title: H929 ID2 24H S2

description: Library name: H-ID2-2-24H


title: AMO1 ID2 24H S2

status: Public on Sep 26 2025

type: SRA

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana Farber Cancer Institute

description: Library name: AM-ID2-2-24H

library_source: transcriptomic

data_processing:
RSeQC for  quality control
STAR RNAseq aligner
VIPER pipeline
Assembly: hg38
Supplementary files format and content: txt file with raw read counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: All myeloma cell lines were cultured in RPMI-1640supplemented with 10% fetal bovine serum, 1% L-glutamine and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 10ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using Roche Kapa Biosystems RiboErase and RNA HyperPrep sample preparation kits from 100ng of RNA.

treatment_protocol: Control and ID2-overexpressing (ID2-OE) cells were incubated with 0.25 µg/ml doxycycline for 24 hours to induce ID2 expression.

tag: cell line

tag: treatment

value: ID2 OE


title: AMO1 Control 24H S1

description: Library name: AM-CNT-1-24H

value: WT


title: KMS20 Control 24H S2

description: Library name: K20-CNT-2-24H


title: H929 Control 24H S1

description: Library name: H-CNT-2-24H


title: H929 Control 24H S2

description: Library name: H-CNT-1-24H


title: AMO1 ID2 24H S1

description: Library name: AM-ID2-1-24H


title: Human kidney epithelial cells mCherry control replicate 1

city: TEL AVIV

first: Naomi

last: Pode-Shakked

address: Weizmann St 6

department: Pediatric Nephrology

country: Israel

institute: Tel Aviv Souraski Medical Center

description:
Library name: 3_AK94P5-Control1
mCherry control hKEpCs, donor AK94P5, biological replicate 1

data_processing:
Quality assessment: FastQC v0.11.9
Trimming and filtering: Trimmomatic v0.39 with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36
Alignment: STAR aligner v2.7.3a to human reference genome GRCh38/hg38
Gene quantification: featureCounts v2.0.1 using GENCODE v32 annotations
Differential expression: DESeq2 v1.30.0 with Benjamini-Hochberg correction; genes with adjusted p-values <0.05 and |log2FC| >1 considered significant
Assembly: GRCh38/hg38
Supplementary files format and content: All_NormData.csv: Normalized expression matrix containing 13,272 genes across 13 samples. Values represent DESeq2 normalized counts
Supplementary files format and content: LFC files: Differential expression results containing gene names, log2FoldChange, padj, and baseMean values
Supplementary files format and content: DE files: Filtered differential expression results for upregulated (Up), downregulated (Dwn), and all significant genes (Res) with fold change >0.58 and p-value <0.05}

molecule: polyA RNA

source_name: adult kidney

growth_protocol:
IMDM + 10% FBS + growth factors (50ng/mL bFGF, 50ng/mL EGF, 5ng/mL SCF)
Primary human adult kidney cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% fetal bovine serum, 1% L-glutamine, 1% penicillin-streptomycin, and growth factors: 50 ng/mL bFGF, 50 ng/mL EGF, and 5 ng/mL SCF (R&D Systems). Cells were maintained at 37'b0C in a humidified atmosphere containing 5% CO2. Cells were passaged using trypsin-EDTA (Gibco) upon reaching 70-80% confluency and used between passages 2-7.

extract_protocol:
Total RNA was extracted from cells at passage 4-6 using RNeasy Mini Kit (Qiagen) with on-column DNase digestion according to manufacturer's instructions. RNA concentration and purity were assessed using NanoDrop spectrophotometer with acceptable 260/280 ratios between 1.8-2.0. RNA integrity was assessed using Agilent 2100 Bioanalyzer with RNA 6000 Nano Kit; only samples with RIN values >8.0 were used.
RNA-Seq libraries were prepared from 1 uc0u956 g total RNA using TruSeq Stranded mRNA Library Prep Kit (Illumina). mRNA was isolated using poly-A selection, fragmented, and reverse transcribed using random hexamer primers. Second-strand cDNA synthesis was performed using dUTP for strand specificity. Following end repair, A-tailing, and adapter ligation, libraries were amplified by PCR for 12-15 cycles. Library quality was assessed using Agilent 2100 Bioanalyzer and quantified by qPCR using KAPA Library Quantification Kit.

treatment_protocol: For lentiviral transduction, hKEpCs were seeded at 5'd710^4 cells per well in 6-well plates and transduced with lentiviral particles at MOI of 5 in the presence of 8 uc0u956 g/mL polybrene. After 24 hours, medium was replaced with fresh REGM containing 10% FBS. Transduced cells were selected with puromycin (2 u956 g/mL) for 7 days. For double transduction, OSR1-expressing cells were additionally transduced with SIX2-encoding virus and selected with puromycin and neomycin.

tag: cell type

value: primary adult kidney epithelial cells

tag: genotype/variation

value: wild type

tag: transfection

value: lentiviral mCherry

value: puromycin selection


title: KT007_PM_positive_cfDNA_5hmC

city: Chicago

first: Lu

last: Gao

state: IL

institute: University of Chicago

description:
Library name: KT007
No

library_source: genomic

data_processing:
All sequencing data was trimmed using Trim Galore44 (version 0.6.7), and subject to quality control analysis using FastQC (version 0.11.9). Results for each sample were collated and analyzed using MultiQC (version 1.21). Samples with at least one of two paired-end files with fewer than 10M unique reads were excluded from all subsequent analysis due to library preparation and/or sequencing failure. This resulted in the exclusion of 7/192 (3.6%) of samples (Supplementary Figure S 1). Reads were mapped to the human genome assembly (GRCh37 hg19) using Bowtie2 (version 2.4.4). 5hmC peaks were called on each sample’s .bam file using MACS3 version (3.0.1). Raw 5hmC-associated read counts for each sample in merged peak-set regions were then determined using featureCounts (version 2.0.3).The resulting merged peak set containing 166,945 hMRs was further filtered into a consensus peak containing 71,597 by excluding peaks occurring on chromosomes X and Y, peaks less than 5,000 bp in length, and peaks that had fewer than 15 counts in > 10% of samples.
Assembly: hg19
Supplementary files format and content: TSV
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: plasma

extract_protocol:
On average 9.7ng (IQR: 9.7-10.0) was obtained from ~5mL of peripheral blood collected from each patient using QIAamp Circulating Nucleic Acid Kit (Qiagen, Cat. No. 55114).
5hmC libraries for all samples were constructed with high-efficiency hmC-Seal technology. According to the requirements of next-generation sequencing, the cfDNA extracted from plasma was end-repaired, 3′-adenylated using the KAPA Hyper Prep Kit (KAPA Biosystems), and then ligated with the Illumina compatible adapters.

tag: tissue

value: plasma

tag: group

value: Surgery only

tag: peritoneal mets

tag: other mets

tag: primary present_at_sampling

tag: primary site

tag: batch


title: KT010_PM_positive_cfDNA_5hmC

description:
Library name: KT010
Yes

value: Chemo + Surgery


title: KT235_PM_positive_cfDNA_5hmC

description:
Library name: KT235
No


title: KT134_PM_positive_cfDNA_5hmC

description:
Library name: KT134
No


title: KT009_PM_positive_cfDNA_5hmC

description:
Library name: KT009
Yes


title: ARPE-19, Meta, macroH2A1, Rep1 (Chip)

city: Minhang

first: deng

last: yongzhuo

state: Shanghai

address: DongchuanoRoad N0.800

country: China

institute: Shanghai Jiao Tong University

description: Library name: ARPE-19_Meta_macroH2A1_Chip, Rep1

data_processing:
Utilize TrimGalore to remove sequencing adapter sequences and low-quality bases from your reads (Q<20)
Use Bowtie2 to align the trimmed single reads to human genome
Use Samtools to remove the unknown chromosome segments mapped reads, unmappable reads and multi-mapped reads The mapped reads are converted to bam format, are de-duplicated by Sambamba markdup
mapped reads are used to identidfy macroH2A1 enriched domains  by normR after normalization by the control (input nucleosome DNA). Genome is divided into 2kb bins,regimeR is used for calling peaks,  significant bins identified by Fisher’s test (P < 0.05) are use exportR to output into Bed files and BigWig files
Assembly: Homo_sapiens.GRCh38.114
Supplementary files format and content: BigWig

source_name: cell line

growth_protocol: All cell lines are kept in a humidified incubator at 37°C temperature with a 5% CO2 supply and cultured in DMEM (GIBCO, Carlsbad, CA, USA) with 10% FBS (GIBCO, Carlsbad, CA, USA) and 1% Pen/Strep antibiotin (GIBCO, Carlsbad, CA, USA).

extract_protocol:
In brief, collected cells are lysis in hypotonic buffer. After centrifugation, then resuspend in PA buffer. Cells are homogenized with a Dounce homogenizer for 10min with intermittent pauses. After removing large debris, supernatant is filtered through 10 μm and 5 μm filters. Chromosomes are centrifuged at 1750 × g for 10 min at 4°C and resuspend in MNase buffer.
Sequencing libraries are generated using approximately 1 ng of DNA per sample with the NEBNext® Ultra™ II DNA Library Prep Kit (E7645S, NEB, Ipswich, MA, USA), and sequencing is conducted on the Illumina® NovaSeq 500 platform. Prior to library preparation, the DNA is extracted using phenol-chloroform and ethanol precipitation. To obtain the DNA, either input mono-nucleosomes or ChIP-purified macroH2A1 nucleosomes are treated overnight at 56°C with 1% SDS and 200 μg/mL Proteinase K (Invitrogen, Carlsbad, CA, USA) following a pre-incubation with 100 μg/mL RNase A (Invitrogen, Carlsbad, CA, USA) to eliminate RNA contamination.

treatment_protocol: Culture cells with 100ng/ml colcemid (Sigma-Aldrich, St. Louis, MO, USA) overnight. After the incubation period, collected cells are lysed for purifing mitotic chromosome

value: cell line

value: human retinal pigment epithelial cell line

value: epithelial cells


title: KT123_PM_positive_cfDNA_5hmC

description:
Library name: KT123
No

value: Chemo only


title: KT082_PM_positive_cfDNA_5hmC

description:
Library name: KT082
No


title: KT006_PM_positive_cfDNA_5hmC

description:
Library name: KT006
Yes


title: KT159_PM_positive_cfDNA_5hmC

description:
Library name: KT159
Yes


title: KT135_PM_positive_cfDNA_5hmC

description:
Library name: KT135
No


title: KT037_PM_positive_cfDNA_5hmC

description:
Library name: KT037
No


title: KT041_PM_positive_cfDNA_5hmC

description:
Library name: KT041
No


title: KT016_PM_positive_cfDNA_5hmC

description:
Library name: KT016
No


title: AMO1 Control 24H S2

description: Library name: AM-CNT-2-24H


title: KT146_PM_positive_cfDNA_5hmC

description:
Library name: KT146
Yes


title: KT011_PM_positive_cfDNA_5hmC

description:
Library name: KT011
Yes


title: KT003_PM_positive_cfDNA_5hmC

description:
Library name: KT003
Yes


title: KT024_PM_positive_cfDNA_5hmC

description:
Library name: KT024
Yes


title: KT019_PM_positive_cfDNA_5hmC

description:
Library name: KT019
Yes


title: KT339_PM_positive_cfDNA_5hmC

description:
Library name: KT339
Yes


title: KT004_PM_positive_cfDNA_5hmC

description:
Library name: KT004
Yes


title: KT334_PM_positive_cfDNA_5hmC

description:
Library name: KT334
Yes


title: KT001_PM_positive_cfDNA_5hmC

description:
Library name: KT001
No


title: KT332_PM_positive_cfDNA_5hmC

description:
Library name: KT332
Yes


title: KT028_PM_positive_cfDNA_5hmC

description:
Library name: KT028
No


title: KT168_PM_positive_cfDNA_5hmC

description:
Library name: KT168
Yes


title: KT301_PM_positive_cfDNA_5hmC

description:
Library name: KT301
No


title: KT136_PM_positive_cfDNA_5hmC

description:
Library name: KT136
No


title: KT165_PM_positive_cfDNA_5hmC

description:
Library name: KT165
Yes


title: KT093_PM_positive_cfDNA_5hmC

description:
Library name: KT093
No


title: KT152_PM_positive_cfDNA_5hmC

description:
Library name: KT152
Yes


title: KT100_PM_positive_cfDNA_5hmC

description:
Library name: KT100
No


title: KT162_PM_positive_cfDNA_5hmC

description:
Library name: KT162
Yes


title: KT092_PM_positive_cfDNA_5hmC

description:
Library name: KT092
No


title: KT078_PM_positive_cfDNA_5hmC

description:
Library name: KT078
Yes

value: Chemo + Radiation + Surgery


title: KT073_PM_positive_cfDNA_5hmC

description:
Library name: KT073
No


title: KT077_PM_positive_cfDNA_5hmC

description:
Library name: KT077
Yes


title: KT069_PM_positive_cfDNA_5hmC

description:
Library name: KT069
No


title: KT057_PM_positive_cfDNA_5hmC

description:
Library name: KT057
No


title: KT067_PM_positive_cfDNA_5hmC

description:
Library name: KT067
No


title: KT068_PM_positive_cfDNA_5hmC

description:
Library name: KT068
No


title: KT055_PM_positive_cfDNA_5hmC

description:
Library name: KT055
No


title: KT047_PM_positive_cfDNA_5hmC

description:
Library name: KT047
Yes


title: KT341_PM_positive_cfDNA_5hmC

description:
Library name: KT341
Yes


title: KT338_PM_positive_cfDNA_5hmC

description:
Library name: KT338
No


title: KT318_PM_positive_cfDNA_5hmC

description:
Library name: KT318
Yes


title: KT305_PM_positive_cfDNA_5hmC

description:
Library name: KT305
No


title: KT322_PM_positive_cfDNA_5hmC

description:
Library name: KT322
Yes


title: KT161_PM_positive_cfDNA_5hmC

description:
Library name: KT161
Yes


title: KT155_PM_positive_cfDNA_5hmC

description:
Library name: KT155
No


title: KT151_PM_positive_cfDNA_5hmC

description:
Library name: KT151
No


title: KT126_PM_positive_cfDNA_5hmC

description:
Library name: KT126
No


title: KT125_PM_positive_cfDNA_5hmC

description:
Library name: KT125
No


title: KT112_PM_positive_cfDNA_5hmC

description:
Library name: KT112
Yes


title: KT096_PM_positive_cfDNA_5hmC

description:
Library name: KT096
No


title: KT083_PM_positive_cfDNA_5hmC

description:
Library name: KT083
No


title: KT052_PM_positive_cfDNA_5hmC

description:
Library name: KT052
Yes


title: KT091_PM_positive_cfDNA_5hmC

description:
Library name: KT091
Yes


title: KT021_PM_positive_cfDNA_5hmC

description:
Library name: KT021
No


title: KT040_PM_positive_cfDNA_5hmC

description:
Library name: KT040
No


title: KT061_PM_positive_cfDNA_5hmC

description:
Library name: KT061
No


title: KT017_PM_positive_cfDNA_5hmC

description:
Library name: KT017
Yes


title: KT018_PM_positive_cfDNA_5hmC

description:
Library name: KT018
Yes


title: KT014_PM_positive_cfDNA_5hmC

description:
Library name: KT014
Yes


title: KT013_PM_positive_cfDNA_5hmC

description:
Library name: KT013
Yes


title: KT008_PM_positive_cfDNA_5hmC

description:
Library name: KT008
Yes


title: KT005_PM_positive_cfDNA_5hmC

description:
Library name: KT005
No

value: Chemo + Radiation


title: KT172_PM_positive_cfDNA_5hmC

description:
Library name: KT172
Yes


title: SHSY_RA4

type: RNA

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

country: Germany

institute: University Hospital Schleswig-Holstein, Campus Kiel

description: Gene expression from retinoic acid-treated SH-SY5Y cells.

hyb_protocol: 3.5 µg fragemented and labeled ssDNA were hybridized on Clariom D arrays for 16 h at 45 °C using the Affymetrix Hybridization Oven 640. The arrays were washed and stained using the Fluidics Station 450 with the protocol FS450_0002.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were processed using the Transcriptome Analysis Console v.4.0.3 (Thermo Fisher Scientific).

label: biotin

label_protocol: 100 ng RNA was used for each sample with the GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations.

growth_protocol: Kelly cells were grown in RPMI 1640 supplemented with 10 % v/v FCS; SH-SY5Y in DMEM + 20 % v/v FCS w/o retinoic acid.

extract_protocol: Total RNA was isolated using the E.Z.N.A Total RNA Kit II (Omega Bio-Tek) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with 5 µM all-trans retinoic acid for 3d.

value: retinoic acid

value: SHSY


title: SHSY_RA2


title: SHSY_RA1


title: KT113_PM_negative_cfDNA_5hmC

description:
Library name: KT113
No


title: SHSY_K4

description: Gene expression from untreated SH-SY5Y cells.

value: control


title: KT046_PM_negative_cfDNA_5hmC

description:
Library name: KT046
No


title: KT142_PM_positive_cfDNA_5hmC

description:
Library name: KT142
Yes


title: SHSY_K3


title: KT025_PM_negative_cfDNA_5hmC

description:
Library name: KT025
No


title: KT020_PM_positive_cfDNA_5hmC

description:
Library name: KT020
No


title: KT036_PM_negative_cfDNA_5hmC

description:
Library name: KT036
Yes


title: SHSY_K2


title: SHSY_K1


title: Kelly_RA4

description: Gene expression from retinoic acid-treated Kelly cells.

value: Kelly


title: KT044_PM_negative_cfDNA_5hmC

description:
Library name: KT044
No


title: KT336_PM_negative_cfDNA_5hmC

description:
Library name: KT336
Yes


title: KT043_PM_negative_cfDNA_5hmC

description:
Library name: KT043
No


title: KT015_PM_positive_cfDNA_5hmC

description:
Library name: KT015
Yes


title: Kelly_RA3


title: KT012_PM_positive_cfDNA_5hmC

description:
Library name: KT012
No


title: Kelly_RA2


title: Kelly_RA1


title: KT370_PM_negative_cfDNA_5hmC

description:
Library name: KT370
No


title: KT371_PM_negative_cfDNA_5hmC

description:
Library name: KT371
No


title: KT117_PM_negative_cfDNA_5hmC

description:
Library name: KT117
No


title: d1A41, d1A42, mESC, Mouse

city: Beijing

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
For all cell types, samples with more than 50,000 remaining contacts were retained for downstream analysis. For mESCs (diploid samples), the haplotype of contacts was phased according to SNP sites. Each chromosome in each sample was treated as a polymer chain, evenly divided into 20kb sections, with each section treated as a particle of the polymer chain. The contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles using the Force-Directed Graph (FDG) algorithm implemented by “hickit”. To assess the quality of the chromatin 3D structure reconstruction, we generated five replicates using different random seeds and calculated the median RMSD for each combination of three replicates. If the median RMSD of the combination with the lowest value was less than 1.5, the first replicate in that combination was used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: dip pairs file: A tab-separated file recording allele-specific contacts that conforms to 4DN Consortium standards with chromosomes
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards with chromosomes

organism: Mus musculus

source_name: mESC

extract_protocol:
• Cell lines We utilized a female mouse embryonic stem cell (mESC) line derived from blastocysts at embryonic day 3.5 (E3.5) from crossbred embryos (female C57BL/6J × male CAST/EiJ). The procedures for derivation and culturing followed the methods provided by Arenas et al. (2006). • Cell culture Cells were cultured on flasks coated with 0.1% gelatin in an ES cell medium containing serum. The medium composition included DMEM (Gibco, 10829018), 15% ESC-grade fetal bovine serum (FBS) (VivaCell, C04002-100), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% P/S (ThermoFisher, 10378016), NEAA (Sigma, M7145), L-Glutamine (Gibco, 25030-081), nucleotides (Millipore, ES-008-D), and 1000 U/ml leukemia inhibitory factor (LIF) (PeproTech, AF-250-02-25UG). Additionally, the medium was supplemented with 2i: 3 μM Gsk3 inhibitor CT99021 (Selleck, S1263) and 1 μM MEK inhibitor PD0325901 (Selleck, S1036).  • Cell differentiation Differentiation was initiated by withdrawing 2i/LIF in DMEM supplemented with 10% FBS, 1% P/S, NEAA, L-Glutamine, nucleotides, and 0.1 mM β-mercaptoethanol. The cells were plated at a density of 1.5 × 10⁴ cells/cm² on 6 well cell culture plates coated with 10 μg/ml fibronectin (GLPBIO, GP23499).
The single-cell preamplification product was diluted to 5ng/ul and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C

value: mESC


title: SHSY_RA3


title: KT369_PM_negative_cfDNA_5hmC

description:
Library name: KT369
No


title: KT031_PM_negative_cfDNA_5hmC

description:
Library name: KT031
No


title: KT368_PM_negative_cfDNA_5hmC

description:
Library name: KT368
No


title: Kelly_K4

description: Gene expression from untreated Kelly cells.


title: Kelly_K3


title: Kelly_K2


title: Kelly_K1


title: KT366_PM_negative_cfDNA_5hmC

description:
Library name: KT366
No


title: KT365_PM_negative_cfDNA_5hmC

description:
Library name: KT365
No


title: KT364_PM_negative_cfDNA_5hmC

description:
Library name: KT364
No


title: KT363_PM_negative_cfDNA_5hmC

description:
Library name: KT363
No


title: KT362_PM_negative_cfDNA_5hmC

description:
Library name: KT362
No


title: KT361_PM_negative_cfDNA_5hmC

description:
Library name: KT361
No


title: KT357_PM_negative_cfDNA_5hmC

description:
Library name: KT357
No


title: Mb1 Cre_Ctrl - pro B, biol rep 5

city: St. Louis

first: George

middle: P.

last: Souroullas

state: MO

address: 660 S. Euclid Av

department: Medicine

institute: Washington University School of Medicine

description: Library name: Sample 33

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
RNA-seq reads were then aligned and quantitated to the appropriate mouse or human genome with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis (SVA).  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Mouse Ensembl GRCm39.113
Supplementary files format and content: tab-delimited text file contains CPM and RPKM values for each sample

source_name: Bone marrow

growth_protocol: B cell progenitors were isolated from mouse bone marrow using FACS and processed for RNA isolation.  Follilcular B cells were isolated from mouse spleen using FACS and processed for RNA isolation.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturer's instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Bone marrow

value: B cell progenitors (pro B)

tag: genotype


title: Mb1 Cre_Ctrl - pro B, biol rep 3

description: Library name: Sample 31


title: KT358_PM_negative_cfDNA_5hmC

description:
Library name: KT358
No


title: Mb1 Cre_Ctrl - pro B, biol rep 6

description: Library name: Sample 34


title: Mb1 Cre_Ctrl - pro B, biol rep 1

description: Library name: Sample 29


title: Mb1 Cre_Ctrl - pro B, biol rep 2

description: Library name: Sample 30


title: Mb1 Cre_Ctrl - pro B, biol rep 4

description: Library name: Sample 32


title: Mb1 Cre_Ctrl - pro B, biol rep 7

description: Library name: Sample 35


title: KT354_PM_negative_cfDNA_5hmC

description:
Library name: KT354
No


title: KT351_PM_negative_cfDNA_5hmC

description:
Library name: KT351
Yes


title: Mb1 Cre_Ctrl - pre B, biol rep 6

description: Library name: Sample 28

value: B cell progenitors (pre B)


title: Mb1 Cre_Ctrl - pre B, biol rep 5

description: Library name: Sample 27


title: KT349_PM_negative_cfDNA_5hmC

description:
Library name: KT349
No

value: plasma


title: Mb1 Cre_Ctrl - pre B, biol rep 3

description: Library name: Sample 25


title: KT348_PM_negative_cfDNA_5hmC

description:
Library name: KT348
No


title: Mb1 Cre_Ctrl - pre B, biol rep 4

description: Library name: Sample 26


title: KT367_PM_negative_cfDNA_5hmC

description:
Library name: KT367
No


title: KT347_PM_negative_cfDNA_5hmC

description:
Library name: KT347
No


title: Mb1 Cre_Ctrl - pre B, biol rep 2

description: Library name: Sample 24


title: KT346_PM_negative_cfDNA_5hmC

description:
Library name: KT346
Yes


title: KT345_PM_negative_cfDNA_5hmC

description:
Library name: KT345
No


title: Mb1 Cre_Ctrl - pre B, biol rep 1

description: Library name: Sample 23


title: Arid2_KO_pro B, biol rep 7

description: Library name: Sample 22


title: Arid2_KO_pro B, biol rep 6

description: Library name: Sample 21


title: KT344_PM_negative_cfDNA_5hmC

description:
Library name: KT344
No

value: Surgery only


title: KT343_PM_negative_cfDNA_5hmC

description:
Library name: KT343
No


title: Arid2_KO_pro B, biol rep 4

description: Library name: Sample 19


title: Arid2_KO_pro B, biol rep 5

description: Library name: Sample 20


title: KT356_PM_negative_cfDNA_5hmC

description:
Library name: KT356
Yes


title: KT167_PM_negative_cfDNA_5hmC

description:
Library name: KT167
No

value: Chemo + Surgery


title: KT131_PM_negative_cfDNA_5hmC

description:
Library name: KT131
Yes


title: Arid2_KO_pro B, biol rep 1

description: Library name: Sample 16


title: KT107_PM_negative_cfDNA_5hmC

description:
Library name: KT107
No


title: Arid2_KO_pro B, biol rep 3

description: Library name: Sample 18


title: KT121_PM_negative_cfDNA_5hmC

description:
Library name: KT121
Yes


title: Arid2_KO_pre B, biol rep 4

description: Library name: Sample 12


title: KT045_PM_negative_cfDNA_5hmC

description:
Library name: KT045
No


title: Arid2_KO_pre B, biol rep 6

description: Library name: Sample 14


title: KT042_PM_negative_cfDNA_5hmC

description:
Library name: KT042
No


title: KT034_PM_negative_cfDNA_5hmC

description:
Library name: KT034
No


title: Arid2_KO_pro B, biol rep 2

description: Library name: Sample 17


title: KT033_PM_negative_cfDNA_5hmC

description:
Library name: KT033
No


title: Arid2_KO_pre B, biol rep 2

description: Library name: Sample 10


title: Arid2_KO_pre B, biol rep 7

description: Library name: Sample 15


title: Arid2_KO_pre B, biol rep 3

description: Library name: Sample 11


title: KT377_non_cancer_control_cfDNA_5hmC

description:
Library name: KT377
n/a


title: KT376_non_cancer_control_cfDNA_5hmC

description:
Library name: KT376
n/a


title: Mb1Cre_Ctrl - Follicular, biol rep 3

description: Library name: Sample 7

source_name: Spleen

value: Spleen

value: Follicular B cells


title: Arid2_KO_pre B, biol rep 1

description: Library name: Sample 9


title: KT032_PM_negative_cfDNA_5hmC

description:
Library name: KT032
No


title: KT374_non_cancer_control_cfDNA_5hmC

description:
Library name: KT374
n/a


title: KT375_non_cancer_control_cfDNA_5hmC

description:
Library name: KT375
n/a


title: Mb1Cre_Ctrl - Follicular, biol rep 2

description: Library name: Sample 6


title: Mb1Cre_Ctrl - Follicular, biol rep 1

description: Library name: Sample 5


title: KT373_non_cancer_control_cfDNA_5hmC

description:
Library name: KT373
n/a


title: Arid2_KO_Follicular, biol rep 4

description: Library name: Sample 4


title: Arid2_KO_pre B, biol rep 5

description: Library name: Sample 13


title: KT330_non_cancer_control_cfDNA_5hmC

description:
Library name: KT330
n/a


title: KT329_non_cancer_control_cfDNA_5hmC

description:
Library name: KT329
n/a


title: Arid2_KO_Follicular, biol rep 2

description: Library name: Sample 2


title: Arid2_KO_Follicular, biol rep 3

description: Library name: Sample 3


title: KT328_non_cancer_control_cfDNA_5hmC

description:
Library name: KT328
n/a


title: Arid2_KO_Follicular, biol rep 1

description: Library name: Sample 1


title: F123 mES cell clonal line (RNA-seq)

city: Stanford

first: Christy

last: Luong

state: CA

address: 269 Campus Dr

department: Department of Dermatology

institute: Stanford University School of Medicine

description:
Library name: F123_mESC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

data_processing:
Reads were aligned to an N-masked genome and transcriptome using STAR. Aligned reads were then split using informative SNPs using SNPsplit for allele-specific analysis. We also kept mapped reads that did not undergo SNPsplit to perform non-allele specific analysis. Transcripts are quantified using Salmon and tximport was used to import and summarize transcripts for downstream gene-level analysis.
Assembly: mm10
Supplementary files format and content: tximport_all_withgenes_merged.csv is a output file from tximport that summarizes Salmon output for gene-level analysis from non-allele specific mapped RNA-seq reads. File contains non-allele specific estimated counts, abundances, and gene_names. Columns are the sample names.
Supplementary files format and content: tximport_allele_specific_all_withgenes_merged.csv is a output file from tximport that summarizes  Salmon output for gene-level analysis from allele specific mapped RNA-seq reads. File contains allele-specific estimated counts, abundances, and gene_names. Columns are the sample names.

growth_protocol: NPCs were differentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF. F123 mESCs were growon on 0.1% gelatin with N2B27 medium with 2i+Lif

extract_protocol:
RNA was extracted with Trizol and purified using Zymo RNA direct-zol mini prep kit.
total RNA was given to Novogene for directional RNA library prep with polyA enrichment

tag: Sex

value: Male

value: mouse embyronic stem cell


title: KT327_non_cancer_control_cfDNA_5hmC

description:
Library name: KT327
n/a


title: CHL27  neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: CH27_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: CHL19 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: CHL19_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: KT324_non_cancer_control_cfDNA_5hmC

description:
Library name: KT324
n/a


title: Mb1Cre_Ctrl - Follicular, biol rep 4

description: Library name: Sample 8


title: KT321_non_cancer_control_cfDNA_5hmC

description:
Library name: KT321
n/a


title: KT323_non_cancer_control_cfDNA_5hmC

description:
Library name: KT323
n/a


title: KT317_non_cancer_control_cfDNA_5hmC

description:
Library name: KT317
n/a


title: CHL25  neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: CHL25_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: KT326_non_cancer_control_cfDNA_5hmC

description:
Library name: KT326
n/a


title: CHL16 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: CHL16_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Ch8 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: Ch8_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: CHL10 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: CHL10_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: KT315_non_cancer_control_cfDNA_5hmC

description:
Library name: KT315
n/a


title: CHL9 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: CHL9_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: KT319_non_cancer_control_cfDNA_5hmC

description:
Library name: KT319
n/a


title: KT313_non_cancer_control_cfDNA_5hmC

description:
Library name: KT313
n/a


title: KT316_non_cancer_control_cfDNA_5hmC

description:
Library name: KT316
n/a


title: KT372_non_cancer_control_cfDNA_5hmC

description:
Library name: KT372
n/a


title: KT312_non_cancer_control_cfDNA_5hmC

description:
Library name: KT312
n/a


title: mE6 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: mE6_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Standard chow scRNA-seq

city: Singapore

first: Zhengwei

last: Wu

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description: Library name: AHT291

library_source: transcriptomic single cell

data_processing:
The scRNA-seq libraries from Parse Biosciences platforms were sequenced using the Illumina NovaSeq 6000 platform. For the Parse data, fastq files from 1 sub-library were demultiplexed into 2 samples using the Trailmaker split-pipe pipeline (v1.0.4p) from Parse Biosciences (https://app.trailmaker.parsebiosciences.com/pipeline, assessed on 5th February 2025.
Assembly: GRCm39
Supplementary files format and content: Provided .rds file for Processed Seurat object for scRNA-seq

source_name: Lung

growth_protocol: In-vivo growth in NSG mice fed with either standard chow or ketogenic diet

extract_protocol:
For the Parse Biosciences platform, the cells were prepared using the Fixation Kit in Evercode™ WT Mini v3 package (Parse Biosciences, Seattle, WA, USA) according to the manufacturer’s protocol. After fixation, the cell count was determined using the TC20™ Automated Cell Counter (Sigma Aldrich). A total of 20,000 cells from dissociated tumor of control diet- and ketogenic diet-fed NSG mice was used, resulting in an average of approximately 10,000 cells per tumor.
These cells were subjected to the Single Cell Whole Transcriptome Kit v2 (Parse Biosciences, Seattle, WA, USA) for library construction

treatment_protocol: Standard diet or ketogenic diet given right before subcutaneous injection of tumor cells

value: Lung

value: Tumor-initiating cells

value: Tumor-initiating cell

value: Standard chow


title: KT311_non_cancer_control_cfDNA_5hmC

description:
Library name: KT311
n/a


title: Ketogenic diet scRNA-seq

description: Library name: AHT292

value: Ketogenic diet


title: KT309_non_cancer_control_cfDNA_5hmC

description:
Library name: KT309
n/a


title: KT308_non_cancer_control_cfDNA_5hmC

description:
Library name: KT308
n/a


title: Rep 1. Input Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

city: Santa Cruz

first: Ali

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

description: Library name: ChIP_input_rep1

data_processing:
ChIP-seq FASTQ files were inspected with FastQC. Low quality reads were removed using Trimmomatic, removing adapter/index sequences, quality filtering (sliding window 4:20) and retaining only reads of 50bp or longer. Data was aligned using Bowtie2, to the mouse mm10 genome. MACS2 was used for peak calling, and only peaks with a q-value > 13 were used for analysis. ChIPSeeker was used to classify peaks based on Gencode VM23 gene annotation
Assembly: mm10
Supplementary files format and content: MACS2 call peak output (q-value >10) in BED format for EV and E2F1 samples

growth_protocol: NIH/3T3 cells were grown in DMEM supplemented with 10% heat-inactivated fetal bovine serum (HIFBS) and 1x penicillin+streptomycin (P/S). For maintaining cultures, cells were split using 0.25% Trypsin + 0.5mM EDTA every 3-4 days at a subcultivation ratio of 1/10. Cells were grown in a humified incubator at 37degC and 5%CO2

extract_protocol:
RNA was extracted following the Zymo RNA microprep kit.
RNA libraries were prepared by Novogene inc using polyA selection and paired-end sequencing and sequenced on the Illumina NovaSeq 6000 (150bp reads)

treatment_protocol: Cells were serum starved (DMEM, 0.25% HIFBS, 1x P/S) for 48 hours. Following this, cells were treated with 500ng/ml doxycycline or 10% HIFBS for up to 24 hours

value: Dox-inducible EV

value: Doxycycline 12 hr


title: Ch1 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: Ch1_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Rep 2. Input Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_input_rep2


title: KT307_non_cancer_control_cfDNA_5hmC

description:
Library name: KT307
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_EV_rep2


title: KT306_non_cancer_control_cfDNA_5hmC

description:
Library name: KT306
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_EV_rep1


title: KT304_non_cancer_control_cfDNA_5hmC

description:
Library name: KT304
n/a


title: Rep 2.Dox-inducible E2F1 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_E2F1_rep2

value: Dox-inducible E2F1


title: Rep 1.Dox-inducible E2F1 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_E2F1_rep1


title: KT303_non_cancer_control_cfDNA_5hmC

description:
Library name: KT303
n/a


title: KT302_non_cancer_control_cfDNA_5hmC

description:
Library name: KT302
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_6hr_rep2

data_processing:
ATAC-seq FASTQ files were inspected with FastQC. Low quality reads were removed using Trimmomatic, removing adapter/index sequences, quality filtering (sliding window 4:20) and retaining only reads of 50bp or longer. Data was aligned using Bowtie2, to the mouse mm10 genome. Reads flagged as PCR duplicates were removed using RmDup, and reads in ENCODE blacklisted regions were removed (mm10.blacklist.v2). MACS2 was used for peak calling, peaks with q value > 50 were used for later analysis. Pooled replicate MACS2 analysis used to combine data from biological replicate experiments. HOMER was used for differential peak signal and motif calling.
Assembly: mm10
Supplementary files format and content: BED files of MACS2 call peak output

extract_protocol:
ATAC sample were prepared according the ActiveMotif ATAC-Seq kit.
ATAC-Seq libraries were prepared according to the ActiveMotif ATAC-Seq kit.

value: 10% Serum 6 hr


title: KT219_non_cancer_control_cfDNA_5hmC

description:
Library name: KT219
n/a

value: plasma


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_12hr_rep1

value: 10% Serum 12 hr


title: KT217_non_cancer_control_cfDNA_5hmC

description:
Library name: KT217
n/a


title: KT215_non_cancer_control_cfDNA_5hmC

description:
Library name: KT215
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_2hr_rep1

value: 10% Serum 2 hr


title: KT218_non_cancer_control_cfDNA_5hmC

description:
Library name: KT218
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_2hr_rep2


title: KT216_non_cancer_control_cfDNA_5hmC

description:
Library name: KT216
n/a


title: KT214_non_cancer_control_cfDNA_5hmC

description:
Library name: KT214
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_EV_dox_12hr_rep2


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_EV_dox_2hr_rep2

value: Doxycycline 2 hr


title: KT213_non_cancer_control_cfDNA_5hmC

description:
Library name: KT213
n/a


title: KT210_non_cancer_control_cfDNA_5hmC

description:
Library name: KT210
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_EV_dox_12hr_rep1


title: KT212_non_cancer_control_cfDNA_5hmC

description:
Library name: KT212
n/a


title: Rep 2. Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_EV_dox_0hr_rep2

value: Doxycycline 0 hr


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_12hr_rep2


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_EV_dox_6hr_rep1

value: Doxycycline 6 hr


title: KT220_non_cancer_control_cfDNA_5hmC

description:
Library name: KT220
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_6hr_rep1


title: Rep 1. Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_EV_dox_0hr_rep1


title: KT205_non_cancer_control_cfDNA_5hmC

description:
Library name: KT205
n/a


title: Rep 2.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_6hr_rep2


title: KT203_non_cancer_control_cfDNA_5hmC

description:
Library name: KT203
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_EV_dox_2hr_rep1


title: KT202_non_cancer_control_cfDNA_5hmC

description:
Library name: KT202
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_EV_dox_6hr_rep2


title: Rep 1.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_12hr_rep1


title: KT209_non_cancer_control_cfDNA_5hmC

description:
Library name: KT209
n/a


title: Rep 1.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_6hr_rep1


title: Rep 2.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_2hr_rep2


title: Rep 2. Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_E2F1_dox_0hr_rep2


title: KT201_non_cancer_control_cfDNA_5hmC

description:
Library name: KT201
n/a


title: KT199_non_cancer_control_cfDNA_5hmC

description:
Library name: KT199
n/a


title: KT198_non_cancer_control_cfDNA_5hmC

description:
Library name: KT198
n/a


title: Rep 2.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_12hr_rep2


title: KT197_non_cancer_control_cfDNA_5hmC

description:
Library name: KT197
n/a


title: Rep 1. Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_E2F1_dox_0hr_rep1


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_12hr_rep2

data_processing:
RNAseq FASTQ files were inspected with FastQC. Low quality reads were removed using Trimmomatic, removing adapter/index sequences, quality filtering (sliding window 4:20) and retaining only reads of 50bp or longer. Data was aligned using HISAT2, unstranded, to the mouse mm10 genome. Featurecounts was used for counting, with Gencode VM23 gene annotation. Count norrmalization and differential gene expression was calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: Normalized counts .csv file with all samples;  .txt for each pairwise comparison against control (time point 0 hr) of differential gene expression


title: KT206_non_cancer_control_cfDNA_5hmC

description:
Library name: KT206
n/a


title: Rep 1.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_2hr_rep1


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_6hr_rep2


title: KT208_non_cancer_control_cfDNA_5hmC

description:
Library name: KT208
n/a


title: KT195_non_cancer_control_cfDNA_5hmC

description:
Library name: KT195
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_2hr_rep2


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_12hr_rep1


title: KT204_non_cancer_control_cfDNA_5hmC

description:
Library name: KT204
n/a


title: KT194_non_cancer_control_cfDNA_5hmC

description:
Library name: KT194
n/a


title: KT193_non_cancer_control_cfDNA_5hmC

description:
Library name: KT193
n/a


title: KT192_non_cancer_control_cfDNA_5hmC

description:
Library name: KT192
n/a


title: KT200_non_cancer_control_cfDNA_5hmC

description:
Library name: KT200
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_2hr_rep1


title: KT191_non_cancer_control_cfDNA_5hmC

description:
Library name: KT191
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_EV_dox_12hr_rep2


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_6hr_rep1


title: KT190_non_cancer_control_cfDNA_5hmC

description:
Library name: KT190
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_EV_dox_6hr_rep2


title: Rep 2. Dox-inducible EV 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_EV_dox_0hr_rep2


title: KT187_non_cancer_control_cfDNA_5hmC

description:
Library name: KT187
n/a


title: KT186_non_cancer_control_cfDNA_5hmC

description:
Library name: KT186
n/a


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_EV_dox_2hr_rep2


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_EV_dox_12hr_rep1


title: KT196_non_cancer_control_cfDNA_5hmC

description:
Library name: KT196
n/a


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_EV_dox_2hr_rep1


title: KT184_non_cancer_control_cfDNA_5hmC

description:
Library name: KT184
n/a


title: Rep 1. Dox-inducible EV 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_EV_dox_0hr_rep1


title: KT183_non_cancer_control_cfDNA_5hmC

description:
Library name: KT183
n/a


title: KT182_non_cancer_control_cfDNA_5hmC

description:
Library name: KT182
n/a


title: KT185_non_cancer_control_cfDNA_5hmC

description:
Library name: KT185
n/a


title: Rep 2.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_E2F1_dox_12hr_rep2


title: Rep 2.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_E2F1_dox_6hr_rep2


title: KT180_non_cancer_control_cfDNA_5hmC

description:
Library name: KT180
n/a


title: Rep 2.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_E2F1_dox_2hr_rep2


title: KT179_non_cancer_control_cfDNA_5hmC

description:
Library name: KT179
n/a


title: KT181_non_cancer_control_cfDNA_5hmC

description:
Library name: KT181
n/a


title: Rep 2. Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_E2F1_dox_0hr_rep2


title: Rep 1.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_E2F1_dox_12hr_rep1


title: KT178_non_cancer_control_cfDNA_5hmC

description:
Library name: KT178
n/a


title: KT189_non_cancer_control_cfDNA_5hmC

description:
Library name: KT189
n/a


title: Rep 1.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_E2F1_dox_6hr_rep1


title: Rep 1.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_E2F1_dox_2hr_rep1


title: KT175_non_cancer_control_cfDNA_5hmC

description:
Library name: KT175
n/a


title: KT177_non_cancer_control_cfDNA_5hmC

description:
Library name: KT177
n/a


title: KT176_non_cancer_control_cfDNA_5hmC

description:
Library name: KT176
n/a


title: Rep 1. Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_E2F1_dox_0hr_rep1


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_EV_dox_6hr_rep1


title: Lambdoid suture, HHIP knockout, sample 15

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: Library name: HHIP_Lam_15_HH

data_processing:
After adapter sequences were removed using Cutadapt  and low-quality bases trimmed from the 3′ ends of reads with a quality score threshold of Q ≤ 20 for stretches exceeding 20 bases, paired-end reads were aligned to the mouse mm10 reference genome using STAR. Gene-level read counts were summarized with featureCounts. The resulting raw paired-end read counts were compiled into a numeric matrix with genes as rows and experiments as columns for downstream differential gene expression analysis using the Bioconductor Limma package.
Gene counts were normalized to FPKM (fragments per kilobase per million mapped reads) using RSEM  in strand-specific mode with default parameters, retaining only genes with expression levels above 1 FPKM in at least 50% of the samples. Additional filtering removed genes with fewer than 50 total reads across all samples or with transcript lengths shorter than 200 nucleotides. Normalization factors were calculated for the filtered data matrix using the TMM (trimmed mean of M-values) method. Subsequently, the data underwent voom mean-variance transformation  to prepare for Limma linear modeling, with sex included as a fixed-effect covariate
A design matrix was constructed to represent the experimental groups, enabling pairwise comparisons across sample groups. Adjusted p-values were calculated using the eBayes method and corrected for multiple comparisons using the Benjamini-Hochberg (BH) procedure, with genes deemed significantly differentially expressed based on a false discovery rate (FDR) threshold of q ≤ 0.05.
Assembly: mm10 genome with Gencode v22 annotations
Supplementary files format and content: Tab delimited featurecounts output file with the following columns: GENCODE V22 gene ID, Chr, Start, End, Strand, Length, total_read_count

source_name: Lambdoid Suture

extract_protocol:
Total RNA was prepared from WT and Hhip-/- paired coronal sutures and individual lambdoid suture strips using the Qiagen RNeasy Minikit (Qiagen, 74104) with on-column DNase digestion (Qiagen, 79254) as described by the manufacturer. Sutures were first homogenized for 40-60 seconds in 350 μl RLT buffer using a disposable Kontes pellet pestle (Fisher Scientific, K749521-1500) and pellet pestle motor (Kimble, 6HAZ6) in 1.5 ml Eppendorf tubes.
RNA-seq libraries were prepared from 50 ng of RNA, between a RIN of 8.2 to 9.6, using the NEBNext Poly(A) Magnetic Isolation Module (New England Biolabs, E7490) and the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, E7775)

treatment_protocol: Coronal and lambdoid sutures were dissected in cold phosphate-buffered saline (PBS) from E18.5 embryos and snap frozen on dry ice. Coronal sutures included the overlapping frontal and parietal bones with osteogenic fronts and the suture mesenchyme between them; lambdoid sutures consisted of one continuous strip that included a narrow margin of bilateral parietal and interparietal bone and the intervening suture and posterior fontanel mesenchyme. Hypodermis and dura mater tissue were removed as far as possible. Care was taken to cleanly separate the lambdoid suture from the underlying cranial cartilage, the tectum posterius, by peeling the tissues apart with fine forceps.

value: Lambdoid Suture

value: Hhip-/-

value: Male


title: Lambdoid suture, HHIP knockout, sample 16

description: Library name: HHIP_Lam_16_HH


title: Chelator, Rep3

city: Chapel Hill

first: Maria

last: Aleman

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

data_processing:
Quality of sequencing fastq files was checked using FastQC and MultiQC. Salmon (v1.10.2) was used for transcript abundance quantification which was then analyzed for differential gene expression using DESeq2 (v3.19).
Significant genes were quantified by passing a read count threshold greater than 10, having an absolute log2 fold change greater than 1 and an adjusted P value less than 0.05. To capture alternative splicing, reads were first mapped to human genome build hg38 from Ensembl{Harrison, 2024 #297} using STAR (v2.7.11b){Dobin, 2013 #298}.
Chi-square tests were used to determine significant differences between observed and expected results. Hypergeometric tests were used to calculate the significance of overlapping datasets, where only co-detected genes or events were used as background.
Spearman's rank correlation test was used in correlation analysis.
Assembly: hg38
Supplementary files format and content: text files include TPM for each sample

growth_protocol: K562 cells were cultured in RPMI 1640 with 10% fetal bovine serum and 1x Anti-Anti and incubated at 37° C with 5% CO2.

extract_protocol:
RNA isolated from cells after treatments was sent to Novogene (Sacramento, CA) for polyA selection and library preparation followed by Illumina sequencing (paired end, 150 cycles). Eighteen to 30 GB of data per sample were collected.
Poly A selection. Performed by Novogene.

treatment_protocol: Cells were treated with 10 µM 21H7 or 100% DMSO (volume-matched) in RPMI 1640 complete media overnight.

value: Iron Chelation


title: Chelator, Rep2


title: Lambdoid suture, HHIP knockout, sample 14

description: Library name: HHIP_Lam_14_HH

value: Female


title: Chelator, Rep1


title: Lambdoid suture, HHIP knockout, sample 13

description: Library name: HHIP_Lam_13_HH


title: Lambdoid suture, wild-type, sample 10

description: Library name: HHIP_Lam_10_WT

value: Wild-type


title: DMSO, Rep2

value: Control


title: DMSO, Rep1


title: h805, snRNAseq

city: Seoul

first: Taehong

last: Min

address: 369, Sangdo-ro, Dongjak-gu, Seoul, Republic of Korea

department: School of Systems Biomedical Science

country: South Korea

institute: Soongsil University

description: 10x Genomics

data_processing:
Data were processed and demultiplexed using cellranger-6.1.2
Assembly: hg38
Supplementary files format and content: cell by gene matrix file

molecule: nuclear RNA

source_name: HCC tissue

extract_protocol:
HCC tissues were mixed with 0.4µl of lysis buffer and incubated on ice for 10 min. After triturating the tissue samples, tissue lysates were centrifuged at 500 rcf for 5 min at 4°C. Emerging supernatant was removed followed by resuspending the tissue lysates in 1 ml nuclei wash and resuspension buffer. Subsequent to the evaluation of cell viability, the single cell suspension underwent the process of cell nuclei sorting using Fluorescence-Activated Cell Sorting (FACS).
For cDNA synthesis and preparation of single-nucleus RNA seq libraries, Single nucleus suspensions were processed using the Chromium Next GEM Single Cell 3' v3.1 (Dual Index) kit to achieve single-cell resolution within a droplet-based system. Following sequencing steps such - selection of barcoded single cells, reverse transcription and PCR was performed subsequently.  Agilent Bioanalyzer was employed to ensure sample quality to establish a sequencing library effectively. Construction of sequencing libraries was conducted on Illumina NovaSeq platform.
snRNA-seq

value: HCC tissue


title: h804, snRNAseq

description: 10x Genomics


title: Coronal suture, wild-type, sample 07

description: Library name: HHIP_Cor_07_WT

source_name: Coronal Suture

value: Coronal Suture


title: Lambdoid suture, wild-type, sample 09

description: Library name: HHIP_Lam_09_WT


title: Coronal suture, HHIP knockout, sample 08

description: Library name: HHIP_Cor_08_HH


title: h802, snRNAseq

description: 10x Genomics


title: h801, snRNAseq

description: 10x Genomics


title: Coronal suture, HHIP knockout, sample 06

description: Library name: HHIP_Cor_06_HH


title: KT174_non_cancer_control_cfDNA_5hmC

description:
Library name: KT174
n/a


title: h800, snRNAseq

description: 10x Genomics


title: h799, snRNAseq

description: 10x Genomics


title: KT173_non_cancer_control_cfDNA_5hmC

description:
Library name: KT173
n/a


title: Coronal suture, wild-type, sample 02

description: Library name: HHIP_Cor_02_WT


title: Coronal suture, wild-type, sample 04

description: Library name: HHIP_Cor_04_WT


title: untagged_rep2

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Merging with bbmerge v. 38.72
Demultiplexing with flexbar v. 3.5.0
UMI extraction with umi_tools extract v. 1.0.0
Alignment to human (hg38)
bigWig generation using bamCoverage 3.3.1
Assembly: hg38
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

source_name: Flp-In T-Rex HEK293

extract_protocol:
Cells were crosslnked with 0.199 mj/cm2 UV-C light,  lysed with 1xNLB buffer, protein-of-interest purified with streptavidin beads, co-purifying RNA isolated with proteinase K digestion and purified with Oligo clean and concentrator-5 columns (Zymo).
Custom library prep, described in Ilik et al., 2020. Isolated RNA is ligated to s-oligo on beads, reverse-transcribed, RNaseH digested, circularized with CircLigase and PCR amplified.
FLASH-seq (Ilik et al., 2020)

value: Flp-In T-Rex HEK293

tag: n-terminal tag

value: untagged

tag: fraction

value: RNAseI digested RNA


title: Coronal suture, wild-type, sample 01

description: Library name: HHIP_Cor_01_WT


title: Lambdoid suture, wild-type, sample 11

description: Library name: HHIP_Lam_11_WT


title: Lambdoid suture, wild-type, sample 12

description: Library name: HHIP_Lam_12_WT


title: PHF3_rep2


title: DMSO, Rep3


title: Retina, si-RORb, scRNA-seq

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

institute: UNIST

description:
Library name: Retina_RORb
10x Genomics

data_processing:
Fastq files were mapped to the mouse reference (mm10). The initial quality control and the combined gene expression matrix were performed using Cell Ranger pipeline (version 8.0.0; 10X Genomics Chromium).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Retinal cells were washed and resuspended in 0.04% BSA/PBS, then counted using a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems).
Single-cell RNA-seq libraries were prepared using the 10x Chromium controller and Next GEM Single Cell 3' Reagent v3.1 kits following the 10x Genomics protocol. Briefly, single-cell Gel Bead-in-emulsion (GEM) was generated with a target recovery of 10,000 cells, and mRNA was barcoded and reverse-transcribed within GEM. Barcoded cDNA was amplified by PCR and processed for 3' Gene Expression Library construction, including enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, and index PCR. Libraries were quantified by qPCR (KAPA) and validated using the Agilent 4200 TapeStation (Agilent technologies). Sequencing was performed on an Illumina NovaSeq platform.

value: Retina

tag: strain

tag: genetic modification

value: P23H Rho mutation

tag: age

value: 1-4 months old

value: intravitreal injection of cp-asiRORB


title: M46 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M46_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

data_processing:
Reads were aligned to an N-masked genome and transcriptome using STAR. Aligned reads were then split using informative SNPs using SNPsplit for allele-specific analysis. We also kept mapped reads that did not undergo SNPsplit to perform non-allele specific analysis. Transcripts are quantified using Salmon and tximport was used to import and summarize transcripts for downstream gene-level analysis.
Assembly: mm10
Supplementary files format and content: tximport_all_withgenes.csv is a output file from tximport that summarizes Salmon output for gene-level analysis from non-allele specific mapped RNA-seq reads. File contains non-allele specific estimated counts, abundances, and gene_names. Columns are the sample names.
Supplementary files format and content: tximport_allele_specific_all_withgenes.csv is a output file from tximport that summarizes  Salmon output for gene-level analysis from allele specific mapped RNA-seq reads. File contains allele-specific estimated counts, abundances, and gene_names. Columns are the sample names.

tag: cell line

tag: cell type

value: neuronal progenitor cells


title: Retina, si-Scramble, scRNA-seq

description:
Library name: Retina_Scramble
10x Genomics

tag: treatment

value: intravitreal injection of cp-asiScramble


title: D16-6-Pass-IWP2

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

data_processing:
Sequence reads were trimmed to remove adaptor sequence/low-quality sequence using Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1).
Hisat2 (v2.0.1) was used to index reference genome sequence. Clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Read count extraction and normalization were performed using HTSeq (v0.6.1)
Differential expression analysis was performed using the DESeq2 Bioconductor package with p-adj < 0.05 as cutoff.
Assembly: hg38
Supplementary files format and content: Microsoft Excel 97-2003 Worksheet containing read counts and FPKM values for each sample

extract_protocol:
RNA was harvested using RNAiso Plus (Takara). 1 μg total RNA was used for library preparation.
cDNA systhesis was carried out using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification  Module. Libraries were prepared using SMRTbell® prep kit 3.0.

value: human embryonic stem cells (ESCs)

value: WT

value: Mesendoderm differentiation with IWP2, D2 passaged

tag: differentiation day


title: PHF3_rep1


title: untagged_rep1


title: M45 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M45_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Male


title: D16-5-Pass-IWP2


title: M43 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M43_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: M42 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M42_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: M41 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M41_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: D16-4-Pass-ctrl

value: Mesendoderm spontaneous differentiation, D2 passaged


title: D16-2-NP-IWP2

value: Mesendoderm differentiation with IWP2, not passaged


title: D16-3-Pass-ctrl


title: M40 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M40_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Coronal suture, HHIP knockout, sample 03

description: Library name: HHIP_Cor_03_HH

tag: tissue

value: Hhip-/-


title: D16-1-NP-IWP2


title: D12-6-Pass-IWP2


title: M39 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M39_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: M38 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M38_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 VR20, Add SSB Post-transcription, Transcribed

city: DAVIS

first: FREDERIC

last: CHEDIN

address: 1 shields avenue

department: MCB

institute: UC DAVIS

description:
Library name: Sample 92
pFC9VR20_PostTxSSB_Transcribed_reference_sequence.fasta.gz

data_processing:
Resulting SMRF-seq fastq files were processed and R-loop footprints were called using the previously published Gargamel pipeline (https://github.com/srhartono/footLoop). R-loops were called using minimum parameters of 50 base pair minimum peak length (-l), at least 20 cytosines present in the R-loop (-w), and cytosine conversion rate (-t) of 55% (high threshold) or 35% (low threshold)
Assembly: all reference sequence used to align the reads is provided
Supplementary files format and content: bed: bed 6 files containing R-loop peaks called with high threshold parameters (-t 55 -w 20 -l 50) or low threshold parameters (-t 35 -w 20 -l50)
Supplementary files format and content: fasta.gz: reference sequence used to align the reads in gzipped FASTA format (linked to the corresponding rep1 sample records)

organism: synthetic construct

source_name: bacterial

growth_protocol: Plasmids were transformed into E. coli DH5α chemically competent cells and single colonies were grown on LB ampicillin agar plates. Single colonies were selected and grown in 300 ml LB culture with 100 µg   / ml of ampicillin in 1 L flasks at either 30° or 37°C overnight with shaking at 200-250 rpm.

extract_protocol:
Negatively supercoiled plasmid substrates were purified by alkaline lysis protocol followed by column cleanup (Qiagen) and eluted into either TE or EB buffer.
Single-Molecule R-loop Footprinting (SMRF-seq) samples were amplified with a combination of forward and reverse primers that each incorporated a unique barcode. The combination of the forward and reverse primer barcodes uniquely identifies each sample within its specific flowcell. Primer binding sequences were designed in Primer3 (10) software and barcodes were generated using a custom Python script. Samples were amplified using Q5U® Hot Start High-Fidelity DNA Polymerase (NEB M0515S) for 25-30 cycles according to the manufacturer’s online protocol. 1-3 μl of bisulfite converted substrate was used for each reaction. In the case that the yield of one reaction was not sufficient, additional reactions using the original bisulfite converted sample were performed and then pooled. The target amplicon size was then purified via agarose gel extraction using BioBasic gel extraction kit (BS654). Sample concentration was quantified via agarose gel electrophoresis against 1kb linear DNA ladder (Thermo Fisher SM0311). SMRT cell PacBio libraries were constructed by the UC Davis DNA Technologies core according to manufacturer’s instructions and sequenced on a PacBio Sequel II instrument. Additional sequencing was performed at the UC Berkeley QB3 sequencing core on a PacBio Revio instrument.

value: bacterial

tag: plasmid

value: pFC9 with VR20 insert

value: Transcribe with T7 RNA Polymerase, Add SSB post-transcription


title: pFC9 VR20, Add SSB Co-transcriptionally, Transcribed, RnaseH1 Treated

description:
Library name: Sample 93
pFC9VR20_CoTxSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase, Add SSB during transcription, Treat with Rnaseh1 before bisulfite treatment


title: pFC9 VR20, Add SSB Co-transcriptionally, Transcribed

description:
Library name: Sample 91
pFC9VR20_CoTxSSB_Transcribed_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase, Add SSB during transcription


title: D12-5-Pass-IWP2


title: pFC9 VR20, Add SSB, Untranscribed

description:
Library name: Sample 90
pFC9VR20_AddSSB_Untranscribed_reference_sequence.fasta.gz

data_processing:
library strategy: Single-molecule R-loop footprinting sequencing (SMRF-seq)
Resulting SMRF-seq fastq files were processed and R-loop footprints were called using the previously published Gargamel pipeline (https://github.com/srhartono/footLoop). R-loops were called using minimum parameters of 50 base pair minimum peak length (-l), at least 20 cytosines present in the R-loop (-w), and cytosine conversion rate (-t) of 55% (high threshold) or 35% (low threshold)
Assembly: all reference sequence used to align the reads is provided
Supplementary files format and content: bed: bed 6 files containing R-loop peaks called with high threshold parameters (-t 55 -w 20 -l 50) or low threshold parameters (-t 35 -w 20 -l50)
Supplementary files format and content: fasta.gz: reference sequence used to align the reads in gzipped FASTA format (linked to the corresponding rep1 sample records)

value: Add SSB


title: M36 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M36_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 VR10, Add SSB Co-transcriptionally, Transcribed, RnaseH1 Treated

description:
Library name: Sample 89
pFC9VR10_CoTxSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: pFC9 with VR10 insert


title: D12-4-Pass-ctrl


title: pFC9 VR10, Add SSB Post-transcription, Transcribed

description:
Library name: Sample 88
pFC9VR10_PostTxSSB_Transcribed_reference_sequence.fasta.gz


title: pFC9 VR10, Add SSB Co-transcriptionally, Transcribed

description:
Library name: Sample 87
pFC9VR10_CoTxSSB_Transcribed_reference_sequence.fasta.gz


title: M35 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M35_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: D12-3-Pass-ctrl


title: pFC9 VR10, Add SSB, Untranscribed

description:
Library name: Sample 86
pFC9VR10_AddSSB_Untranscribed_reference_sequence.fasta.gz


title: M33 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M33_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: D12-2-NP-IWP2


title: pFC9, Add SSB Co-transcriptionally, Transcribed, RnaseH1 Treated

description:
Library name: Sample 85
pFC9_CoTxSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz


title: pFC9, Add SSB Co-transcriptionally, Transcribed

description:
Library name: Sample 83
pFC9_CoTxSSB_Transcribed_reference_sequence.fasta.gz


title: pFC9, Add SSB Post-transcription, Transcribed

description:
Library name: Sample 84
pFC9_PostTxSSB_Transcribed_reference_sequence.fasta.gz


title: M32 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M32_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: M31 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M31_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: D12-1-NP-IWP2


title: pFC9, Add SSB, Untranscribed

description:
Library name: Sample 82
pFC9_AddSSB_Untranscribed_reference_sequence.fasta.gz


title: pFC9 with NtBspQI Target Site 3, Add NtBspQI (Nicked), Transcribed, rep2

description:
Library name: Sample 51
pFC9NtBspQITargetSite3_AddNtBspQI_Nicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: pFC9 with NtBspQI Target Site 3 Insert

value: Add NtBspQI (nick at site 3), Transcribe with T7 RNA Polymerase


title: M30 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M30_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: Day-10-passaged

data_processing:
Sequence reads were trimmed to remove adaptor sequence/low-quality sequence using Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1).
Hisat2 (v2.0.1) was used to index reference genome sequence. Clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Read count extraction and normalization were performed using HTSeq (v0.6.1)
Differential expression analysis was performed using the DESeq2 Bioconductor package with p-adj < 0.05 as cutoff.
Assembly: hg38
Supplementary files format and content: read counts and FPKM values for each sample

value: human embryonic stem cells (ESCs)


title: pFC9 with NtBspQI Target Site 3, Add NtBspQI (Nicked), Untranscribed, rep2

description:
Library name: Sample 49
pFC9NtBspQITargetSite3_AddNtBspQI_Nicked_NoSSB_Untranscribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 3)


title: M28 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M28_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with NtBspQI Target Site 3, Add NtBspQI (Nicked), Transcribed, RnaseH1 Treated, rep2

description:
Library name: Sample 53
pFC9NtBspQITargetSite3_AddNtBspQI_Nicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 3), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: pFC9 with NtBspQI Target Site 3, No NtBspQI (Not Nicked), Transcribed, RnaseH1 Treated, rep2

description:
Library name: Sample 47
pFC9NtBspQITargetSite3_AddNtBspQI_NotNicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: pFC9 with NtBspQI Target Site 3, No NtBspQI (Not Nicked), Transcribed, rep2

description:
Library name: Sample 45
pFC9NtBspQITargetSite3_AddNtBspQI_NotNicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase


title: Day-10-NP-ctrl

value: WT

value: Mesendoderm spontaneous differentiation, not passaged


title: pFC9 with NtBspQI Target Site 2, Add NtBspQI (Nicked), Transcribed, RnaseH1 Treated, rep2

description:
Library name: Sample 41
pFC9NtBspQITargetSite2_AddNtBspQI_Nicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: bacterial

value: pFC9 with NtBspQI Target Site 2 Insert

value: Add NtBspQI (nick at site 2), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: Day-7-passaged

value: Mesendoderm spontaneous differentiation, D2 passaged


title: pFC9 with NtBspQI Target Site 3, No NtBspQI (Not Nicked), Untranscribed, rep2

description:
Library name: Sample 43
pFC9NtBspQITargetSite3_AddNtBspQI_NotNicked_NoSSB_Untranscribed_reference_sequence.fasta.gz


title: pFC9 with NtBspQI Target Site 2, Add NtBspQI (Nicked), Untranscribed, rep2

description:
Library name: Sample 37
pFC9NtBspQITargetSite2_AddNtBspQI_Nicked_NoSSB_Untranscribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 2)


title: pFC9 with NtBspQI Target Site 2, No NtBspQI (Not Nicked), Untranscribed, rep2

description:
Library name: Sample 31
pFC9NtBspQITargetSite2_AddNtBspQI_NotNicked_NoSSB_Untranscribed_reference_sequence.fasta.gz


title: pFC9 with NtBspQI Target Site 2, No NtBspQI (Not Nicked), Transcribed, rep2

description:
Library name: Sample 33
pFC9NtBspQITargetSite2_AddNtBspQI_NotNicked_NoSSB_Transcribed_reference_sequence.fasta.gz


title: pFC9 with NtBspQI Target Site 2, No NtBspQI (Not Nicked), Transcribed, RnaseH1 Treated, rep2

description:
Library name: Sample 35
pFC9NtBspQITargetSite2_AddNtBspQI_NotNicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz


title: pFC9 with NtBspQI Target Site 1, Add NtBspQI (Nicked), Transcribed, RnaseH1 Treated, rep2

description:
Library name: Sample 29
pFC9NtBspQITargetSite1_AddNtBspQI_Nicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: pFC9 with NtBspQI Target Site 1 Insert

value: Add NtBspQI (nick at site 1), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: M21 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M21_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Male


title: pFC9 with NtBspQI Target Site 2, Add NtBspQI (Nicked), Transcribed, rep2

description:
Library name: Sample 39
pFC9NtBspQITargetSite2_AddNtBspQI_Nicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 2), Transcribe with T7 RNA Polymerase


title: M26 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M26_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: Day-7-NP-IWP2

value: human embryonic stem cells (ESCs)

value: Mesendoderm differentiation with IWP2, not passaged


title: M25 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M25_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: M27 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M27_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Day-3-passaged


title: Day-7-NP-ctrl


title: M19 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M19_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with sgRNA Target Site 3, Add Cas9 (Nicked), Transcribed

description:
Library name: Sample 16
pFC9sgRNATargetSite3_AddCas9_Nicked_Transcribed_reference_sequence.fasta.gz

value: pFC9 with sgRNA Target Site 3 insert

value: Add Cas9 (nick at site 3), Transcribe with T7 RNA Polymerase


title: Day-3-NP-IWP2


title: pFC9 with sgRNA Target Site 3, Add Cas9 (Nicked), Untranscribed

description:
Library name: Sample 15
pFC9sgRNATargetSite3_AddCas9_Nicked_Untranscribed_reference_sequence.fasta.gz

value: Add Cas9 (nick at site 3)


title: M24 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M24_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with NtBspQI Target Site 1, Add NtBspQI (Nicked), Untranscribed, rep2

description:
Library name: Sample 25
pFC9NtBspQITargetSite1_AddNtBspQI_Nicked_NoSSB_Untranscribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 1)


title: M20 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M20_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Day-3-NP-ctrl

value: WT

value: Mesendoderm spontaneous differentiation, not passaged


title: pFC9 with sgRNA Target Site 2, Add Cas9 (Nicked), Transcribed

description:
Library name: Sample 13
pFC9sgRNATargetSite2_AddCas9_Nicked_Transcribed_reference_sequence.fasta.gz

value: bacterial

value: pFC9 with sgRNA Target Site 2 insert

value: Add Cas9 (nick at site 2), Transcribe with T7 RNA Polymerase


title: pFC9 with NtBspQI Target Site 1, No NtBspQI (Not Nicked), Transcribed, rep2

description:
Library name: Sample 21
pFC9NtBspQITargetSite1_AddNtBspQI_NotNicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase


title: pFC9 with NtBspQI Target Site 1, Add NtBspQI (Nicked), Transcribed, rep2

description:
Library name: Sample 27
pFC9NtBspQITargetSite1_AddNtBspQI_Nicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: pFC9 with NtBspQI Target Site 1 Insert

value: Add NtBspQI (nick at site 1), Transcribe with T7 RNA Polymerase


title: pFC9 with NtBspQI Target Site 1, No NtBspQI (Not Nicked), Transcribed, RnaseH1 Treated, rep2

description:
Library name: Sample 23
pFC9NtBspQITargetSite1_AddNtBspQI_NotNicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: Day-5-NP-ctrl


title: pFC9 with NtBspQI Target Site 1, No NtBspQI (Not Nicked), Untranscribed, rep2

description:
Library name: Sample 19
pFC9NtBspQITargetSite1_AddNtBspQI_NotNicked_NoSSB_Untranscribed_reference_sequence.fasta.gz


title: Day-10-NP-IWP2


title: pFC9 with sgRNA Target Site 2, Add Cas9 (Nicked), Untranscribed

description:
Library name: Sample 12
pFC9sgRNATargetSite2_AddCas9_Nicked_Untranscribed_reference_sequence.fasta.gz

value: Add Cas9 (nick at site 2)


title: pFC9 with sgRNA Target Site 1, Add Cas9 (Nicked), Transcribed, RnaseH1 Treated, biorep2

description:
Library name: Sample 11
pFC9sgRNATargetSite1_AddCas9_Nicked_Transcribed_RnaseH1_rep2_reference_sequence.fasta.gz

value: pFC9 with sgRNA Target Site 1 insert

value: Add Cas9 (nick at site 1), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1) before bisulfite treatment


title: pFC9 with sgRNA Target Site 1, Add Cas9 (Nicked), Transcribed, rep2

description:
Library name: Sample 9
pFC9sgRNATargetSite1_AddCas9_Nicked_Transcribed_rep2_reference_sequence.fasta.gz

value: Add Cas9 (nick at site 1), Transcribe with T7 RNA Polymerase


title: pFC9 with sgRNA Target Site 3, Add Cas9 (Nicked), Transcribed, RnaseH1 Treated

description:
Library name: Sample 17
pFC9sgRNATargetSite3_AddCas9_Nicked_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: pFC9 with sgRNA Target Site 3 insert

value: Add Cas9 (nick at site 3), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1) before bisulfite treatment


title: M15 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M15_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Male

value: neuronal progenitor cells


title: M18 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M18_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Day-1

value: human embryonic stem cells (ESCs)

value: WT

value: Mesendoderm spontaneous differentiation


title: M13 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M13_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9 with sgRNA Target Site 1, Add Cas9 (Nicked), Untranscribed

description:
Library name: Sample 7
pFC9sgRNATargetSite1_AddCas9_Nicked_Untranscribed_reference_sequence.fasta.gz

value: bacterial

value: Add Cas9 (nick at site 1)


title: pFC9 with sgRNA Target Site 2, Add Cas9 (Nicked), Transcribed, RnaseH1 Treated

description:
Library name: Sample 14
pFC9sgRNATargetSite2_AddCas9_Nicked_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: pFC9 with sgRNA Target Site 2 insert

value: Add Cas9 (nick at site 2), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1) before bisulfite treatment


title: M17 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M17_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Day-5-passaged

value: Mesendoderm spontaneous differentiation, D2 passaged


title: pFC9 with sgRNA Target Site 1, Add Cas9 (Nicked), Transcribed, RnaseH1 Treated, biorep1

description:
Library name: Sample 10
pFC9sgRNATargetSite1_AddCas9_Nicked_Transcribed_RnaseH1_rep1_reference_sequence.fasta.gz


title: Day-5-NP-IWP2

value: Mesendoderm differentiation with IWP2, not passaged


title: M14 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M14_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S11 Monocyte, High Salt (190mmol/L NaCl)

city: Nashville

first: Ashley

last: Mutchler

address: 1005 Dr. D.B. Todd Jr. Boulevard

institute: Meharry Medical College

description:
Library name: Sample 22
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-22_S22

data_processing:
Using the R package, the FASTQ data files from the paired-end sequencing analysis were aligned with TopHat 2 for each sample against the human GRCh38 reference genome assembly. Quality control for the RNAseq data occurred during the following stages: 1) RNA quality; 2) raw read data (FASTQ); 3) alignment; 4) gene expression. Quality control for the raw data and alignment were performed using QC3 , and the MultiRankSeq method was used for expression analysis. Raw data false discovery rate (FDR < 0.05) was used to correct for multiple hypothesis testing.
Assembly: human GRCh38
Supplementary files format and content: excel file containing  FPKM values and DESeq2 paired-analysis

source_name: Peripheral blood

extract_protocol:
Rneasy Midi Kit (Qiagen) according to manufacturer's protocol
Targeted analysis of polyadenylated transcripts was performed using the Illumina Tru-seq RNA sample prep kit

value: Peripheral blood

value: Monocytes

value: High salt (190 mmol/L NaCl)


title: Day-2


title: pFC9, Add Cas9 (Not Nicked), Transcribed, RnaseH1 Treated

description:
Library name: Sample 6
pFC9_AddCas9_NotNicked_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Add Cas9 (not nicked), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: pFC9, Add Cas9 (Not Nicked), Transcribed

description:
Library name: Sample 5
pFC9_AddCas9_NotNicked_Transcribed_reference_sequence.fasta.gz

value: Add Cas9 (not nicked), Transcribe with T7 RNA Polymerase


title: pFC9 with sgRNA Target Site 1, Add Cas9 (Nicked), Transcribed, rep1

description:
Library name: Sample 8
pFC9sgRNATargetSite1_AddCas9_Nicked_Transcribed_rep1_reference_sequence.fasta.gz

value: pFC9 with sgRNA Target Site 1 insert

value: Add Cas9 (nick at site 1), Transcribe with T7 RNA Polymerase


title: S09 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 20
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-20_S20


title: miR183_mim

city: Jinan

first: Shu

middle: Li

last: zhuang

state: China/Shandong

address: Department of General Surgery, Qilu Hospital, Shandong University, 107, Jinan Culture Road, Jinan, 250012, China.

department: Qilu Hospital

institute: Shandong University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Supplementary files format and content: Homo_sapiens.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

growth_protocol: The total RNA of cholangiocarcinoma cell line QBC-939 overexpressing NC, miR-182-5p, miR-183-5p was extracted using Trizol reagent.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We overexpressed NC, miR-182-5p and miR-183-5p in cholangiocarcinoma cell line QBC-939, respectively.

value: CCA cells


title: M08 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M08_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Male

value: neuronal progenitor cells


title: S08 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 19
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-19_S19


title: S10 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 21
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-21_S21


title: M12 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M12_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: M10 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M10_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: miR182_mim

value: WT


title: NC

value: oe-NC


title: pFC9, Add Cas9 (Not Nicked), Untranscribed

description:
Library name: Sample 4
pFC9_AddCas9_NotNicked_Untranscribed_reference_sequence.fasta.gz

value: bacterial

value: Add Cas9 (not nicked)


title: S07 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 18
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-18_S18


title: M07 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M07_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: pFC9, No Cas9 (Not Nicked), Transcribed, RnaseH1 Treated

description:
Library name: Sample 3
pFC9_NoCas9_NotNicked_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: pFC9, No Cas9 (Not Nicked), Transcribed

description:
Library name: Sample 2
pFC9_NoCas9_NotNicked_Transcribed_reference_sequence.fasta.gz

value: Transcribe with T7 RNA Polymerase


title: ALL survivor 135

type: genomic

city: Montréal

first: Daniel

last: Sinnett

state: Québec

address: 3175 Chem. de la Côte-Sainte-Catherine

department: Research Center

country: Canada

institute: CHU Sainte-Justine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC V1.0 Beadchip using standard Illumina protocol

scan_protocol: standard  protocol for Illumina HiScan

data_processing:
The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.
normalized betas

label: Cy3 and Cy5

source_name: Whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications.

value: Whole blood

value: Female

tag: age at sample collection


title: ALL survivor 136


title: M06 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M06_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: Day-0

value: human embryonic stem cells (ESCs)

value: Mesendoderm spontaneous differentiation


title: ALL survivor 134


title: pFC9, No Cas9 (Not Nicked), Untranscribed

description:
Library name: Sample 1
pFC9_NoCas9_NotNicked_Untranscribed_reference_sequence.fasta.gz


title: S06 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 17
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-17_S17

value: Peripheral blood

value: Monocytes

value: High salt (190 mmol/L NaCl)


title: M11 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M11_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: S05 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 16
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-16_S16


title: M05 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M05_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads


title: ALL survivor 133


title: pFC9 with NtBspQI Target Site 3, Add NtBspQI (Nicked), Transcribed, RnaseH1 Treated, rep1

description:
Library name: Sample 52
pFC9NtBspQITargetSite3_AddNtBspQI_Nicked_NoSSB_Transcribed_RnaseH1_reference_sequence.fasta.gz

value: pFC9 with NtBspQI Target Site 3 Insert

value: Add NtBspQI (nick at site 3), Transcribe with T7 RNA Polymerase, Treat with Rnaseh1 before bisulfite treatment


title: S04 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 15
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-15_S15


title: M04 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M04_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: Male


title: ALL survivor 132


title: pFC9 with NtBspQI Target Site 3, Add NtBspQI (Nicked), Transcribed, rep1

description:
Library name: Sample 50
pFC9NtBspQITargetSite3_AddNtBspQI_Nicked_NoSSB_Transcribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 3), Transcribe with T7 RNA Polymerase


title: S03 Monocyte, High Salt (190mmol/L NaCl)

description:
Library name: Sample 14
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-14_S14


title: ALL survivor 131


title: pFC9 with NtBspQI Target Site 3, Add NtBspQI (Nicked), Untranscribed, rep1

description:
Library name: Sample 48
pFC9NtBspQITargetSite3_AddNtBspQI_Nicked_NoSSB_Untranscribed_reference_sequence.fasta.gz

value: Add NtBspQI (nick at site 3)


title: S02 Monocyte, High  Salt (190mmol/L NaCl)

description:
Library name: Sample 13
Ex vivo salt treatment of primary monocytes from 11 donors
3696-AK-13_S13


title: ALL survivor 130


title: M02 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M02_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads

value: neuronal progenitor cells


title: M03 neuronal progenitor cell clonal line (RNA-seq)

description:
Library name: M03_NPC
directional RNA library preparation with PolyA enrichment. Sequenced with 150 x 150bp for ~40 million paired end reads