions.
Sequencing libraries were prepared following the SMARTer Stranded Total RNA-seq Kit v2 – Pico Input (Takara Bio, cat. no. 634411).

value: Neurons


title: TdTomato+ cells collected from +/+;Aldh1l1+;tdT+/- 9 weeks old mouse brain (Replicate 3)

description: Library name: WT_F_3


title: Wild type ZmNFYA1, replicate 2

tag: cultivar

value: wild type


title: Horse

description:
Library name: Horse
Bulk RNA-seq from cortex

value: Cortex


title: TdTomato+ cells collected from +/+;Aldh1l1+;tdT+/- 9 weeks old mouse brain (Replicate 2)

description: Library name: WT_F_2


title: Mutant ZmMYBR6, replicate 1

tag: age


title: Monkey DRG from control skin 3

city: Baltimore

first: Pang-Yen

last: Tseng

address: 655 W. Lombard St.

department: Pain and Translational Symptom Science

institute: University of Maryland Baltimore

description:
Library name: Vehicle3
MnemDRG_TPM.csv
MnemDRG_counts.csv

data_processing:
Sequencing reads were aligned to reference transcriptomes using kallisto
Assembly: Ensembl mouse reference transcriptome GRCm38.v98; NCBI Macaca nemestrina Annotation Release 101, Mnem_1.0 (GCF_000956065.1)
Supplementary files format and content: Transcript per million (TPM)
Supplementary files format and content: counts

organism: Macaca nemestrina

source_name: DRG

extract_protocol:
The total RNA from fresh frozen mouse or monkey DRG were purified with Direct-zol RNA Miniprep kit (Zymo Research)
RNA-sequencing libraries were prepared and sequenced at NIDCD/NIDCR Genomics and Computational Biology Core

value: DRG

value: Vehicle


title: TdTomato+ cells collected from +/+;Aldh1l1+;tdT+/- 9 weeks old mouse brain (Replicate 1)

description: Library name: WT_F_1


title: Wild type ZmMYBR6, replicate 2

value: Endosperm

value: 15 DAP


title: Wild type ZmMYBR6, replicate 1


title: BLZ_Jung_Tam_4

description: Library name: N126-15


title: Wild type ZmMYBR6, replicate 3


title: BLZ_Jung_Oil_4

description: Library name: N126-11

value: Oil


title: 7815Tp

city: Limoges

first: Nathalie

last: Faumont

address: Rue Bernard Descottes

department: Centre de Biologie et de Recherche en Santé

country: France

institute: Université e Limoges

data_processing:
STAR package
Pair-end reads were aligned to the GRCm39 genome with the Gencode gtf version vM33.
STAR count reads belonging to genes declared in the transcriptome gtf file. This file is from the Gencode base (https://www.gencodegenes.org/mouse/release_M33.html)
Reads normalisation was done with the R package EdgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Spleen

extract_protocol:
Negative selection of spleen B-cells was performed with the Pan B Cells isolation kit of Miltenyi® (Miltenyi Biotec, Bergisch Gladbach, Germany). Then, cells were labeled with the anti-CD19-BV510 monoclonal antibody (BD Biosciences, Franklin Lakes, NJ) for cell sorting. CD19pos TOM+ and TOM- B-cells from TOM-AID mice and CD19pos TOM-/YFP-, TOM+/YFP- and TOM+/YFP+ from REL-AID mice were sorted on a Facs Aria III Cell Sorter (BD Biosciences). Total RNA was extracted with the RNeasy Kit (Qiagen, Les Ulis, France) following the manufacturer’s protocol and quantified with the NanoDrop One (Thermo Scientific™, Walham, MA).
Purification of polyA mRNA was done from 100ng total RNA with the Magnetic mRNA Isolation Kit (New England Biolabs, Ipswich, MA). Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations (New England Biolabs). Fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing were performed.

treatment_protocol: Mouse Immunization consisted of an intraperitoneal injection of 2.109 sheep red blood cells (SRBCs; SARL Atlantis France) on day 0 and monthly thereafter. Tamoxifen, purchased from Gibco (Gibco Thermo Fisher Scientific France, Illkirch-Graffenstaden, France), was administrated by gavage at 400 mg/kg on day 0, 2 and 4.  Then SRBC immunization boost were performed monthly until month 2

value: Spleen

value: sorted CD19pos tdTomato positive B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato

value: Tamoxifen gavage and sheep red blood cell immunization


title: Monkey DRG from control skin 1

description:
Library name: Vehicle1
MnemDRG_TPM.csv
MnemDRG_counts.csv


title: BLZ_Jung_Tam_1

description: Library name: N126-12

value: Brain

value: Microglia


title: BLZ_Jung_Oil_3

description: Library name: N126-10

value: Cx3cr1CreERT2(Jung) Hetero; Rosa26YFP Hetero


title: Monkey DRG from control skin 2

description:
Library name: Vehicle2
MnemDRG_TPM.csv
MnemDRG_counts.csv


title: Mutant ZmABI47, replicate 3

value: mutant


title: Monkey DRG from SADBE-treated skin 3

description:
Library name: SADBE3
MnemDRG_TPM.csv
MnemDRG_counts.csv

value: SADBE


title: Mutant ZmABI47, replicate 2


title: 7813TpYp

value: sorted CD19pos tdTomato positive YFP negative B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato_REL_YFP


title: Monkey DRG from SADBE-treated skin 2

description:
Library name: SADBE2
MnemDRG_TPM.csv
MnemDRG_counts.csv


title: BLZ_Littman_Tam_4

description: Library name: N126-07

value: Cx3cr1CreERT2(Litt) Hetero


title: 7813-7000-7001TpYn


title: Mutant ZmABI47, replicate 1


title: Monkey DRG from SADBE-treated skin 1

description:
Library name: SADBE1
MnemDRG_TPM.csv
MnemDRG_counts.csv

value: DRG


title: 7813Tn

value: sorted CD19pos tdTomato negative YFP negative B-cells


title: Rabbit, rep2, snATAC

description:
Library name: Rabbit2_snATAC
Rabbit2_filtered_feature_bc_matrix.h5

organism: Oryctolagus cuniculus

value: cortex


title: BLZ_Littman_Tam_2

description: Library name: N126-05


title: BLZ_Jung_Oil_2

description: Library name: N126-09


title: 7812Tp


title: Wild type ZmABI47, replicate 2

value: Endosperm

value: 15 DAP

value: wild type


title: BLZ_Littman_Tam_1

description: Library name: N126-04


title: BLZ_Jung_Oil_1

description: Library name: N126-08

value: Oil


title: Rabbit, rep1, snATAC

description:
Library name: Rabbit1_snATAC
Rabbit1_filtered_feature_bc_matrix.h5


title: Wild type ZmABI47, replicate 1


title: 7815Tn

value: Spleen

value: sorted CD19pos tdTomato negative B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato


title: BLZ_Littman_Oil_3

description: Library name: N126-03

value: Brain

value: Microglia


title: BLZ_Littman_Oil_2

description: Library name: N126-02


title: 7812Tn

value: Tamoxifen gavage and sheep red blood cell immunization


title: Rabbit, rep1, snRNA

description: Library name: Rabbit1_snRNA


title: Mutant ZmBZIP43, replicate 2

value: mutant


title: Rabbit, rep2, snRNA

description: Library name: Rabbit2_snRNA


title: 7810Tp

value: sorted CD19pos tdTomato positive B-cells


title: BLZ_Littman_Oil_1

description: Library name: N126-01


title: Rabbit, rep2, NEUN sorted

description:
Library name: Rabbit2-NEUN
NeuN+ RNA-seq from crotex

value: Cortex

value: Neurons


title: Mutant ZmBZIP43, replicate 3


title: 7810Tn


title: 7569TpYp

value: sorted CD19pos tdTomato positive YFP positive B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato_REL_YFP


title: Rabbit, rep1, NEUN sorted

description:
Library name: Rabbit1-NEUN
NeuN+ RNA-seq from crotex


title: Mutant ZmBZIP43, replicate 1


title: CUTTL1 cells Actinomycin D 360min, STM2457, rep3

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

description:
CUTTL1 ActD STM2457 360min_3
ActinomycinD_normalized_counts.tsv

data_processing:
Data was mapped to the reference genome (GRCh38.105 assembly) using STAR (version STAR/2.7.11b) and differential expression analysis was performed with DESeq2 (version 1.42.1).
Assembly: hg38
Supplementary files format and content: DESeq2 normalized counts, .csv format

source_name: blood

growth_protocol: RPMI 20%FBS

extract_protocol:
RNA was extracted using ‘miRNeasy Mini’ (217004, Qiagen Benelux BV, Venlo, The Netherlands) or ‘miRNeasy Micro’ (217084, Qiagen Benelux BV) kits, and DNA digestion was done on-column according to the manufacturer’s protocol.
RNA extracted as described above was further used for full length RNA sequencing utilizing the Watchmaker total mRNA library preparation kit (7BK0001-096, Watchmaker Genomics, Boulder, CO, USA) according to manufacturer’s instructions). Prepared libraries were further sequenced using the AVITI sequencer (Element Biosciences, San Diego, USA) using the AVITI 2x150 High Output Sequencing Kit (860-00001, Element Biosciences, San Diego, USA).

value: blood

value: T-ALL

value: WT

value: Actinomycin D, 10uM, 360min, STM2457


title: BLZ_Littman_Tam_3

description: Library name: N126-06

value: Cx3cr1CreERT2(Litt) Hetero


title: 7569Tn

value: Spleen

value: sorted CD19pos tdTomato negative YFP negative B-cells


title: Wild type ZmBZIP43, replicate 3

value: Endosperm

value: 15 DAP

value: wild type


title: Wild type ZmABI47, replicate 3


title: CUTTL1 cells Actinomycin D 360min, STM2457, rep2

description:
CUTTL1 ActD STM2457 360min_2
ActinomycinD_normalized_counts.tsv


title: Rabbit, rep2

description:
Library name: Rabbit2
Bulk RNA-seq from cortex

source_name: Cortex


title: Rabbit, rep1

description:
Library name: Rabbit1
Bulk RNA-seq from cortex


title: 7568TpYp

value: Tamoxifen gavage and sheep red blood cell immunization


title: Wild type ZmBZIP43, replicate 2


title: CUTTL1 cells Actinomycin D 360min, STM2457, rep1

description:
CUTTL1 ActD STM2457 360min_1
ActinomycinD_normalized_counts.tsv


title: 7568Tn


title: CUTTL1 cells Actinomycin D 360min, DMSO, rep3

description:
CUTTL1 ActD DMSO 360min_3
ActinomycinD_normalized_counts.tsv

value: Actinomycin D, 10uM, 360min


title: parthenote3 [RNA-seq]

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

description: Library name: PA3

data_processing:
To remove adapters and low-quality reads from the raw RNA-seq data, we utilized Trimmomatic (v0.39), applying parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Using the STAR aligner (v2.7.11b), the cleaned reads were aligned to the reference genome (Sscrofa11.1/susScr11) with default parameters.
Uniquely mapped reads were retrieved with SAMtools and were subsequently deduplicated using Picard MarkDuplicate.
Assembly: susScr11
Supplementary files format and content: Quantification files in plain-text format (.sf).

organism: Sus scrofa

source_name: whole embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA, total RNA was isolated and fragmented.
To select poly-A tails and construct cDNA libraries, 1 µg of total RNA was used with the TruSeq RNA Sample Prep Kit v.2.

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: whole embryo

value: parthenogenesis


title: NeuN+ ATAC-seq, Rabbit, rep2

city: Huntsville

first: J.

last: Cochran

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: ATAC_Rabbit2-NEUN

data_processing:
Samples were processed using the standard ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline v.1.7.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: ATAC-seq peak calls, tagAlign alignment files

extract_protocol:
After centrifugation to remove sucrose gradient, nuclei were labeled by resuspending the pellet in 1 mL blocking buffer with NeuN-488 antibody (Millipore, cat. no. MAB377X) at 1:4,000 and 4,6-diamidino-2-phenylindole at 1:20,000 for at least 30 minutes at 4°C with rotation. Nuclei were then centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was removed the pellet was resuspended in 500 μL cold 1% BSA in PBS with RNase Inhibitor. Nuclei were then filtered through a 35 μm filter, washing the filter with an additional 100 μL 1% BSA in PBS. Nuclei were then sorted using a Sony MA900 device with a 70-μm nozzle and pressure not exceeding a pressure setting of 7. Gates were set to capture those populations that were positive for 488 signal (NeuN+). Both the NeuN+ and NeuN- populations were collected and held at 4°C . Purity of selected samples was typically >95% based on reanalysis of sorted samples.
Approximately 100,000 NeuN+ nuclei were isolated from cortex tissues and used for ATAC-seq library preparation as per standard protocols (PMID: 24097267, PMID: 25559105, PMID: 28846090) with the following modifications. Briefly, 50 μL of cold 5x lysis buffer was added to sorted nuclei to reach a final concentration of 1x (1- mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and incubated for 20 min on ice followed by centrifugation for 10 minutes. The transposition reaction was incubated for 30 minutes at 37°C with agitation at 1000 rpm (Illumina Tagment DNA Enzyme and Buffer kit, cat. no. 20034198). After column clean up via the QIAGEN MinElute Reaction Cleanup kit (QIAGEN, cat. no. 28204) and PCR amplification of libraries, an additional clean up with AMPure XP beads (0.8X ratio) was performed with two 80% ethanol washes before quantification using a DNA High-Sensitivity chip on a 2100 BioAnalyzer (Agilent). Libraries were sequenced paired-end with the Illumina dual indexes on a NovaSeq X Plus 10 B 300 cycle flowcell targeting 100 million reads per sample.

value: Cortex

value: Neurons


title: CUTTL1 cells Actinomycin D 360min, DMSO, rep2

description:
CUTTL1 ActD DMSO 360min_2
ActinomycinD_normalized_counts.tsv


title: 7567TpYp

value: sorted CD19pos tdTomato positive YFP negative B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato_REL_YFP


title: 7567T-7569T-7568TpYn


title: NeuN+ ATAC-seq, Rabbit, rep1

description: Library name: ATAC_Rabbit1-NEUN


title: parthenote1 [RNA-seq]

description: Library name: PA1


title: 7566TpYp

value: sorted CD19pos tdTomato negative YFP positive B-cells


title: CUTTL1 cells Actinomycin D 180min, STM2457, rep3

description:
CUTTL1 ActD STM2457 180min_3
ActinomycinD_normalized_counts.tsv

value: blood

value: T-ALL

value: WT

value: Actinomycin D, 10uM, 180min, STM2457


title: CUTTL1 cells Actinomycin D 180min, STM2457, rep2

description:
CUTTL1 ActD STM2457 180min_2
ActinomycinD_normalized_counts.tsv


title: control6 [RNA-seq]

description: Library name: CN6

value: untreated


title: 7567Tn

value: Spleen

value: sorted CD19pos tdTomato negative YFP negative B-cells


title: Cat, rep1, snATAC

description:
Library name: Cat1351_snATAC
Cat1351_filtered_feature_bc_matrix.h5

value: cortex


title: control5 [RNA-seq]

description: Library name: CN5


title: 7566TpYn

value: Tamoxifen gavage and sheep red blood cell immunization


title: CUTTL1 cells Actinomycin D 180min, STM2457, rep1

description:
CUTTL1 ActD STM2457 180min_1
ActinomycinD_normalized_counts.tsv


title: control4 [RNA-seq]

description: Library name: CN4


title: 7566Tn


title: Wild type ZmBZIP43, replicate 1

value: Endosperm

value: 15 DAP

value: wild type


title: Cat, rep3, snRNA

description: Library name: Cat2079_snRNA


title: Cat, rep2, snRNA

description: Library name: Cat2066_snRNA


title: parthenote2 [RNA-seq]

description: Library name: PA2

value: whole embryo

value: parthenogenesis


title: CUTTL1 cells Actinomycin D 180min, DMSO, rep3

description:
CUTTL1 ActD DMSO 180min_3
ActinomycinD_normalized_counts.tsv

value: Actinomycin D, 10uM, 180min


title: control2 [RNA-seq]

description: Library name: CN2


title: Cat, rep1, snRNA

description: Library name: Cat1351_snRNA


title: 7001TpYp

value: sorted CD19pos tdTomato positive YFP positive B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato_REL_YFP


title: control3 [RNA-seq]

description: Library name: CN3


title: 7001Tn


title: Cat2079, NEUN sorted

description:
Library name: Cat2079-NEUN
NeuN+ RNA-seq from crotex

value: Cortex

value: Neurons


title: Cat, rep3, snATAC

description:
Library name: Cat2079_snATAC
Cat2079_filtered_feature_bc_matrix.h5


title: CUTTL1 cells Actinomycin D 180min, DMSO, rep1

description:
CUTTL1 ActD DMSO 180min_1
ActinomycinD_normalized_counts.tsv

value: blood

value: T-ALL

value: WT


title: CUTTL1 cells Actinomycin D 360min, DMSO, rep1

description:
CUTTL1 ActD DMSO 360min_1
ActinomycinD_normalized_counts.tsv

value: Actinomycin D, 10uM, 360min


title: Cat, rep2, snATAC

description:
Library name: Cat2066_snATAC
Cat2066_filtered_feature_bc_matrix.h5


title: 7000TpYp

value: Spleen


title: Cat2079, rep3

description:
Library name: Cat2079
Bulk RNA-seq from cortex


title: 7000Tn

value: sorted CD19pos tdTomato negative YFP negative B-cells


title: Cat2066, rep2

description:
Library name: Cat2066
Bulk RNA-seq from cortex


title: Nodose_2

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

country: Canada

institute: Queen's University

description: Library name: Sample_5

data_processing:
Illumina NextSeq500 platform with 75-cycle single-end reads
Basecalling was performed using Illumina RTA 2.4.11, and demultiplexing was done with bcl2fastq 2.20 (allowing one mismatch in the index).
Trimmomatic was used to remove adapter sequences and low-quality bases from the 3′ end of each read, and the resulting high-quality reads were aligned to the GRCm38 mouse genome using STAR v2.5.11, which also generated gene-level read counts.
Assembly: GRCm38
Supplementary files format and content: Tab Separated Values (.tsv) files including raw counts of every sample
Supplementary files format and content: Tab Separated Values (.tsv) files includingTPM of isoform transcripts of gene transcripts every sample

source_name: jugular-nodose complex

extract_protocol:
ThermoFisher PureLink™ RNA Micro Scale Kit
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing

value: jugular-nodose complex

value: TRPV1+ vagal sensory neurons


title: Nodose_3

description: Library name: Sample_6


title: Cat1351, rep1

description:
Library name: Cat1351
Bulk RNA-seq from cortex


title: 3998Tn

value: Tamoxifen gavage and sheep red blood cell immunization


title: CUTTL1 cells Actinomycin D 60min, STM2457, rep2

description:
CUTTL1 ActD STM2457 60min_2
ActinomycinD_normalized_counts.tsv

value: Actinomycin D, 10uM, 60min, STM2457


title: CUTTL1 cells Actinomycin D 60min, STM2457, rep1

description:
CUTTL1 ActD STM2457 60min_1
ActinomycinD_normalized_counts.tsv


title: Nodose_1

description: Library name: Sample_4


title: CUTTL1 cells Actinomycin D 180min, DMSO, rep2

description:
CUTTL1 ActD DMSO 180min_2
ActinomycinD_normalized_counts.tsv


title: Horse, snATAC

description:
Library name: Horse_snATAC
Horse_filtered_feature_bc_matrix.h5

organism: Equus caballus

value: cortex


title: CUTTL1 cells Actinomycin D 60min, DMSO, rep3

description:
CUTTL1 ActD DMSO 60min_3
ActinomycinD_normalized_counts.tsv

value: Actinomycin D, 10uM, 60min


title: Horse, snRNA

description: Library name: Horse_snRNA


title: 3346Tn

value: sorted CD19pos tdTomato negative B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato


title: Cancer_3

description: Library name: Sample_3

data_processing:
Illumina NextSeq500 platform with 75-cycle single-end reads
Basecalling was performed using Illumina RTA 2.4.11, and demultiplexing was done with bcl2fastq 2.20 (allowing one mismatch in the index).
Trimmomatic was used to remove adapter sequences and low-quality bases from the 3′ end of each read, and the resulting high-quality reads were aligned to the GRCm38 mouse genome using STAR v2.5.11, which also generated gene-level read counts.
Assembly: GRCm38
Supplementary files format and content: Tab Separated Values (.tsv) files including raw counts of every sample
Supplementary files format and content: Tab Separated Values (.tsv) files including FPKM and TPM of isoform transcripts of gene transcripts every sample


title: CUTTL1 cells Actinomycin D 60min, DMSO, rep2

description:
CUTTL1 ActD DMSO 60min_2
ActinomycinD_normalized_counts.tsv


title: control1 [RNA-seq]

description: Library name: CN1

value: whole embryo

value: untreated


title: CUTTL1 cells Actinomycin D 60min, DMSO, rep1

description:
CUTTL1 ActD DMSO 60min_1
ActinomycinD_normalized_counts.tsv


title: Cancer_1

description: Library name: Sample_1


title: Cancer_2

description: Library name: Sample_2


title: 3340Tp

value: sorted CD19pos tdTomato positive B-cells


title: Cow, NEUN sorted

description:
Library name: Cow-NEUN
NeuN+ RNA-seq from crotex

value: Cortex

value: Neurons


title: 3340Tn


title: Cow

description:
Library name: Cow
Bulk RNA-seq from cortex


title: CUTTL1 cells Actinomycin D 60min, STM2457, rep3

description:
CUTTL1 ActD STM2457 60min_3
ActinomycinD_normalized_counts.tsv

value: blood

value: T-ALL

value: WT


title: CUTTL1 cells Actinomycin D 20min, STM2457, rep3

description:
CUTTL1 ActD STM2457 20min_3
ActinomycinD_normalized_counts.tsv

value: Actinomycin D, 10uM, 20min, STM2457


title: 3337Tp

value: Spleen


title: A549-Reference

city: Gothenburg

first: Volkan

last: Sayin

address: Medicinaregatan 1F

department: Department of Surgery

country: Sweden

institute: University of Gothenburg

description: Library name: Sample 5

data_processing:
Sequencing adapters and low-quality bases are trimmed using Trimmomatic 0.38
MACS2 2.1.2 was used for peak calling to identify open chromatin region
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Lung Tumor

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2.

extract_protocol:
cell suspensions of 500,000 cells were sent for further processing to an external facility at  Genewiz (Azenta).
Samples were further processed by 150-bp-paired-end sequencing on an Illumina HiSeq 2500 at the external facility

treatment_protocol: CRISPR-mediated knockout was used to generate BACH1-knockout cells, while WT cells served as controls.

value: Lung Tumor

value: epithelial cells


title: DNA_REP3

first: Yihan

last: Lin

address: No.5 Yiheyuan Road, Haidian

institute: Peking University

description: Library name: Sample 21

data_processing:
Trimmomatic 0.39 was used to remove the 5' end 15-bp low quality sequence of the FASTQ file. BWA 0.7.17-r1188 was employed to map the resulting cleaned reads to the reference sequence. The resulting bam files were processed using a command mpileup from samtools to generate bcf file. To precisely profile the mutational frequency, nucleotides with sequencing quality score below Q30 were discarded. Then, custom Bash and Python scripts were used to extract the mutation information and calculate the mutation frequency.
Assembly: trVLP-ASV genome sequence
Supplementary files format and content: An excel file containing the mutation frequency information for each mutation type in each sample

organism: Mesocricetus auratus

source_name: kidney

growth_protocol: BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 μg/ml streptomycin, and 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
For each sample, supernatants containing trVLPs were collected, and RNA was extracted using TRIzol LS Reagent (HaiGene, #B1901), and the RNA was extracted following the manufacturer's protocol.
Approximately 100 ng of RNA was reverse transcribed into cDNA using the HiScript III First-Strand cDNA Synthesis Kit (Vazyme, R312-02) with sequence-specific primer (Sindis-gsp-R2: tgcgcctcctcggaaatacg). Subsequently, 5 µL of the cDNA was used as a template for PCR amplification in a 50 µL reaction volume with KOD One PCR Master Mix. The PCR was performed for 28 cycles using primers designed to target specific regions of the trVLP genome, such as the mCherry region. The PCR products were sequenced using the Fast Next-Generation Sequencing (NGS) service by a Miseq merchine from Tsingke Biotechnology.

treatment_protocol: trVLP-ASV transduction

value: kidney

value: BHK-21 cells

value: fibroblast cells

value: expressing nsP4 and human ACE2

value: trVLP-ASV transduction

tag: batch


title: CUTTL1 cells Actinomycin D 20min, STM2457, rep2

description:
CUTTL1 ActD STM2457 20min_2
ActinomycinD_normalized_counts.tsv


title: A549-KO-1_CHIP

description: Library name: Sample 4

value: A549 sg2 BACH1 KO


title: 3337Tn

value: sorted CD19pos tdTomato negative B-cells

value: C57/BL6 background, heterozygous AID.CREert2_tdTomato

value: Tamoxifen gavage and sheep red blood cell immunization


title: 3346Tp

value: sorted CD19pos tdTomato positive B-cells


title: A549-WT-3_CHIP

description: Library name: Sample 3

value: A549 WT


title: CUTTL1 cells Actinomycin D 20min, STM2457, rep1

description:
CUTTL1 ActD STM2457 20min_1
ActinomycinD_normalized_counts.tsv

value: blood

value: T-ALL


title: DNA_REP1

description: Library name: Sample 19


title: 105_RNAseq Lung_PBS/SAL

city: Chapel Hill

first: Lanazha

last: Belfield-Simpson

address: 125 Mason Farm Rd

institute: Univeristy of North Carolina at Chapel Hill

data_processing:
Raw data in fastq files were mapped to reference genome/transcriptome using STAR aligner to generate .BAM files.
Gene expression was estimated based on the BAM file with transcript assembler, StringTie v2, and saved as count and TPM values.
Assembly: GRCm39 and Gencode vM33
Supplementary files format and content: Estimated raw count in tab-delimited text.
Supplementary files format and content: Estimated TPM (transcripts per million mapped reads) in tab-delimited text.

source_name: Lung

extract_protocol:
Total RNA was isolated from Whole Lung using the Quick-RNA Microprep kit (Zymo Research).
Standard RNA-seq with PolyA selection, 20M paired end reads per sample, Illumina, 2x150bp.

treatment_protocol: Male wild type (C57Bl/6;stock no. 000664, Bar Harbor, Maine) mice between 7-8 weeks of age were utilized for all studies. Mice received five oropharyngeal instillations of 10 µg HDM (Greer, catalog number: XPB70D3A2.5) in 50µl (HDM mice) or PBS (Ca2+, Mg2+ free, 50µl) (PBS mice) at 2-3 day intervals. Twenty-four hours after the fifth instillation of HDM (HDM mice) or PBS (PBS mice), mice received 100 µL of 2 mg Combustion Products (CP)/ml saline or 100 µL saline (controls) by oropharyngeal instillation. At 24 hours post instillation, animals were euthanized by isoflurane overdose immediately prior to lung harvest. Lungs were flash frozen and stored at -80*C prior to RNA isolation.

value: Lung

value: PBS and Saline


title: CUTTL1 cells Actinomycin D 20min, DMSO, rep3

description:
CUTTL1 ActD DMSO 20min_3
ActinomycinD_normalized_counts.tsv

value: WT

value: Actinomycin D, 10uM, 20min


title: 104_RNAseq Lung_PBS/SAL


title: A549-WT-2_CHIP

description: Library name: Sample 2

value: Lung Tumor

value: epithelial cells


title: CUTTL1 cells Actinomycin D 20min, DMSO, rep2

description:
CUTTL1 ActD DMSO 20min_2
ActinomycinD_normalized_counts.tsv


title: DAY6-REP2

description: Library name: Sample 17

value: kidney

value: BHK-21 cells

value: fibroblast cells


title: 102_RNAseq Lung_PBS/CP

value: PBS and CP


title: A549-WT-1_CHIP

description: Library name: Sample 1


title: CUTTL1 cells Actinomycin D 20min, DMSO, rep1

description:
CUTTL1 ActD DMSO 20min_1
ActinomycinD_normalized_counts.tsv


title: 101_RNAseq Lung_PBS/CP


title: A549-sg2-BACH1-KO-1

description:
Library name: Sample 4
04_5042Gothenburg_A549-sg2-BACH1-KO-1_RNA_hs_i121

data_processing:
Reads aligned to the ENSEMBL GRCh38 genome using STAR RNA-Seq aligner.
Differential expression analyzed with DESeq2 software.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalised counts for each sample

source_name: Lung tumor

growth_protocol: A549 cells were cultured in DMEM at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification Kit.
RNA libraries prepared using Illumina-compatible library preparation kits.

treatment_protocol: CRISPR-mediated knockout was used for BACH1-KO cells, WT cells served as controls.

value: Lung tumor

value: A549 BACH1 KO


title: A549-sg2-BACH1-KO-2

description:
Library name: Sample 5
05_5042Gothenburg_A549-sg2-BACH1-KO-2_RNA_hs_i122


title: DAY6-REP1

description: Library name: Sample 16

value: expressing nsP4 and human ACE2

value: trVLP-ASV transduction


title: 100_RNAseq Lung_HDM/SAL

value: HDM and Saline


title: DAY4-REP3

description: Library name: Sample 15


title: DNA_REP2

description: Library name: Sample 20


title: A549-sg2-BACH1-KO-3

description:
Library name: Sample 6
06_5042Gothenburg_A549-sg2-BACH1-KO-3_RNA_hs_i123


title: 98_RNAseq Lung_HDM/CP

value: HDM and CP


title: CUTTL1 cells Actinomycin D 0min, DMSO, rep3

description:
CUTTL1 ActD DMSO 0min_3
ActinomycinD_normalized_counts.tsv

value: blood

value: T-ALL

value: Actinomycin D, 10uM, 0min


title: CUTTL1 cells Actinomycin D 0min, STM2457, rep2

description:
CUTTL1 ActD STM2457 0min_2
ActinomycinD_normalized_counts.tsv

value: WT

value: Actinomycin D, 10uM, 0min, STM2457


title: A549-WT-2

description:
Library name: Sample 2
02_5042Gothenburg_A549-WT-2_RNA_hs_i119

value: A549 WT


title: DAY6-REP3

description: Library name: Sample 18


title: 97_RNAseq Lung_HDM/CP

value: Lung


title: CUTTL1 cells Actinomycin D 0min, STM2457, rep1

description:
CUTTL1 ActD STM2457 0min_1
ActinomycinD_normalized_counts.tsv


title: DAY4-REP2

description: Library name: Sample 14

value: kidney


title: DAY14-REP3

description: Library name: Sample 12

value: BHK-21 cells


title: A549-WT-1

description:
Library name: Sample 1
01_5042Gothenburg_A549-WT-1_RNA_hs_i118

value: epithelial cells


title: DAY14-REP2

description: Library name: Sample 11

value: fibroblast cells


title: CUTTL1 cells Actinomycin D 0min, STM2457, rep3

description:
CUTTL1 ActD STM2457 0min_3
ActinomycinD_normalized_counts.tsv


title: 96_RNAseq Lung_HDM/CP


title: CUTTL1 cells Actinomycin D 0min, DMSO, rep1

description:
CUTTL1 ActD DMSO 0min_1
ActinomycinD_normalized_counts.tsv


title: DAY14-REP1

description: Library name: Sample 10


title: 81_RNAseq Lung_PBS/SAL

value: PBS and Saline


title: Moderate MASLD sample 3, female, LaminB1 ChIP

city: Pittsburgh

first: Irina

middle: M

last: Bochkis

state: PA

address: 707A Scaife Hall, 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

description:
LaminB1_H_F_moderate_MASLD.bed
H F LaminB1 moderate MASLD 3

data_processing:
Reads were aligned to human genome (hg19; NCBI build 37) using BWA v0.7.12 (Li and Durbin 2009). Duplicate reads were removed using Picard v 1.134 (http://picard.sourceforge.net). Reads (Phred score ≥ 30) that aligned uniquely were used for subsequent analysis. Data from three human patients were merged for FOXA2 and lamin B1 binding (three normal and three MASLD). Epic peak caller 16 (https://github.com/biocore-ntnu/epic2) was used to determine lamin B1–associated domains in human patients (hg19 as species, window size of 10 kb, gap size of three, FDR 5%). PeakSeq 17 was used to identify FOXA2 bound peaks against input Normals (FDR 5%, Q-value < 0.07).
Assembly: hg19
Supplementary files format and content: bed files with peak calls from PeakSeq with the following columns: chromosome, begin coordinate, end coordinate, q-value

source_name: Liver

extract_protocol:
Snap-frozen mouse or human liver (100 mg) was used to prepare chromatin. Briefly, liver tissue was minced in cold PBS and cross-linked in 1% formaldehyde/PBS for 15 min with constant rotation in a Labquake tube rotator. Cross-linking was quenched by adding glycine to a final concentration of 0.125M. Nuclear lysate was sonicated using a Diagenode Bioruptor Pico for 14 cycles (30 sec on/30 sec off). FOXA2- specific rabbit antiserum (Seven Hills Bioreagents WRAB-1200) and rabbit antibody to lamin B1 (Abcam Ab16048), were used for immunoprecipitation.
Libraries were made according to standard Illumina protocol (end-repair of ChIP DNA, addition of A base to the 3′-ends, adapter ligation, and amplification). We used multiplex adapters for sequencing and Kapa HiFi DNA polymerase (Kapa Biosystems) for PCR amplification (16 cycles). Library fragments were isolated using Pippin HT agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 and NextSeq 2000 instruments following the manufacturer’s protocols.

value: Liver

tag: subject status

value: Moderate MASLD

tag: chip antibody

value: LaminB1 ChIP


title: 99_RNAseq Lung_HDM/SAL

value: HDM and Saline


title: CUTTL1 cells,  METTL3KD, sh 366,rep3

description:
CUTTL1 METTL3KD sh366_3
METTL3KD_normalized_counts.tsv


title: Moderate MASLD sample 1, female, LaminB1 ChIP

description:
LaminB1_H_F_moderate_MASLD.bed
H F LaminB1 moderate MASLD 1


title: CUTTL1 cells,  METTL3KD, sh 366,rep2

description:
CUTTL1 METTL3KD sh366_2
METTL3KD_normalized_counts.tsv


title: Moderate MASLD sample 2, female, LaminB1 ChIP

description:
LaminB1_H_F_moderate_MASLD.bed
H F LaminB1 moderate MASLD 2


title: DAY4-REP1

description: Library name: Sample 13

value: expressing nsP4 and human ACE2

value: trVLP-ASV transduction


title: 80_RNAseq Lung_PBS/SAL


title: DAY10-REP3

description: Library name: Sample 9


title: A549-WT-3

description:
Library name: Sample 3
03_5042Gothenburg_A549-WT-3_RNA_hs_i120

value: Lung tumor


title: DAY10-REP2

description: Library name: Sample 8


title: CUTTL1 cells Actinomycin D 0min, DMSO, rep2

description:
CUTTL1 ActD DMSO 0min_2
ActinomycinD_normalized_counts.tsv

value: blood

value: T-ALL

value: Actinomycin D, 10uM, 0min


title: 76_RNAseq Lung_PBS/CP

value: PBS and CP


title: DAY10-REP1

description: Library name: Sample 7


title: CUTTL1 cells,  METTL3KD, sh 366,rep1

description:
CUTTL1 METTL3KD sh366_1
METTL3KD_normalized_counts.tsv


title: CUTTL1 cells,  METTL3KD, sh 677,rep3

description:
CUTTL1 METTL3KD sh677_3
METTL3KD_normalized_counts.tsv


title: Mild MASLD sample 3, female, LaminB1 ChIP

description:
LaminB1_H_F_mild_MASLD.bed
H F LaminB1 mild MASLD 3

value: Mild MASLD


title: 75_RNAseq Lung_PBS/CP

value: Lung


title: Mild MASLD sample 2, female, LaminB1 ChIP

description:
LaminB1_H_F_mild_MASLD.bed
H F LaminB1 mild MASLD 2


title: CUTTL1 cells,  METTL3KD, sh 677,rep2

description:
CUTTL1 METTL3KD sh677_2
METTL3KD_normalized_counts.tsv


title: 48H-REP3

description: Library name: Sample 6

value: kidney

value: BHK-21 cells


title: 72_RNAseq Lung_HDM/SAL


title: Mild MASLD sample 1, female, LaminB1 ChIP

description:
LaminB1_H_F_mild_MASLD.bed
H F LaminB1 mild MASLD 1


title: 48H-REP2

description: Library name: Sample 5

value: fibroblast cells


title: CUTTL1 cells,  METTL3KD, sh 677,rep1

description:
CUTTL1 METTL3KD sh677_1
METTL3KD_normalized_counts.tsv


title: Normal Liver sample 3, female, LaminB1 ChIP

description:
LaminB1_H_F_normal_liver.bed
H F LaminB1 Normal 3

value: healthy


title: 67_RNAseq Lung_HDM/CP

value: HDM and CP


title: Normal Liver sample 2, female, LaminB1 ChIP

description:
LaminB1_H_F_normal_liver.bed
H F LaminB1 Normal 2

value: Liver


title: CUTTL1 cells shControl, METTL3_matched, rep3

description:
CUTTL1 shCTR_METTL3_3
METTL3KD_normalized_counts.tsv

value: WT


title: 66_RNAseq Lung_HDM/CP


title: 79_RNAseq Lung_PBS/SAL

value: PBS and Saline


title: 48H-REP1

description: Library name: Sample 4

value: expressing nsP4 and human ACE2


title: 24H-REP3

description: Library name: Sample 3

value: trVLP-ASV transduction


title: CUTTL1 cells shControl, METTL3_matched, rep2

description:
CUTTL1 shCTR_METTL3_2
METTL3KD_normalized_counts.tsv


title: Normal Liver sample 1, female, LaminB1 ChIP

description:
LaminB1_H_F_normal_liver.bed
H F LaminB1 Normal 1

value: LaminB1 ChIP


title: 24H-REP2

description: Library name: Sample 2


title: CUTTL1 cells shControl, METTL3_matched, rep1

description:
CUTTL1 shCTR_METTL3_1
METTL3KD_normalized_counts.tsv

value: blood


title: Moderate MASLD sample 3, female, Foxa2 ChIP

description:
Foxa2_H_F_moderate_MASLD.bed
H F Foxa2 moderate MASLD 3

value: Moderate MASLD

value: Foxa2 ChIP


title: Moderate MASLD sample 2, female, Foxa2 ChIP

description:
Foxa2_H_F_moderate_MASLD.bed
H F Foxa2 moderate MASLD 2


title: 24H-REP1

description: Library name: Sample 1


title: 59_RNAseq Lung_PBS/CP

value: PBS and CP


title: Moderate MASLD sample 1, female, Foxa2 ChIP

description:
Foxa2_H_F_moderate_MASLD.bed
H F Foxa2 moderate MASLD 1


title: 61_RNAseq Lung_PBS/SAL


title: Thymocytes 1

description:
Thymocytes 1
TALL_Thymus_normalized_counts.tsv

source_name: Thymus

value: Thymus

value: Thymocytes


title: VIR-7831_rep1

description: Library name: Sample 23

data_processing:
Trimmomatic 0.39 was used to remove the 5' end 15-bp low quality sequence of the FASTQ file. BWA 0.7.17-r1188 was employed to map the resulting cleaned reads to the reference sequence. The resulting bam files were processed using a command mpileup from samtools to generate bcf file. To precisely profile the mutational frequency, nucleotides with sequencing quality score below Q30 were discarded. Then, custom Bash and Python scripts were used to extract the mutation information and calculate the mutation frequency.
Assembly: trVLP-ASV genome sequence
Supplementary files format and content: An Excel file for each sample, containing the mutation frequency information for each type of mutation in the RBD region.

extract_protocol:
For each sample, supernatants containing trVLPs were collected, and RNA was extracted using TRIzol LS Reagent (HaiGene, #B1901), and the RNA was extracted following the manufacturer's protocol.
Approximately 100 ng of RNA was reverse transcribed into cDNA using the HiScript III First-Strand cDNA Synthesis Kit (Vazyme, R312-02) with sequence-specific primer (Sindis-gsp-R2: tgcgcctcctcggaaatacg). Subsequently, 5 µL of the cDNA was used as a template for PCR amplification in a 50 µL reaction volume with KOD One PCR Master Mix. The PCR was performed for 28 cycles using primers designed to target specific regions of the trVLP genome, such as the RBD region. The PCR products were sequenced using the Fast Next-Generation Sequencing (NGS) service by a Miseq merchine from Tsingke Biotechnology.

treatment_protocol: trVLP-ASV transduction and antibody treatment

value: kidney

value: VIR-7831 antibody


title: Mild MASLD sample 3, female, Foxa2 ChIP

description:
Foxa2_H_F_mild_MASLD.bed
H F Foxa2 mild MASLD 3

value: Mild MASLD


title: Thymocytes 2

description:
Thymocytes 2
TALL_Thymus_normalized_counts.tsv


title: 58_RNAseq Lung_PBS/CP

value: Lung


title: SA55_rep2_JN.1

description: Library name: Sample 22

value: BHK-21 cells

value: fibroblast cells

value: SA55 antibody


title: T-ALL PDX 3

description:
T-ALL PDX 3
TALL_Thymus_normalized_counts.tsv

value: T-ALL blasts

value: Leukemic blasts

value: WT