title: distal, WENR-minus, input, biol rep 3

city: Baltimore

first: Lijing

last: Yang

state: MD

address: 3400 N. Charles St.

institute: Johns Hopkins university

data_processing:
Trimmomatic v0.39 was used to trim the ChIP-Seq reads and FastQC was used again to check whether the adaptors were eliminated successfully
Bowtie2 v2.4.5 was used to align reads to the mouse (mm10) genome.
Samtools v1.13 was applied to delete the duplicate alignments.
Peak calling performed by Macs2 v2.2.7.1 peak caller with parameters ‘callpeak -f BAM -g mm -B -q 0.01’ and matched input was set as control
Assembly: BigWig files were generated using deeptools v3.5.1.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: distal colon

growth_protocol: Proximal and distal colon organoids were cultured in ENSW-plus medium at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 minutes. After quenching and cell lysis, chromatin was sonicated using a bioruptor (diagenode).
DNA extracted from 6 wells of organoids. Chipmentation method (Schmidl et al , 2015; PMID: 26280331) was applied to build the libraries. ChIP-seq libraries were prepared using Kapa HiFi HotStart Ready Mix kit complemented with Nextera XT index kit from Illmina. Post amplification libraries were size selected at 200-500 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Organoids were cultured in ENSW-minus medium for 3 days or continue to be cultured in ENSW-plus medium.

value: distal colon

value: organoid

value: Mouse distal colon

value: Cross homozygous tdTomato reporter (B6;129S6- t(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mouse with  heterozygous Cre-inducible BrafV600E mouse(B6.129P2(Cg)-Braftm1Mmcm/J) to generate heterozygous Cre-inducible BRAFV600E with heterozygous tdTomato reporter.

value: WENR-minus


title: P23-45_40min_input_gp64_replica1

status: Public on Dec 12 2023

type: SRA

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

description:
P23-45_40min_input_gp64_1
Replica 1

library_source: genomic

data_processing:
The adapters and low-quality sequences were eliminated by the Skoltech Genomics Core Facility.
ChIP-seq reads were aligned to P23-45 genome with the second long terminal repeat ommited ([1...83630] of the GenBank accession OP542242) using bowtie2 (version 2.4.1).
Samtools (version 1.10) software was used to convert .sam files to .bam format and to filter the reads. Filtering was performed using the following parameters: -F 4 (to remove all unmapped reads), -f 2 (to keep only the reads mapped in a proper pair), -q 1 (to skip the alignments with mapQuality < 1).
BedGraph files were generated using  MACS2 (version 2.2.7.1) with default settings.
Assembly: GenBank accession OP542242
Supplementary files format and content: bedGraph

molecule: genomic DNA

organism: Thermus thermophilus HB8

source_name: bacterial

growth_protocol: Bacterial cells were grown in an orbital shaker at 70°C in liquid medium (0.8% tryptone, 0.4% NaCl, 0.2% yeast extract, 0.5 mM MgSO4, and 0.5 mM CaCl2 in “Vittel” mineral water). Cells were grown until an optical density at 600 nm of around 0.2 and infected with P23-45 bacteriophage at a multiplicity of infection 10. At 5, 20, and 40 min post infection 200 ml of cells were collected.

extract_protocol:
Infected cells were fixed with 1% formaldehyde for 20 minutes. The cross-linking reaction was stopped by the addition of dry glycine up to the final concentration of 0.5 M. Cells were incubated for 20 min with agitation. The cells were harvested by centrifugation and washed twice with ice-cold TBS (10 mM Tris-HCl pH 7.6, 150 mM NaCl). The cells were lysed and DNA was sheared by sonication to an average size of 200 – 500 bp. Immunoprecipitation was performed using corresponding antibodies and Sera-Mag SpeedBeads Protein A/G Sepharose magnetic beads (GEHealth).
DNA libraries were generated by the Skoltech Genomics Core Facility using Swift Accel-NGS 1S Kit (Swift Biosciences) following the manufacturer’s instructions.

tag: infection

value: P23-45 bacteriophage

tag: cell type

value: bacterial

tag: chip antibody


title: Lepr-cKO 4wpc contra [KO-176Snc]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

library_source: transcriptomic

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5 was used to align the reads to the GRCm38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes
Assembly: GRCm38 version 97
Supplementary files format and content: Tab-delimited gene counts

molecule: total RNA

organism: Mus musculus

source_name: sciatic nerve endoneurium

extract_protocol:
Tissues were microdissected in ice-cold PBS and stored at -80°C in 1ml TRIZOL (Thermofisher). RNA was extracted using the illustra RNAspin Mini RNA isolation kit from GE Healthcare (25-0500-70). RNA-sequencing was performed  at the NGS- Integrative Genomics (NIG) Core Unit Institute of Human Genetics of University Medical Center Göttingen (UMG).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: sciatic nerve endoneurium

tag: strain background

tag: genotype

tag: treatment

value: control 4wpc


title: 210329_Tfh_Bob1KO_1

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

country: Japan

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

data_processing:
Illumina NovaSeq Sysyem software v1.6 used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence and poly-A/T tail using cutadapt v1.2.1 and PRINSEQ v0.19.2.
Trimmed sequence reads were mapped to GRCm38/mm10 using TopHat v2.0.13.
Read count extraction and normalization were performed using Cufflinks v 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was extracted from FACS sorted Tfh cells by using Trizol reagent. 0.7 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing following manufacturer's protocols.

treatment_protocol: FoxP3-GFP-Bob1 floxed mice and FoxP3-GFP-CD4 conditional Bob1 KO mice were immunized by intraperitoneal administration of 100 ug of NP49-CGG in complete Freund's adjuvant. Spleens were collected these immunized mice at day 7. Single-cell suspensions from spleens were labeled with fluorophore-labeld antibodies and FACS sorted Tfh cells (CD3+CD4+CXCR5+PD-1+GFP-) using FACSAria II and III.

value: spleen

value: CD4+ Tfh cells

value: NP-CGG in CFA i.p. day 7


title: 3603_OF2A_4-3-B6-M6

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: nuclear RNA + genomic DNA

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM file were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmCT-seq

molecule: nuclear RNA

organism: Homo sapiens

source_name: OF2A human BA46

extract_protocol: Library prepared following protocol described in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female


title: Lepr-cKO 4wpc contra [KO-169Snc]


title: P23-45_40min_gp96_replica1

description:
P23-45_40min_gp96_1
Replica 1

value: against P23-45 gp96 (first 1540 amino acid residues) (custom)


title: proximal, WENR-plus, input, biol rep 3

source_name: proximal colon

value: proximal colon

tag: cell line

value: Mouse proximal colon

value: WENR-plus


title: Lepr-cKO 4wpc contra [KO-175Snc]


title: 3603_OF2A_4-3-B6-M18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-N17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-M17

description: nuclear RNA + genomic DNA


title: distal, WENR-minus, input, biol rep 2

value: distal colon

value: organoid


title: Lepr control 4wpc ipsi [WT-178Sni]

value: Leprfl/fl

value: injured 4wpc


title: Lepr-cKO 4wpc contra [KO-177Snc]


title: 3603_OF2A_4-3-B6-M5

description: nuclear RNA + genomic DNA


title: Lepr control 4wpc ipsi [WT-173Sni]


title: P23-45_20min_input_gp64_replica1

description:
P23-45_20min_input_gp64_1
Replica 1

value: P23-45 bacteriophage


title: distal, WENR-plus, input,  biol rep 3

value: Mouse distal colon

value: Cross homozygous tdTomato reporter (B6;129S6- t(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mouse with  heterozygous Cre-inducible BrafV600E mouse(B6.129P2(Cg)-Braftm1Mmcm/J) to generate heterozygous Cre-inducible BRAFV600E with heterozygous tdTomato reporter.


title: proximal, WENR-minus, input,  biol rep 2

value: WENR-minus


title: 3603_OF2A_4-3-B6-L6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-L5

description: nuclear RNA + genomic DNA


title: Lepr control 4wpc ipsi [WT-171Sni]

value: sciatic nerve endoneurium


title: proximal, WENR-minus, input,  biol rep 3


title: P23-45_20min_gp96_replica1

description:
P23-45_20min_gp96_1
Replica 1

value: bacterial


title: P23-45_5min_input_gp96_replica1

description:
P23-45_5min_input_gp96_1
Replica 1


title: proximal, WENR-plus, input, biol rep 2


title: distal, WENR-minus, input, biol rep 1


title: P23-45_20min_gp64_replica1

description:
P23-45_20min_gp64_1
Replica 1

value: against P23-45 gp64 (custom)


title: distal, WENR-plus, input,  biol rep 2


title: P23-45_20min_input_gp96_replica1

description:
P23-45_20min_input_gp96_1
Replica 1


title: P23-45_40min_gp64_replica1

description:
P23-45_40min_gp64_1
Replica 1


title: 3603_OF2A_4-3-B6-L18

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Lepr control 4wpc contra [WT-178Snc]

value: control 4wpc


title: 3603_OF2A_4-3-B6-L17

description: nuclear RNA + genomic DNA

value: Female


title: P23-45_5min_gp96_replica1

description:
P23-45_5min_gp96_1
Replica 1

value: against P23-45 gp96 (first 1540 amino acid residues) (custom)


title: distal, WENR-plus, input,  biol rep1


title: proximal, WENR-minus, input,  biol rep 1

value: proximal colon

value: Mouse proximal colon


title: P23-45_5min_input_gp64_replica1

description:
P23-45_5min_input_gp64_1
Replica 1


title: Lepr control 4wpc contra [WT-173Snc]


title: 3603_OF2A_4-3-B6-K6

description: nuclear RNA + genomic DNA


title: Lepr control 4wpc contra [WT-170Snc]


title: 3603_OF2A_4-3-B6-K18

description: nuclear RNA + genomic DNA


title: Lepr control 4wpc contra [WT-168Snc]


title: proximal, WENR-plus, input, biol rep 1

value: WENR-plus


title: P23-45_5min_gp64_replica1

description:
P23-45_5min_gp64_1
Replica 1


title: distal, WENR-plus, cdx2,  biol rep 3

value: distal colon

value: organoid


title: 3603_OF2A_4-3-B6-J6

description: nuclear RNA + genomic DNA


title: Lepr control 4wpc ipsi [WT-170Sni]

value: Leprfl/fl

value: injured 4wpc


title: P23-45_40min_gp96

value: P23-45 bacteriophage

tag: time

value: 40 min


title: distal Cdx2-sgRNA WENR-minus biol rep 2

data_processing:
Sequence reads were aligned using Salmon v1.1.0  an using the gencode.vM23 version for mapping to genes.
Standard alignment parameters were used by running following code: “salmon quant -i salmon_index_gencode.vM23 -l A -p 8 -1 <read1> -2 <read2> -o <output_file_name>”.
Transcript-level estimates were performed using R package tximport v1.20.0.
Transcript names to gene ids mappings were performed using the Bioconductor/R database TxDb.Mmusculus.UCSC.mm10.knownGene.
Salmon v1.1 +B33-aligned data was imported using tximport v1.20.0 +B27 and differential gene expression analyses were performed using DESeq2 v1.32.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA Sample Prep Kit following manufacturer's protocols.

treatment_protocol:
Proximal and distal colon organoids were treated with scramble-sgRNA or Cdx2-sgRNA. Follwed with 2 weeks of antibiotic screening, pick up single clone of Cdx2-sgRNA group of transduced organoids. The single clone originated transduced organoid with Cdx2 frameshift mutation was used for further experiment.
Before extracting the RNA for builing the libraries, organoids were cultured in ENSW-minus medium for 3 days or continue to be cultured in ENSW-plus medium.

value: Mouse distal colon

value: Cross homozygous tdTomato reporter (B6;129S6- t(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mouse with  heterozygous Cre-inducible BrafV600E mouse(B6.129P2(Cg)-Braftm1Mmcm/J) to generate heterozygous Cre-inducible BRAFV600E with heterozygous tdTomato reporter.

value: Cdx2-sgRNA, WENR-minus


title: 3603_OF2A_4-3-B6-K17

description: nuclear RNA + genomic DNA


title: distal, WENR-minus, cdx2, biol rep 3

value: WENR-minus


title: distal scramble-sgRNA WENR-minus biol rep 2

value: scramble-sgRNA, WENR-minus


title: P23-45_20min_input

value: bacterial

value: 20 min


title: 3603_OF2A_4-3-B6-J18

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: P23-45_40min_input


title: 3603_OF2A_4-3-B6-K5

description: nuclear RNA + genomic DNA


title: Lepr control 4wpc contra [WT-171Snc]

value: sciatic nerve endoneurium

value: control 4wpc


title: proximal, WENR-minus,cdx2,  biol rep 3

value: proximal colon

value: Mouse proximal colon


title: distal Cdx2-sgRNA WENR-plus biol rep 2

value: distal colon

value: organoid

value: Cdx2-sgRNA, WENR-plus


title: 3603_OF2A_4-3-B6-J5

description: nuclear RNA + genomic DNA


title: P23-45_40min_gp64

value: P23-45 bacteriophage

value: 40 min

value: against P23-45 gp64 (custom)


title: proximal, WENR-plus, cdx2, biol rep 3

value: Cross homozygous tdTomato reporter (B6;129S6- t(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mouse with  heterozygous Cre-inducible BrafV600E mouse(B6.129P2(Cg)-Braftm1Mmcm/J) to generate heterozygous Cre-inducible BRAFV600E with heterozygous tdTomato reporter.

value: WENR-plus


title: P23-45_20min_gp96

value: against P23-45 gp96 (first 1540 amino acid residues) (custom)


title: distal, WENR-minus, cdx2, biol rep 2

value: Mouse distal colon

value: WENR-minus


title: proximal Cdx2-sgRNA WENR-minus biol rep 2

value: Cdx2-sgRNA, WENR-minus


title: distal, WENR-plus, cdx2,  biol rep 2


title: distal scramble-sgRNA WENR-plus biol rep 2

value: scramble-sgRNA, WENR-plus


title: 3603_OF2A_4-3-B6-J17

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: P23-45_20min_gp64

value: bacterial

value: 20 min


title: 3603_OF2A_4-3-B6-I6

description: nuclear RNA + genomic DNA


title: proximal Cdx2-sgRNA WENR-plus biol rep 2

value: proximal colon

value: Mouse proximal colon


title: 3603_OF2A_4-3-B6-I18

description: nuclear RNA + genomic DNA


title: proximal scramble-sgRNA WENR-minus biol rep 2

value: organoid

value: scramble-sgRNA, WENR-minus


title: proximal, WENR-minus,cdx2,  biol rep 2


title: proximal, WENR-plus, cdx2, biol rep 2


title: proximal scramble-sgRNA WENR-plus biol rep 2


title: 3603_OF2A_4-3-B6-I5

description: nuclear RNA + genomic DNA


title: distal, WENR-minus, cdx2, biol rep 1

value: distal colon


title: Lg7742a WGS MiSeq 2

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Offline base calling of ONT reads was performed with Guppy 5.0.7 and the R9.4.1 450bps SUP model on NVIDIA Tesla V100 GPUs.
Direct 5-methylcytosine modification calling in all contexts from the ONT WGS reads was performed with Megalodon v2.5.0 with the dna_r9.4.1_450bps_modbases_5mc_hac model and Guppy v5.0.7 on NVIDIA Tesla V100 GPUs. Calls for Cs with fewer than 5 supporting reads were discarded, and the resulting bedMethyl files were split by cytosine context (CpG, CHG, CHH) using bedtools v2.30.0 intersect. Fractional methylation calls at each cytosine were adjusted to a [0..1] scale, and the bedMethyl files were converted to bigWig format. Profiles over genomic regions were calculated as for the WGBS libraries.
ONT reads were aligned to their respective reference assemblies with minimap2 v2.24-r1122 “-x map-ont --MD”. Single nucleotide variants and indels shorter than 50 bp (SNVs) were called using Clair3 v0.1-r12 with options “--min_contig_size=1000000 --platform ont --model_path /opt/models/r941_prom_sup_g5014”. Structural variants (SVs) were called with Sniffles2 v2.0.7 with default options. SNVs and SVs were filtered using RTG Tools v3.12.1 (https://github.com/RealTimeGenomics/rtg-tools) with options “vcffilter --min-read-depth=10 --min-genotype-quality=20”, and homozygous calls were removed with “vcffilter --remove-hom”.
Illumina gDNA reads were aligned to the reference assemblies with bwa-mem2 v2.2.1 and coverage was calculated over 1bp bins with deeptools v3.5.2 “bamCoverage --samFlagExclude 2304 --ignoreDuplicates --binSize 1 --normalizeUsing CPM”.
Supplementary files format and content: ONT 5mC BigWigs: Consensus 5mC calls from Megalodon split by context. In the bigwig coverage tracks (1bp bins), positive values are used for cytosines on the top reference strand, negative for the bottom strand.
Supplementary files format and content: VCFs: heterozygous variant calls made with the same reads used for assembly aligned to their respective assembled references.

organism: Lemna gibba

source_name: whole frond

growth_protocol: Sterile cultures were obtained from the Rutgers Duckweed Stock Cooperative and cultivated in 50 mL Schenk and Hildebrandt (SH) medium with 1% sucrose at pH 5.6 at 23°C under a 16 hour photoperiod of approximately 30 μmol/m2/s per second of white fluorescent light. For HMW DNA extraction, culture flasks were covered in foil and grown in the dark for up to 2 weeks prior to harvest to deplete excess carbohydrates. Cultures were then flash frozen in liquid N2 and stored at -80ºC.

extract_protocol:
High molecular weight (HMW) DNA extractions were performed using either a modified CTAB prep followed by a high-salt low-ethanol starch cleanup (Pacific Biosciences), or nuclear extraction as follows:  CTAB prep (Lg7742a, Lj8627, Wa8730): 4 g frozen tissue was ground three times under liquid N2 with a mortar and pestle and transferred to 20 mL pre-warmed lysis buffer (100 mM Tris-HCl pH 9.0, 2% w/v CTAB, 1.4 M NaCl, 20 mM EDTA, 2% PVP-10, 1% 2-mercaptoethanol, 0.1% sarkosyl, 100ug/mL Proteinase K), briefly vortexed, and then incubated at 65ºC for 1 hour with periodic mixing by gentle inversion. The lysate was extracted with 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) and then 1 vol. of chloroform:isoamyl alcohol in phase-lock gel tubes. HMW DNA was precipitated from the aqueous phase in a 50 mL falcon tube by the addition of 0.1 vol. 3M NaOAc pH 5.2 followed by 0.7 vol. Isopropanol. After gentle swirling but no inversion mixing, precipitated salt in the upper phase was pipetted off and HMW DNA was hooked out with a bent pasteur pipette, washed by dipping in 70% EtOH, air-dried for 2 minutes, and resuspended in 200 uL Tris-Cl pH 8.5 (EB). The DNA solution was treated with 2 uL 20 mg/mL RNase A at 37ºC for 20 minutes followed by 2 uL 50 mg/mL Proteinase K at 50ºC for 30 minutes. 194 uL EB, 100 uL 5M NaCl, and 2 uL 0.5 M EDTA were added and organic solvent extractions were performed as before (1x P:C:IA and 1x C:IA). 0.3 vol. EtOH was added followed by centrifugation at 16,000 x g for 15 minutes to precipitate carbohydrates. The supernatant was poured into a new tube and 1.7 vol. of EtOH was added to precipitate HMW DNA, followed by hooking with a pasteur pipette, a 70% EtOH wash, drying, and resuspension in 50 uL EB.  Nuclear prep (Lm7210, Lm9252, Lj7182, Lj9421, Lt9434): as previously described with modifications.
Long-read data for Lg7742a, Lj8627, and Wa8730 were collected over multiple years as the MinION sequencing platform matured. Various protocols and both the SQK-LSK108 and SQK-LSK109 kits were used to prepare libraries for sequencing on multiple flow cell revisions. Here we describe the method used to produce the most recent runs in this study: 2 µg HMW DNA was sheared by 20 passes through a P1000 pipette tip and size-selected using 0.8 vol of custom SPRI beads. The SQK-LSK109 1D Genomic DNA Protocol was followed with the following modifications: Incubation times for all enzymatic reactions were extended to 20 minutes; cleanups following the repair reaction and adapter ligation were performed with 1 vol and 0.8 vol, respectively, of custom SPRI beads rather than Ampure XP; bead elutions were carried out at 37ºC until evenly resuspended; completed libraries were eluted in 24 uL Oxford EB, and half of this volume was mixed with LB and SQB and loaded onto an R9.4.1 rev. D flow cell. After about 20 hours the run was stopped, the Nuclease Flush protocol was performed, and the flow cell re-primed. 6 uL of the remaining library was mixed with 6 uL EB and the loading reagents, loaded onto the flow cell, and the run restarted.  Libraries for Lj7182, Lj9421, Lm7210, Lm9252, and Lt9434 were prepared as previously described and sequenced on R9.4.1 flow cells on the PromethION platform. Short read WGS libraries for Lg7742a and Lj8627 were prepared from 2µg of HMW gDNA using the Illumina TruSeq DNA PCR-Free kit (Illumina, cat#20015962) and sequenced on an Illumina MiSeq (PE 250bp, PE 300bp) or HiSeq 2500 instrument (PE 150bp). Libraries for other Lemna accessions were prepared as described for the NCBI SRA experiment SRX7624904, and previously published libraries were used for Wa8730 (SRX8008794, SRX8008795).

value: whole frond


title: 3603_OF2A_4-3-B6-H6

description: nuclear RNA + genomic DNA


title: distal Cdx2-sgRNA WENR-minus biol rep 1

value: Cross homozygous tdTomato reporter (B6;129S6- t(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mouse with  heterozygous Cre-inducible BrafV600E mouse(B6.129P2(Cg)-Braftm1Mmcm/J) to generate heterozygous Cre-inducible BRAFV600E with heterozygous tdTomato reporter.


title: P23-45_5min_gp96

value: P23-45 bacteriophage

value: 5 min


title: P23-45_5min_gp64

value: against P23-45 gp64 (custom)


title: Lg7742a WGS MiSeq 1


title: distal Cdx2-sgRNA WENR-plus biol rep 1

value: Mouse distal colon

value: Cdx2-sgRNA, WENR-plus


title: proximal, WENR-minus,cdx2,  biol rep 1

value: WENR-minus


title: 3603_OF2A_4-3-B6-H5

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: proximal, WENR-plus, cdx2, biol rep 1

value: WENR-plus


title: 3603_OF2A_4-3-B6-I17

description: nuclear RNA + genomic DNA

value: Female


title: 3603_OF2A_4-3-B6-H18

description: nuclear RNA + genomic DNA


title: P23-45_5min_input

value: bacterial


title: distal scramble-sgRNA WENR-minus biol rep 1


title: distal scramble-sgRNA WENR-plus biol rep 1

value: scramble-sgRNA, WENR-plus


title: 3603_OF2A_4-3-B6-H17

description: nuclear RNA + genomic DNA


title: Lm9252 WGS ONT

organism: Lemna minor


title: Lt9434 WGS ONT

organism: Lemna turionifera


title: proximal Cdx2-sgRNA WENR-minus biol rep 1

value: proximal colon

value: Mouse proximal colon

value: Cdx2-sgRNA, WENR-minus


title: SkM EX4

city: Shanghai

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

country: China

institute: Fudan University

data_processing:
The clean reads were mapped to the reference genome (mm10) using STAR (2.7.10a).
Quantification of gene expression was calculated using RSEM (v1.2.28).
Subsequently, differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. GO enrichment analysis and KEGG pathway analysis was performed by clusterProfiler (4.2.2) with different expSubsequently, differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. GO enrichment analysis and KEGG pathway analysis was performed by clusterProfiler (4.2.2) with different expression genes.
Assembly: mm10
Supplementary files format and content: csv files include counts values for each samples

source_name: gastrocnemius muscle tissue

extract_protocol:
Trizol method was used to extract Total RNA according to manufacturer’s instructions. RNA quality was measured using the AgTrizol method was used to extract Total RNA according to manufacturer’s instructions. RNA quality was measured using the Agilent 2100 Bioanalyzer (RNA 6000 Nano Kit; Agilent Technologies, Santa Clara, CA, USA).
cDNA libraries for each sample were constructed as reported previously (Yao et al., 2022).
Libraries were sequenced on BGIseq500 platform (BGI-Shenzhen, China), using 150 bp paired-end reads aimed at 30 million reads per sample.

value: gastrocnemius muscle tissue

value: WT

value: treadmill running exercise training


title: SkM EX3


title: 3603_OF2A_4-3-B6-G6

description: nuclear RNA + genomic DNA


title: distal, WENR-plus, cdx2,  biol rep1

value: distal colon

value: organoid

value: Cross homozygous tdTomato reporter (B6;129S6- t(ROSA)26Sortm9(CAG-tdTomato)Hze/J) mouse with  heterozygous Cre-inducible BrafV600E mouse(B6.129P2(Cg)-Braftm1Mmcm/J) to generate heterozygous Cre-inducible BRAFV600E with heterozygous tdTomato reporter.


title: Lm7210 WGS ONT

value: whole frond


title: proximal Cdx2-sgRNA WENR-plus biol rep 1

value: Cdx2-sgRNA, WENR-plus


title: 3603_OF2A_4-3-B6-G5

description: nuclear RNA + genomic DNA


title: Lj8627 WGS ONT

organism: Lemna japonica


title: proximal scramble-sgRNA WENR-minus biol rep 1

value: scramble-sgRNA, WENR-minus


title: SkM EX2


title: 3603_OF2A_4-3-B6-G18

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: SkM CE3

value: calorie restriction combined with treadmill running exercise training


title: 3603_OF2A_4-3-B6-G17

description: nuclear RNA + genomic DNA

value: Female


title: SkM EX1


title: 6436

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

description: Sample from GSE213789

data_processing:
FASTQC passed reads were quantified in mapping-based mode using Salmon v1.4.0 using a decoy-aware transcriptome index generated using GENCODE mouse reference assembly (GRCm39, M26 release)
Transcript abundance estimates were coallated  for gene-level quantification using the tximport function in DESeq2
Differential gene expression and pathway analysis was performed using un-normalized gene level counts as input for Omics Playground v2.8.2
Assembly: GRCm39, M26 release
Supplementary files format and content: salmon_raw_genelevel_counts.txt (contains un-normalized gene-level counts used for downstream analysis in Omics Playground v2.8.2 ) and  Gene Symbol

molecule: polyA RNA

source_name: Nf1 flox/flox PostnCre+ trigeminal nerve

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus Mini kit.
800ng total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.

value: Nf1 flox/flox PostnCre+

value: plexiform neurofibroma


title: 6792

description: Sample from GSE213789


title: Wa8730 WGS ONT

organism: Wolffia australiana


title: proximal scramble-sgRNA WENR-plus biol rep 1

value: proximal colon

value: scramble-sgRNA, WENR-plus


title: Mouse Common Bile Duct [BD1]

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: 10X Chromium Single Cell RNAseq

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Cell Ranger
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrix with cell barcode

source_name: Common Bile Duct

extract_protocol:
Common bile duct was harvested, digested to single cell suspension, and loaded into 10X Chromium
Single Cell RNAseq libraries of polyadenylated mRNA was prepared using chromium 10X singlecell 3' v2 chemistry according to the manufacturer’s instructions.

tag: strain

value: male

value: Common Bile Duct

tag: disease status

value: Healthy


title: 3603_OF2A_4-3-B6-F6

description: nuclear RNA + genomic DNA


title: 6264

description: Sample from GSE213789


title: D0_D4_D11_D40

city: Houston

first: FENG

last: WANG

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

description:
This Sample represents time points D0, D4, D11, and D40.
scRNA-seq

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software.
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/ software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting. cDNA inserts were aligned to the mm10/GRCm38 reference genome.
Only confidently mapped, non-PCR duplicates with valid barcodes and UMIs were used to generate the gene–barcode matrix.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx: gene–barcode matrix.

source_name: Bone marrow

extract_protocol:
Bone marrow was collected at d0, d4, d11, d40 from Rad223 treatment. After sorting for CD117+ cells from 3 mice/timepoint, each timepoint was tagged with oligo-tagged antibodies to uniquely label cells from distinct samples (https://cite-seq.com/cell-hashing/).
Samples were pooled and single-cell RNA-seq libraries were prepared using Single Cell 3′ Reagent Kits v.2: Chromium Single Cell 3′ Library & Gel Bead Kit v.2, PN-120237; Single Cell 3′ Chip Kit v.2 PN-120236; and i7 Multiplex Kit PN-120262 (10x Genomics) following the Single Cell 3′ Reagent Kits v.2 User Guide (Manual Part no. CG00052 Rev A).

value: Bone marrow CD117+ cells

tag: time point

value: mixed sample (non-demultiplexed)


title: 3603_OF2A_4-3-B6-F5

description: nuclear RNA + genomic DNA


title: SkM CE2

value: gastrocnemius muscle tissue

value: WT


title: 6891

description: Sample from GSE213789


title: SkM CE1


title: R3

city: cahgnzhou

first: Wendong

last: Gu

address: NO.185, juqianjie road

institute: The Third Affiliated Hospital of Soochow University

description: 10x genomics

data_processing:
Use of Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome), the analysis software provided by 10x Genomics, to filter data, compare, quantify, and identify the recovered cells from the raw data, and finally obtain the gene expression matrix of each cell.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
The hippocampus of rats was dissected at two months after whole-brain 20Gy irradiation. Place a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 x PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm² pieces, the tissues were washed with 1 x PBS. Tissues were dissociated into single cells in dissociation solution in 37℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1x PBS containing 10% fetal bovine serum (FBS, V/V), then pipetting 5-10 times with a Pasteur pipette. The resulting cell suspension was filtered by passing through 70-30 um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1x PBS (0.04%BSA) and added with 1 ml 1x red blood cell lysis buffer (MACS 130-094-183,10x) and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in100μl Dead Cell Removal MicroBeads (MACS 130-090-101) and remove dead cells using MiltenyiDead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1xPBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4℃ (repeat twice). The cell pellet was resuspended in 50μl of 1xPBS (0.04%BSA). The overall cell viability was confirmed by trypan blue exclusion, which needed to be above 85%, single-cell suspensions were counted using a haemocytometer/Countess II Automated Cell Counter and concentration adjusted to700-1200 cells/p1.
RNA libraries were prepared with Chromium Single cell 3’Reagent v3 Kits according to the manufacturer’s protocol.

value: hippocampus

value: irradiation


title: R2

description: 10x genomics


title: 6491

description: Sample from GSE213789


title: R1

description: 10x genomics


title: SkM control4

value: chow diet


title: 3603_OF2A_4-3-B6-F17

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: SkM control3


title: N3

description: 10x genomics

value: control


title: 6441

description: Sample from GSE213789


title: 3603_OF2A_4-3-B6-E6

description: nuclear RNA + genomic DNA

value: Female


title: SkM control2


title: 3603_OF2A_4-3-B6-E5

description: nuclear RNA + genomic DNA


title: SkM control1


title: SkM CR3

value: calorie restriction


title: N1

description: 10x genomics


title: 6721

description: Sample from GSE213789

source_name: Nf1 flox/flox PostnCre- trigeminal nerve

value: Nf1 flox/flox PostnCre-

value: normal nerve


title: N2

description: 10x genomics


title: 6616

description: Sample from GSE213789


title: SRC12-T1a

city: Stanford

first: Ajay

last: Subramanian

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

description: Bulk RNAseq

data_processing:
FASTQ files were quasi-aligned to Gencode version 27 transcript models, and expression levels were summarized using Salmon.
After restricting to protein coding genes, expression levels per gene were summarized as TPM.
Assembly: GRCh38.
Supplementary files format and content: Tab-delimited text file, including TPM for each sample.

source_name: Undifferentiated pleomorphic sarcoma

extract_protocol:
Bulk RNA was isolated from two to three 1 mm FFPE cores per sample using RNAstorm FFPE RNA Extraction Kits (Cell Data Sciences).
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq v2-Pico Input Mammalian Kits (Takara Bio USA, Inc.).

tag: individual

value: Undifferentiated pleomorphic sarcoma

value: Tumor

value: Ipilimumab/nivolumab/cryotherapy


title: 3603_OF2A_4-3-B6-E17

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-E18

description: nuclear RNA + genomic DNA


title: 6428

description: Sample from GSE213789


title: SkM CR2


title: 6385

description: Sample from GSE213789


title: SRC09-T2a

description: Bulk RNAseq

source_name: Leiomyosarcoma

value: Leiomyosarcoma


title: 6375

description: Sample from GSE213789


title: 3603_OF2A_4-3-B6-D6

description: nuclear RNA + genomic DNA


title: SRC06-T2a

description: Bulk RNAseq


title: 3603_OF2A_4-3-B6-D5

description: nuclear RNA + genomic DNA


title: BAT EX4

source_name: brown adipose tissue

value: brown adipose tissue

value: treadmill running exercise training


title: 6172

description: Sample from GSE213789


title: SRC05-T2a

description: Bulk RNAseq


title: 3603_OF2A_4-3-B6-D18

description: nuclear RNA + genomic DNA


title: 6803T

source_name: Nf1 flox/flox Arf flox/flox PostnCre+ malignant peripheral nerve sheath tumor

value: Nf1 flox/flox Arf flox/flox PostnCre+

value: malignant peripheral nerve sheath tumor


title: BAT EX3

value: WT


title: 3603_OF2A_4-3-B6-D17

description: nuclear RNA + genomic DNA


title: BAT EX2


title: 6773T


title: SkM CR1

value: gastrocnemius muscle tissue


title: 3603_OF2A_4-3-B6-C5

description: nuclear RNA + genomic DNA


title: BAT EX1


title: 3603_OF2A_4-3-B6-C18

description: nuclear RNA + genomic DNA


title: 6699T


title: ES489, sam2∆/sam2∆ replicate 2

city: Highland Heights

first: Erin

last: Strome

state: KY

address: Nunn Drive, Northern Kentucky University

department: Department of Biological Sciences

institute: Northern Kentucky University

data_processing:
Sequences were aligned to Saccharomyces cerevisiae (yeast) reference genome, R64-1-1 (GCF_000146045.2) using tophat2 v2.0.13 resulting in aligned bam files. The input reads had an alignment rate of around 94 percent and ranged from 6 to 30 million raw reads.
Differential expression was calculated using cufflinks-cuffdiff2 v2.2.1 for three comparisons sam1KO vs WT, sam2KO vs WT, sam1KO vs sam2KO.
Assembly: R64-1-1 (GCF_000146045.2)
Supplementary files format and content: all_genes_count_table.tsv: Tab-delimited file output by cuffnorm v2.2.1 containing raw counts for all genes (rows) identified by both gene_id and locus across all samples (columns).

organism: Saccharomyces cerevisiae

growth_protocol: Samples were grown in synthetic complete (SC) media altered to match each strains' genotypic requirements (sam1∆/sam1∆: addition of G418, and sam2∆/sam2∆: removal of leucine). Samples were grown at 30°C overnight with agitation to mid-exponential phase (OD600 = 0.5-0.6).

extract_protocol:
RNA extraction follows the RNA Isolation procedure from the TRIzol Reagent protocol (Ambion Cat #15596-018). RNA Purification was completed using the RNeasy RNA Cleanup protocol and spin columns, estimating for up to 1mg of RNA (Midi kit), from Qiagen, with DNase treatment on the columns and removal by subsequent washes. RNA quantity and quality were assessed via Nanospec and gel analysis.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.

value: sam2 knockout


title: BAT CE4

value: calorie restriction combined with treadmill running exercise training


title: 6771T


title: 3603_OF2A_4-3-B6-F18

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3603_OF2A_4-3-B6-C6

description: nuclear RNA + genomic DNA

value: Female


title: BAT CE3


title: 3603_OF2A_4-3-B6-C17

description: nuclear RNA + genomic DNA


title: ES489, sam2∆/sam2∆ replicate 3


title: ES489, sam2∆/sam2∆ replicate 1


title: ES119, sam1∆/sam1∆ replicate 3

value: sam1 knockout


title: BAT CE2


title: ES119, sam1∆/sam1∆ replicate 2


title: SRC01-T1a

description: Bulk RNAseq


title: BAT CE1


title: ES119, sam1∆/sam1∆ replicate 1


title: 3603_OF2A_4-3-B6-B6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-B5

description: nuclear RNA + genomic DNA


title: 6390T


title: Myometrium_SPA3_80_A_spatial

city: Paterna

first: Raul

last: Pérez-Moraga

state: Valencia

address: Rda. de Narcís Monturiol, 11, Bloque C

country: Spain

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

description: 10x Genomics

data_processing:
sc/snRNA-seq data processing and filtering Raw sequences were demultiplexed, aligned, and counted using the CellRanger software suite (v 6.0.2) for nuclei and whole cell gene expression calculations, which takes advantage of intronic reads to improve sensitivity and sequencing depth (human reference genome GRCh38-2020-A). Technical artifacts due to ambient RNA contamination were reduced with CellBender (0.2.0), and low-quality droplets and barcodes were filtered out in four quality control-based consecutive steps throughout the analysis: (i) low UMIcount barcode removal using an EmptyDrops-based method; (ii) cells/nuclei marked as doublets by DoubletFinder (2.0.3) and scds (1.6.0) tools – the hybrid approach from the scds R package was used to avoid removing false-positive doublets; (iii) cells/nuclei with median absolute deviation (MAD) > 3 in two of three basic quality control metrics: number of detected features, number of counts and mitochondrial ratio. These cell-tocount matrices were integrated and corrected using Seurat and Harmony functions, as described below. A final filtering step, (iv), was applied alongside different rounds of clustering, where the obtained clustered cells/nuclei with less than 750 features/cell, more than 25% mitochondrial ratio, and/or showing a pattern of high doublet-scoring plus no gene marker associated expression (during manual cell type annotations), were also removed. Nuclei droplets were similarly processed, and quality controls were applied with the only specific criteria to remove nuclei with MAD > 2 in mitochondrial ratio per sample.  Processed samples were merged and saved into h5ad objects. Spatial transcriptomics data processing: Spatial transcriptomics data processing used the Space Ranger v2.0.1 to align sequence data to the GRCh38-2020-A reference genome, followed by tissue and fiducial detection of spots and counting barcodes/unique molecular identifiers (UMIs) to generate featurebarcode matrices. These matrices were loaded into Seurat, and quality control filtering was performed based on the number of reads and detected genes per spot. Next, a reference matrix was built with informative genes from scRNA-Seq data (with a mean expression in a specific cell type at least 0.75 log fold higher than other cell types and removal of top 1% genes with the highest expression dispersion). Conditional autoregressive-based deconvolution was used to estimate cell composition in each spatial transcriptomics spot and build refined high-resolution maps of cell proportions and gene expression using the CARD package. Cell proportions estimated by CARD were normalized using the min-max method to validate differential abundance detected by scRNA-seq, while the spatial count matrix was processed using total count and lognormalization for validating differential expression detected by scRNA-seq.
1): Cellbender data: This contains the Cellbender output with the filtered matrix counts in h5 file format. 2): Raw count matrix: This contains the unfiltered count matrix generated by CellRanger. 3): Various h5ad files that contain the integrated cells of the dataset, along with zoomed views of different main cell populations.
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: h5ad single-cell object with barcode metadata
Supplementary files format and content: tar archive with raw count matrix data (MTX, TSV) and cellbender processed h5ad counts.
Library strategy: Spatial Transcriptomics

source_name: Myometrium

extract_protocol:
Uterine tissues from the twenty recruited patients (n=3 samples per patient) were maintained in preservation solution (HypoThermosol® FRS) after surgery and further dissociated within 24 h of tissue retrieval to isolate the myometrial layer, which was achieved by removing the endometrium, serosa, and necrotic areas with a sterile scalpel. As previously described75, myometrial samples were rinsed in a wash buffer solution containing Hank's Balanced Salt Solution (HBSS) (ThermoFisher Scientific, Grand Island, NY) and 1% antibiotic-antimycotic solution (ThermoFisher Scientific) to remove blood and mucus. Samples were then divided for different purposes; snap-frozen in liquid nitrogen or formalin fixation/paraffin embedding (FFPE) for further histological characterization, while the remaining tissue was carefully manually minced into small pieces (<1 mm3 ) and digested at 37°C using an enzymatic process for single-cell dissociation. Subsequently, cell suspensions were passed through a 50-mm polyethylene filter (Partec, Celltrics) to remove cell clumps and undigested tissue and then dissociated to single cells by incubating with 400μL TrypLE Select (ThermoFisher Scientific) for 20 min at 37°C to obtain single-cell suspensions. 100μL DNase I (Sigma-Aldrich) was then added to digest extracellular genomic DNA, and cells were treated with ACK Lysing Buffer (ThermoFisher Scientific) to induce hypotonic shock to avoid red blood cell contamination. The resulting cell suspension was pipetted, passed through a 100-μm cell filter, and centrifuged at 1000 rpm for 5 min. The cell pellet was resuspended in Dulbecco's Modified Eagle's Medium (DMEM, Sigma-Aldrich) supplemented with 2% fetal bovine serum (Labclinics) and 10 mM HEPES (ThermoFisher Scientific) as a myometrial-enriched suspension at a concentration of 1x106 cells/mL. Cell concentration and viability were measured using trypan blue with an EVE™ automated cell counter (NanoEnTek). Dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec) cells, with cell suspensions reaching a viability of ≥70%.
Nuclei isolation for snRNA-seq from myometrial cell suspensions: A previously described snRNA-seq procedure was followed to increase the number of recovered cells from the human myometrium. After thawing and centrifuging cell samples, the supernatant was removed, and myometrial cell pellets were resuspended in 1 mL of lysis buffer on ice for 15 min. Samples were then transferred to a 15 mL conical tube and centrifuged at 500 g for 5 min at 4°C. The resulting cell pellets were resuspended in 1× ST buffer within the 100-200 µL range, and nuclei solutions were passed through a 40 µm Falcon cell strainer. The concentration and viability of nuclei were evaluated using an EVE™ automated cell counter (NanoEnTek) with trypan blue. Finally, ~10,000 single-nuclei suspensions were loaded onto Chromium Chips for the Chromium Single Cell 3′ Library preparation according to the manufacturer's recommendations (10x Genomics). Single-cell capture, library preparation, and sequencing: To profile single cells/nuclei from three different areas of the human myometrium (anterior, posterior, and fundus), scRNA-seq analysis was performed using the 10X Chromium system (10X Genomics, Pleasanton, CA, USA). Approximately 17,000 cells or nuclei were loaded onto a 10X G Chip to obtain Gel Bead-in-emulsions (GEMs) each containing an individual cell. GEMs were used to generate barcoded cDNA libraries following the manufacturer's protocol (Single Cell 3' Reagent Kit v3.1, 10X Genomics) and quantified using the TapeStation High Sensitivity D5000 kit (Agilent, Germany). Subsequently, gene expression libraries were constructed using 1-100 ng of each amplified cDNA library and quantified using the TapeStation High Sensitivity D1000 kit (Agilent, Germany) to determine the average fragment size and library concentration. Libraries were normalized, diluted, and sequenced on the Illumina NovaSeq 6000 system (Illumina, USA) according to the manufacturer's instructions. Spatial transcriptomics: The systematic mapping of cells and gene activity to tissue locations used the Visium Spatial Gene Expression Reagent Kit (10X Genomics). Eight full-thickness uterine samples were examined from eight women - three peri-menopausal (under 55 years old) and five post-menopausal (equal to or older than 55 years old). First, the quality of preserved RNA in FFPE blocks was evaluated based on the percentage of RNA fragments above 200 base pairs (DV200). Next, 7 µm-thick tissue sections were sampled using a semi-automated microtome (ThermoScientific HM340E). Per the manufacturer's protocol, each section was mounted onto a 6.5x6.5 mm capture area of the Visium Spatial Gene Expression Slide (PN-2000233). Capture areas contain approximately 5,000 barcoded spots, providing an average resolution of 1-10 cells (10X Genomics). Tissue sections were then deparaffinized, hH&E stained, and uncrosslinked according to the manufacturer's protocol (10X Genomics) with minor modifications. Brightfield images were taken using a 10X objective (Plan APO) on a Nikon Eclipse Ti2. Images were stitched together using NIS-Elements software (Nikon) and exported as .tiff files. Following imaging and uncrosslinking, the Visium Spatial Gene Expression Slide & Reagent for FFPE kit (10XGenomics) was used for library construction. All steps (cDNA synthesis and amplification, library construction, and post-library construction quality control) were carried out according to the manufacturer's protocol. The libraries were sequenced on a HiSeqX (Illumina), 50PE (2x 150bp), applying 1% Phix. Sequencing depth was calculated with the formula (Coverage Area x total spots on the Capture Area) x 50,000 read pairs/spot. Sequencing was performed using the following read protocol: read 1: 28 cycles; i7 index read: 10 cycles; i5 index read: 10 cycles; read 2: 90 cycles. Following sequencing, data was visualized to determine each gene expression's spatial location and degree.

tag: biopsy origin

value: A

tag: seurat id

value: Myometrium

tag: treatment stage

value: Postmenopause

tag: patient

tag: protocol

value: spatial


title: ES76, wildtype, control cells replicate 3


title: Myometrium_SPA3_72_A_spatial

description: 10x Genomics

tag: tissue

value: Perimenopause


title: BAT control3

tag: genotype

value: chow diet


title: Myometrium_SPA1_71_A_spatial

description: 10x Genomics


title: 3603_OF2A_4-3-B6-B18

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-3-B6-B17

description: nuclear RNA + genomic DNA


title: BAT control2

value: brown adipose tissue

tag: treatment


title: 6782T


title: BAT CR4

value: calorie restriction


title: Myometrium_SPA1_56_A_spatial

description: 10x Genomics


title: BAT control1


title: NFE2L2_KO_clone_134, replicate 3

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

data_processing:
Quality control for raw sequencing reads was performed using the FastQC (v0.11.9) and MultiQC (v1.09)
Quality, adapters and contamination filtering were performed using the Trimmomatic command-line tool
Processed reads were aligned to the NCBI GRCh38 human reference using STAR (v2.7.1a)
Transcript assembly and the number of reads per gene were determined using Stringtie (RNA-seq)
Differentially expressed genes were identified using the DESeq2 R/Bioconductor package. Extended gene annotations (including HGNC gene symbol, description and transcript type) were obtained using the biomaRt R/Bioconductor package
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (RNA-seq)

growth_protocol: Panc-1 cells were cultured in 10% FBS DMEM (Euroclone, Milan, Italy) with 5% CO2 at 37C. Media were supplemented with 10% FBS, L-glutamine (2 mm), penicillin (100 U·mL−1), and streptomycin (100 μg·mL−1) (Lonza, Basel, Switzerland).

extract_protocol:
Panc-1 cells were lysed using Tri Reagent (Molecular Research Center, USA). Total RNA was treated with DNAse I (NEB, USA) and purified with RNA Clean & Concentrator (Zymo Research, USA). RNA-seq poli A enriched transcripts library preparation and sequencing were performed at BMR-Genomics (Padua, Italy) following Illumina specifications.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 following manufacturer's protocols.

treatment_protocol:
None
None

tag: cell type

value: Human Pancreas Cancer Cell Line

value: NFE2L2 KO

value: Day 2


title: BAT CR3

value: WT


title: Myometrium_SPA3_55_A_spatial

description: 10x Genomics


title: Myometrium_SPA1_54_A_spatial

description: 10x Genomics


title: ES76, wildtype, control cells replicate 1


title: NFE2L2_KO_clone_134, replicate 2


title: 3603_OF2A_4-3-B6-A18

description: nuclear RNA + genomic DNA

tag: brain region

tag: age


title: Myometrium_SPA1_45_A_spatial

description: 10x Genomics


title: 3603_OF2A_4-3-B6-A17

description: nuclear RNA + genomic DNA

tag: Sex


title: NFE2L2_KO_clone_134, replicate 1

tag: cell line

tag: time


title: BAT CR1


title: Myometrium_SPA1_04_A_spatial

description: 10x Genomics


title: Wild-type cells, replicate 3


title: 3603_OF2A_4-2-B6-P4

description: nuclear RNA + genomic DNA


title: Cbx5 KO EAE, rep3

city: Paris Cedex 05

first: Christian

last: MUCHARDT

address: Sciences Sorbonne Université Campus Pierre et Marie Curie 7-9, Quai Saint Bernard - Bât A, 2ème étage

department: UMR8256 – Biological Adaptation and Ageing

country: France

institute: CNRS

description: RNA-seq: lncRNA directional library preparation with rRNA depletion (Ribo-Zero Magnetic Kit), quantitation, pooling and PE 150 sequencing (30G raw data) on Illumina HiSeq 2500 platform.

data_processing:
Mapping was carried out with STAR (v2.6.0b) against the mm10 mus musculus primary assembly from Ensembl (parameters: --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterMultimapNmax 1)
The SAM files were converted to BAM files and sorted by coordinate using samtools (v1.7)
BigWigs files were generated using Deeptools (v3.1.3)
Differentially expressed genes were obtained using DESeq2 (v1.18.1)
Assembly: mm10
Supplementary files format and content: Supplementary files include RNA-seq data in bigWig format (mm10 version of the mouse genome) and a gene expression analysis carried out with DeSeq2. Please note that one of the control mice (sample 1) was heterozygote for the Cbx5 mutation (Cbx5+/-). This mouse unexpectedly displayed a transcriptional phenotype very close to that of the Cbx5-/-, suggesting that the activity of the Cbx5 protein was dose dependent. The RNA-seq data from this mouse were not included in the gene expression analysis.

extract_protocol:
CD4+ mouse T cells were purified from spleenocytes using the Miltenyi kit 130-104-454. Total RNA was extracted by Trizol LS (Thermo Fisher Scientific, ref. 10296028), according to the manufacturer's protocol.
Total RNA library preparation and sequencing were performed by Novogene Co., Ltd, as a lncRNA sequencing service

treatment_protocol: EAE: to prepare the MOG35-55 emulsion for immunization, we first calculated the total volume required and then prepared 1.5 to 2 times that amount to account for potential losses during the process. Each mouse received a subcutaneous injection of 200 µl of a mixture containing MOG35-55 peptide solution and Complete Freund's Adjuvant (CFA) in a 1:1 ratio. The MOG35-55 peptide solution was prepared by diluting lyophilized 200 µg of the peptide per mouse with ddH2O to achieve a final concentration of 2 mg/mL, which was then stored at -20°C. CFA was prepared by grinding 100 mg of desiccated Mycobacterium tuberculosis H37RA and adding 10 mL of Incomplete Freund's Adjuvant (IFA) to create a 10 mg/mL CFA stock solution that could be stored at 4°C. Just prior to immunization, CFA was diluted with IFA to reach a final concentration of 2 mg/mL, with thorough mixing. The MOG35-55 and CFA were then mixed in a 1:1 ratio until the final concentration of 1 mg/mL was achieved. This emulsion, a critical step for immunization, was carefully prepared to ensure proper emulsification. After verification of its stability, the emulsion was drawn into syringes for subsequent use. In addition to the MOG35-55 emulsion, pertussis toxin was prepared and administered. For each mouse, 400 ng of pertussis toxin in 200 µl of PBS was injected intraperitoneally on the day of immunization and repeated two days later. Pertussis toxin was reconstituted by dissolving 50 µg in 500 µl of ddH2O to create a 100 µg/mL stock solution, which was stored at 4°C. To achieve the required concentration for immunization, the stock solution was diluted 1:50 with PBS. Finally, to ensure proper identification and monitoring, individual mice were marked, typically by using color markings on the tail base. A second dose of pertussis toxin was administered on day two after the initial immunization to complete the immunization process. Procedure was stopped on day 14 for the preparation of RNAs.

value: Cbx5 KO EAE


title: Wild-type cells, replicate 2


title: 3603_OF2A_4-2-B6-P3

description: nuclear RNA + genomic DNA


title: GAS MPARK7KO rep4

data_processing:
The clean reads were mapped to the reference genome (mm10) using STAR (2.7.10a).
Quantification of gene expression was calculated using RSEM (v1.2.28).
Differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. GO enrichment analysis and KEGG pathway analysis was performed by clusterProfiler (4.2.2) with different expression genes.
Assembly: mm10
Supplementary files format and content: csv files include counts values for each samples

source_name: gas

extract_protocol:
GAS tissues from immobilized muscle-specific DJ-1 knockout (MPARK7KO) mice and flox mice were extracted for RNA sequencing.
cDNA libraries for each sample were constructed as reported previously (Yao et al., 2022).
Libraries were sequenced on BGIseq500 platform (BGI-Shenzhen, China), using 150 bp paired-end reads aimed at 30 million reads per sample.

value: Gastrocnemius muscle

value: skeletal muscle PARK7KO

value: immobilization-induced muscle atrophy


title: ES76, wildtype, control cells replicate 2


title: 3603_OF2A_4-3-B6-A5

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: GAS MPARK7KO rep3


title: 3603_OF2A_4-3-B6-A6

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-P16

description: nuclear RNA + genomic DNA


title: GAS MPARK7KO rep2


title: Cbx5 KO EAE, rep2


title: Wild-type cells, replicate 1


title: 3603_OF2A_4-2-B6-P15

description: nuclear RNA + genomic DNA


title: wt EAE, rep2

value: wt EAE


title: Cbx5 KO EAE, rep1


title: GAS MPARK7KO rep1


title: wt EAE, rep3


title: BAT CR2


title: 3603_OF2A_4-2-B6-O4

description: nuclear RNA + genomic DNA


title: GAS WT rep3


title: Viperin KO_VSHV_7 dpi

type: RNA

city: Jeju

last: Shanaka

address: Ara-dong

department: Marine life Sciences

country: South Korea

institute: Jeju National University

description:
Test
SAMPLE 19

data_processing:
The qPCR primers for gene expression analysis were designed according to the guidelines for the publication of quantitative realtime PCR experiments (MIQE) experiments
Fold Change worksheet reports test/control. The respective test value was divided with the respective control value.

label: SYBR Green

organism: Danio rerio

source_name: Internal tissue

label_protocol: All qPCR reactions were performed in triplicate in a reaction volume of 10 μL containing 4 μL of cDNA template, 0.4 μL of each qPCR primer (10 pmol/μL), 5.0 μL of 2× TB Green® Premix Ex Taq™ II (TaKaRa, Japan), and 1.2 μL of PCR-grade water. Reactions were run in a Real-Time system Thermal Cycler Dice™ system III TP950 (TaKaRa, Japan) under the following conditions: 95 °C for 10 s, followed by 45 cycles at 95 °C for 5 s, 60 °C for 10 s, and 72 °C for 20 s, and a final cycle at 95 °C for 5 s, 60 °C for 30 s, and 95 °C for 15 s.

growth_protocol: Wild-type (WT) and viperin-/- zebrafish were maintained as previously described by Avdesh at el. Water used in tanks was maintained at constant pH (pH 6.8–7.5), conductivity (500–800 mS), and temperature (28°C ± 0.5°C) during the fish rearing. The zebrafish facility’s light and dark cycle consisted of 14:10 h. The fish were fed three times with the Artemia diet. The Jeju National University Animal Ethics Committee reviewed and approved this study

extract_protocol: TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) was used for RNA extraction.

treatment_protocol: Three-month-old adult male zebrafish were used for the VHSV challenge experiments. The fish were adapted to the experimental temperature described in the mortality experiment and injected with 1 × 105 TCID50/mL of VHSV. After the initial injection, the VHSV copy number was checked at 12 h postinfection (hpi) to evaluate the injection process.

value: Internal tissues

value: Viperin KO

tag: infection

value: VSHV

value: 7 dpi


title: GAS WT rep1


title: GAS WT rep2


title: Viperin KO_VSHV_5 dpi

description:
Test
SAMPLE 18

value: 5 dpi


title: Sp9509 small RNA 3

data_processing:
Sequencing adapters were trimmed using skewer v0.2.2 and 4nt randomer sequences were removed from both ends of each read with fastp v0.20.1 with options “--trim_front1 4 --trim_tail1 4 --length_required 10 --length_limit 35 --disable_adapter_trimming --trim_poly_g -q 20 --unqualified_percent_limit 10”. Reads mapping perfectly to annotated structural RNAs and organelles were removed, and those remaining were aligned to the genomes with ShortStack v4.0.0 using options “--mincov 0.5 --mmap f --dn_mirna --knownRNAs <miRBase 22.1 mature plant sequences>”. Separate ShortStack runs with merged biological replicates were performed for microRNA discovery, and microRNAs identified by ShortStack were annotated by top BLAST hit of the mature sequence to miRBase 22.1. Alignments were split by size class and bigWig coverage tracks computed with deepTools “bamCoverage --binSize 1 --normalizeUsing CPM”.
Supplementary files format and content: BigWig coverage tracks of merged replicates for each size class of 20nt - 24nt small RNA.
Supplementary files format and content: Small RNA clusters annotated by ShortStack 4 (GFF3) for merged replicates.

organism: Spirodela polyrhiza

extract_protocol:
RNA was extracted from 3 biological replicates of 100mg of frozen tissue for each accession using the Quick-DNA/RNA Miniprep kit (Zymo) following manufacturer’s instructions with the following modifications: frozen tissue was ground under LN2 with a mortar and pestle and resuspended in the Shield solution. It was refrozen in LN2, thawed, and treated with Proteinase K, and frozen again after the addition of lysis buffer. After thawing, samples were centrifuged at full speed, RT for 3 min. to remove debris, and the manufacturer’s protocol was followed as described. Afterwards, samples were DNase treated, enriched for RNAs 17-200 nt in length, and concentrated using the RNA Clean & Concentrator kit (Zymo).
Libraries were prepared with the NEXTflex Small RNA-Seq Kit v3 (Perkin Elmer) following manufacturer instructions and sequenced on a NextSeq 500 (SE 75).

value: whole frond


title: Cbx5 KO, rep2

value: Cbx5 KO


title: Viperin KO_VSHV_1 dpi

description:
Test
SAMPLE 16

value: 1 dpi


title: Viperin KO_VSHV_3 dpi

description:
Test
SAMPLE 17

value: 3 dpi


title: Sp9509 small RNA 2


title: Cbx5 KO, rep1


title: 3603_OF2A_4-2-B6-N4

description: nuclear RNA + genomic DNA


title: WT_VSHV_9 dpi

description:
Test
SAMPLE 15

value: WT

value: 9 dpi


title: Sp9509 small RNA 1


title: wt, rep3

value: wt


title: 3603_OF2A_4-2-B6-N3

description: nuclear RNA + genomic DNA


title: Viperin KO_VSHV_9 dpi

description:
Test
SAMPLE 20


title: wt, rep2


title: 3603_OF2A_4-2-B6-O3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-O16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-N15

description: nuclear RNA + genomic DNA


title: wt EAE, rep1


title: WT_VSHV_7 dpi

description:
Test
SAMPLE 14


title: WT_VSHV_5 dpi

description:
Test
SAMPLE 13


title: Cbx5 KO, rep3


title: C. elegans, mbl-1c(syb5299) mutant, L4, IP sample, rep 3

city: Helsinki

first: Jens

last: Verbeeren

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

description: NovaSeq PE 150

data_processing:
Reads were mapped to the C. elegans reference (WBcel235 assembly) with BWA.
MACS2 was used for peak calling.
Diffbind was used to call differentially represented peaks between input and immunoprecipitated samples.
Assembly: WBcel235 assembly
Supplementary files format and content: Peak data files in narrowpeak format.
Supplementary files format and content: Bed alignment files.
Supplementary files format and content: Excel files with peak data and transcript features.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Animals were synchronized by bleaching, plated as L1 larvae on NGM plates seeded with OP50, grown at 20C, and collected at the L4 stage.

extract_protocol:
TRIzol RNA purification
Unenriched RNA samples were fragmented to 250 bp and reverse transcribed to cDNA with random primers. cDNAs were dA-tailed and DNA fragments with A tail were ligated to sequencing adaptors. Final DNA library was obtained by PCR amplification. After the construction of the library, the initial quantification was done with Qubit 2.0, and the library was diluted to 1ng/l. Then the insertion size of the library was detected with NGS3K. If meeting the expectation, the accurate concentration of the library was quantified by Q-PCR (library effective concentration > 2nM) to ensure the quality of the library.

value: whole organism

value: L4 stage


title: Breast tissue from normal patient 0131

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Libraries were sequenced on an Illumina NextSeq 500/2000.
Read alignment and count summarization were performed using spaceranger v1.3.0 using the Illumina BCL files as input.
Assembly: GRCh38
Supplementary files format and content: h5 files contain genewise read counts for all spots. Row names are Ensembl IDs and column names are 10x spatial barcodes used to identify spots.
Supplementary files format and content: csv files contain the spatial coordinates of the visium spots
Supplementary files format and content: png files contain the tissue H&E images
Library strategy: Visium Spatial Transcritpomics

source_name: Mammary gland

extract_protocol:
OCT-embedded frozen tissues were sectioned, placed on Visium slides and imaged
Libraries were prepared according to the 10x Visium Spatial Transcritpomics protocol

value: Mammary gland

value: Normal

value: female


title: 3603_OF2A_4-2-B6-M4

description: nuclear RNA + genomic DNA

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM file were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmCT-seq

source_name: OF2A human BA46

extract_protocol: Library prepared following protocol described in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: C. elegans, mbl-1c(syb5299) mutant, L4, IP sample, rep 2

description: NovaSeq PE 150


title: Cbx5+/-, rep1


title: 3603_OF2A_4-2-B6-O15

description: nuclear RNA + genomic DNA


title: Breast tissue from normal patient 0059


title: WT_VSHV_3 dpi

description:
Test
SAMPLE 12

value: Internal tissues

value: VSHV


title: WT_VSHV_1 dpi

description:
Test
SAMPLE 11


title: C. elegans, mbl-1c(syb5299) mutant, L4, IP sample, rep 1

description: NovaSeq PE 150


title: 3603_OF2A_4-2-B6-M3

description: nuclear RNA + genomic DNA


title: Breast tissue from BRCA2 mutation carrier 210727


title: C. elegans, mbl-1c(syb5299) mutant, L4, RNA input, rep 3

description: NovaSeq PE 150


title: 3603_OF2A_4-2-B6-M16

description: nuclear RNA + genomic DNA


title: Breast tissue from BRCA2 mutation carrier1218


title: Viperin KO_PBS_9 dpi

description:
Test
SAMPLE 10

value: Viperin KO

value: PBS


title: C. elegans, mbl-1c(syb5299) mutant, L4, RNA input, rep 2

description: NovaSeq PE 150


title: Viperin KO_PBS_5 dpi

description:
Test
SAMPLE 8

value: 5 dpi


title: Viperin KO_PBS_3 dpi

description:
Test
SAMPLE 7


title: 3603_OF2A_4-2-B6-N16

description: nuclear RNA + genomic DNA


title: Viperin KO_PBS_7 dpi

description:
Test
SAMPLE 9

value: 7 dpi


title: C. elegans, mbl-1c(syb5299) mutant, L4, RNA input, rep 1

description: NovaSeq PE 150


title: C. elegans, mbl-1(syb4345) mutant, L4, small RNA, rep 2

description: NovaSeq SE 50

data_processing:
Reads were mapped to the C. elegans reference (WBcel235 assembly) using the Bowtie algorithm.
Expression of known and unique miRNA was analyzed and normalized by TPM.
DESeq2 R package  was used for differential expression analysis.
Assembly: WBcel235 assembly
Supplementary files format and content: Excel file includes raw counts for each sample.
Supplementary files format and content: Excel files including significantly differentially expressed miRNAs (compared to wt) for each sample.

extract_protocol:
TRIzol method
Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing with SE50. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.


title: C. elegans, mbl-1(syb4345) mutant, L4, small RNA, rep 3

description: NovaSeq SE 50


title: Viperin KO_PBS_1 dpi

description:
Test
SAMPLE 6

value: 1 dpi


title: Breast tissue from BRCA2 mutation carrier 0259 rep 1


title: ERBB3-hi luminal progenitor cells from Patient 0408 [WT-hi-0408]

data_processing:
Libraries were sequenced on an Illumina Nextseq 500. Each sample was sequenced on two separate runs resulting in two techinical replicates of each except for the ERBB3-lo sample from patient 0059.
Reads were aligned to the human genome hg38 by the align function of the Rsubread software tool version 2.2.2.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Read counts from the technical replicates of the same sample were summed up together.
Assembly: hg38
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy kit and Dnase treated.
40 ng of total RNA (or a minimum of 10 ng of total RNA for smaller cell number samples) was used to construct libraries following Ilumina's recommended protocol for TruSeq RNA Library Prep Kit v2.

value: Luminal progenitor

tag: group

value: WT


title: 3603_OF2A_4-2-B6-M15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-L15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-L4

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-L16

description: nuclear RNA + genomic DNA


title: WT_PBS_9 dpi

description:
Control
SAMPLE 5

value: 9 dpi


title: C. elegans, mbl-1(syb4318) mutant, L4, small RNA, rep 3

description: NovaSeq SE 50

value: whole organism


title: ERBB3-lo luminal progenitor cells from Patient 0017 [WT-lo-0017]


title: 3603_OF2A_4-2-B6-K16

description: nuclear RNA + genomic DNA


title: WT_PBS_5 dpi

description:
Control
SAMPLE 3


title: 3603_OF2A_4-2-B6-K3

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-K4

description: nuclear RNA + genomic DNA


title: C. elegans, mbl-1(syb4318) mutant, L4, small RNA, rep 2

description: NovaSeq SE 50

value: L4 stage


title: ERBB3-lo luminal progenitor cells from Patient 0111 [WT-lo-0111]

value: Mammary gland


title: WT_PBS_7 dpi

description:
Control
SAMPLE 4


title: WT_PBS_3 dpi

description:
Control
SAMPLE 2

value: 3 dpi


title: WT_PBS_1 dpi

description:
Control
SAMPLE 1


title: C. elegans, mbl-1(syb4318) mutant, L4, small RNA, rep 1

description: NovaSeq SE 50


title: ERBB3-lo luminal progenitor cells from Patient 0408 [WT-lo-0408]

value: female


title: ERBB3-hi luminal progenitor cells from Patient 0017 [WT-hi-0017]


title: dTrmt10A RNAi basal m6A-IP SYS rep3

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

data_processing:
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with MeTPeak for peak calling and RADAR for differential peak calling.
Assembly: dm6
Supplementary files format and content: bigWig files for each condition were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM)
Library strategy: m6A-seq

organism: Drosophila melanogaster

source_name: head

growth_protocol: DaGal4> Control RNAi (Vienna 60100), DaGal4> dTrmt10A RNAi(Vienna 100720), or DaGal4> UAS-dTrmt10A (This work/ DGRC Stock 1619899) Drosophila crosses set up in 25 degree incubator. Male progeny collected 1-2 days post eclosion for treatment and RNA extraction.

extract_protocol:
For m6A-IP seq flies were flash frozen and head tissue was collected into cold RNAse free tubes. Total RNA was extracted from 200 Drosophila Heads per replicate using Trizol/ chloroform extraction. PolyA+ mRNA was obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module. PolyA+ RNA was fragmented using the NEB Next Magnesium Fragmentation Module (NEB, E6150S) for 4 minutes at 95 °C for a 250 ng sample of polyA+ RNA, and RNA was repurified using the Zymo RNA clean & concentrator -5 kit (Zymo, R1013). 10% of the fragmented polyA+ RNA was saved as an input control for sequencing. M6A -immunoprecipitation was done using the EpiMark N6-Methyladenosine Enrichment kit protocol with some minor alteration. 30ul of protein G magnetic beads (NEB, #S1430) were washed and resuspended in IP buffer (150mM NaCl, 10mM Tris-HCL, 0.1% NP-40). 4ul of synaptic systems antibody (SYS, 202003) was conjugated to protein G-magnetic beads (NEB, S1430S) for 2 hours at 4°C. Beads/ antibody were washed twice in IP buffer. ~1μg PolyA+ RNA was incubated with beads/antibody in IP buffer supplemented with 0.1% SUPERase-In RNase Inhibitor (Thermo Fisher; AM2696) for 2 hours at 4°C. After incubation, RNA/beads/antibody are washed twice in IP buffer, twice in low salt IP buffer (50mM NaCl, 10mM Tris-HCL, 0.1% NP-40), and twice in high salt IP buffer (500mM NaCl, 10mM Tris-HCL, 0.1% NP-40). RNA is eluted from beads with 25μl of RLT buffer twice and elution was pooled and concentrated using Zymo RNA clean and concentrator kit-5 (R1015). Libraries were made using SMARTer Stranded Total RNA-Seq Kit V2 without rRNA depletion(takarabio, 634411) for IPed and input RNA, and sequenced using illumina HiSeq with 40M paired end reads (2x150bp). Library preparation and sequencing was done by Admera Health. Three biological replicates per genotype and condition were done with Synaptic Systems m6A antibody.
Libraries were made using SMARTer Stranded Total RNA-Seq Kit V2 without rRNA depletion (takarabio, 634411) for IPed and input RNA,  sequenced using illumina HiSeq with 40M paired end reads (2x150bp).

treatment_protocol: male progeny were collected and anesthetized. Tissue was collected in basal conditions, immediately post Heat stress (HS), flies were placed into clear vials (20 flies per vial) and were HS for 30 minutes at 38.5°C.

tag: ip antibody

value: SYS

tag: heat shock condition

value: basal

value: DaGal4> Trmt10A RNAi


title: dTrmt10A RNAi basal m6A-IP SYS rep1


title: ERBB3-lo luminal progenitor cells from Patient 0059 [BRCA2-lo-0059]


title: 3603_OF2A_4-2-B6-K15

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: C. elegans, mbl-1(tm1563) mutant, L4, small RNA, rep 3

description: NovaSeq SE 50


title: C. elegans, mbl-1(tm1563) mutant, L4, small RNA, rep 2

description: NovaSeq SE 50


title: C. elegans, mbl-1(syb4345) mutant, L4, small RNA, rep 1

description: NovaSeq SE 50


title: ERBB3-hi luminal progenitor cells from Patient 0111 [WT-hi-0111]


title: 3603_OF2A_4-2-B6-J4

description: nuclear RNA + genomic DNA


title: C. elegans, mbl-1(tm1563) mutant, L4, small RNA, rep 1

description: NovaSeq SE 50


title: ERBB3-hi luminal progenitor cells from Patient 0059 [BRCA2-hi-0059]


title: dTrmt10A RNAi basal m6A-IP SYS rep2


title: 3603_OF2A_4-2-B6-J16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-J3

description: nuclear RNA + genomic DNA


title: ERBB3-hi luminal progenitor cells from Patient 01.0021.0323 [BRCA2-hi-01.0021.0323]


title: C. elegans, wild-type, L4, small RNA, rep 3

description: NovaSeq SE 50


title: dTrmt10A RNAi basal input SYS rep3

description: input for m6A-IP-seq

data_processing:
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with MeTPeak for peak calling and RADAR for differential peak calling.
Assembly: dm6
Supplementary files format and content: bigWig files for each condition were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM)


title: 3603_OF2A_4-2-B6-J15

description: nuclear RNA + genomic DNA


title: dTrmt10A RNAi basal input SYS rep2

description: input for m6A-IP-seq


title: C. elegans, wild-type, L4, small RNA, rep 1

description: NovaSeq SE 50


title: 3603_OF2A_4-2-B6-I4

description: nuclear RNA + genomic DNA


title: ERBB3-hi luminal progenitor cells from Patient 0046 [BRCA2-ERBB3-hi-0046]


title: 3603_OF2A_4-2-B6-I3

description: nuclear RNA + genomic DNA


title: dTrmt10A RNAi basal input SYS rep1

description: input for m6A-IP-seq


title: ERBB3-lo luminal progenitor cells from Patient 0046 [BRCA2-ERBB3-lo-0046]


title: C. elegans, mbl-1(syb4345) mutant, L4, rep 3

description: NovaSeq PE 150

data_processing:
Reads were mapped to the C. elegans reference (WBcel235 assembly) using the HISAT2 algorithm
DESeq2 R package  was used for differential expression analysis
rMATS was used for detection of differential alternative splicing.
Assembly: WBcel235 assembly
Supplementary files format and content: Excel file includes raw counts for each sample.
Supplementary files format and content: Excel files including significantly differentially expressed genes (compared to wt) for each sample
Supplementary files format and content: Excel files with differential alternative splicing events (compared to wt). A3SS: alternative 3' splice sites. A5SS: alternative 5' splice sites. MXE: mutual exclusive alternative exons. RI: retained introns. SE: skipped exons.

extract_protocol:
TRIzol method
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.


title: UAS-dTrmt10A HS m6A-IP SYS rep3

value: 30 minute heat shock

value: DaGal4> UAS-Trmt10A


title: ERBB3-lo luminal progenitor cells from Patient 01.0021.0323 [BRCA2-lo-01.0021.0323]


title: ERBB3-lo luminal progenitor cells from Patient 0010 [WT-lo-0010]

data_processing:
Libraries were sequenced on an Illumina Nextseq 500.
Reads were aligned to the human genome hg38 by the align function of the Rsubread software tool version 2.10.5.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy kit and Dnase treated.
100 ng of total RNA (or a minimum of 10 ng of total RNA for lower cell number samples) was used to construct libraries following Ilumina's recommended protocol for TruSeq RNA Library Prep Kit v2.


title: ERBB3-hi luminal progenitor cells from Patient 0010 [WT-hi-0010]


title: 3603_OF2A_4-2-B6-I16

description: nuclear RNA + genomic DNA


title: C. elegans, mbl-1(syb4345) mutant, L4, rep 1

description: NovaSeq PE 150


title: C. elegans, mbl-1(syb4345) mutant, L4, rep 2

description: NovaSeq PE 150


title: C. elegans, wild-type, L4, small RNA, rep 2

description: NovaSeq SE 50


title: UAS-dTrmt10A HS m6A-IP SYS rep1


title: ERBB3-lo luminal progenitor cells from Patient 0907 [WT-lo-0907]


title: C. elegans, mbl-1(syb4318) mutant, L4, rep 2

description: NovaSeq PE 150


title: C. elegans, mbl-1(syb4318) mutant, L4, rep 3

description: NovaSeq PE 150


title: ERBB3-hi luminal progenitor cells from Patient 0034 [WT-hi-0034]


title: ERBB3-hi luminal progenitor cells from Patient 0907 [WT-hi-0907]


title: 3603_OF2A_4-2-B6-H4

description: nuclear RNA + genomic DNA


title: UAS-dTrmt10A HS input SYS rep3

description: input for m6A-IP-seq


title: UAS-dTrmt10A HS input SYS rep2

description: input for m6A-IP-seq


title: 3603_OF2A_4-2-B6-H16

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-H3

description: nuclear RNA + genomic DNA


title: ERBB3-lo luminal progenitor cells from Patient 0034 [WT-lo-0034]


title: C. elegans, mbl-1(tm1563) mutant, L4, rep 3

description: NovaSeq PE 150


title: 3603_OF2A_4-2-B6-H15

description: nuclear RNA + genomic DNA


title: ERBB3-hi luminal progenitor cells from Patient 15.002.1 [BRCA2-hi-15.002.1]


title: 3603_OF2A_4-2-B6-G4

description: nuclear RNA + genomic DNA


title: UAS-dTrmt10A basal m6A-IP SYS rep3


title: C. elegans, mbl-1(tm1563) mutant, L4, rep 2

description: NovaSeq PE 150


title: UAS-dTrmt10A HS m6A-IP SYS rep2


title: 3603_OF2A_4-2-B6-I15

description: nuclear RNA + genomic DNA


title: UAS-dTrmt10A basal m6A-IP SYS rep2


title: ERBB3-lo luminal progenitor cells from Patient 15.002.1 [BRCA2-lo-15.002.1]


title: C. elegans, mbl-1(tm1563) mutant, L4, rep 1

description: NovaSeq PE 150


title: ERBB3-hi luminal progenitor cells from Patient 0046 [BRCA2-hi-0046]


title: C. elegans, wild-type, L4, rep 3

description: NovaSeq PE 150


title: ERBB3-lo luminal progenitor cells from Patient 0046 [BRCA2-lo-0046]


title: C. elegans, mbl-1(syb4318) mutant, L4, rep 1

description: NovaSeq PE 150


title: 3603_OF2A_4-2-B6-G15

description: nuclear RNA + genomic DNA


title: 3603_OF2A_4-2-B6-G16

description: nuclear RNA + genomic DNA


title: ERBB3-hi luminal progenitor cells from Patient 0111 [BRCA2-hi-0111]


title: UAS-dTrmt10A basal input SYS rep1

description: input for m6A-IP-seq


title: ERBB3-lo luminal progenitor cells from Patient 0111 [BRCA2-lo-0111]


title: 3603_OF2A_4-2-B6-F4

description: nuclear RNA + genomic DNA


title: UAS-dTrmt10A basal m6A-IP SYS rep1


title: 3603_OF2A_4-2-B6-F16

description: nuclear RNA + genomic DNA


title: Control-KK- HS m6A-IP SYS rep3


title: C. elegans, wild-type, L4, rep 2

description: NovaSeq PE 150


title: 3603_OF2A_4-2-B6-G3

description: nuclear RNA + genomic DNA


title: Chip_Exp2_D7_3

city: Boston

first: Donald

last: Ingber

state: Massachusetts

address: 3 Blackfan Circle, CLSB 5th Floor

institute: Wyss Institute for Biologically Inspired Engineering at Harvard University

description: Epithelial cells of cervix from donor 7 cultured in organ chip

data_processing:
The paired reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GRCh38.p7
Supplementary files format and content: raw counts

source_name: cervix

growth_protocol: Cell were grown using Hank’s Buffer Saline Solution (HBSS) in the apical channel while being fed through the basal channel by  cervical differentiation medium (LifeLine Cell Technology, Cat. no. LL-0072+5 nM estradiol-17β (E2)+ 50 µg/mL Ascorbic acid.

extract_protocol: Total RNA was isolated from the cell lysate of the cervical epithelial cells of chips and Transwells using RNeasy Micro Kit (QIAEGN, Cat. No. 74004)

value: cervix

value: primary

value: epithelial

tag: donor

tag: ethnicity

value: caucasian

tag: setup

value: organ chip

tag: flow regimen

value: continuous

tag: technical replicate


title: Chip_Exp2_D7_2

tag: tissue


title: ERBB3-hi luminal progenitor cells from Patient 0148 [WT-hi-0148]

value: Luminal progenitor

tag: patient

tag: genotype

value: WT


title: UAS-dTrmt10A basal input SYS rep3

description: input for m6A-IP-seq


title: 3603_OF2A_4-2-B6-F15

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

description: nuclear RNA + genomic DNA

tag: brain region


title: UAS-dTrmt10A HS input SYS rep1

description: input for m6A-IP-seq


title: Control-KK- HS m6A-IP SYS rep2


title: ERBB3-hi luminal progenitor cells from Patient 0151 [WT-hi-0151]

value: Mammary gland

tag: cell type


title: Chip_Exp2_D7_1

tag: Sex

value: female


title: Control-KK- HS m6A-IP SYS rep1

value: SYS


title: C. elegans, wild-type, L4, rep 1

description: NovaSeq PE 150

value: whole organism

tag: treatment

value: L4 stage


title: 3603_OF2A_4-2-B6-E4

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age


title: ML population from Patient 0399 [WT-ML-0399]

data_processing:
Libraries were sequenced on an Illumina NextSeq 500.
Reads were aligned to the human genome hg38 by the align function of the Rsubread software tool version 1.33.5.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy kit and Dnase treated.
A minimum of 10 ng of total RNA was used to construct libraries following Ilumina's recommended protocol for TruSeq RNA Library Prep Kit v2.

value: ML


title: UAS-dTrmt10A basal input SYS rep2

description: input for m6A-IP-seq

value: basal


title: 3603_OF2A_4-2-B6-F3

description: nuclear RNA + genomic DNA

value: Female


title: 3603_OF2A_4-2-B6-E3

description: nuclear RNA + genomic DNA


title: Control-KK- HS input SYS rep3

description: input for m6A-IP-seq

value: 30 minute heat shock


title: Chip_Exp2_D6_3

description: Epithelial cells of cervix from donor 6 cultured in organ chip

value: cervix

tag: cell line

value: primary

value: hispanic


title: Basal population from Patient 0399 [WT-Basal-0399]

value: Basal


title: LP population from Patient 0399 [WT-LP-0399]

value: LP


title: Control-KK- HS input SYS rep1

description: input for m6A-IP-seq


title: Chip_Exp2_D6_2

value: epithelial

value: organ chip

value: continuous


title: Chip_Exp2_D6_1

value: female


title: ML population from Patient 0174 [WT-ML-0174]

value: Mammary gland

value: WT


title: LP population from Patient 0174 [WT-LP-0174]


title: Control-KK- HS input SYS rep2

description: input for m6A-IP-seq


title: 3603_OF2A_4-2-B6-E16

description: nuclear RNA + genomic DNA


title: Chip_Exp2_D5_2

description: Epithelial cells of cervix from donor 5 cultured in organ chip

value: african american


title: 3603_OF2A_4-2-B6-E15

description: nuclear RNA + genomic DNA

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3603_OF2A_4-2-B6-D3

description: nuclear RNA + genomic DNA


title: Chip_Exp2_D5_3


title: 3603_OF2A_4-2-B6-D4

description: nuclear RNA + genomic DNA


title: Control-KK- basal m6A-IP SYS rep3

value: SYS


title: Chip_Exp2_D5_1


title: ML population from Patient 0025 [WT-ML-0025]

value: ML


title: 3603_OF2A_4-2-B6-D16

description: nuclear RNA + genomic DNA

value: Female


title: Control-KK- basal m6A-IP SYS rep2

value: basal


title: Control-KK- basal input SYS rep3

description: input for m6A-IP-seq


title: 3603_OF2A_4-2-B6-D15

description: nuclear RNA + genomic DNA


title: LP population from Patient 0025 [WT-LP-0025]


title: Chip_Exp1_D7_2

value: cervix

value: caucasian

value: periodic


title: Control-KK- basal input SYS rep2

description: input for m6A-IP-seq


title: Chip_Exp1_D7_1

value: primary


title: Basal population from Patient 0025 [WT-Basal-0025]

value: Basal


title: 3603_OF2A_4-2-B6-C4

description: nuclear RNA + genomic DNA


title: Chip_Exp1_D6_2

value: epithelial

value: hispanic


title: ML population from Patient 0004 [BRCA2-ML-0004]


title: Chip_Exp1_D6_1

value: organ chip


title: 3603_OF2A_4-2-B6-C3

description: nuclear RNA + genomic DNA


title: Lt9434 WGS NovaSeq

city: Cold Spring Harbor

last: Martienssen

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Offline base calling of ONT reads was performed with Guppy 5.0.7 and the R9.4.1 450bps SUP model on NVIDIA Tesla V100 GPUs.
Direct 5-methylcytosine modification calling in all contexts from the ONT WGS reads was performed with Megalodon v2.5.0 with the dna_r9.4.1_450bps_modbases_5mc_hac model and Guppy v5.0.7 on NVIDIA Tesla V100 GPUs. Calls for Cs with fewer than 5 supporting reads were discarded, and the resulting bedMethyl files were split by cytosine context (CpG, CHG, CHH) using bedtools v2.30.0 intersect. Fractional methylation calls at each cytosine were adjusted to a [0..1] scale, and the bedMethyl files were converted to bigWig format. Profiles over genomic regions were calculated as for the WGBS libraries.
ONT reads were aligned to their respective reference assemblies with minimap2 v2.24-r1122 “-x map-ont --MD”. Single nucleotide variants and indels shorter than 50 bp (SNVs) were called using Clair3 v0.1-r12 with options “--min_contig_size=1000000 --platform ont --model_path /opt/models/r941_prom_sup_g5014”. Structural variants (SVs) were called with Sniffles2 v2.0.7 with default options. SNVs and SVs were filtered using RTG Tools v3.12.1 (https://github.com/RealTimeGenomics/rtg-tools) with options “vcffilter --min-read-depth=10 --min-genotype-quality=20”, and homozygous calls were removed with “vcffilter --remove-hom”.
Illumina gDNA reads were aligned to the reference assemblies with bwa-mem2 v2.2.1 and coverage was calculated over 1bp bins with deeptools v3.5.2 “bamCoverage --samFlagExclude 2304 --ignoreDuplicates --binSize 1 --normalizeUsing CPM”.
Supplementary files format and content: ONT 5mC BigWigs: Consensus 5mC calls from Megalodon split by context. In the bigwig coverage tracks (1bp bins), positive values are used for cytosines on the top reference strand, negative for the bottom strand.
Supplementary files format and content: VCFs: heterozygous variant calls made with the same reads used for assembly aligned to their respective assembled references.

source_name: whole frond

extract_protocol:
High molecular weight (HMW) DNA extractions were performed using either a modified CTAB prep followed by a high-salt low-ethanol starch cleanup (Pacific Biosciences), or nuclear extraction as follows:  CTAB prep (Lg7742a, Lj8627, Wa8730): 4 g frozen tissue was ground three times under liquid N2 with a mortar and pestle and transferred to 20 mL pre-warmed lysis buffer (100 mM Tris-HCl pH 9.0, 2% w/v CTAB, 1.4 M NaCl, 20 mM EDTA, 2% PVP-10, 1% 2-mercaptoethanol, 0.1% sarkosyl, 100ug/mL Proteinase K), briefly vortexed, and then incubated at 65ºC for 1 hour with periodic mixing by gentle inversion. The lysate was extracted with 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) and then 1 vol. of chloroform:isoamyl alcohol in phase-lock gel tubes. HMW DNA was precipitated from the aqueous phase in a 50 mL falcon tube by the addition of 0.1 vol. 3M NaOAc pH 5.2 followed by 0.7 vol. Isopropanol. After gentle swirling but no inversion mixing, precipitated salt in the upper phase was pipetted off and HMW DNA was hooked out with a bent pasteur pipette, washed by dipping in 70% EtOH, air-dried for 2 minutes, and resuspended in 200 uL Tris-Cl pH 8.5 (EB). The DNA solution was treated with 2 uL 20 mg/mL RNase A at 37ºC for 20 minutes followed by 2 uL 50 mg/mL Proteinase K at 50ºC for 30 minutes. 194 uL EB, 100 uL 5M NaCl, and 2 uL 0.5 M EDTA were added and organic solvent extractions were performed as before (1x P:C:IA and 1x C:IA). 0.3 vol. EtOH was added followed by centrifugation at 16,000 x g for 15 minutes to precipitate carbohydrates. The supernatant was poured into a new tube and 1.7 vol. of EtOH was added to precipitate HMW DNA, followed by hooking with a pasteur pipette, a 70% EtOH wash, drying, and resuspension in 50 uL EB.  Nuclear prep (Lm7210, Lm9252, Lj7182, Lj9421, Lt9434): as previously described with modifications.
Long-read data for Lg7742a, Lj8627, and Wa8730 were collected over multiple years as the MinION sequencing platform matured. Various protocols and both the SQK-LSK108 and SQK-LSK109 kits were used to prepare libraries for sequencing on multiple flow cell revisions. Here we describe the method used to produce the most recent runs in this study: 2 µg HMW DNA was sheared by 20 passes through a P1000 pipette tip and size-selected using 0.8 vol of custom SPRI beads. The SQK-LSK109 1D Genomic DNA Protocol was followed with the following modifications: Incubation times for all enzymatic reactions were extended to 20 minutes; cleanups following the repair reaction and adapter ligation were performed with 1 vol and 0.8 vol, respectively, of custom SPRI beads rather than Ampure XP; bead elutions were carried out at 37ºC until evenly resuspended; completed libraries were eluted in 24 uL Oxford EB, and half of this volume was mixed with LB and SQB and loaded onto an R9.4.1 rev. D flow cell. After about 20 hours the run was stopped, the Nuclease Flush protocol was performed, and the flow cell re-primed. 6 uL of the remaining library was mixed with 6 uL EB and the loading reagents, loaded onto the flow cell, and the run restarted.  Libraries for Lj7182, Lj9421, Lm7210, Lm9252, and Lt9434 were prepared as previously described and sequenced on R9.4.1 flow cells on the PromethION platform. Short read WGS libraries for Lg7742a and Lj8627 were prepared from 2µg of HMW gDNA using the Illumina TruSeq DNA PCR-Free kit (Illumina, cat#20015962) and sequenced on an Illumina MiSeq (PE 250bp, PE 300bp) or HiSeq 2500 instrument (PE 150bp). Libraries for other Lemna accessions were prepared as described for the NCBI SRA experiment SRX7624904, and previously published libraries were used for Wa8730 (SRX8008794, SRX8008795).

value: whole frond


title: Control-KK- basal input SYS rep1

description: input for m6A-IP-seq


title: Lj8627 WGS MiSeq 2


title: Control-KK- basal m6A-IP SYS rep1


title: 3603_OF2A_4-2-B6-C16

description: nuclear RNA + genomic DNA


title: Basal population from Patient 0004 [BRCA2-Basal-0004]

value: Mammary gland

value: female


title: LP population from Patient 0004 [BRCA2-LP-0004]

value: LP


title: Chip_Exp1_D5_2

value: african american


title: Chip_Exp1_D5_1


title: Lj8627 WGS MiSeq 1


title: TW_D7_3

description: Epithelial cells of cervix from donor 7 cultured in transwell

value: transwell

value: static


title: Basal population from Patient 0174 [WT-Basal-0174]

value: WT