title: PID022_TM1_P1_1_1

description: Library name: PID022_TM1_P1_1_1

value: Tumor

value: renal cell carcinoma

value: ccRCC

value: Lung metastasis


title: Liver, Py 6hpi, biol rep3

status: Public on Jul 20 2026

type: SRA

city: Seattle

first: Alexis

last: Kaushansky

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

country: USA

institute: Seattle Children’s Research Institute

description: Library name: Sample 12

library_source: transcriptomic

data_processing:
Sequences were aligned and raw gene counts acquired using the BioJupies platform (https://maayanlab.cloud/biojupies/) with default parameters.
Assembly: mm10
Supplementary files format and content: xls file containing raw gene counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was extracted from homogenized livers using trizol and chloroform.
Library construction and sequencing  were conducted by Novogene using paired-end sequencing using the NovaSeq X Plus platform.

tag: tissue

value: liver

tag: disease state

value: Py liver-stage

tag: time

value: 6 hpi

tag: strain


title: sample_510_GABA, Oxford Nanopore methylation

city: La Jolla

first: Eran

middle: A

last: Mukamel

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

description:
Library name: sample_510_GABA
sample ID=sample_510_GABA; donor=510; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing

library_source: genomic

data_processing:
Pod5 files generated with Oxford Nanopore PromethION were used as the input for basecalling using Dorado (v.0.9.1). Modified basecalling mode that can recognize both 5mC and 5hmC was activated using the Super Accurate (SUP) modified basecalling model “dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v3” in the Dorado “basecaller” subcommand (simplex mode), with “--modified-bases-threshold” set to 0.05 and “--min_qscore” set to 9. Basecalled sequences were saved in unmapped BAM files, where the modification information was saved in the MM and ML tags. These reads were then aligned to the hg38 human reference genome with minimap2 (v2.28-r1209) with the “-ayx lr:hq” parameters. Modkit (v0.4.1) “pileup” subcommand was then used to create bedMethyl files for all cytosines, CG or CH sites with “--max-depth” set to 100000 and “--sampling-frac” set to 0.01. Summarized statistics of 5mC or 5hmC in gene body or 100kb genomic bins were computed using the Modkit “stats” subcommand with “--min-coverage” set to 1.
Assembly: GRCh38
Supplementary files format and content: bedMethyl files contain genomic positions, coverage, and native DNA methylation calls generated with modkit; .tbi files are tabix indexes.
Supplementary files format and content: Processed data file 2 is the tabix index (.tbi) for the corresponding bedMethyl file.

molecule: genomic DNA

organism: Homo sapiens

source_name: human prefrontal cortex

growth_protocol: Not applicable; postmortem human brain tissue was used.

extract_protocol:
Genomic DNA was isolated from sorted Glu or MGE-GABA nuclei from human prefrontal cortex.
Native genomic DNA ligation libraries were prepared for Oxford Nanopore sequencing.

treatment_protocol: None.

value: human prefrontal cortex

tag: cell type

value: MGE-GABA


title: WI-38 cells, single-fraction, 110mGy, 5hmC, rep4

city: Chalk River

first: Richard

middle: B.

last: Richardson

state: Ontario

address: 286 Plant Rd

department: Radiobiology and Health

country: Canada

institute: Canadian Nuclear Laboratories

description: Library name: SF110 H4

data_processing:
Quality control was conducted using FastQ Screen (v0.4.1) and FastQC (v0.11.9).
Trimming was performed using TrimGalore (v0.6.6) with parameters: --clip_R1 1; --clip_R2 1; --three_prime_clip_R1 1; - three_prime_clip_R2 1; --trim-n; --length 50; -q 20 and --stringency 5. Quality of trimmed filtered reads was revaluated using FastQC (v0.11.9).
Alignment to the human reference genome GRCh38 was conducted using BWA (v0.7.17) in the paired-end mode of the BWA-MEM algorithm with the default parameter settings.
Mapped read files (*.sam) were converted to sorted BAM files by SAMtools (v1.11). Unmapped reads were filtered out using SAMtools (v1.11).
Bioconductor package MEDIPS (v1.40.0) was used to identify differentially hydroxymethylated regions (DhMRs) between controls and irradiated cells for both regimens with ws=50 bp; shift=0 and uniq=1.
Differential coverage was calculated using the edgeR function in MEDIPS with minRowSum=5 and TMM normalization. P-values were adjusted for multiple testing using the FDR method. Statistically significant methylation coverage results were selected using the criteria of FDR<0.05.
Genomic annotation was carried out using HOMER (v4.11). Neighboring significant regions located within the same chromosome, and with the same annotation and Gene ID, were merged using an in-house Python script.
Assembly: GRCh38
Supplementary files format and content: Bam files include only mapped sorted reads for each sample
Supplementary files format and content: RData files include differential coverage results using the edgeR function (edgeR_control_treatment). When available, it also includes specific data extracted from the "edgeR_control_treatment" file as follows:  differential coverage results with unadjusted P value<0.05 (edgeR.sna_control_treatment), differential coverage results with FDR<0.1 (edgeR.s0.1_control_treatment), differential coverage results with FDR<0.05 (edgeR.s0.05_control_treatment), differential coverage results with FDR<0.05 of hyperDhMRs (hyper_control_treatment), differential coverage results with FDR<0.05 of hypoDhMRs (hypo_control_treatment)

growth_protocol: WI-38 cells were maintained in EMEM medium supplemented with 10% fetal bovine serum (FBS), 50 U/mL Penicillin, 50 µg/mL Streptomycin, and 2 mM L-Glutamine in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total DNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol with minor modifications.
Cell pellets were resuspended in PBS and treated with proteinase K and RNase A. The DNA-loaded spin columns were washed three times with buffer AW2. DNA was then eluted in Tris-EDTA (TE) buffer (low EDTA, pH 8.0) after 5 m at RT. DNA samples displayed A260/A280 ratios in the range of 1.8 to 2.0 and A260/A230 ratios higher than 2.1.
DNA was sheared into ~200 bp fragments using a Covaris S220 focused ultrasonicator. Libraries were constructed with 1.2 μg of DNA using a NEBNext Ultra II DNA library prep kit for Illumina following the manufacturer’s guidelines. Immunoprecipitation with a 5hmC antibody was conducted using a Diagenode hMeDIP kit as described in the manufacturer’s protocol with a starting volume of 15 µL. The immunoprecipitated adaptor-ligated DNA and Input fraction were purified with a Diagenode IPure kit v2 according to the manufacturer’s instructions.
The libraries from the Input fraction and IP DNA were linked to unique dual index primers (New England Biolabs) and amplified by PCR using a NEBNext Ultra II DNA library prep kit for Illumina with 7 cycles for the Input and 8 for the IP samples. The PCR products were further purified and size selected using NEBNext sample purification beads. Libraries were quantified using a KAPA library quantification kit.

treatment_protocol:
Cells were irradiated to seven doses of americium-241 α-sources ranging from 2.0 to 2,200 mGy using two exposure regimens, a single-fraction where the total dose was given at once, and a multi-fraction method, where the total dose was equally distributed over 14 consecutive days.
Cells in both exposure regimens were trypsinized and collected after the last irradiation following 1 h incubation at 37 °C in a 5% CO2 humidified atmosphere. Collected cells were immediately flash-frozen in liquid nitrogen and subsequently stored at -80 °C.

tag: cell line

value: Human fibroblast from 3-month-old female lung tissue

tag: treatment

value: alpha-irradiation

tag: dose (mgy)

tag: radiation regimen

value: single-fraction

tag: total number_of_fractions

tag: antibody

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: Liver, Py 6hpi, biol rep2

description: Library name: Sample 11


title: sample_18_GLU, Oxford Nanopore methylation

description:
Library name: sample_18_GLU
sample ID=sample_18_GLU; donor=18; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing

value: Glu


title: WI-38 cells, single-fraction, 110mGy, 5hmC, rep3

description: Library name: SF110 H3


title: Rhizopus microsporus gcn5 mutant input ChIP-seq

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description:
Library name: gcn5_input
input ChIP-seq in gcn5 mutant R. microsporus

data_processing:
Raw reads trimmed with Trim Galore. Aligned to Rhizopus microsporus genome (Rhimi59_2_AssemblyScaffolds.fasta; 79 scaffolds) with Bowtie2 v2.4.x. Duplicates removed with Picard MarkDuplicates v2.x.
BigWig files generated with deepTools bamCoverage (CPM normalisation). Input-normalised log2-ratio bigWigs computed with deepTools bamCompare (CPM). Files in GEO = input-normalised log2 ratio (one per ChIP sample); input samples = CPM bigWig.
Peaks called with MACS2 v2.2.x vs matched input. Narrow: --nomodel --extsize 200. Broad: --broad. Lost peaks: WT peaks with <20% overlap in mutant (bedtools intersect -v -f 0.20). Peak files referenced in processed data file 2 column (not deposited as bigWig).
Assembly: Rhizopus microsporus NCBI assembly Rhimi59_2 (Rhimi59_2_AssemblyScaffolds.fasta; 79 scaffolds). Gene annotation: Rhimi59_2 JGI MycoCosm official gene models.
Supplementary files format and content: coverage bigbig (.bw) files for each sample

organism: Rhizopus microsporus

source_name: mycelium

growth_protocol: Rhizopus microsporus WT and deletion strains (set1 mutant, gcn5 mutant) were cultured in PDA medium at 30°C under standard conditions. Biomass for ChIP-seq and RNA-seq was harvested from mid-log phase liquid cultures.

extract_protocol:
Cells were cross-linked with 1% formaldehyde (10 min, RT) and quenched with 125 mM glycine. Cells were lysed by bead-beating. Chromatin was sheared to 150–300 bp by sonication. IP was performed overnight at 4°C with antibodies: H3K4me1 (Abcam ab8895), H3K4me3 (Abcam ab8580), H3K27ac (Abcam ab4729), RNApol II (8WG16), using protein A/G beads. Libraries were prepared from IP-enriched DNA and matched input controls.
Standard Illumina library preparation from ChIP DNA or rRNA-depleted RNA. Paired-end 150 bp sequencing.

treatment_protocol: No drug or chemical treatment was applied. Standard growth until mid-log phase for all strains.

value: gcn5 mutant

tag: genotype

value: GCN5 deletion (H3K27 acetyltransferase, SAGA complex)

tag: chip antibody

value: N/A — input chromatin

value: mycelium


title: Rhizopus microsporus gcn5 mutant beads ChIP-seq

description:
Library name: gcn5_beads
beads ChIP-seq in gcn5 mutant R. microsporus

value: N/A — bead-only control


title: Liver, Py 6hpi, biol rep1

description: Library name: Sample 10


title: sample_18_GABA, Oxford Nanopore methylation

description:
Library name: sample_18_GABA
sample ID=sample_18_GABA; donor=18; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing


title: Rhizopus microsporus gcn5 mutant RNApol ChIP-seq

description:
Library name: gcn5_RNApol
RNApol ChIP-seq in gcn5 mutant R. microsporus

value: RNA Polymerase II 8WG16


title: Liver, Pc day 20, biol rep5

description: Library name: Sample 9

value: Pc blood-stage

value: 20 dpi


title: sample_1535_GLU, Oxford Nanopore methylation

description:
Library name: sample_1535_GLU
sample ID=sample_1535_GLU; donor=1535; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing


title: WI-38 cells, single-fraction, 110mGy, 5hmC, rep1

description: Library name: SF110 H1


title: WI-38 cells, single-fraction, 110mGy, 5hmC, rep2

description: Library name: SF110 H2


title: Rhizopus microsporus gcn5 mutant H3K27ac ChIP-seq

description:
Library name: gcn5_H3K27ac
H3K27ac ChIP-seq in gcn5 mutant R. microsporus

value: H3K27ac (Abcam ab4729)


title: sample_1535_GABA, Oxford Nanopore methylation

description:
Library name: sample_1535_GABA
sample ID=sample_1535_GABA; donor=1535; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing


title: WI-38 cells, single-fraction, 23mGy, 5hmC, rep4

description: Library name: SF23 H4


title: Liver, Pc day 20, biol rep4

description: Library name: Sample 8

value: liver


title: Rhizopus microsporus gcn5 mutant H3K4me3 ChIP-seq

description:
Library name: gcn5_H3K4me3
H3K4me3 ChIP-seq in gcn5 mutant R. microsporus

value: H3K4me3 (Abcam ab8580)


title: Liver, Pc day 20, biol rep3

description: Library name: Sample 7


title: sample_1065_GLU, Oxford Nanopore methylation

description:
Library name: sample_1065_GLU
sample ID=sample_1065_GLU; donor=1065; brain region=human prefrontal cortex; cell type=Glu; assay=native DNA Oxford Nanopore methylation sequencing

value: human prefrontal cortex


title: WI-38 cells, single-fraction, 23mGy, 5hmC, rep3

description: Library name: SF23 H3

value: Human fibroblast from 3-month-old female lung tissue


title: Liver, Pc day 20, biol rep2

description: Library name: Sample 6


title: sample_1065_GABA, Oxford Nanopore methylation

description:
Library name: sample_1065_GABA
sample ID=sample_1065_GABA; donor=1065; brain region=human prefrontal cortex; cell type=MGE-GABA; assay=native DNA Oxford Nanopore methylation sequencing

value: MGE-GABA


title: Rhizopus microsporus gcn5 mutant H3K4me1 ChIP-seq

description:
Library name: gcn5_H3K4me1
H3K4me1 ChIP-seq in gcn5 mutant R. microsporus

value: H3K4me1 (Abcam ab8895)


title: WI-38 cells, single-fraction, 23mGy, 5hmC, rep2

description: Library name: SF23 H2

value: alpha-irradiation

value: single-fraction

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: Rhizopus microsporus set1 mutant input ChIP-seq

description:
Library name: set1_input
input ChIP-seq in set1 mutant R. microsporus

value: set1 mutant

value: SET1 deletion (H3K4 methyltransferase)


title: Day 11 post wound induction Langerhans cells

city: East Lansing

first: Axel

middle: Dizan

last: Schmitter-Sanchez

state: MI

address: 775 Woodlot Dr

department: Medicine

institute: Michigan State University

description:
Library name: Day11_Wound_LC_scRNA
10X genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, alignment, and gene counting were executed using the 10x Genomics Cell Ranger software pipeline (version 9.0.0) 'count' command. Reads were mapped tracking both exonic and intronic sequences during quantification.
Assembly: Mouse GRCm39 (including eGFP and tdTomato transgenic reporter sequences).
Supplementary files format and content: An HDF5 formatted binary file (filtered_feature_bc_matrix.h5) containing the filtered single-cell gene-barcode expression matrix of raw UMI counts.

molecule: polyA RNA

source_name: Ear epidermis

extract_protocol:
Day 11 post wound induction of 6 mouse ears were incubated epidermis side up in 2.5% Trypsin solution at 37°C for 90 min, and the epidermis was removed from the dermis. Single cell suspension was achieved by mincing, cutting, and running the sample through a 70 µm filter. Samples were then enriched for LCs by magnetic sorting following the standard protocol from the Epidermal Langerhans Cell MicroBead Kit (Miltenyi Biotec).
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3' Reagent Kit (v3 chemistry) targeting polyadenylated transcripts, according to the manufacturer's protocol.

treatment_protocol: Wound induction was performed by softly applying microneedles (Skinmedix, micro needle dermal stamp 0.2 mm)

value: Ear epidermis

value: Langerhans cells

tag: age

value: 8 weeks

tag: Sex

value: male


title: Liver, Pc day 20, biol rep1

description: Library name: Sample 5

value: Pc blood-stage

value: 20 dpi


title: Rhizopus microsporus set1 mutant beads ChIP-seq

description:
Library name: set1_beads
beads ChIP-seq in set1 mutant R. microsporus

value: N/A — bead-only control

value: mycelium


title: WI-38 cells, single-fraction, 23mGy, 5hmC, rep1

description: Library name: SF23 H1


title: WI-38 cells, single-fraction, 11mGy, 5hmC, rep4

description: Library name: SF11 H4


title: Rhizopus microsporus set1 mutant RNApol ChIP-seq

description:
Library name: set1_RNApol
RNApol ChIP-seq in set1 mutant R. microsporus

value: RNA Polymerase II 8WG16


title: S. cerevisiae, rny1D, OD600=0.2 to log, repC

city: Portland

first: Jennifer

middle: F.

last: Garcia

state: Maine

address: 716 Stevens Avenue

department: School of Biological Sciences, College of Arts and Sciences

institute: University of New England

description: Library name: rny1D-SC113_RepC

data_processing:
Raw sequencing reads were first processed to remove adapter sequences and low-quality bases/reads using Trim Galore! (Galaxy Version 0.6.7)
Quality-trimmed reads were mapped and counted using Sailfish (Galaxy Version 0.10.1.1) and the reference transcriptome (rna.fna) from the NCBI RefSeq assembly GCF_000146045.2
Differential gene expression analysis was performed on the Sailfish count files using DESeq2 (Galaxy Version 2.11.40.7).
Assembly: Saccharomyces cerevisiae S288C genome build SGD R64-3-1 and NCBI RefSeq assembly GCF_000146045.2
Supplementary files format and content: Tab-delimited file containing Normalized Sequence Counts per RNA-seq Library
Supplementary files format and content: Tab-delimited file containing Variance Stabilizing Transformed (VST) log-like data per RNA-seq Library

organism: Saccharomyces cerevisiae

source_name: Sacchromyces cerevisiae

growth_protocol: Yeast strains were streaked from frozen stocks onto selective SC media plates and grown at 25-30°C for 1-3 days. Cells were then cultured in synthetic complete (SC) liquid media overnight at 30°C with shaking. Overnight cultures were diluted to an OD600 of 0.2 in fresh SC medium and incubated at 30°C with shaking until mid-log phase, then harvested by centrifugation and immediately flash-frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from frozen cell pellets using a phenol-chloroform-LET extraction protocol.
Enriched poly(A)+ mRNA was isolated from 5 µg of intact total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Purified mRNA was fragmented at 94°C for 8 minutes, followed by first- and second-strand cDNA synthesis, end-repair, dA-tailing, and adaptor ligation. Libraries were purified and enriched via PCR (13 cycles).

value: Sacchromyces cerevisiae

value: Synthetic Complete (SC) media, 30°C, exponential growth


title: Liver, UI, biol rep 3

description: Library name: Sample 3

value: liver

value: uninfected


title: S. cerevisiae, rny1D, OD600=0.2 to log, repB

description: Library name: rny1D-SC113_RepB


title: Rhizopus microsporus set1 mutant H3K27ac ChIP-seq

description:
Library name: set1_H3K27ac
H3K27ac ChIP-seq in set1 mutant R. microsporus

value: H3K27ac (Abcam ab4729)


title: Liver, UI, biol rep 2

description: Library name: Sample 2


title: S. cerevisiae, rny1D, OD600=0.2 to log, repA

description: Library name: rny1D-SC113_RepA


title: WI-38 cells, single-fraction, 11mGy, 5hmC, rep3

description: Library name: SF11 H3

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

value: single-fraction

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: WI-38 cells, single-fraction, 11mGy, 5hmC, rep2

description: Library name: SF11 H2


title: Liver, UI, biol rep 1

description: Library name: Sample 1


title: Rhizopus microsporus set1 mutant H3K4me3 ChIP-seq

description:
Library name: set1_H3K4me3
H3K4me3 ChIP-seq in set1 mutant R. microsporus

value: set1 mutant

value: SET1 deletion (H3K4 methyltransferase)

value: H3K4me3 (Abcam ab8580)


title: Rhizopus microsporus set1 mutant H3K4me1 ChIP-seq

description:
Library name: set1_H3K4me1
H3K4me1 ChIP-seq in set1 mutant R. microsporus

value: H3K4me1 (Abcam ab8895)


title: WI-38 cells, single-fraction, 2mGy, 5hmC, rep4

description: Library name: SF2 H4


title: S. cerevisiae, WT, OD600=0.2 to log, repB

description: Library name: WT-SC112_RepB

value: WT


title: Rhizopus microsporus WT input ChIP-seq

description:
Library name: WT_input
input ChIP-seq in WT R. microsporus

value: wild-type

value: N/A — input chromatin


title: S. cerevisiae, WT, OD600=0.2 to log, repA

description: Library name: WT-SC112_RepA


title: C3_DM+Wash_Rep3

city: Atlanta

first: Eli

last: Chlan

state: GA

address: 1365 Clifton Rd N E Building B

institute: Emory University

description:
Library name: 25094R-01-60v1
25094R.01.60v1

data_processing:
Quality control was performed using an Agilent Bioanalyzer to ensure all RNA samples had an RNA Integrity Number (RIN) greater than 7. Libraries were prepared using NEBNext Ultra (11) Directional Kit with Poly A Selection and sequenced on the Illumina NovaSeq X Plus (2X150) platform at 40M paired-end reads per sample. Sequencing reads were aligned to the Mus musculus genome assembly GRCm39 (mm39) using STAR aligner (v2.7.1a). Gene-level quantification was performed using featureCounts. Genes with fewer than 40 raw counts in more than 20% of total samples were excluded. Data were normalized using the DESeq2 R package.
Assembly: Transcripts were aligned to the Mus musculus genome assembly GRCm39 (mm39).
Supplementary files format and content: Raw count values in csv format.

source_name: retina

growth_protocol: Mice were maintained in standard housing conditions with ad libitum access to food and water.  All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and performed in accordance with institutional guidelines.

extract_protocol:
RNA was isolated from mouse retina tissue using Qiagen RNeasy kit (Cat no.: 74106; Qiagen; Hilden, Germany) according to the manufacturer’s protocols.
NEBNext Ultra (II) Directional RNA Library Prep Kit with Poly A Selection was used to generate libraries for sequencing.

value: retina

value: M

tag: cohort

tag: conditions

value: DM+Wash

tag: disease

value: DM

value: Washout


title: C3_DM+Wash_Rep2

description:
Library name: 25094R-01-59v1
25094R.01.59v1

tag: tissue


title: Rhizopus microsporus WT beads ChIP-seq

description:
Library name: WT_beads
beads ChIP-seq in WT R. microsporus

value: N/A — bead-only control

value: mycelium


title: WI-38 cells, single-fraction, 2mGy, 5hmC, rep2

description: Library name: SF2 H2

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation


title: h0_3

city: Yan Tai

first: Qiao

middle: Zi

last: Zhao

address: China Agr Univ, Yantai Ins

country: China

institute: CAU

description: Library name: S3445688

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end  reads were generated.Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads.
Assembly: The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Supplementary files format and content: The CSV file containing both counts and FPKM values.

organism: Strongylocentrotus intermedius

source_name: coelomocyte

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: coelomocyte

tag: time

value: LD


title: WI-38 cells, single-fraction, 2mGy, 5hmC, rep3

description: Library name: SF2 H3

value: single-fraction

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: C3_DM+Wash_Rep1

description:
Library name: 25094R-01-58v1
25094R.01.58v1

tag: strain


title: Rhizopus microsporus WT RNApol ChIP-seq

description:
Library name: WT_RNApol
RNApol ChIP-seq in WT R. microsporus

value: RNA Polymerase II 8WG16

tag: cell type


title: h0_2

description: Library name: S3445687


title: WI-38 cells, single-fraction, 2mGy, 5hmC, rep1

description: Library name: SF2 H1

tag: cell line


title: Rhizopus microsporus WT H3K27ac ChIP-seq

description:
Library name: WT_H3K27ac
H3K27ac ChIP-seq in WT R. microsporus

value: WT

value: H3K27ac (Abcam ab4729)


title: WI-38 cells, single-fraction, 0mGy, 5hmC, rep4

description: Library name: SF0 H4

tag: treatment

value: Sham


title: Rhizopus microsporus WT H3K4me3 ChIP-seq

description:
Library name: WT_H3K4me3
H3K4me3 ChIP-seq in WT R. microsporus

value: wild-type

value: H3K4me3 (Abcam ab8580)


title: C3_DM+Cont_Rep3

description:
Library name: 25094R-01-56v1
25094R.01.56v1

value: retina

value: M

value: DM+Cont

value: Continued


title: h12_3

description: Library name: S3445682


title: Rhizopus microsporus WT H3K4me1 ChIP-seq

description:
Library name: WT_H3K4me1
H3K4me1 ChIP-seq in WT R. microsporus

value: H3K4me1 (Abcam ab8895)

value: mycelium


title: WI-38 cells, single-fraction, 220mGy, 5hmC, rep2

description: Library name: SF220 H2

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

tag: dose (mgy)


title: C3_DM+Cont_Rep2

description:
Library name: 25094R-01-55v1
25094R.01.55v1

value: DM


title: h12_2

description: Library name: S3445681

value: coelomocyte

value: LD


title: WI-38 cells, single-fraction, 0mGy, 5hmC, rep2

description: Library name: SF0 H2

tag: radiation regimen

value: single-fraction

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: PDO MSK107Li, ZFP36L2 gRNA2 generated clone 2, replicate 2

city: New York

first: Qingwen

last: Jiang

state: NY

address: 417 East 68th Street, 1725

institute: memorial sloan kettering cancer center

description: Library name: MSK107Li_ZFP36L2_KO2_C2_2

data_processing:
Quality control and trimming: Raw read quality was assessed using FastQC (v0.12.1). Reads were quality-filtered using fastp (v0.24.0) with poly-X tail trimming, 3′ quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Alignment: Filtered reads were aligned to the human reference genome (hg38) using STAR (v2.7.11) with non-canonical splice junction removal. Aligned reads were coordinate-sorted using samtools (v1.22.1).
Deduplication: PCR and optical duplicates were removed by UMI-based deduplication using UMIcollapse (v1.1.0).
Alignment QC: Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC (v5.0.4) and Qualimap (v2.3), aggregated into a QC report using MultiQC (v1.32).
Gene-level quantification: Gene expression was quantified using featureCounts (subread v2.1.1) with strand-specific counting, fractional assignment of multi-mapping reads, using exons and 3′ UTRs as feature identifiers, grouped by gene_id. Gene counts were TMM-normalized for sample-sample correlation analysis.
Assembly: GRCh38
Supplementary files format and content: CSV file with TMM normalized gene counts.

growth_protocol: Patient-derived organoids were cultured and expanded in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). Cells are embedded and plated in 40 μL domes of 3:1 Matrigel (Corning) :HISC medium mixture in suspension culture plates. After Matrigel domes solidified at 37 °C for 30 minutes, HISC medium supplemented with Y-27632 (MedChemExpress) was added to the well. Medium was refreshed every two days.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Total RNA was submitted to Plasmidsaurus (plasmidsaurus.com) for 3′ end RNA-seq library preparation and sequencing. Libraries were generated using a 3′ end counting approach with unique molecular identifiers (UMIs) incorporated during cDNA synthesis to enable PCR duplicate removal. Approximately 20 million raw Illumina reads were generated per sample, yielding ~10 million deduplicated reads after UMI-based deduplication.

treatment_protocol: Organoids were cultured in intestinal growth factor-free (IGFF) medium for 13 days to induce differentiation, then dissociated into single cells and passaged into HISC medium; samples were harvested on day 7 of dedifferentiation.

value: CRC PDO

value: ZFP36L2 KO2


title: C3_DM+Cont_Rep1

description:
Library name: 25094R-01-54v1
25094R.01.54v1


title: h12_1

description: Library name: S3445680


title: WI-38 cells, single-fraction, 0mGy, 5hmC, rep1

description: Library name: SF0 H1

value: Sham

tag: total number_of_fractions


title: PDO MSK107Li, ZFP36L2 gRNA2 generated clone 2, replicate 1

description: Library name: MSK107Li_ZFP36L2_KO2_C2_1


title: Rag1_7

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Library name: Rag1_7

data_processing:
Base calling was performed with Illumina BaseCaller to generate BCL files, followed by demultiplexing to FASTQ using bcl2fastq v2.17.1.14. Read quality was assessed with FastQC v0.11.5. Reads were aligned to the Mus musculus reference genome (Ensembl GRCm38) using STAR v2.5 allowing up to 2 mismatches per 50 bp. Gene-level counts were generated using featureCounts v1.5.0-p1 with the Ensembl annotation Mus_musculus.GRCm38.84.gtf. Differential expression analysis was performed in R/Bioconductor using DESeq2 v1.8.2; candidate genes were filtered at |log2 fold change| > 1 and FDR-adjusted p-value < 0.05. Gene annotation was performed with biomaRt v2.24.1 (Mus musculus dataset).
Assembly: GRCm39
Supplementary files format and content: generated using featureCounts; rows correspond to genes (Ensembl gene ID and gene symbol), columns correspond to samples, and values represent integer read counts (raw_counts.csv). A second matrix contains DESeq2 size-factor–normalized counts with the same gene and sample structure (normalized_counts.csv).

source_name: skin

growth_protocol: Dermal ILC2s were sorted and purified from skin of 30 wild-type and 16 Rag1⁻/⁻ mice.

extract_protocol:
Total RNA was extracted from sorted dILC2s and RNA integrity (RIN) was assessed using a Fragment Analyzer
Libraries were prepared from 200 ng total RNA using TruSeq RNA Sample Prep Kit v2 (Illumina), quality-checked for size (~290–320 bp), and sequenced on an Illumina HiSeq 4000 (single-end 1×50 bp; ~30M reads/sample).

treatment_protocol: No ex vivo stimulation; freshly sorted dILC2s were used for RNA-seq.

value: skin

value: innate lymphoid cells type 3


title: C3_DM+Veh_Rep3

description:
Library name: 25094R-01-53v1
25094R.01.53v1

value: retina

value: M

value: DM+Veh

value: Vehicle


title: HeLa cells, siCDC5L, biol rep 3

city: Shanghai

first: Shunyi

last: Li

state: Shanghai

address: 100 Haike Rd, Building 13

department: Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

data_processing:
RaNA-seq Version 1.0 (https://ranaseq.eu/)
Reads were processed with Salmon software to obtain the expression quantification.
The differential expression analysis were performed with the limma.
Assembly: hg38
Supplementary files format and content: xlsx, row counts and limma normalized abundance measurement for each Sample

source_name: Uterus; Cervix

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

extract_protocol:
RNA was harvested using RNAiso Plus (TaKaRa).
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L).

value: Uterus; Cervix

value: HeLa

value: epithelial cells

value: CDC7L knockdown


title: PDO MSK107Li, ZFP36L2 gRNA2 generated clone 1, replicate 2

description: Library name: MSK107Li_ZFP36L2_KO2_C1_2


title: Rag1_2

description: Library name: Rag1_2


title: C3_DM+Veh_Rep2

description:
Library name: 25094R-01-52v1
25094R.01.52v1

value: DM


title: PDO MSK107Li, ZFP36L2 gRNA2 generated clone 1, replicate 1

description: Library name: MSK107Li_ZFP36L2_KO2_C1_1


title: HeLa cells, siCDC5L, biol rep 2

value: CDC6L knockdown


title: C3_DM+Veh_Rep1

description:
Library name: 25094R-01-51v1
25094R.01.51v1


title: B6J_13

description: Library name: B6J_13

value: innate lymphoid cells type 2

value: WT (B6)


title: HeLa cells, siCDC5L, biol rep 1

value: CDC5L knockdown


title: PDO MSK107Li, ZFP36L2 gRNA1 generated clone 2, replicate 2

description: Library name: MSK107Li_ZFP36L2_KO1_C2_2

value: CRC PDO

value: ZFP36L2 KO1


title: C3_Ctrl+Wash_Rep3

description:
Library name: 25094R-01-50v1
25094R.01.50v1

value: Ctrl+Wash

value: Ctrl

value: Washout


title: B6J_6

description: Library name: B6J_6

value: skin


title: PDO MSK107Li, ZFP36L2 gRNA1 generated clone 2, replicate 1

description: Library name: MSK107Li_ZFP36L2_KO1_C2_1


title: HeLa cells, siControl, biol rep 3

value: WT


title: C3_Ctrl+Wash_Rep2

description:
Library name: 25094R-01-49v1
25094R.01.49v1

value: retina

value: M


title: B6J_5

description: Library name: B6J_5


title: HeLa cells, siControl, biol rep 2

value: Uterus; Cervix

value: HeLa


title: Liver, UI, biol rep 4

description: Library name: Sample 4

value: liver

tag: disease state

value: uninfected


title: PDO MSK107Li, ZFP36L2 gRNA1 generated clone 1, replicate 2

description: Library name: MSK107Li_ZFP36L2_KO1_C1_2

tag: genotype


title: C3_Ctrl+Wash_Rep1

description:
Library name: 25094R-01-48v1
25094R.01.48v1


title: Liver, Combo, replicate 2

city: South San Francisco

first: Russell

last: Fletcher

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

description:
Library name: SRZ4_combo
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 8.0.0
Data exploration, normalization, dimension reduction, clustering, DE, and GSEA analyses were done in R (version 4.3.2)
Assembly: GRCm39
Supplementary files format and content: matrix file of raw, prefiltered UMI counts
Supplementary files format and content: Tab-separated values files of prefiltered cell barcodes
Supplementary files format and content: Tab-separated values files of prefiltered features/genes
Supplementary files format and content: log2  of scran normalized counts matrix as tab delimited text file
Supplementary files format and content: QC, batch, experimental condition, cell type data in tab delimited text file

growth_protocol: Mice were obtained from Jackson Laboratories (Bar Harbor, ME, USA). All animal experimentation was in accordance with the ‘‘Guide for the Care and Use of Laboratory Animals’’ prepared by the National Academy of Sciences. Protocols for animal experimentation were approved by the Surrozen Institutional Animal Care and Use Committee. 7-week-old C57Bl/6J female mice were acclimatized 4-5 per cage a minimum of two days prior to the experiment. Mice were kept 12/12-hour light/dark cycle in a 30% to 70% humidity environment and room temperature ranging from 20°C to 26°C.

extract_protocol:
At 48-hours of the experiment, livers were perfused with a collagenase solution to dissociate the cells, and live cells were then purified by FACS.
Standard 10x Genomics Chromium 3’ v2 scRNA-seq reagents were used. Approximately 2000-3000 cells were loaded per channel. Cells from one animal replicate were captured per channel. Standard 10x Genomics Chromium 3’ v2 scRNA-seq RT, cDNA amplification, and sequencing library preparation protocols were followed. Multiplexed sequencing libraries were sequenced on Illumina Hi Seq 4000 S1 lanes, averaging about 50,000 reads per cell.

treatment_protocol: Mice were dosed intraperitoneally once with either 1.3 mg/kg of an Anti-Bgal antibody or with 0.3 mg/kg of the WNT mimetic R2M3-26 plus 0.46 mg/kg Fc-RSPO2, and mice livers were collected at 48-hours after treatment.

value: liver cells

value: 6-8 weeks old


title: HeLa cells, siControl, biol rep 1

value: epithelial cells


title: PDO MSK107Li, ZFP36L2 gRNA1 generated clone 1, replicate 1

description: Library name: MSK107Li_ZFP36L2_KO1_C1_1


title: C3_Ctrl+Cont_Rep3

description:
Library name: 25094R-01-47v1
25094R.01.47v1

value: Ctrl+Cont

value: Continued


title: S. cerevisiae, WT, OD600=0.2 to log, repC

description: Library name: WT-SC112_RepC

value: Sacchromyces cerevisiae

value: Synthetic Complete (SC) media, 30°C, exponential growth


title: WI-38 cells, single-fraction, 11mGy, 5hmC, rep1

description: Library name: SF11 H1

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

value: single-fraction

tag: antibody

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: Liver, Combo, replicate 1

description:
Library name: SRZ3_combo
10x Genomics

tag: age


title: PDO MSK107Li, Control, culture 2, replicate 2

description: Library name: MSK107Li_Ctrl_C2_2

value: CRC PDO

value: Control


title: HeLa cells, Input

data_processing:
Illumina platform are transformed to short reads by base calling and these short reads are recorded in FASTQ format.
ChIP-seq reads were quality controlled with Fastp (version 0.23.1).
ChIP-seq reads were aligned using bowtie2 (2.2.5).
ChIP-seq reads were sorted and filtered using samtools.
The peak calling was done by MACS2 ( 2.2.7.1) in broad peak calling mode with q-value (minimum false discovery rate) cutoff set to 0.05 for peak detection.
Assembly: hg38
Supplementary files format and content: txt, bed, bw, fasta (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was  digested into fragments using micrococcal nuclease.
The purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit （NEB, USA, Catalog #: E7645L）for ChIP-seq library preparation.

value: Uterus; Cervix

tag: chip antibody


title: C3_Ctrl+Cont_Rep2

description:
Library name: 25094R-01-46v1
25094R.01.46v1

value: retina

tag: Sex

value: M

tag: cohort

value: Ctrl


title: Liver, Anti-Bgal, replicate 2

description:
Library name: SRZ2_AntiBgal
10x Genomics

value: liver

value: liver cells


title: C3_DM+Wash_Rep4

description:
Library name: 25094R-01-61v1
25094R.01.61v1

tag: conditions

value: DM+Wash

tag: disease

value: DM

value: Washout


title: HeLa cells, HA1

tag: tissue

value: HeLa

value: epithelial cells


title: Liver, Anti-Bgal, replicate 1

description:
Library name: SRZ1_AntiBgal
10x Genomics

value: 6-8 weeks old


title: C3_Ctrl+Cont_Rep1

description:
Library name: 25094R-01-45v1
25094R.01.45v1

tag: strain

value: Ctrl+Cont

value: Continued


title: AML PDX TUH96_P2 EPIC methylation

type: genomic

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

description:
TUH96_P2
Model TUH96 timepoint P2

hyb_protocol: Samples were hybridized to the Infinium MethylationEPIC BeadChip following the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the Illumina iScan system.

data_processing:
Raw IDAT files were processed in R using the minfi package. Data were normalized with preprocessNoob and beta values were extracted.
Beta values represent the ratio of methylated probe intensity over total intensity (methylated + unmethylated).

label: biotin

source_name: xenografted human AML cells

label_protocol: DNA was bisulfite converted and labeled according to the Illumina Infinium MethylationEPIC protocol.

growth_protocol: AML patient-derived xenograft cells were expanded in immunodeficient mice.

extract_protocol: Genomic DNA was extracted from AML PDX cells using standard DNA extraction procedures.

treatment_protocol: No treatment was applied prior to DNA extraction.

value: xenografted human AML cells

value: AML cells

value: not applicable

value: no treatment


title: PDO MSK107Li, Control, culture 1, replicate 2

description: Library name: MSK107Li_Ctrl_C1_2

tag: cell type

value: CRC PDO

value: Control


title: C3_Ctrl+Veh_Rep3

description:
Library name: 25094R-01-44v1
25094R.01.44v1

value: retina

value: M

value: Ctrl+Veh

value: Ctrl

value: Vehicle


title: AML PDX TUH96_P1 EPIC methylation

description:
TUH96_P1
Model TUH96 timepoint P1

tag: cell line


title: PDO MSK107Li, Control, culture 1, replicate 1

description: Library name: MSK107Li_Ctrl_C1_1


title: C3_Ctrl+Veh_Rep2

description:
Library name: 25094R-01-43v1
25094R.01.43v1

tag: treatment


title: ipscTG, inflammatory soup treated, rep3, lane2

city: Cardiff

first: Viola

last: Volpato

address: Maindy Rd

department: UK DRI

country: United Kingdom

institute: Cardiff University

description: Library name: TG_INFL_repl3_lane2

data_processing:
We used the pipelines “mkfastq” and “count” from the Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/) to demultiplex raw base call files into FASTQ files, and to perform alignment, barcode counting and UMI counting. Multiple sequencing runs (two HiSeq4000 lanes) of the same library were combined by the “count” pipeline. Barcodes and UMIs were filtered using default settings to generate gene-barcode matrix.
Assembly: GRCh38
Supplementary files format and content: tab separated file with genes expression (rows) and cells (columns).
Supplementary files format and content: tab separated file with cells (rows) and metadata (columns).

source_name: iPSCs

extract_protocol:
iPSC-TG nociceptors were washed in PBS with 0.04% BSA and re-suspended at a concentration of ~1500cells/μl before capturing single cells in droplets on Chromium 10x Genomics platform.
Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide:  CG00052 Rev B.  Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851).  Quantification of library construction was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tapestation (Agilent.  5067-5584). Libraries were sequenced on Illumina HiSeq4000 platform to achieve an average of 42,000 reads per cell.

value: iPSCs

value: StemBANCC iPSC line SBAD03-01

value: TG nociceptors

value: treated


title: ipscTG, inflammatory soup treated, rep3, lane1

description: Library name: TG_INFL_repl3_lane1


title: AML PDX TUH96_P0 EPIC methylation

description:
TUH96_P0
Model TUH96 timepoint P0

source_name: peripheral blood

value: peripheral blood


title: C3_Ctrl+Veh_Rep1

description:
Library name: 25094R-01-42v1
25094R.01.42v1


title: Gastroid, SPON2 Treated, 3

city: NASHVILLE

first: James

middle: R

last: Goldenring

state: TN

address: 2213 Garland Avenue

department: Epithelial Biology Center

institute: Vanderbilt University

description:
Library name: Sample 6
Row name in Human_SPON2_mRNA_bulk_seq_Filter_features_Filtered_counts.txt: 13956-JR-6_S1

data_processing:
Reads trimmed and aligned to hg38 (hg38_ensembl_release91_v2) using STAR 2.7.8a in Partek Flow v12.8.0
Reads quantified against annotation model hg38_refseq_v83_17_11_01_v2
Features with maximum count ≤ 1.0 excluded (noise reduction)
Remaining features normalized by median-ratio method
Differential expression performed with DESeq2 in Partek Flow; SPON2-treated relative to control; FDR ≤ 0.05 considered significant
GSEA performed on median-ratio normalized counts; MSigDB Hallmark, Transcription Factor Targets, and KEGG (hsa_v14_25_11_05); FDR ≤ 0.05 significant, 0.05 < FDR ≤ 0.2 considered exploratory
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file containing gene-level counts (fractional due to multi-isoform read distribution) for all samples after exclusion of features with maximum count ≤ 1 in partek flow and before normalization

source_name: Gastric Corpus

growth_protocol: Dissociated gastroids in Human IntestiCult Medium (StemCell Technologies) were plated onto collagen-coated Transwell inserts (200 μL apical, 300 μL basal). Media was replaced at 48 hours. Cells were allowed to proliferate and adhere for 7 days. On day 7, apical medium was aspirated to establish an air-liquid interface (ALI). Allowed to grow and maintained for 14 more days as outlined in the treatment protocol section.

extract_protocol:
Cell pellets were preserved in RNALater and centrifuged at 1000Xg. RNA was extracted using the Qiagen RNeasy Micro Kit with on-column DNase treatment. RNA concentration was assessed by Qubit fluorometry and RNA integrity was determined using the Agilent 4200 TapeStation System.
RNA libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit (NEB, cat. #E3330) with 250ng input per sample. Poly(A) selection was used to enrich for mRNA. Libraries were sequenced on an Illumina NovaSeq X Plus at paired-end 150bp. Done at VANTAGE Core, Vanderbilt University.

treatment_protocol: At ALI initiation, basal medium was replaced with either fresh IntestiCult Medium (negative control), or 20 ng/mL recombinant human SPON2. ALI culture was maintained for 14 days with basal medium changed every other day and apical secretions removed daily.

value: Gastric Corpus

value: Gastric Organoids/G05C

value: Gastric Epithelial Cells

value: SPON2 Treated Media

tag: time

value: 3 Weeks


title: ipscTG, inflammatory soup treated, rep2, lane2

description: Library name: TG_INFL_repl2_lane2


title: C3_DM+Cont_Rep4

description:
Library name: 25094R-01-57v1
25094R.01.57v1

value: DM+Cont

value: DM

value: Continued


title: h0_1

description: Library name: S3445686

value: coelomocyte

value: LD


title: AML PDX TUH93_P2 EPIC methylation

description:
TUH93_P2
Model TUH93 timepoint P2

value: xenografted human AML cells

value: AML cells

value: not applicable

value: no treatment


title: Gastroid, SPON2 Treated, 2

description:
Library name: Sample 5
Row name in Human_SPON2_mRNA_bulk_seq_Filter_features_Filtered_counts.txt: 13956-JR-5_S1


title: ipscTG, inflammatory soup treated, rep2, lane1

description: Library name: TG_INFL_repl2_lane1

value: iPSCs

value: StemBANCC iPSC line SBAD03-01

value: TG nociceptors


title: C2_DM+Wash_Rep3

description:
Library name: 25094R-01-41v1
25094R.01.41v1

value: retina

value: M

value: DM+Wash

value: Washout


title: WI-38 cells, single-fraction, 0mGy, 5hmC, rep3

description: Library name: SF0 H3

value: Human fibroblast from 3-month-old female lung tissue

value: Sham

tag: dose (mgy)

tag: radiation regimen

value: single-fraction

value: anti-5hmC (monoclonal mouse antibody - Diagenode #C15200200)


title: AML PDX TUH93_P1 EPIC methylation

description:
TUH93_P1
Model TUH93 timepoint P1


title: C2_DM+Wash_Rep2

description:
Library name: 25094R-01-40v1
25094R.01.40v1

value: DM


title: AML PDX TUH93_P0 EPIC methylation

description:
TUH93_P0
Model TUH93 timepoint P0

value: peripheral blood


title: Gastroid, SPON2 Treated, 1

description:
Library name: Sample 4
Row name in Human_SPON2_mRNA_bulk_seq_Filter_features_Filtered_counts.txt: 13956-JR-4_S1

value: Gastric Corpus

value: Gastric Organoids/G05C

value: Gastric Epithelial Cells

value: SPON2 Treated Media

value: 3 Weeks


title: ipscTG, inflammatory soup treated, rep1, lane2

description: Library name: TG_INFL_repl1_lane2

value: iPSCs

value: StemBANCC iPSC line SBAD03-01

value: treated


title: Gastroid, Control, 3

description:
Library name: Sample 3
Row name in Human_SPON2_mRNA_bulk_seq_Filter_features_Filtered_counts.txt: 13956-JR-3_S1


title: C2_DM+Wash_Rep1

description:
Library name: 25094R-01-39v1
25094R.01.39v1

value: retina

value: M


title: ipscTG, inflammatory soup treated, rep1, lane1

description: Library name: TG_INFL_repl1_lane1

value: TG nociceptors


title: Gastroid, Control, 2

description:
Library name: Sample 2
Row name in Human_SPON2_mRNA_bulk_seq_Filter_features_Filtered_counts.txt: 13956-JR-2_S1


title: AML PDX TUH84_P2 EPIC methylation

description:
TUH84_P2
Model TUH84 timepoint P2

value: xenografted human AML cells

value: AML cells

value: not applicable

value: no treatment


title: C2_DM+Cont_Rep4

description:
Library name: 25094R-01-38v1
25094R.01.38v1

value: DM+Cont

value: DM

value: Continued


title: ipscTG, control, rep3, lane2

description: Library name: TG_CTR_repl3_lane2

value: control


title: AML PDX TUH84_P1 EPIC methylation

description:
TUH84_P1
Model TUH84 timepoint P1


title: Gastroid, Control, 1

description:
Library name: Sample 1
Row name in Human_SPON2_mRNA_bulk_seq_Filter_features_Filtered_counts.txt: 13956-JR-1_S1

value: Gastric Corpus

value: Gastric Organoids/G05C

value: Gastric Epithelial Cells


title: C2_DM+Cont_Rep3

description:
Library name: 25094R-01-37v1
25094R.01.37v1


title: AML PDX TUH84_P0 EPIC methylation

description:
TUH84_P0
Model TUH84 timepoint P0

value: peripheral blood


title: ipscTG, control, rep3, lane1

description: Library name: TG_CTR_repl3_lane1

value: iPSCs

value: StemBANCC iPSC line SBAD03-01


title: PACERR overexpression with hnRNPL motif deleted, HDL treaed, rep3

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description:
Library name: Delta3-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

data_processing:
Data analyses were performed by GENEWIZ from Azenta Life Sciences (South Plainfield, NJ), as follows: sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b (default parameters).
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: hg38
Supplementary files format and content: subread_gene_quants.csv is a comma-delimited file containing the unnormalized read counts for each gene across all samples (gene x sample format). The first and last columns contain the Ensembl gene IDs and common gene names, respectively. The remaining columns contain gene counts for each sample in the study.

growth_protocol: THP-1 monocytes (ATCC TIB-202) were grown in RPMI supplemented with 2 mM L-glutamine, 10 mM HEPES, 1 mM sodium pyruvate, 4500 mg/L glucose, 1500 mg/L sodium bicarbonate, 0.05 mM beta-mercaptoethanol, 10% FBS and 1% pencillin/streptomycin

extract_protocol:
Total RNA was isolated using TRIzol reagent and Zymo Research Direct-zol RNA MicroPrep columns. Tissues were lysed with steel beads using the Qiagen tissue lyser in the presence of Trizol.
Libraries were prepared by GENEWIZ from Azenta Life Sciences (South Plainfield, NJ), using the NEBNext Ultra II RNA Library Prep Kit for Illumina (non-stranded, polyA), according to manufacturer's protocols.

treatment_protocol: THP-1 monocytes were stably transfected with pMSCV-PIG retrovirus produced by HEK293T cells transiently transfected with pMSCV-PIG-empty vector, pMSCV-PIG-PACERR or pMSCV-PIG-deltaPACERR and selected using  5 μg/ml puromycin. Once stably transfected, monocytes were differentiated into macrophages with 10 nM phorbol-12-myristate acetate (PMA) for 72 hours before treatment with 50µg/ml HDL for 24 hours.

value: macrophages

tag: vector

value: pMSCV-PIG PACERR overexpression with hnRNPL motif deleted

value: HDL 24hours

tag: sequencing barcode

value: AGCGATAG+GGCAGCTA


title: ipscTG, control, rep2, lane2

description: Library name: TG_CTR_repl2_lane2

value: TG nociceptors


title: C2_DM+Cont_Rep2

description:
Library name: 25094R-01-36v1
25094R.01.36v1

value: retina

value: M


title: AML PDX TUH83_P2 EPIC methylation

description:
TUH83_P2
Model TUH83 timepoint P2

value: xenografted human AML cells

value: AML cells

tag: genotype

value: not applicable

value: no treatment


title: PACERR overexpression with hnRNPL motif deleted, HDL treaed, rep2

description:
Library name: Delta2-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: CGTACTAG+ATCCTGTG


title: ipscTG, control, rep2, lane1

description: Library name: TG_CTR_repl2_lane1

value: control


title: C2_DM+Cont_Rep1

description:
Library name: 25094R-01-35v1
25094R.01.35v1

value: DM+Cont

value: DM

value: Continued


title: PACERR overexpression with hnRNPL motif deleted, HDL treaed, rep1

description:
Library name: Delta1-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: CGAGGCTC+TCTGAAAC


title: AML PDX TUH83_P1 EPIC methylation

description:
TUH83_P1
Model TUH83 timepoint P1


title: C2_DM+Veh_Rep3

description:
Library name: 25094R-01-34v1
25094R.01.34v1

value: DM+Veh

value: Vehicle


title: AML PDX TUH83_P0 EPIC methylation

description:
TUH83_P0
Model TUH83 timepoint P0

value: peripheral blood


title: ipscTG, control, rep1, lane2

description: Library name: TG_CTR_repl1_lane2

value: iPSCs

value: StemBANCC iPSC line SBAD03-01


title: PACERR overexpression with hnRNPL motif deleted, untreated, rep3

description:
Library name: Delta3
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: macrophages

value: pMSCV-PIG PACERR overexpression with hnRNPL motif deleted

value: untreated

value: CGGCTATG+GGCAGCTA


title: ipscTG, control, rep1, lane1

description: Library name: TG_CTR_repl1_lane1

value: TG nociceptors


title: PACERR overexpression with hnRNPL motif deleted, untreated, rep2

description:
Library name: Delta2
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: AAAGATAC+ATCCTGTG


title: C2_DM+Veh_Rep1

description:
Library name: 25094R-01-32v1
25094R.01.32v1

value: retina

value: M


title: AML PDX TUH76_P1 EPIC methylation

description:
TUH76_P1
Model TUH76 timepoint P1

value: xenografted human AML cells

value: AML cells

value: not applicable

value: no treatment


title: 11421 donor, 4 Week old WT neurons treated with DMSO, replicate3

city: Genova

first: Chiara

last: Pedicone

address: Largo Rosanna Benzi, 10

department: Neuroscienze Sperimentali

country: Italy

institute: IRCCS Azienda Ospedaliera Metropolitana Policlinico San Martino

description: Library name: 2A07-DMSO-3

data_processing:
Reads were aligned to the GRCh38 reference genome using STAR v2.7.9a with default parameters. Transcript abundance was estimated with RSEM v1.3.1.
Quality control was conducted using Picard v2.21.1 to assess read counts, duplication rates, ribosomal RNA contamination, strand specificity, and GC bias.
Duplicate removal was performed with Picard MarkDuplicates. Lowly expressed genes (CPM ≤ 0.3 in <30% of samples) and transcripts ≤50 bp were filtered out.
Normalization was performed using conditional quantile normalization (CQN) to correct for GC content and gene length biases, followed by limma-trend normalization.
Differential expression analysis was conducted using DESeq2, adjusting for relevant covariates.
Assembly: Hg38
Supplementary files format and content: Comma separated value file of raw read counts

source_name: iPSC derived Neurons

growth_protocol: 4 weeks old neurons differentiated from NPC with Dual Smad protocol.

extract_protocol:
Qiagen RNAeasy Mini extraction of total RNA
poly-A selection and sequencing 150bp 30 mil reads/sample.

treatment_protocol: 24h treatment with 10 uM Anastrozole or DMSO

tag: genotype/treatment

value: iPSC derived Neurons

tag: donor

value: WT

value: DMSO

tag: batch


title: AML PDX TUH76_P2 EPIC methylation

description:
TUH76_P2
Model TUH76 timepoint P2


title: PACERR overexpression with hnRNPL motif deleted, untreated, rep1

description:
Library name: Delta1
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: TAAGGCGA+TCTGAAAC


title: C2_Ctrl+Wash_Rep3

description:
Library name: 25094R-01-31v1
25094R.01.31v1

tag: Sex

tag: cohort

value: Ctrl+Wash

value: Ctrl

value: Washout


title: AML PDX TUH76_P0 EPIC methylation

description:
TUH76_P0
Model TUH76 timepoint P0

value: peripheral blood


title: 11421 donor, 4 Week old WT neurons treated with DMSO, replicate2

description: Library name: 2A07-DMSO-2


title: PACERR overexpression, HDL treated, rep3

description:
Library name: P3-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: macrophages

value: pMSCV-PIG PACERR overexpression

value: HDL 24hours

value: TCTCGCGC+GGCAGCTA


title: 11421 donor, 4 Week old WT neurons treated with DMSO, replicate1

description: Library name: 2A07-DMSO-1


title: C2_Ctrl+Wash_Rep2

description:
Library name: 25094R-01-30v1
25094R.01.30v1

value: retina

value: M

tag: conditions

tag: disease


title: AML PDX TUH10_P2 EPIC methylation

description:
TUH10_P2
Model TUH10 timepoint P2

tag: tissue

value: xenografted human AML cells

value: AML cells


title: PACERR overexpression, HDL treated, rep2

description:
Library name: P2-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

tag: cell type

value: TAAGGCGA+ATCCTGTG


title: C2_Ctrl+Wash_Rep1

description:
Library name: 25094R-01-29v1
25094R.01.29v1

tag: strain


title: 11421 donor, 4 Week old WT neurons treated with Anastrozole, replicate3

description: Library name: 2A07-Anast-3

tag: cell line

value: iPSC derived Neurons

tag: treatment

value: Anastrozole


title: AML PDX TUH10_P1 EPIC methylation

description:
TUH10_P1
Model TUH10 timepoint P1

value: not applicable

value: no treatment


title: C2_Ctrl+Cont_Rep3

description:
Library name: 25094R-01-28v1
25094R.01.28v1

value: Ctrl+Cont

value: Continued


title: AML PDX TUH10_P0 EPIC methylation

description:
TUH10_P0
Model TUH10 timepoint P0


title: 11421 donor, 4 Week old WT neurons treated with Anastrozole, replicate2

description: Library name: 2A07-Anast-2

value: WT


title: PACERR overexpression, HDL treated, rep1

description:
Library name: P1-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: GCTACGCT+TCTGAAAC


title: C2_Ctrl+Cont_Rep2

description:
Library name: 25094R-01-27v1
25094R.01.27v1

value: Ctrl


title: PACERR overexpression, untreated, rep3

description:
Library name: P3
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: macrophages

value: pMSCV-PIG PACERR overexpression

value: untreated

value: CGAGGCTC+ATCCTGTG


title: 11421 donor, 4 Week old WT neurons treated with Anastrozole, replicate1

description: Library name: 2A07-Anast-1


title: AML PDX TUH102_P2 EPIC methylation

description:
TUH102_P2
Model TUH102 timepoint P2


title: PACERR overexpression, untreated, rep2

description:
Library name: P2
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: CAAGGTGA+ATCCTGTG


title: C2_Ctrl+Cont_Rep1

description:
Library name: 25094R-01-26v1
25094R.01.26v1

value: retina

value: M


title: 11362 donor, 4 Week old WT neurons treated with DMSO, replicate3

description: Library name: C11-DMSO-3

value: DMSO


title: AML PDX TUH102_P1 EPIC methylation

description:
TUH102_P1
Model TUH102 timepoint P1

value: xenografted human AML cells

value: AML cells


title: PACERR overexpression, untreated, rep1

description:
Library name: P1
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: TGGAGCTG+TCTGAAAC


title: 11362 donor, 4 Week old WT neurons treated with DMSO, replicate2

description: Library name: C11-DMSO-2

value: iPSC derived Neurons


title: C2_Ctrl+Veh_Rep3

description:
Library name: 25094R-01-25v1
25094R.01.25v1

value: Ctrl+Veh

value: Vehicle


title: AML PDX TUH102_P0 EPIC methylation

description:
TUH102_P0
Model TUH102 timepoint P0

value: peripheral blood

value: not applicable

value: no treatment


title: Empty vector, HDL treated, rep3

description:
Library name: EV3-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: macrophages

value: pMSCV-PIG empty vector

value: HDL 24hours

value: TCCGCGAA+GGCAGCTA


title: 11362 donor, 4 Week old WT neurons treated with DMSO, replicate1

description: Library name: C11-DMSO-1

value: WT


title: AML PDX TUH06_P2 EPIC methylation

description:
TUH06_P2
Model TUH06 timepoint P2


title: C2_Ctrl+Veh_Rep2

description:
Library name: 25094R-01-24v1
25094R.01.24v1

value: retina

value: Ctrl


title: C2_Ctrl+Veh_Rep1

description:
Library name: 25094R-01-23v1
25094R.01.23v1

value: M


title: PDO MSK107Li, Control, culture 2, replicate 1

description: Library name: MSK107Li_Ctrl_C2_1

value: CRC PDO

value: Control


title: AML PDX TUH06_P1 EPIC methylation

description:
TUH06_P1
Model TUH06 timepoint P1

value: xenografted human AML cells

value: AML cells


title: 11362 donor, 4 Week old WT neurons treated with Anastrozole, replicate3

description: Library name: C11-Anast-3

value: iPSC derived Neurons

value: Anastrozole


title: Empty vector, HDL treated, rep2

description:
Library name: EV2-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: TGGAGCTG+ATCCTGTG


title: 11362 donor, 4 Week old WT neurons treated with Anastrozole, replicate2

description: Library name: C11-Anast-2


title: C1_DM+Cont_Rep4

description:
Library name: 25094R-01-18v1
25094R.01.18v1

value: DM+Cont

value: DM

value: Continued


title: Empty vector, HDL treated, rep1

description:
Library name: EV1-HDL
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: macrophages

value: pMSCV-PIG empty vector

value: CGTACTAG+TCTGAAAC


title: AML PDX TUH06_P0 EPIC methylation

description:
TUH06_P0
Model TUH06 timepoint P0

value: peripheral blood

value: not applicable

value: no treatment


title: Empty vector, untreated, rep3

description:
Library name: EV3
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: untreated

value: GCTACGCT+ATCCTGTG


title: C1_DM+Cont_Rep3

description:
Library name: 25094R-01-17v1
25094R.01.17v1

value: retina

value: M


title: AML PDX PAR27_P2 EPIC methylation

description:
PAR27_P2
Model PAR27 timepoint P2

value: xenografted human AML cells

value: AML cells


title: 11362 donor, 4 Week old WT neurons treated with Anastrozole, replicate1

description: Library name: C11-Anast-1

value: iPSC derived Neurons

value: WT

value: Anastrozole


title: Empty vector, untreated, rep2

description:
Library name: EV2
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: TGGCACCT+ATCCTGTG


title: 11421 donor, 4 Week old R406W neurons treated with DMSO, replicate3

description: Library name: 11421-DMSO-3

value: R406W mutant

value: DMSO


title: Empty vector, untreated, rep1

description:
Library name: EV1
Libraries pooled and sequenced together on a 25B flowcell (2x150bp reads)

value: macrophages

value: pMSCV-PIG empty vector

value: AAAGATAC+TCTGAAAC


title: C1_DM+Cont_Rep2

description:
Library name: 25094R-01-16v1
25094R.01.16v1

value: DM+Cont

value: DM

value: Continued


title: C1_DM+Cont_Rep1

description:
Library name: 25094R-01-15v1
25094R.01.15v1


title: 11421 donor, 4 Week old R406W neurons treated with DMSO, replicate2

description: Library name: 11421-DMSO-2


title: AML PDX PAR27_P0 EPIC methylation

description:
PAR27_P0
Model PAR27 timepoint P0

source_name: bone marrow

value: bone marrow

value: not applicable

value: no treatment


title: AML PDX PAR27_P1 EPIC methylation

description:
PAR27_P1
Model PAR27 timepoint P1

value: xenografted human AML cells


title: HaCaT-All in one control -3

city: Nottingham

first: Mohammed

last: Ahmed

address: Clifton Lane

institute: Nottingham Trent University

description: Library name: Sample 6

data_processing:
Human mRNA Sequencing (WOBI) NovaSeq X Plus Series (PE150). In brief, quality of RNA reads was assessed using Fastqc (v0.12.1) for presence of adapters and low-quality reads. Reads were aligned to the GRCh38.p14 genome using STAR (v2.7.10b) and read counts for each gene was evaluated using Feature Counts from the SubRead package (v2.0.1). Raw counts were input to Rstudio (v4.2.2) for further analyses. Normalization and differential gene expression analysis between groups were performed using EdgeR (v3.38.4). Genes with a Benjamini-Hochberg false discovery rate <0.05 were considered significant. Normalized counts were used to generate heatmaps for gene expression level using pHeatmap package (v1.0.12) and differentially expressed genes were plot as a Volcano plot using Enhanced Volcano package (v1.14.0). Gene ontology analysis was performed with significant enrichment threshold of P<0.01 and Q<0.05 using Cluster Profiler package (v4.4.4) and annotated using the org.Hs.e.g.db database (v3.15.0). Barcode plots were generated using the Limma package (v3.52.4). Principal component analysis (PCA) was conducted using PCA tools package (v2.14.0).
Assembly: hg38 (GRCh38.p14)
Supplementary files format and content: csv differentiali gene expression plus signifacnce (p values) comparison of CRISPR-Cas9 ELF5 control (ELF5-Control) comapred to CRISPR-ELF5KO samples (ELF5-KO)

source_name: HaCaT

growth_protocol: Cell culture of immortalised human keratinocytes (HaCaT; 300493, 2B Scientific) was grown in DMEM (Fisher UK) respectively, supplemented with 10% heat-inactivated fetal bovine serum (Fisher Uk, UK), 100U/ml penicillin (Fisher UK, UK), 100µg/ml streptomycin (Fisher UK, UK), and 2mM L-glutamine (Fisher UK), at 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated using the Zymo Direct-zol RNA kit (Cambridge Biosciences, UK).
ELF5-Control and ELF5-KO cells were cultured as described above, and total RNA was extracted using the Zymo Direct-zol RNA kit. Samples were sent to Novogene (Cambridge, United Kingdom) for RNA sequencing using Human mRNA Sequencing (WOBI) NovaSeq X Plus Series (PE150).

value: HaCaT

value: Immortalised Human keratinocytes

value: CRISPR-Control


title: C1_Ctrl+Cont_Rep3

description:
Library name: 25094R-01-14v1
25094R.01.14v1

value: retina

value: M

value: Ctrl+Cont

value: Ctrl


title: HaCaT-All in one control -2

description: Library name: Sample 5


title: 11421 donor, 4 Week old R406W neurons treated with DMSO, replicate1

description: Library name: 11421-DMSO-1

value: iPSC derived Neurons

value: R406W mutant

value: DMSO


title: C1_Ctrl+Cont_Rep2

description:
Library name: 25094R-01-13v1
25094R.01.13v1


title: 11421 donor, 4 Week old R406W neurons treated with Anastrozole, replicate3

description: Library name: 11421-Anast-3

value: Anastrozole


title: HaCaT-All in one control -1

description: Library name: Sample 4


title: C1_Ctrl+Cont_Rep1

description:
Library name: 25094R-01-12v1
25094R.01.12v1


title: 11421 donor, 4 Week old R406W neurons treated with Anastrozole, replicate2

description: Library name: 11421-Anast-2


title: C1_DM+Veh_Rep4

description:
Library name: 25094R-01-07v1
25094R.01.07v1

value: DM+Veh

value: DM

value: Vehicle


title: HaCaT-All in one Elf5 KO -3

description: Library name: Sample 3


title: HaCaT-All in one Elf5 KO -2

description: Library name: Sample 2


title: 11421 donor, 4 Week old R406W neurons treated with Anastrozole, replicate1

description: Library name: 11421-Anast-1


title: C1_DM+Veh_Rep3

description:
Library name: 25094R-01-06v1
25094R.01.06v1


title: 11362 donor, 4 Week old R406W neurons treated with DMSO, replicate3

description: Library name: 11362-DMSO-3


title: HaCaT-All in one Elf5 KO -1

description: Library name: Sample 1


title: C1_DM+Veh_Rep2

description:
Library name: 25094R-01-05v1
25094R.01.05v1


title: 11362 donor, 4 Week old R406W neurons treated with DMSO, replicate2

description: Library name: 11362-DMSO-2


title: C2_DM+Veh_Rep2

description:
Library name: 25094R-01-33v1
25094R.01.33v1


title: C1_DM+Veh_Rep1

description:
Library name: 25094R-01-04v1
25094R.01.04v1


title: 11362 donor, 4 Week old R406W neurons treated with DMSO, replicate1

description: Library name: 11362-DMSO-1


title: Alicyclobacillus acidocaldarius KCTC 1825 PacBio methylome

city: Seodaemun-gu

first: Jae-Yoon

last: Sung

state: Seoul

address: YERP B118DA, Yonsei University

department: Biotechnology

country: South Korea

institute: Yonsei University

description:
Library name: KCTC1825_PacBio_methylome
PacBio HiFi whole-genome sequencing sample used for complete genome assembly and kinetic detection of m6A and m4C DNA modifications; the SRA source file alias is A_DSM446.hifi_reads.bam.

data_processing:
PacBio HiFi reads with a minimum read QV of 20 were processed with SMRT Link 25.2.0.266456 using the Microbial Genome Analysis workflow. Reads were assembled, circularized, rotated, polished, and aligned to the resulting complete genome assembly.
Strand-specific kinetic information was prepared with ccs-kinetics-bystrandify. Reads were aligned with pbmm2 using a minimum gap-compressed identity of 98%, a minimum aligned length of 50 bp, and 8 threads.
Base modifications were called with ipdSummary v2.0 in 24 shards with 8 workers per shard, using a p-value threshold of 0.001 and identification of m4C and m6A.
Sequence motifs were identified with pbmotifmaker using a minimum score of 35 and reprocessed with a minimum methylated fraction of 0.3. Modification and motif reporting used a modification QV cutoff of 35.
Processed outputs were generated as per-base kinetic calls in CSV, base-modification calls in GFF3, motif summaries in CSV, and motif-annotated modification sites in GFF3.
Assembly: GCF_059033385.1 (ASM5903338v1; complete genome), paired GenBank assembly GCA_059033385.1. Chromosome CM180098.1 and plasmid pKCTC1825 JCADBT010000002.1.
Supplementary files format and content: Gzip-compressed CSV and GFF3 files. basemods.csv contains per-position kinetic statistics including modification score, IPD ratio, and coverage; basemods.gff contains genome-wide m4C, m6A, and other modified-base calls.
Supplementary files format and content: motifs.csv summarizes detected motif sequences, modification types, modified fractions, site counts, mean scores, mean IPD ratios, and coverage; motifs.gff contains modification sites annotated with motif identifiers. Analysis contig ctg.s1 corresponds to chromosome CM180098.1 and ctg.s2 corresponds to plasmid pKCTC1825 (JCADBT010000002.1).

organism: Alicyclobacillus acidocaldarius subsp. acidocaldarius

source_name: bacterial cell

extract_protocol:
High-molecular-weight genomic DNA was extracted from Alicyclobacillus acidocaldarius strain KCTC 1825 (DSM 446) for PacBio HiFi sequencing. The extraction method and kit were not documented in the sequencing analysis files available for this submission.
A PacBio HiFi whole-genome sequencing library was prepared from high-molecular-weight genomic DNA and sequenced on a PacBio Revio instrument. Detailed library preparation kit information was not documented in the sequencing analysis files available for this submission.

treatment_protocol: No experimental treatment was applied.

value: bacterial cell


title: GFP_neg/Tdtomato_neg CAFs

city: Charlottesville

first: Robert

middle: Weldon

last: Barnes

state: VA

address: 409 Lane Rd

department: Biomedical Engineering

institute: University of Virginia

description: Library name: file4

data_processing:
Raw sequencing data from the 10x Genomics platform were processed with Cell Ranger (v10.0.0) to perform read alignment and generate UMI count matrices. Alignment was carried out against the mouse reference genome (GRCm39; refdata-gex-GRCm39-2024-A), obtained from the 10x Genomics website, using the STAR aligner. Gene expression was then quantified per cell from the number of unique UMIs detected, and the resulting filtered gene-by-cell count matrices were used as input for subsequent single-cell analysis. Cells which expressed fewer than 100 or more than 6000 features and more than 10% mitochondrial DNA were filtered out. After removing these low quality cells, the R package Seurat (5.0) was used to perform unsupervised clustering on cells. Cell counts were normalized using LogNormalize and multiplied by a scaling factor of 10000. The top 2000 highly variable genes were used to perform a principle component analysis. The Louvain algorithy was used to cluster cells by the top 25 PCs and Uniform Manifold Approximation and Projection (UMAP) was used to visualize cell clusters.
Assembly: GRCm39
Supplementary files format and content: All processed data files are in .mtx format

source_name: B16-F1-OVA tumor

growth_protocol: B16-F1-OVA tumor cells (doi: 10.4049/jimmunol.177.9.6081) (4 x 10E5) in 200 uL phosphate-buffered saline were intraperitoneally injected into Cxcl13-cre-tdTomato (doi: 10.1016/j.immuni.2017.05.008) X R26R-eGFPflox (B6;129-Gt(ROSA)26Sortm2Sho/J)  mice and allowed to establish for 14 days prior to harvest.

extract_protocol:
Resected tumors were collected in RPMI-1640 (Corning) supplemented with 2% FBS (Sigma), 15 mM HEPES, 2 mM L-glutamine, 1 mM sodium pyruvate, 1X essential and non-essential amino acids, gentamicin (all from Gibco), transferred into RPMI-1640 containing 0.4 mg/ml collagenase II (Fisher/Worthington), 0.1 mg/ ml collagenase-dispase, and 50 ug/mL DNase I, minced into small fragments with scissors, and digested for 40 min at 37ºC. Digested cell suspensions were homogenized, filtered through 70 um mesh (Miltenyi Biotec) and depleted of red blood cells with Red Blood Cell Lysing Buffer Hybri-Max at RT for 10 min. Cells were washed and stained with anti-CD16/CD32 and biotinylated anti-PDPN for 1 hour in Awesome MACS buffer (PBS containing 0.5% BSA [Sigma Aldrich], 20mM EDTA [Fisher], 2.5mM dextrose [Sigma Aldrich], 2 mM L-glutamine, 1 mM sodium pyruvate, and 1X essential and non-essential amino acids). Podoplanin+ cells were enriched using anti-biotin magnetic beads on LS-MACS manual columns (Miltenyi Biotec), and stained with anti-CD45 (Biolegend), anti-CD31 (eBio), and anti-podoplanin (Biolegend) in Awesome MACS buffer for 30 min. After staining cells were resuspended in Awesome MACS containing DAPI (0.2 µg/ml) and sorted as described below.  Cells were sorted using a BD Influx System (Becton Dickinson) into BSA-pretreated Eppendorf tubes containing 4% ultra-pure BSA (Sigma) in PBS. CD45neg CD31neg podoplaninhi cancer associated fibroblasts were sorted into tdTomatoneg eGFPneg, tdTomato+ eGFPneg, tdTomato+ eGFP+, and tdTomatoneg eGFP+ subpopulations. Viable cells were enumerated using a Cell Drop instrument (Denovix). Live sorted subpopulations were processed for RNA extraction and indexed libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit.  Single cells were processed using the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) to the vendor’ specifications. Illumina NextSeq 2000 were used to sequence the bulk and single cel libraires according to validated standard operating procedures established by the University of Virginia Genome Analysis and Technology Core, RRID:SCR_018883.
Live sorted subpopulations were processed for RNA extraction and indexed libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit.  Single cells were processed using the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) to the vendor’ specifications. Illumina NextSeq 2000 were used to sequence the single cell libraires according to validated standard operating procedures established by the University of Virginia Genome Analysis and Technology Core, RRID:SCR_018883.

tag: host strain

value: B16-F1-OVA tumor

value: Fibroblast


title: C1_Ctrl+Veh_Rep3

description:
Library name: 25094R-01-03v1
25094R.01.03v1

value: Ctrl+Veh


title: 11362 donor, 4 Week old R406W neurons treated with Anastrozole, replicate3

description: Library name: 11362-Anast-3


title: GFP_pos/Tdtomato_pos CAFs

description: Library name: file3


title: C1_Ctrl+Veh_Rep2

description:
Library name: 25094R-01-02v1
25094R.01.02v1


title: 11362 donor, 4 Week old R406W neurons treated with Anastrozole, replicate2

description: Library name: 11362-Anast-2


title: GFP_neg/Tdtomato_pos CAFs

description: Library name: file2


title: C1_Ctrl+Veh_Rep1

description:
Library name: 25094R-01-01v1
25094R.01.01v1


title: 11362 donor, 4 Week old R406W neurons treated with Anastrozole, replicate1

description: Library name: 11362-Anast-1


title: GFP_pos/Tdtomato_neg CAFs

description: Library name: file1


title: Late 2C STARR input

status: Public on Jul 19 2026

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

description:
Library name: L2C_STARR_input
L2C-embryo-STARR.xlsx

data_processing:
*library strategy: STARR-seq
2CLC STARRseq: The raw reads of STARR-seq and input were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were aligned to the mouse mm10 genome using bowtie2 with the options: -p 48 --very-sensitive --end-to-end --no-unal --phred33 -X 2000’. Alignment bam files were transformed into read coverage files (bigwig format) using deepTools with the RPKM normalization method. Genome coverage was computed with deeptools using the pybigwig function. Enriched genomic peaks were called using a 500bp sliding window algorithm, with a sliding step of 250 bp, using custom scripts. For every 500bp window in the genome, the number of reads falling in that window for a given sample (normalized by RPKM method) was divided by the number of reads in that window for the corresponding input file (also normalized by RPKM method). Enriched regions were initially formed by taking all 500bp windows whose signal-over-input value exceeds a 2-fold threshold. Finally, any remaining overlaps among regions were merged, to produce the final peak calls.
Late 2C STARRseq: We constructed a genome containing only our target sequences of interest. Then we mapped the cleaned sequencing data back to this reference genome using Bowtie2. Samtools was used to count the number of sequencing reads mapped to each reference sequence.
Assembly: mm10
Supplementary files format and content: bigwig, normalized counts matrix

source_name: embryo

extract_protocol:
The polyadenylated mRNAs were captured using the Magnetic mRNA Isolation Kit (S1550S, NEB)
STARR-seq libraries were constrcted using the published UMI-STARR-seq protocol

value: embryo

value: late 2cell


title: Late 2C STARR rep2

description:
Library name: L2C_STARR_rep2
L2C-embryo-STARR.xlsx


title: 2C like cells STARR rep2

description: Library name: 2CLC_STARR_rep2

source_name: DUX-induced E14Tg2a

value: DUX-induced E14Tg2a

value: DUX-induced 2CLCs


title: 2C like cells  STARR rep1 [2C_1_S6_L004]

description: Library name: 2C like cells  STARR rep1 [2C_1_S6_L004]


title: C407, scRNA-seq

city: Bunkyo-ku

first: Akiyasu

last: Iwase

state: Tokyo

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description:
Fluidigm C1
C407

data_processing:
Sequence reads from fastq files were mapped by HISAT2 version 2.1.0. Gene expression counts were calculated with the featureCounts function from the Rsubread version 1.34.7 package using R
Assembly: mm10
Supplementary files format and content: Fluidigm_raw_counts.txt. Tab-separated matrix files include raw counts for each single-cell
Supplementary files format and content: Fluidigm_SCT_counts.txt. Tab-separated matrix files include normalized counts by SCTransform from Seurat for each single-cell

source_name: heart

extract_protocol:
Cardiac NCCs labeled by Wnt1-Cre; R26-EYFP mice at E11.5, 12.5, 14.5 and 17.5 around sub-region of aorticopulmonary septum were dissociated by using 0.25 w/v% trypsin / 1 mmol/L EDTA・4Na solution (Wako) at 37 °C, 15 minutes. Enzymes were neutralized with equal volume of DMEM (Wako) with 10% fetal bovine serum (FBS) (SIGMA). Cell suspensions were filtered through a 35 μm nylon mesh cell strainer（FALCON 352235.  Cells were kept on ice until cell sorting. Cell sorting was performed in a fluorescence-activated cell sorting (FACS) AriaⅡcell sorter (BD Biosciences).
EYFP-positive single cells were captured on the Fluidigm C1 Medium-cell (10-17 μm cell diameter) integrated fluidic circuit (IFC) for single cell cDNA libraries for mRNA sequencing. EYFP-positive cells were loaded on the IFC chips at concentration of 300 cells per μL. All captured cells were photographed to check whether cells were truly EYFP-positive and were dissociated for single cells by using KEYENCE BZ-X710. Single cell cDNAs were prepared on Fluidigm C1 system by using SMARTer v4 Ultra Input Low RNA kit for the Fluidigm C1 System (Clontech). Only single cell cDNAs confirmed by imaging data were performed quality check (QC) by using Agilent 2200 TapeStation system and quantified by Qubit (Thermo Fisher). High quality cDNAs were further constructed sequencing libraries by using Nextera XT DNA Sample Preparation Kit (Illumina). Each single cell cDNAs were sequenced 50 pair-end on the Illumina HiSeq 2500.

value: heart

value: Wnt1-Cre; R26-EYFP


title: NK92MI, DMSO treated rep3

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

description:
Library name: DMSO-3
Count.Human.txt

data_processing:
Raw RNA-seq data were preprocessed using fastp (v0.23.4), an ultra-fast all-in-one FASTQ preprocessor, with default parameters to ensure high-quality reads. Processed reads were then aligned to the GRCm38/mm10 (for mouse) or GRCh38/hg38 (for human) reference genome using STAR (v2.7.11b), allowing a maximum of 2 mismatches per read alignment. Gene-level quantification was performed using HTSeq (v2.0.3) to generate raw read counts. Differentially expressed genes (DEGs) were identified using DESeq2 R package with the following thresholds: absolute log₂ fold change (|log₂FC|) > 0.5 and Benjamini-Hochberg (BH)-adjusted P value < 0.01.
Assembly: GRCh38/hg38 for Homo sapiens GRCm38/mm10 for Mus musculus
Supplementary files format and content: text format of the raw read count for each gene

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.


title: 2C like cells STARR input

description: Library name: 2CLC_STARR_input


title: GFP positive p300

description:
Library name: p300_GFPpos
ChIP-seq for p300 (EP300) in DUX-induced 2C-like cells

data_processing:
Raw reads were demultiplexed and converted to FASTQ format.
Reads were trimmed for adapter and low-quality sequences, then aligned to the mouse mm10 (GRCm38) reference genome using Bowtie2.
Assembly: mm10
Supplementary files format and content: bigWig files containing normalized ChIP-seq read coverage (reads per million, RPM) across the mm10 genome for each sample.

extract_protocol:
ChIP-seq libraries were constrcted using the published ULI-NChIP-seq protocol
ChIP-seq libraries were constrcted using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645S, NEB) and the NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (E7335S, NEB)


title: GFP negative p300

description:
Library name: p300_GFPneg
ChIP-seq for p300 (EP300) in GFP-negative mESCs

value: mESC


title: RECQL4-deficient, Cyclin E overexpression, 3 Gy

city: Kitakyushu

first: Masaoki

last: Kohzaki

state: Fukuoka

address: 1-1 Iseigaoka Yahatanishi-ku

department: Institute of Industrial Ecological Sciences

institute: University of Occupational and Environmental Health, Japan

description:
Affymetrix CytoScan HD Array
RecQL4_3Gy_CyclinE_OE_clone2_151201

hyb_protocol: Genomic DNA was processed and hybridized to the Affymetrix CytoScan HD Array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the GeneChip Scanner according to the manufacturer's recommendations.

data_processing:
The original experiments were analyzed using an earlier version of Chromosome Analysis Suite (ChAS). For GEO submission, archived CEL files were reprocessed using ChAS version 4.5 to generate CYCHP files. Copy number analysis was performed using the hg19 (GRCh37) human reference genome.
Primary data consist of raw CEL files generated using the Affymetrix CytoScan HD Array. Processed CYCHP files were generated using Chromosome Analysis Suite (ChAS) version 4.5.

source_name: RECQL4-deficient U2OS cells

label_protocol: Genomic DNA labeling was performed according to the manufacturer's protocol for the Affymetrix CytoScan HD Array.

growth_protocol: U2OS cells (WT and RECQL4-deficient) were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol: Genomic DNA was extracted from cultured U2OS cells using standard procedures.

treatment_protocol: WT and RECQL4-deficient U2OS cells carrying a Tet-off Cyclin E expression construct were cultured under non-induced (NE) or Cyclin E-overexpressing (OE) conditions. Cells were exposed or not exposed to 3 Gy ionizing radiation prior to genomic DNA extraction.

tag: irradiation

value: 3 Gy

tag: cyclin e induction

value: Cyclin E induction


title: Parse sublibrary 2

city: Odense M

first: Xuan

last: Wang

address: Munkebjergvænget 14, Thriges Kollegium Edison A

department: IMM

country: Denmark

institute: University of Southern Denmark

description: Library name: Sample2

data_processing:
FASTQ files were processed using the Trailmakers pipeline (Parse Biosciences), which includes demultiplexing, read alignment, and generation of gene-cell count matrices. Reads were mapped to the GRCm38 (mm10) mouse reference genome.
Downstream analysis was performed in R using the Seurat package (v4.0). Mitochondrial genes are used to calculate the mitochondrial concentration, cells which has 10% more mitochondrial genes are moved and the poor quality cells (less than 100 genes expressed) and poor quality genes (present in less than 3 cells) are removed from the quality control stages. Cell type annotation was performed based on the expression of established marker genes for the major cortical population. Developmental trajectory inference was performed using CytoTRACE v2 which estimates differentiation states and reconstructs lineage trajectories
Assembly: mm10
Supplementary files format and content: unfiltered 10x input for scanpy or Seurat

source_name: mouse cortex

extract_protocol:
Plugged C57BL/6J females were purchased from Janvier Labs and E0.5 was defined as the morning on which the vaginal plug appeared. Mice were subjected to in utero electroporation and embryos harvested as previously described41. Electroporation was performed using the pCAG-mScarlet-3XFlag vector encoding for Nfib-WT, Nfib-S265A, Hmgn3-WT, Hmgn3-S78A, and an empty vector served as a control. In brief, plasmids were prepped using an NncleoBond Xtra Maxi Endotoxin-free Plasmid maxi kit (Cat no: 740424.10) and plasmid concentration adjusted to 1.5 μg/μl. Pregnant mice were anaesthetised with isofluorane at E13.5 and ∼1.5 μl of plasmid solution was injected into the ventricle of embryonic brains. The plasmids were electroporated into the dorsal ventricular zone with six pulses of 30 V, 50 ms each at 1 s interval delivered through platinum electrodes using round electrodes CUY650P5 and Nepa Gene electroporator (NEPA21 Type II). After four days of electrophoration (E17.5), the brain tissues were processed for the analyses. For the isolation of electroporated cells from E17.5, the dorsolateral neocortex was dissected, and a single cell suspension was produced from two to three hemispheres per condition using the MACS Neural Tissue Dissociation kit containing papain (Miltenyi Biotec, 130-092-628). The cells were resuspended to 1 million cells/ml in FACS buffer (3%BSA, 1mM EDTA in HBSS w/o Ca2+ and Mg2+), passed through a 40-μm filter and immediately processed by FACS on a five-laser Invitrogen BIGFOOT cell sorter. For each condition, 30,000 to 100,000 cells were collected in 1.5 mL DNA LoBind tubes containing FACS buffer. scRNA-seq libraries were generated according to Parse Biosciences protocols: Evercode Cell Fixation v3 and Evercode WT Mini v3. For cell fixation, FACS sorted single cell suspensions were centrifuged for 10 min at 200g at 4°C in 15-ml BSA-coated Falcon tubes and resuspended in Cell Prefixation Buffer with BSA 7.5% (Gibco) in 15-ml BSA-coated Falcon tubes. Cell suspensions were incubated in fixation solution followed by the addition of permeabilization solution and stop buffer, according to the manufacturer’s instructions. Cell suspensions were frozen using a Mr. Frosty Freezing container (Sigma-Aldrich) at −80°C until further use. Samples barcoding and sub-libraries were prepared using the Evercode WT Mini v3 as per the manufacturer's instructions and sequenced on a NovaSeq 6000 instrument.
Single-cell transcriptomic libraries were prepared using the Evercode WT Mini kit (Parse Biosciences, Chemistry v3) according to the manufacturer’s protocol. Sequencing was performed on two sublibraries

value: mouse cortex

value: neuron


title: 2C like cells  STARR rep1 [2C_1_S6_L002]

description: Library name: 2C like cells  STARR rep1 [2C_1_S6_L002]


title: Parse sublibrary 1

description: Library name: Sample1


title: neuron, E17.5_NFIB_WT_R2

description: Library name: Sample10

data_processing:
Cut&Run was performed on IUE FACS sorted cells to profile the genome-wide binding of Nfib wild-type (WT) and S265A mutant, Hmgn3-WT and S78A mutant. The experiment included two biological replicates for each condition and IgG served as a control. The sequencing reads were subjected to quality control using FastQC (v0.12.1) and adapter trimming with Cutadapt (v4.6). Reads were aligned to the mouse reference genome mm10 using Bowtie2 (v2.4.4), followed by duplicate removal and quality filtering using Picard (v3.1.0) and Samtools (v1.15.1). Peaks were called using MACS2 and  ChIPseeker was used for downstream genomic analysis and annotation. Signal tracks were generated using DeepTools (v3.5.1) for visualization.
Assembly: mm10
Supplementary files format and content: bigwig files for IGV
Library strategy: CUT&Run

extract_protocol:
Plugged C57BL/6J females were purchased from Janvier Labs and E0.5 was defined as the morning on which the vaginal plug appeared. Mice were subjected to in utero electroporation and embryos harvested as previously described41. Electroporation was performed using the pCAG-mScarlet-3XFlag vector encoding for Nfib-WT, Nfib-S265A, Hmgn3-WT, Hmgn3-S78A, and an empty vector served as a control. In brief, plasmids were prepped using an NncleoBond Xtra Maxi Endotoxin-free Plasmid maxi kit (Cat no: 740424.10) and plasmid concentration adjusted to 1.5 μg/μl. Pregnant mice were anaesthetised with isofluorane at E13.5 and ∼1.5 μl of plasmid solution was injected into the ventricle of embryonic brains. The plasmids were electroporated into the dorsal ventricular zone with six pulses of 30 V, 50 ms each at 1 s interval delivered through platinum electrodes using round electrodes CUY650P5 and Nepa Gene electroporator (NEPA21 Type II). After four days of electrophoration (E17.5), the brain tissues were processed for the analyses. For the isolation of electroporated cells from E17.5, the dorsolateral neocortex was dissected, and a single cell suspension was produced from two to three hemispheres per condition using the MACS Neural Tissue Dissociation kit containing papain (Miltenyi Biotec, 130-092-628). The cells were resuspended to 1 million cells/ml in FACS buffer (3%BSA, 1mM EDTA in HBSS w/o Ca2+ and Mg2+), passed through a 40-μm filter and immediately processed by FACS on a five-laser Invitrogen BIGFOOT cell sorter. For each condition, 30,000 to 100,000 cells were collected in 1.5 mL DNA LoBind tubes containing FACS buffer. scRNA-seq libraries were generated according to Parse Biosciences protocols: Evercode Cell Fixation v3 and Evercode WT Mini v3. For cell fixation, FACS sorted single cell suspensions were centrifuged for 10 min at 200g at 4°C in 15-ml BSA-coated Falcon tubes and resuspended in Cell Prefixation Buffer with BSA 7.5% (Gibco) in 15-ml BSA-coated Falcon tubes. Cell suspensions were incubated in fixation solution followed by the addition of permeabilization solution and stop buffer, according to the manufacturer’s instructions. Cell suspensions were frozen using a Mr. Frosty Freezing container (Sigma-Aldrich) at −80°C until further use. Samples barcoding and sub-libraries were prepared using the Evercode WT Mini v3 as per the manufacturer's instructions and sequenced on a NovaSeq 6000 instrument. CUT&RUN experiments were performed on E17.5 IUE sorted cells using specific antibodies for the following proteins: Flag (Sigma, M2 clone F1804), and normal IgG. Biological replicates were generated for all the CUT&RUN assays. Samples were prepared following the EpiCypher CUTANA ChIP/CUT&RUN Kit protocol (Epicypher, SKU: 14-1048). An IgG antibody served as a negative control to evaluate non-specific background signal from chromatin captured during immunoprecipitation, and an E. Coli spike-in control was added for normalizing enrichment during analysis. CUT&RUN libraries were prepared according to the CUTANA™ CUT&RUN Library Prep Kit (Epicypher) for Illumina, and each sample was uniquely barcoded with the Multiplex Oligos for Illumina. Libraries were pooled and sequenced using 75 base pair paired-end reads on the NovaSeq 6000 platform, obtaining a sequencing depth of at least 10 million reads per sample.
CUT&RUN libraries were prepared according to the CUTANA™ CUT&RUN Library Prep Kit (Epicypher) for Illumina, and each sample was uniquely barcoded with the Multiplex Oligos for Illumina. Libraries were pooled and sequenced using 75 base pair paired-end reads on the NovaSeq 6000 platform, obtaining a sequencing depth of at least 10 million reads per sample.

value: WT


title: Late 2C STARR rep1

description:
Library name: L2C_STARR_rep1
L2C-embryo-STARR.xlsx


title: neuron, E17.5_NFIB_WT_R1

description: Library name: Sample9


title: neuron, E17.5_NFIB_Mu_R2

description: Library name: Sample8


title: neuron, E17.5_NFIB_Mu_R1

description: Library name: Sample7


title: RECQL4-deficient, Cyclin E overexpression

description:
Affymetrix CytoScan HD Array
RecQL4_CyclinE_OE_clone2_151201

value: 0 Gy


title: neuron, E17.5_Hmgn3_WT_R1

description: Library name: Sample5


title: neuron, E17.5_Hmgn3_WT_R2

description: Library name: Sample6


title: RECQL4-deficient, Cyclin E not induced, 3 Gy

description:
Affymetrix CytoScan HD Array
RecQL4_3Gy_CyclinE_NE_clone2_151201

value: no


title: neuron, E17.5_Hmgn3_Mu_R2

description: Library name: Sample4


title: neuron, E17.5_Hmgn3_Mu_R1

description: Library name: Sample3


title: neuron, E17.5_phos_batch_igg_ctrl_R2

description: Library name: Sample2

value: empty vector


title: RECQL4-deficient, Cyclin E not induced

description:
Affymetrix CytoScan HD Array
RecQL4_CyclinE_NE_clone2_151201


title: neuron, E17.5_phos_batch_igg_ctrl_R1

description: Library name: Sample1


title: Donor 6 RINSC 0 Gy

city: Kingston

first: Michael

last: Antosh

state: RI

address: 2 Lippitt Rd

institute: University of Rhode Island

description: Library name: Sample 52

data_processing:
Alignment: HISAT2
Quality check: FastQC
Analysis: deseq2
Assembly: GRCh38 Reference Genome
Supplementary files format and content: normalized data,from deseq2 output (csv file)
Supplementary files format and content: read counts (csv file)

source_name: Whole blood

growth_protocol: Sampled from donors under IRB protocol IRB-AAAS5693 at Columbia University.

extract_protocol:
Blood samples preserved in PAXgene RNA stabilization reagent were sent to Azenta, where total RNA was extracted followed by globin reduction.
QIAGEN Fast Select rRNA HMR and Globin Kit, plus NEGNext Ultra II RNA Library preparation kit.  Note: sequencer model number listed may be incorrect.

treatment_protocol: Each sample was irradiated with 42% photons and 58% neutrons, at either the RINSC source or the RARAF source.

value: Whole blood

tag: irradiation site

value: RINSC

tag: radiation dose_(gy)

tag: age

value: Female


title: lncRNAseq GFP positive_rep3

description: Library name: lncRNAseq_GFPpos_rep3

data_processing:
The raw RNA-seq reads were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to the mouse Gencode (vM15) transcriptome with RSEM. Gene expression values were normalized across samples using the variance modeling tool DESeq2
Assembly: mm10
Supplementary files format and content: Tab-separated values files

extract_protocol:
Cellular total RNA was collected using a Trizol extraction method
RNA libraries were constrcted using the Illumina Ribo-Zero plus rRNA Depletion kit (20037135, Illumina)


title: lncRNAseq GFP positive_rep2

description: Library name: lncRNAseq_GFPpos_rep2


title: WT, Cyclin E overexpression, 3 Gy

description:
Affymetrix CytoScan HD Array
WT_3Gy_CyclinE_OE_clone2_151201

source_name: WT U2OS cells

tag: genotype


title: lncRNAseq GFP positive_rep1

description: Library name: lncRNAseq_GFPpos_rep1


title: lncRNAseq GFP negative_rep3

description: Library name: lncRNAseq_GFPneg_rep3


title: lncRNAseq GFP negative_rep2

description: Library name: lncRNAseq_GFPneg_rep2


title: RECQL4-deficient parental clone

description:
Affymetrix CytoScan HD Array
RecQL4_original_clone_151117