title: VSMC_sample_8_E47_KO

description: Library name: sample_8

data_processing:
Base calling and quality control performed by Novogene Inc. FastQC was used to assess quality. Reads were aligned to the murine genome GENCODE v49 GCh38 primary assembly using HISAT and reads counts were generated using Feature Counts
Assembly: GRCm38.99 (mm10) chr_patch_hapl_scaff gtf file
Supplementary files format and content: Raw read counts output from Feature counts.

source_name: Aorta

growth_protocol: Cells were revived from cryorecovery in TC-treated dishes.

extract_protocol:
Cells were lysed in cell culture plates with Trizol and RNA was manually extracted and resuspended in water and sent to Novogene Inc. for library prep.
Unstranded mRNAseq standard input Illumina polyA enrichment library prep

value: Aorta

value: Vascular Smooth Muscle Cells

value: E47 KO


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 24hr, rep3

status: Public on Jan 09 2026

type: SRA

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

country: USA

institute: Northwestern University

description:
Library name: RNA-seq_chromatin_Adult_30m-24hr_3
Adult_opto30m-24hr.bigwig

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to the mm10 reference genome with HISAT2 using the public server at https://usegalaxy.org/, normalized by library size, and visualized using bigwig files. Gene annotations were derived using GENCODE version M11. Differential gene expression analyses were performed using pair-wise negative binomial tests with edgeR and the false discovery rate (FDR) was calculated for all genes. Gene ontology analyses of differentially expressed genes were performed using DAVID (Dennis et al., 2003) Knowledgebase v2025_1 with a background of all H3K4me3-marked genes in the adult mouse cerebellum.
Assembly: mm10
Supplementary files format and content: bigwig files

molecule: nuclear RNA

organism: Mus musculus

source_name: anterior dorsal cerebellar vermis

extract_protocol:
For NEUROD1/2 knockout mice, cerebella were removed, microdissected, and total RNA from ADCV was extracted with Trizol. For optostimulation, the medial part of the ADCV was homogenized and spun down. The supernatant was removed and the RNA in the pellet representing the chromatin fraction was extracted with Trizol. Purified RNA was treated with NEBNext rRNA depletion kit  (#E6310).
RNA libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (#E7760).

treatment_protocol: For AAV injection, 0.5 µl of AAV9-gRNA-mCherry (titer 1x10^13vg/ml) was delivered to the ADCV using a fine glass pipette connected to a microinjector system (Nanoinject II, Drummond) and mounted in the stereotaxic frame (Stoelting). Optogenetic stimulation of ADCV granule neurons was performed using a 450nm diode blue laser (Opto Engine, 200mW) coupled to a multimode fiber cable (Oz Optics) with 68 mW of power at the tip of the fiber delivered through a fiber optic cannula. Each 100 ms optogenetic stimulus was composed of a 50 Hz train of 10 ms pulses and was delivered at 30 second intervals. Animals were stimulated over a 10 minute period, or over a 30 minute period and returned to their homecage.

tag: tissue

value: anterior dorsal cerebellar vermis

tag: cell type

value: cerebellar cells

tag: genotype

value: Math1-Cre; ChR2YFP-GN

tag: treatment

value: optostimulation 30 minutes, return to homecage 1 day


title: VSMC_sample_5_E47_WT

city: Charlottesville

first: Brett

middle: P

last: Ransegnola

state: VA

address: 755 Walker Square, Apt 2D

institute: UVA SOM

description: Library name: sample_5

molecule: total RNA

value: E47 WT


title: VSMC_sample_6_E47_WT

description: Library name: sample_6


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep27

description:
Library name: RNA-seq_chromatin_Adult_homecage_27
Adult_home_set7.bigwig

value: home cage control


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep25

description:
Library name: RNA-seq_chromatin_Adult_homecage_25
Adult_home_set7.bigwig


title: VSMC_sample_3_E12_KO

description: Library name: sample_3

value: E12 KO


title: SMARCA4_PROTAC2.bio2.tech3

city: Cambridge

first: Xuan

last: He

address: Lensfield Road

department: Chemistry

country: United Kingdom

institute: University of Cambridge

description: Library name: SMARCA4_PROTAC2.bio2.tech3

library_source: genomic

data_processing:
Reads from each sample were trimmed using fastp (version 0.23.4)  with a quality threshold of 25 (-q 25). The trimmed reads were aligned to the reference genome hg38 using Bowtie2 (version 2.5.2)  with the options --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 1500. Duplicates were marked using MarkDuplicates from Picard (version 3.1.0)  and subsequently removed with SAMtools (version 1.18)  using the -F 1804 option. Reads mapped to mitochondrial DNA were also removed. To visualize the aligned profiles, bamCoverage from deepTools (version 3.5.5)  was used to generate bigWig files from the alignments with options: -bs 10 --normalizeUsing CPM --effectiveGenomeSize 2913022398 --extendReads --minFragmentLength 10 --maxFragmentLength 1000.
Assembly: hg38
Supplementary files format and content: bigwig files for mapping profiles visualization

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human osteosarcoma U2OS cells (ATCC, HTB-96) were cultured in phenol red-free Dulbecco’s modified Eagle medium (DMEM) (high glucose and l-glutamine plus, Gibco, catalogue number 21063045) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Gibco, catalogue number 10082147) and 1 mM sodium pyruvate. This formulation is hereafter referred to as full-growth DMEM. Cells were incubated at 37 °C in a humidified atmosphere containing 5% CO₂ and were passaged at least twice following thawing before experimental use.

extract_protocol:
The CUT&Tag protocol was adapted from previously described procedures. U2OS cells were cultured to 70–80% confluence and treated with 2 μM of G4L-PROTAC for 6 h before harvesting. To facilitate cellular uptake of the compound, 6 μL of Endo-Porter (Endo-Porter PEG: 1 mM Endo-Porter in 10% polyethylene glycol, 1500 MW, aqueous) was added per 1 mL of culture medium together with G4L-PROTAC. Then the cells were detached using Accutase (Gibco, Cat. No. A1110501), quenched with full-growth DMEM, and centrifuged at 200 × g for 5 minutes. The resulting cell pellets were fixed in 0.1% (w/v) formaldehyde in PBS for 2 minutes at room temperature and quenched with 110 mM glycine. Cells were then centrifuged at 300 × g for 5 minutes at 4 °C, washed, and resuspended in cold wash buffer (20 mM HEPES, pH 7.5, 150 mM KCl, 0.5 mM spermidine, cOmplete EDTA-free protease inhibitor cocktail, Roche, Cat. No. 11836170001). Cells were either used immediately or cryopreserved in wash buffer supplemented with 10% DMSO at −80 °C. A final cell concentration of 6 million cells per ml was used for subsequent steps. Concanavalin A beads (15 μl per sample; Bangs Laboratories, Cat. No. BP531) were washed twice with binding buffer (20 mM HEPES, pH 7.5, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂) and resuspended in 10 μl of the same buffer. A 100 μl suspension of cells was combined with 10 μl of pre-washed beads in 0.2 ml PCR tubes and mixed on an Intelli Mixer RM-2M (ELMI) using mode C3 (cycle: 6 s at 108°, 6 s at 252°, 12 s pause) at 20 rpm for 10 minutes at room temperature. Bead-bound cells were gently washed twice with 100 μl wash buffer using a magnetic stand and resuspended in 100 μl of a 1:100 diluted 1st antibody solution. Control samples without 1st antibody were included. The incubations were carried out on the same mixer at 4 ℃ overnight. To remove unbound 1st antibodies, cells were washed three times with 200 μl of Dig-wash buffer (wash buffer with 0.05% digitonin), followed by incubation with 100 μl of guinea pig anti-rabbit IgG secondary antibody (antibodies-online, Cat. No. ABIN101961) diluted 1:100 in Dig-wash buffer for 1 hour at room temperature on the mixer. The pA-Tn5 adapter complex (2 μM) was prepared as previously described and diluted 1:200 in Dig-300 buffer (20 mM HEPES, pH 7.5, 300 mM KCl, 0.5 mM spermidine, 0.01% digitonin, protease inhibitors) . Cells were washed three times with 200 μl Dig-wash buffer to remove excess antibodies before being incubated with 100 μl of pA-Tn5 complex for 1 hour on the mixer at room temperature. Subsequently, cells were washed three times in 200 μl Dig-300 buffer to eliminate unbound pA-Tn5 and resuspended in 200 μl of tagmentation buffer (Dig-300 with 10 mM MgCl₂) for 1 hour at 37 °C on the mixers. After tagmentation, cells were washed twice in 200 μl TAPS buffer (10 mM TAPS, 0.2 mM EDTA), then resuspended in 100 μl extraction buffer (10 mM Tris-HCl, pH 8.0, 0.5 mg/ml proteinase K [Thermo Scientific, Cat. No. EO0491], 0.5% SDS). Samples were incubated at 55 °C for 1.5 hours at 800 rpm. DNA was purified using the DNA Clean & Concentrator-5 kit (Zymo Research, Cat. No. D4013) and eluted in 25 μl elution buffer following a 10-minute incubation at room temperature.
For library amplification, 21 μl of tagmented DNA was combined with 2 μl each of uniquely barcoded v2 Ad1.x and Ad2.x primers (10 μM each) , and 25 μl of NEBNext Ultra II Q5 2× PCR Master Mix (New England Biolabs, Cat. No. M0544). PCR cycling conditions were: 72 °C for 5 min; 98 °C for 30 s; followed by 10 cycles of 98 °C for 10 s and 63 °C for 10 s; and a final extension at 72 °C for 1 min. Libraries were purified with 1.3× volume (65 μl) of Ampure XP beads (Beckman Coulter, Cat. No. A63882), incubated at room temperature for 10 min, and washed twice with 80% ethanol. DNA was eluted in 25 μl of 10 mM Tris-HCl (pH 8.0). Library size distribution was verified using the TapeStation with High Sensitivity D1000 ScreenTape (Agilent, Cat. No. 5067-5584), and concentrations were quantified using the NEBNext Library Quant Kit (New England Biolabs, Cat. No. E7630L). Pooled libraries were size-selected by adding 0.4× volume Ampure XP beads, transferring the supernatant to a new tube, then adding 1.3× volume Ampure XP beads for final cleanup. Beads were washed twice with 80% ethanol and DNA was eluted in 30 μl of 10 mM Tris-HCl, pH 8.0. Sequencing was performed on an Illumina NextSeq 2000 using the NextSeq 1000/2000 P2 reagent kit (100 cycles, Cat. No. 20046811). Experiments were carried out in two biological replicates with two technical replicates each.

tag: cell line

value: WT


title: SMARCA4_PROTAC2.bio2.tech2

description: Library name: SMARCA4_PROTAC2.bio2.tech2

treatment_protocol: U2OS cells were cultured to 70–80% confluence and treated with 2 μM of G4L-PROTAC for 6 h before harvesting. To facilitate cellular uptake of the compound, 6 μL of Endo-Porter (Endo-Porter PEG: 1 mM Endo-Porter in 10% polyethylene glycol, 1500 MW, aqueous) was added per 1 mL of culture medium together with G4L-PROTAC.


title: VSMC_sample_7_E47_KO

description: Library name: sample_7


title: VSMC_sample_4_E12_KO

description: Library name: sample_4


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep24

description:
Library name: RNA-seq_chromatin_Adult_homecage_24
Adult_home_set7.bigwig


title: VSMC_sample_1_E12_WT

description: Library name: sample_1

value: E12 WT


title: SMARCA4_PROTAC2.bio1.tech2

description: Library name: SMARCA4_PROTAC2.bio1.tech2


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep23

description:
Library name: RNA-seq_chromatin_Adult_homecage_23
Adult_home_set7.bigwig


title: SMARCA4_PROTAC2.bio2.tech1

description: Library name: SMARCA4_PROTAC2.bio2.tech1


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep26

description:
Library name: RNA-seq_chromatin_Adult_homecage_26
Adult_home_set7.bigwig


title: Sample3, Nulliparous, scRNAseq

city: Santa Cruz

first: Paloma

last: Medina

state: CA

address: 1156 High St.

institute: University of California Santa Cruz

description:
Library name: Sample 3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the mouse genome (mm10). Additionally, we integrated an 18m NP data set from Tabula Muris Senis. For quality control, we used Scanpy’s ‘scanpy.pp.calculate_qc_metrics’, ‘scanpy.pp.filter_genes’, and scanpy.pp.filter_cells.  We applied filters to eliminate (1) genes that are detected in less than 3 cells, (2) cells that have less than 200 genes, (3) cells with gene counts < 600 or > 8,000, (4) cells with total counts of UMIs per cell < 2,000 or > 12,000, and (5) cells with mitochondrial gene ratio > 1.5%. The mitochondrial gene ratio was defined as the percentage of UMIs mapped to mitochondrial genes compared to non-mitochondrial genes within each cell; cells with a high ratio are indicative of non-viable or apoptotic cells. Doublets were identified using Scrublet and these cells were then filtered out. After filtering, the datasets were concatenated, the UMI counts for each cell were then normalized using a target sum of 1e4, and then log transformed using ‘scanpy.pp.log1p’, which computes X=log(X+1), where log denotes the natural logarithm.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Mammary Gland

extract_protocol:
L2-5 and R2-5 mammary glands were harvested, minced, and chemically digested overnight in Advanced DMEM F/12 with 1% PSA, gentle collagenase/hyaluronidase, and DNAse I at 37C, 5% CO2, and added humidity. Partially digested glands were then mechanically digested by pipetting with a serological pipette until no tissue pieces were visible. Digested glands were washed with staining buffer (Hank’s Balanced Salt Solution, 2% Bovine Calf Serum, 1% PSA) and centrifuged (1500RPM) at 4C for 5 minutes. Red blood cells were lysed with 5mL of ACK Lysis buffer for 5 minutes, and cells were washed with 15mL of staining buffer. Cells were treated with 0.25% Trypsin with EDTA and gently pipetted continuously for 2-3 minutes to digest the basement membrane. Cells were then treated with DNAse I and Dispase and pipetted continuously for 2-3 minutes to prevent clumping. The single-cell suspension was then filtered through a 40um mesh strainer and pelleted via centrifugation (1500RPM, 4C, 5 minutes).
We performed scRNA-seq from mammary glands of 18m NP and 18m P mice using 10x chromium scRNA-seq (n=3 mice/group) as per manufacture’s protocol using the 5’ Gene expression workflow. Libraries were sequenced on the Illumina NovoSeq 6000 Platform by Medgenome, Inc.

value: Mammary Gland

value: C57Bl/6 WT


title: SMARCA4_PROTAC2.bio1.tech1

description: Library name: SMARCA4_PROTAC2.bio1.tech1


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 12hr, rep4

description:
Library name: RNA-seq_chromatin_Adult_30m-12hr_4
Adult_opto30m-12hr.bigwig

value: optostimulation 30 minutes, return to homecage 12 hours


title: mESC, EED rescue 24h, WT background, HA-EED ChIP, Rep1

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

description: Library name: ChIPseq_HAEED_EEDrescue_WT_24h_Rep1

data_processing:
Sequenced reads from experiments were mapped with Bowtie2 using default parameters.
SAM and BAM files were cleaned up and sorted using samtools and bedtools. Duplicates were marked using picard tool.
Bigwig files and heatmap were generated using deeptools.
Peaks were called using MACS3.
Assembly: mm10, dm6
Supplementary files format and content: bigwig, broadpeak

source_name: E14 mESC

growth_protocol: Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), l-glutamine, penicillin-streptomycin, nonessential amino acids, 0.1 mM β mercaptoethanol, leukemia inhibitory factor, and 2i inhibitors, which include 1 μM mitogen-activated protein kinase kinase 1/2 inhibitor (PD0325901) and 3 μM glycogen synthase kinase 3 inhibitor (CHIR99021) on 0.1% gelatin-coated plates, grown in 37 degree and 5% CO2.

extract_protocol:
Cells were fixed with 1% Formaldehyde. After qenching and cell lysis, chromatin was sonicated using Diagenode bioruptor.
Libraries for ChIP-seq were prepared according to manufacturer's instructions (Illumina). Briefly, IP'ed DNA (∼5 ng) was end-repaired using End-It Repair Kit (Epicenter), tailed with deoxyadenine using Klenow exo− (New England Biolabs), and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-400bp were size selected using Agencourt AMPure XP beads, and subjected to PCR amplification using Q5 DNA polymerase (New England Biolabs).

treatment_protocol: 4-Hydroxytamoxifen treatment for 0 or 24 hr

value: E14 mESC

value: HA-EED rescue, WT background

value: 4-Hydroxytamoxifen treatment for 24h


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 12hr, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-12hr_2
Adult_opto30m-12hr.bigwig


title: mESC, EED rescue 24h, WT background, H3K27me3 ChIP, Rep1

description: Library name: ChIPseq_H3K27me3_EEDrescue_WT_24h_Rep1


title: SMARCA4_PROTAC1.bio2.tech2

description: Library name: SMARCA4_PROTAC1.bio2.tech2


title: VSMC_sample_2_E12_WT

description: Library name: sample_2

value: Aorta

value: Vascular Smooth Muscle Cells


title: Late-tumor 3

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

description:
Library name: L-R2L2
10X Genomics

data_processing:
demultiplexing, barcoded processing, gene counting were done using 10X cellranger tools v8.0.1
Assembly: mouse mm39
Supplementary files format and content: tab delimited barcode, features, and matrix files

source_name: brain

extract_protocol:
steps to extract nuclei followed a slightly modified version of the 10X nuclei isolation kit (cat# 1000493) protocol for gene expression libraries. The frozen tissue was dissociated in lysis buffer and filtered. At the debris removal step, we replaced the 10X kit solution with Miltenyi’s debris removal solution (cat# 130-109-398) and followed Miltenyi’s protocol.  After debris removal, the nuclei were resuspended in 0.1% BSA in PBS and continued following the 10X nuclei isolation kit protocol. Nuclei yield ranged from 5,000-20,000/mg.
After nuclei extraction, the purified nuclei were transported to the CUNY ASRC’s epigenetics core at a concentration of 10e6/mL for 10X 3’ Gene Expression library preparation (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268). Samples were sequenced with a target of 10,000 nuclei per sample and 40,000 reads per nuclei a Novaseq 6000 sequencer

value: brain


title: SMARCA4_PROTAC1.bio2.tech3

description: Library name: SMARCA4_PROTAC1.bio2.tech3


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 12hr, rep3

description:
Library name: RNA-seq_chromatin_Adult_30m-12hr_3
Adult_opto30m-12hr.bigwig

value: anterior dorsal cerebellar vermis

value: cerebellar cells


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 12hr, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-12hr_1
Adult_opto30m-12hr.bigwig

value: Math1-Cre; ChR2YFP-GN


title: Late-tumor 1

description:
Library name: L-L3
10X Genomics


title: Sox10 cKO skin wound 3, Day 4 following injury

city: Zurich

first: Adrian

last: Salas-Bastos

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description:
Library name: Sox10 cKO wound 3
10x Genomics

data_processing:
scRNAseq CTL and Sox10 cKO wounds: FASTQ files were mapped against a customized Mus musculus genome annotation file (GRCm39 assembly, release M26 [2021-04-20]), plus the transgenes tdTomato using 10x Genomics Cell Ranger (version  6.0.2) with default parameters. Count matrices were imported into R (version 4.0.2) using the Bioconductor package, DropletUtils (version 1.18.1) and combined in a SingleCellExperiment object using the SingleCellExperiment package (version 1.10.1). Cells filtering was performed with the scater package by applying sample specific thresholds after exploratory analysis. More specifically, cells with more than 300 features, and mitochondrial percentage lower than 10-20% were kept. Doublet cells were removed with scDblFinder (version 1.12.0). Cells passing the filters were kept in the SingleCellExperiment object and subsequently converted into the anndata format using the zellkonverter package (version 1.16.0). The filtered count matrix stored in the object was used as input for scvi tools algorithm (version 1.2.2.post2), for normalization, batch correction and data denoising. Cluster partitions were computed by leiden algorithm using scanpy.tl.leiden function from the scanpy package (version 1.10.4). Further downstream analyses were performed in R using as input the denoised expression data.
Assembly: customized Mus musculus genome annotation file (GRCm39 assembly, release M26 [2021-04-20]), plus the transgenes tdTomato
Supplementary files format and content: The processed files are compressed .tar.gz files containing a subfolder with the barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files for each sample

source_name: Regenerating skin wound

extract_protocol:
One skin wound was processed per sample. Skin tissue was minced into small pieces, then digested with 10 ml of DMEM/F12 containing 1.5 mg/ml collagenase I, 10% FBS for 2 hours at 37°C with agitation. Samples were centrifuged, and the cell-containing supernatant was passed through a 40-μm cell strainer and set aside on ice. The remaining skin pieces were further digested with 2 ml DMEM/F12 containing 0.025% Trypsin-EDTA  and 2 mM EDTA for 5 minutes at 37°C with agitation. Trypsin was inactivated and the remaining skin pieces were passed three times through an 18G needle and five times through a 21G needle. The digested skin suspension was then filtered through a 40-μm cell strainer and combined with the previously obtained cell suspension that was kept on ice. Samples were washed once with HBSS, centrifuged, and resuspended in DMEM/F12 medium containing 10% FBS, 1% Penicillin-Streptomycin, and 1:1000 Protector RNase Inhibitor. Debris and cell clumps were filtered out manually using 40-μm mesh filters. Dead cells were then removed with EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, #17899), according to manufacturer’s instructions.
Single cell libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics). 7000 cells per sample were targeted for capture. Each library was sequenced on the Illumina NovaSeq 6000 platform to achieve approximately 50000 reads per cell.

treatment_protocol: Tmx induced loss of Sox10 in peripheral glial cells (Sox10  cKO samples). Four circular full-thickness excisional wounds of 5 mm of diameter were generated on the lower back skin of each animal, two on each side, 1 cm of the midline of the animal and roughly 2 cm apart from each other.

value: Regenerating skin wound

value: 8-10 weeks old

value: female

value: Sox10 cKO

tag: batch

value: C


title: Sox10 cKO skin wound 2, Day 4 following injury

description:
Library name: Sox10 cKO wound 2
10x Genomics

value: B


title: Sox10 cKO skin wound 1, Day 4 following injury

description:
Library name: Sox10 cKO wound 1
10x Genomics

value: A


title: Late-tumor 2

description:
Library name: L-L5
10X Genomics


title: Early-tumor  3

description:
Library name: E-R2L5
10X Genomics


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep20

description:
Library name: RNA-seq_chromatin_Adult_homecage_20
Adult_home_set6.bigwig

value: home cage control


title: CTL skin wound 3, Day 4 following injury

description:
Library name: CTL skin wound 3
10x Genomics

value: CTL


title: CTL skin wound 2, Day 4 following injury

description:
Library name: CTL skin wound 2
10x Genomics


title: Early-tumor  2

description:
Library name: E-R2L3
10X Genomics


title: SMARCA4_PROTAC1.bio2.tech1

description: Library name: SMARCA4_PROTAC1.bio2.tech1

value: WT


title: Early-tumor  1

description:
Library name: E-L2
10X Genomics


title: Sample14

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

description:
Library name: S14
10x Genomics 3' gene expression v3.1

data_processing:
Samples were demultixpled, aligned, and counted using CellRanger v8.0.1.
Assembly: Mmul10
Supplementary files format and content: Tab separated value files and matrix files

extract_protocol:
Fresh frozen tissue samples were homogenized and used to generate nuclei suspensions as detailed in accompanying manuscript.
Libraries were constructed using the manufacturer protocol for the 10x Genomics dual index 3' gene expression assay v3.1

value: SNI

value: 3 days


title: CTL skin wound 1, Day 4 following injury

description:
Library name: CTL skin wound 1
10x Genomics


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep22

description:
Library name: RNA-seq_chromatin_Adult_homecage_22
Adult_home_set6.bigwig


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep21

description:
Library name: RNA-seq_chromatin_Adult_homecage_21
Adult_home_set6.bigwig


title: SMARCA4_PDS.bio2.tech3

description: Library name: SMARCA4_PDS.bio2.tech3

value: PDS


title: Sample12

description:
Library name: S12
10x Genomics 3' gene expression v3.1

value: brain


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 270m, rep4

description:
Library name: RNA-seq_chromatin_Adult_30m-270m_4
Adult_opto30m-270m.bigwig

value: anterior dorsal cerebellar vermis

value: optostimulation 30 minutes, return to homecage 4 hours


title: Sample11

description:
Library name: S11
10x Genomics 3' gene expression v3.1


title: SMARCA4_PDS.bio1.tech2

description: Library name: SMARCA4_PDS.bio1.tech2


title: SMARCA4_PROTAC1.bio1.tech2

description: Library name: SMARCA4_PROTAC1.bio1.tech2


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 270m, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-270m_2
Adult_opto30m-270m.bigwig

value: cerebellar cells

value: Math1-Cre; ChR2YFP-GN


title: Sample6

description:
Library name: S6
10x Genomics 3' gene expression v3.1

value: 3 months


title: Sample8

description:
Library name: S8
10x Genomics 3' gene expression v3.1

value: 3 weeks


title: Sample10

description:
Library name: S10
10x Genomics 3' gene expression v3.1


title: Sample5

description:
Library name: S5
10x Genomics 3' gene expression v3.1


title: FUS_PROTAC3.bio2.tech1

description: Library name: FUS_PROTAC3.bio2.tech1


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep18

description:
Library name: RNA-seq_chromatin_Adult_homecage_18
Adult_home_set5.bigwig


title: Sample4

description:
Library name: S4
10x Genomics 3' gene expression v3.1


title: FUS_PROTAC3.bio1.tech2

description: Library name: FUS_PROTAC3.bio1.tech2


title: Sample13

description:
Library name: S13
10x Genomics 3' gene expression v3.1


title: SMARCA4_PROTAC1.bio1.tech1

description: Library name: SMARCA4_PROTAC1.bio1.tech1


title: Canrenone1

city: Rochester

first: Ieng Lam

last: Lei

state: MN

address: 321 3rd Ave Sw

institute: Mayo Clinic

description:
Library name: sample10
Singleron

data_processing:
The counting matrix of single cell was processed using CeleScope.
Assembly: hg38
Supplementary files format and content: tar compressed files including barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz

source_name: Heart tissue

extract_protocol:
Nuclei was isolated from the heart tissue. RNA was examined using bioanalyzer for QC.
The libraries construct in Singleron INC following the manufacturer's protocol.

value: Heart tissue

tag: sample group

value: Canrenone

value: Perfused


title: SMARCA4_PDS.bio2.tech1

description: Library name: SMARCA4_PDS.bio2.tech1


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep16

description:
Library name: RNA-seq_chromatin_Adult_homecage_16
Adult_home_set5.bigwig


title: FUS_PROTAC2.bio2.tech2

description: Library name: FUS_PROTAC2.bio2.tech2


title: HTK2

description:
Library name: sample8
Singleron

value: HTK


title: SMARCA4_PDS.bio1.tech1

description: Library name: SMARCA4_PDS.bio1.tech1


title: SMARCA4_PDS.bio2.tech2

description: Library name: SMARCA4_PDS.bio2.tech2


title: HTK1

description:
Library name: sample7
Singleron


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 150m, rep4

description:
Library name: RNA-seq_chromatin_Adult_30m-150m_4
Adult_opto30m-150m.bigwig

value: optostimulation 30 minutes, return to homecage 2 hours


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep19

description:
Library name: RNA-seq_chromatin_Adult_homecage_19
Adult_home_set6.bigwig

value: home cage control


title: AF2

description:
Library name: sample5
Singleron

value: AF

value: Store only


title: mESC, EED rescue 24h, EPOPJARID2dKO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPJARID2dKO_24h

value: E14 mESC

value: HA-EED rescue, EPOPJARID2dKO background

value: 4-Hydroxytamoxifen treatment for 24h


title: Sample7

description:
Library name: S7
10x Genomics 3' gene expression v3.1

value: brain

value: SNI


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 150m, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-150m_2
Adult_opto30m-150m.bigwig

value: anterior dorsal cerebellar vermis

value: cerebellar cells


title: Canrenone2

description:
Library name: sample11
Singleron


title: FUS_PROTAC3.bio2.tech2

description: Library name: FUS_PROTAC3.bio2.tech2

value: WT


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 270m, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-270m_1
Adult_opto30m-270m.bigwig

value: Math1-Cre; ChR2YFP-GN

value: optostimulation 30 minutes, return to homecage 4 hours


title: Canrenone3

description:
Library name: sample12
Singleron

value: Heart tissue

value: Canrenone


title: Sample9

description:
Library name: S9
10x Genomics 3' gene expression v3.1

value: 3 weeks


title: FUS_PROTAC1.bio2.tech2

description: Library name: FUS_PROTAC1.bio2.tech2


title: Sample3

description:
Library name: S3
10x Genomics 3' gene expression v3.1

value: No SNI

value: 3 months


title: FUS_PROTAC3.bio1.tech1

description: Library name: FUS_PROTAC3.bio1.tech1


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep17

description:
Library name: RNA-seq_chromatin_Adult_homecage_17
Adult_home_set5.bigwig

value: home cage control


title: mESC, EED rescue 0h, EPOPKO background, H3K27me3 ChIP,Rep2

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPKO_0h_Rep2

value: HA-EED rescue,EPOPKO background

value: 4-Hydroxytamoxifen treatment for 0h


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 150m, rep3

description:
Library name: RNA-seq_chromatin_Adult_30m-150m_3
Adult_opto30m-150m.bigwig

value: optostimulation 30 minutes, return to homecage 2 hours


title: Sample2

description:
Library name: S2
10x Genomics 3' gene expression v3.1


title: HTK3

description:
Library name: sample9
Singleron

value: HTK

value: Perfused


title: FUS_PROTAC2.bio2.tech1

description: Library name: FUS_PROTAC2.bio2.tech1


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep15

description:
Library name: RNA-seq_chromatin_Adult_homecage_15
Adult_home_set5.bigwig


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 270m, rep3

description:
Library name: RNA-seq_chromatin_Adult_30m-270m_3
Adult_opto30m-270m.bigwig


title: AF3

description:
Library name: sample6
Singleron

value: AF

value: Store only


title: mESC, EED rescue 0h, EPOPKO background, H3K27me3 ChIP,Rep1

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPKO_0h_Rep1

value: E14 mESC


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 150m, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-150m_1
Adult_opto30m-150m.bigwig

value: anterior dorsal cerebellar vermis

value: cerebellar cells


title: mESC, EED rescue 0h, EPOPJARID2dKO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPJARID2dKO_0h

value: HA-EED rescue,EPOPJARID2dKO background


title: Donor1

description:
Library name: sample1
Singleron

value: Heart tissue

value: Donor


title: FUS_PROTAC2.bio1.tech2

description: Library name: FUS_PROTAC2.bio1.tech2

value: WT


title: FUS_PROTAC2.bio1.tech1

description: Library name: FUS_PROTAC2.bio1.tech1


title: mESC, EED rescue 24h, EPOPMTF2dKO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPMTF2dKO_24h

value: HA-EED rescue, EPOPMTF2dKO background

value: 4-Hydroxytamoxifen treatment for 24h


title: Sample1

description:
Library name: S1
10x Genomics 3' gene expression v3.1

value: brain

value: No SNI

value: 3 months


title: FUS_PDS.bio2.tech2

description: Library name: FUS_PDS.bio2.tech2

value: PDS


title: Donor3

description:
Library name: sample3
Singleron


title: mESC, EED rescue 0h, EPOPMTF2dKO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPMTF2dKO_0h

value: HA-EED rescue,EPOPMTF2dKO background

value: 4-Hydroxytamoxifen treatment for 0h


title: Donor2

description:
Library name: sample2
Singleron


title: AF1

description:
Library name: sample4
Singleron

value: AF


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 90m, rep4

description:
Library name: RNA-seq_chromatin_Adult_30m-90m_4
Adult_opto30m-90min.bigwig

value: Math1-Cre; ChR2YFP-GN

value: optostimulation 30 minutes, return to homecage 1 hour


title: mESC, EED rescue 24h, JARID2KO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_JARID2KO_24h

value: E14 mESC

value: HA-EED rescue, JARID2KO background


title: FUS_PDS.bio1.tech2

description: Library name: FUS_PDS.bio1.tech2


title: mESC, EED rescue 24h, EPOPKO background, H3K27me3 ChIP,Rep2

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPKO_24h_Rep2

value: HA-EED rescue, EPOPKO background


title: FUS_PROTAC1.bio1.tech2

description: Library name: FUS_PROTAC1.bio1.tech2


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 90m, rep3

description:
Library name: RNA-seq_chromatin_Adult_30m-90m_3
Adult_opto30m-90min.bigwig

value: anterior dorsal cerebellar vermis

value: cerebellar cells


title: FUS_PDS.bio1.tech1

description: Library name: FUS_PDS.bio1.tech1

value: WT


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 90m, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-90m_2
Adult_opto30m-90min.bigwig


title: mESC, EED rescue 24h, EPOPKO background, H3K27me3 ChIP,Rep1

description: Library name: ChIPseq_H3K27me3_EEDrescue_EPOPKO_24h_Rep1


title: mESC, EED rescue 0h, JARID2KO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_JARID2KO_0h

value: HA-EED rescue,JARID2KO background


title: FUS_PROTAC1.bio2.tech1

description: Library name: FUS_PROTAC1.bio2.tech1


title: custom_chrY_genomic_control_FICO3_WT_Tau

city: Bethesda

first: Mirit

middle: I

last: Aladjem

state: MD

address: 37 Convent Dr. Building 37, Room 5068D

department: DNA Replication Group

institute: National Cancer Institute

description: Library name: custome_chrY_genomic_control_FICO3_WT_Tau.bam

data_processing:
Raw bam files were generated from fastq files of ChIP-seq or NS-seq after QC, trimmimming, QC, aligned to T2T and custome buid with BWA.
Assembly: T2T-assembly and custome-build assembly from PRJNA1181812
Supplementary files format and content: Bed file format showing:NS-seq peaks
Supplementary files format and content: BigWig files

source_name: iPSC

extract_protocol:
Nascent Strand DNA from exponetially growing cell cultures were isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S). A paired end sequncing was performed for all NS-seq samples.

value: iPSC


title: mESC, EED rescue 0h, JARID2MTF2dKO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_JARID2MTF2dKO_0h

value: HA-EED rescue,JARID2MTF2dKO background


title: custom_chrY_genomic_control_FICO3_PHP

description: Library name: custome_chrY_genomic_control_FICO3_PHP.bam


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 90m, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-90m_1
Adult_opto30m-90min.bigwig


title: custom_chrY_genomic_control_FICO3

description: Library name: custome_chrY_genomic_control_FICO3.bam


title: FUS_PDS.bio2.tech1

description: Library name: FUS_PDS.bio2.tech1


title: DLD1 cells, Triptolide treated, Replicate 2

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: DLD1 Triptolide 2

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated using a copy number aware UMI deduplicator. Pipeline available at https://github.com/laurabiggins/TrAEL-seq Samples were imported into Seqmonk v1.49.1, truncated to a single base, then quantified either as total read count or as strand bias (R-F)/(R+F) equivalent to RFD. Assembly: GRCm38
Assembly: GRCh38
Supplementary files format and content: Replication Fork Direction and Read Count data in 50KB windows
Supplementary files format and content: dld1 pc9 summaries.txt

growth_protocol: Undifferentiated H9 hESCs were maintained on Vitronectin-coated plates (Thermo Fisher Scientific, A14700) in TeSR-E8 media (StemCell Technologies, 05990) and Essential 8 Medium (Gibco, A1517001) under 5% O2, 5% CO2 at 37 °C. DLD-1 cells were maintained in 75 cm2 flasks (Thermo Fisher Scientific, 156499 & 159910) in RPMI-1640 media (PAN Biotech, P04- 18500) with 10% (v/v) FBS (Fetal Bovine Serum) (Thermo Fisher Scientific, 10270-106), and 100 I.U/mL penicillin-streptomycin (Thermo Fisher Scientific, 15140122) under 5% CO2 at 37 °C. Cells were passaged with trypsin-EDTA 0.05% solution (Invitrogen, 25300062) and kept for a maximum of 20 passages. IMR90 ER:HRASG12V (IMR90 ER:RAS) fibroblasts were gifted from Prof. Masashi Narita at the CRUK Cambridge Institute. Cells were cultured in DMEM (Thermo Fisher Scientific, 31053028) with 10% (v/v) FBS (Thermo Fisher Scientific, 10270-106), 2 mM L-Glutamine (Thermo Fisher Scientific, 25030081), 100 I.U/mL penicillin-streptomycin (Thermo Fisher Scientific, 15140122) and 1 mM sodium pyruvate (Thermo Fisher Scientific, 11360070) under 5% CO2 at 37 °C. For passaging and collection, cells were detached with TrypLE™ Express Enzyme (Thermo Fisher Scientific, 12604013) and centrifuged at 300 g for 3 min.

extract_protocol:
1-2x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl multiplexed TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: For time course experiments, IMR90 ER:RAS cells were seeded in 10-15 cm dishes (Thermo Fisher Scientific, 150350) and the following day were treated with 4-hydroxy tamoxifen (4OHT) (Sigma, H7904) at a final concentration of 100 nM. 4OHT was replenished every 2-3 days. Cells were fully senescent following 6 days of treatment with 4OHT. Hydroxyurea (Merck H78627) was used at 20-100 µM for 2 hours, Ceralasertib (Merck TA9H11E41972) at 1 µM for 24 hours, palbociclib (Thermo Fisher Scientific 16430568)  at 16 nM for 24 hours, triptolide (Thermo Fisher Scientific PG490) at 3 µM for 4 hours.

value: Triptolide (3 µM)


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep9

description:
Library name: RNA-seq_chromatin_Adult_homecage_9
Adult_home_set3.bigwig

value: home cage control


title: FUS_PROTAC1.bio1.tech1

description: Library name: FUS_PROTAC1.bio1.tech1


title: DLD1 cells, Cerelasertib treated, Replicate 1

description: Library name: DLD1 ATRi 1

value: Cerelasertib (1 µM)


title: mESC, EED rescue 0h, MTF2KO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_MTF2KO_0h

value: HA-EED rescue, MTF2KO background


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep13

description:
Library name: RNA-seq_chromatin_Adult_homecage_13
Adult_home_set3.bigwig


title: PC9 cells, untreated control for palbociclib condition

description: Library name: PC9 control

value: Untreated


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep11

description:
Library name: RNA-seq_chromatin_Adult_homecage_11
Adult_home_set4.bigwig


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep14

description:
Library name: RNA-seq_chromatin_Adult_homecage_14
Adult_home_set4.bigwig


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep12

description:
Library name: RNA-seq_chromatin_Adult_homecage_12
Adult_home_set3.bigwig


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep8

description:
Library name: RNA-seq_chromatin_Adult_homecage_8
Adult_home_set3.bigwig


title: PC9 cells, Palbociclib treated, Replicate 1

description: Library name: PC9 palbociclib 1

value: Palbociclib (16 nM)


title: custom_chrY_Fico3_WT_Tau_with_Dox_rep1

description: Library name: custome_chrY_Fico3_WT_Tau_with_Dox_rep1.bam


title: DLD1 cells, Cerelasertib treated, Replicate 2

description: Library name: DLD1 ATRi 2


title: mESC, EED rescue 24h, JARID2MTF2dKO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_JARID2MTF2dKO_24h

value: HA-EED rescue, JARID2MTF2dKO background

value: 4-Hydroxytamoxifen treatment for 24h


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep10

description:
Library name: RNA-seq_chromatin_Adult_homecage_10
Adult_home_set4.bigwig

value: Math1-Cre; ChR2YFP-GN


title: mESC, EED rescue 24h, MTF2KO background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_MTF2KO_24h

value: E14 mESC


title: custom_chrY_Fico3_WT_Tau_rep2

description: Library name: custome_chrY_Fico3_WT_Tau_rep2.bam


title: DLD1 cells, untreated control for ATRi condition

description: Library name: DLD1 control


title: mESC, EED rescue 0h, WT background, H3K27me3 ChIP

description: Library name: ChIPseq_H3K27me3_EEDrescue_WT_0h

value: HA-EED rescue, WT background

value: 4-Hydroxytamoxifen treatment for 0h


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 1hr, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-1hr_2
Adult_opto30m-1hr.bigwig

value: anterior dorsal cerebellar vermis

value: cerebellar cells

value: optostimulation 30 minutes, return to homecage 30 minutes


title: custom_chrY_Fico3_WT_Tau_rep1

description: Library name: custome_chrY_Fico3_WT_Tau_rep1.bam

value: iPSC


title: DLD1 cells, untreated, replicate 2

description: Library name: DLD1 control 2


title: PC9 cells, Palbociclib treated, Replicate 2

description: Library name: PC9 palbociclib 2


title: custom_chrY_Fico3_WT_Tau_with_Dox_rep2

description: Library name: custome_chrY_Fico3_WT_Tau_with_Dox_rep2.bam


title: mESC, EED rescue 24h, EPOPKO background, HA-EED ChIP,Rep2

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPKO_24h_Rep2

value: HA-EED rescue, EPOPKO background


title: mESC, EED rescue 0h, EPOPJARID2dKO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPJARID2dKO_0h

value: HA-EED rescue,EPOPJARID2dKO background


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 40m, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-40m_2
Adult_opto30m-40m.bigwig

value: optostimulation 30 minutes, return to homecage 10 minutes


title: DLD1 cells, HU treated, 100 µM

description: Library name: DLD1 100uM HU

value: Hydroxyurea (100 µM)


title: mESC, EED rescue 0h, EPOPKO background, HA-EED ChIP,Rep2

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPKO_0h_Rep2

value: HA-EED rescue,EPOPKO background


title: mESC, EED rescue 24h, WT background, H3K27me3 ChIP, Rep2

description: Library name: ChIPseq_H3K27me3_EEDrescue_WT_24h_Rep2


title: DLD1 cells, Triptolide treated, Replicate 1

description: Library name: DLD1 Triptolide 1

value: Triptolide (3 µM)


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 1hr, rep3

description:
Library name: RNA-seq_chromatin_Adult_30m-1hr_3
Adult_opto30m-1hr.bigwig


title: custom_chrY_Fico3_with_Dox_rep2

description: Library name: custome_chrY_Fico3_with_Dox_rep2.bam


title: DLD1 cells, untreated, replicate 1

description: Library name: DLD1 control 1

value: Untreated


title: mESC, EED rescue 24h, EPOPKO background, HA-EED ChIP,Rep1

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPKO_24h_Rep1


title: DLD1 cells, DRB treated, Replicate 2

description: Library name: DLD1 DRB 2

value: DRB (100 µM)


title: custom_chrY_Fico3_rep1

description: Library name: custome_chrY_Fico3_rep1.bam


title: custom_chrY_Fico3_with_Dox_rep1

description: Library name: custome_chrY_Fico3_with_Dox_rep1.bam


title: DLD1 cells, DRB treated, Replicate 1

description: Library name: DLD1 DRB 1


title: mESC, EED rescue 24h, EPOPJARID2dKO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPJARID2dKO_24h

value: HA-EED rescue, EPOPJARID2dKO background

value: 4-Hydroxytamoxifen treatment for 24h


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 40m, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-40m_1
Adult_opto30m-40m.bigwig

value: Math1-Cre; ChR2YFP-GN


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 1hr, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-1hr_1
Adult_opto30m-1hr.bigwig


title: DLD1 cells, HU treated, 50 µM

description: Library name: DLD1 50uM HU

value: Hydroxyurea (50 µM)


title: PC9 cells, untreated

description: Library name: PC9


title: mESC, EED rescue 24h, EPOPMTF2dKO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPMTF2dKO_24h

value: E14 mESC

value: HA-EED rescue, EPOPMTF2dKO background


title: custom_chrY_Fico3_PHP_with_Dox_rep2

description: Library name: custome_chrY_Fico3_PHP_with_Dox_rep2.bam


title: custom_chrY_Fico3_rep2

description: Library name: custome_chrY_Fico3_rep2.bam


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep7

description:
Library name: RNA-seq_chromatin_Adult_homecage_7
Adult_home_set2.bigwig

value: anterior dorsal cerebellar vermis

value: cerebellar cells

value: home cage control


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep6

description:
Library name: RNA-seq_chromatin_Adult_homecage_6
Adult_home_set2.bigwig


title: custom_chrY_Fico3_PHP_rep2

description: Library name: custome_chrY_Fico3_PHP_rep2.bam

value: iPSC


title: custom_chrY_Fico3_PHP_with_Dox_rep1

description: Library name: custome_chrY_Fico3_PHP_with_Dox_rep1.bam


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep5

description:
Library name: RNA-seq_chromatin_Adult_homecage_5
Adult_home_set2.bigwig


title: DLD1 cells, untreated

description: Library name: DLD1


title: RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep2

description:
Library name: RNA-seq_chromatin_Adult_10m-10m_2
Adult_opto10m-10m.bigwig

value: optostimulation 10 minutes


title: NF2_VS3, Naïve

city: Columbus

first: Long-Sheng

last: Chang

address: 575 Children's Crossroad

institute: Abigail Wexner Institute at Nationwide Children's Hospital

description:
Library name: Naïve_NF2_VS3
10x Genomics

data_processing:
Demultiplexed scRNA-seq fastq files were input into the Cell Ranger pipeline (version 6.1.2) from 10x Genomics to align reads to the hg19 human reference sequence and generate barcoded count matrices of gene expression data. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: hg19
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5

source_name: NF2-mutated schwannoma

extract_protocol:
Fresh surgically-removed VS tissues were placed in DMEM or saline and transported to the lab for preparing single cell suspension. Tissues were dissociated by enzymatic digestion with collagenase/dispase at 37 C on a GentleMACs dissociator. Dissociated cells were cryopreserved in 10% dimethyl sulfoxide in DMEM containing 10% FBS until processing on the 10X Genomics’ Chromium Single Cell platform and sequencing on a NovaSeq 6000 System (Illumina)
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, VS tumor cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: NF2-mutated schwannoma


title: custom_chrY_Fico3_PHP_rep1

description: Library name: custome_chrY_Fico3_PHP_rep1.bam


title: RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep4

description:
Library name: RNA-seq_chromatin_Adult_10m-10m_4
Adult_opto10m-10m.bigwig


title: mESC, EED rescue 24h, JARID2KO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_JARID2KO_24h

value: HA-EED rescue, JARID2KO background


title: DLD1 cells, HU treated, 20 µM

description: Library name: DLD1 20uM HU

value: Hydroxyurea (20 µM)


title: mESC, EED rescue 0h, EPOPKO background, HA-EED ChIP,Rep1

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPKO_0h_Rep1

value: HA-EED rescue,EPOPKO background

value: 4-Hydroxytamoxifen treatment for 0h


title: RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep3

description:
Library name: RNA-seq_chromatin_Adult_10m-10m_3
Adult_opto10m-10m.bigwig


title: custom_chr21_genomic_control_FICO3_WT_Tau

description: Library name: custome_chr21_genomic_control_FICO3_WT_Tau.bam


title: NF2_VS, bevacizumab-treated

description:
Library name: bevacizumab-treated_NF2_VS
10x Genomics


title: NF2_VS2, Naïve

description:
Library name: Naïve_NF2_VS2
10x Genomics


title: RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep1

description:
Library name: RNA-seq_chromatin_Adult_10m-10m_1
Adult_opto10m-10m.bigwig


title: mESC, EED rescue 0h, EPOPMTF2dKO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_EPOPMTF2dKO_0h

value: HA-EED rescue,EPOPMTF2dKO background


title: RNA-seq of MDA-MB-231  replicate 3

city: Beijing

first: Qing

last: Fang

state: Haidian District

address: YiHeYuan Road

department: School of Life Sciences

country: China

institute: Peking University

description:
Library name: MDAMB231_RNAseq_rep3
RNA-seq of MDA-MB-231  replicate 3
counts_MCF10A_MDAMB231.txt

data_processing:
Nucleo-seq and WGS Data Process:Raw paired-end reads of Nucleo-seq and WGS were trimmed with TrimGalore v0.0.6 and aligned to UCSC human reference genome assembly (hg19) using Bowtie2 v2.2.5 with default parameters. Low quality mapped reads were removed using SAMtools v1.13 under parameter ‘-q 30’ and duplicated reads were removed via Picard MarkDuplicates. Bigwig files for track plotting were transformed from bam files with uniquely mapped reads using deepTools v3.5.5 bamCoverage with parameters ‘--normalizeUsing RPKM --binSize 50’. High mappability and uniquely mapped reads were prepared in bam format for the following identification of NAD.
Nucleo-C and in situ Hi-C Data Process: Raw paired-end reads of Nucleo-C and in situ Hi-C were trimmed with TrimGalore v0.0.6 and preprocessed by the HiC-Pro v2.11.4, paired-end reads were aligned to human reference genomes hg19 using bowtie2 v2.3.5 in two steps. The .allValidPairs files were transformed to .hic files by Juicer (v 1.22.01) pre command. Genome were divided into specific size bin and counted the valid pairs of each bin. We used 500 kb, 100 kb, 50 kb, 25 kb, and 10 kb bin size to generate original interaction matrix, and then Observed/Expected matrix was used to correct the original interaction matrix using R package strawr. The 100 kb corrected matrix was used to identify AB compartments in in situ Hi-C datasets. NADs-NADs interactions quantification as well as heatmap visualization were performed in Observed/Expected matrixes at 25 kb/10 kb.
RNA-seq Data Prcess: Raw paired-end reads were trimmed with TrimGalore v0.0.6 and aligned to UCSC human reference genome assembly (hg19) using STAR v2.6.1b with the following parameters: ‘--outSAMtype BAM SortedByCoordinate, --outSAMunmapped Within KeepPairs, --quantMode TranscriptomeSAM GeneCounts’. The counts matrix of gene expression was quantified using featureCounts with parameter ‘-t exon -g gene_id’. Differential analysis of gene expression was conducted with R package DESeq2 v1.46.0 and DEGs were defined with abs(log2FoldChange) > 1 and p-value < 0.05. Bigwig files of gene expression were transformed from mapped bam files via deepTools v3.5.5 bamCoverage with parameters ‘--normalizeUsing RPKM --binSize 50’.
Assembly: Assembly: hg19
Supplementary files format and content: bedgraph,hic
Supplementary files format and content: counts matrix

molecule: polyA RNA

growth_protocol: Human cervical cancer cells (HeLa) and human triple negative breast adenocarcinoma cells MDA-MB-231 were maintained in the medium (DMEM; Thermo, C11995500BT) supplemented with 10% fetal bovine serum (FBS; Gibco, 10099141), 100 units/mL penicillium and 100 μg/mL streptomycin (Thermo Fisher, 15140122) at 37°C in a 5% CO2 cell culture incubator. Human colon cancer cells (HCT116) were a gift from the laboratory of J. Wang. Human normal mammary gland epithelial cell line MCF10A were maintained in the commercially available complete medium (Pricella, CM-0525-125) following the manufacturer’s protocol. Human B lymphoid cells (GM12878) were cultured in the medium (RPMI 1640; Thermo Fisher, 11875093) containing 10% fetal bovine serum, 100 units/mL penicillium and 100 μg/mL streptomycin.

extract_protocol:
Nucleoli Extraction and Purification: Nuclei were isolated from crosslinked cells (1% formaldehyde) using lysis buffers and SDS/Triton X-100 treatment. Purified nuclei were sonicated to release nucleoli, which were then separated from nuclear debris by filtration and purified through a S2/S3 density gradient centrifugation;Nucleoli Staining and Fluorescence-Activated Nucleoli Sorting:Purified nucleoli were stained with a PE-conjugated anti-NPM1 antibody. Using a flow cytometer calibrated with size-standardized beads, nucleoli were identified as PE-positive particles measuring 500-1300 nm in diameter and sorted for subsequent analysis.
Intact nuclei or sorted nucleoli were re-crosskined for WGS preparation, or digested in situ with DpnII restriction enzyme and re-ligated for Nucleo-C Library Construction. For WGS and Nucleo-seq, libraries were conducted based on Tn5 tagmentation and adapter addition via TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502/503), according to total input DNA amount (TD502 for 4–6 ng DNA, TD503 for 1–2 ng DNA), respectively acoording to the manufacturer’s instruction.The final library was size-selected (300-500bp) for paired-end sequencing on an Illumina platform. For minimized Hi-C and Nucleo-C, proteins were degraded with proteinase K, crosslinks were reversed, and DNA was purified via ethanol precipitation.The digested DNA was fragmented using dsDNA Fragmentase. Biotinylated fragments were captured on streptavidin beads, followed by end repair, adapter ligation, and PCR amplification (11-13 cycles). The final library was size-selected (300-500bp) for paired-end sequencing on an Illumina platform. For RNA-seq, cells were collected using TRNzol reagent and subsequently constructed for RNA extraction and sequencing. The RNA library preparation was performed by using NEBNext UltraTM RNA Library Prep Kit for Illumina, followed by size selection with AMPure XP Beads. Sequencing was performed using Illumina's sequencing-by-synthesis technology.

value: Human triple negative breast cancer cell line

value: wild type


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep3

description:
Library name: RNA-seq_chromatin_Adult_homecage_3
Adult_home_set1.bigwig


title: NF2_VS1, Naïve

description:
Library name: Naïve_NF2_VS1
10x Genomics


title: mESC, EED rescue 24h, JARID2MTF2dKO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_JARID2MTF2dKO_24h

value: HA-EED rescue, JARID2MTF2dKO background

value: 4-Hydroxytamoxifen treatment for 24h


title: RNA-seq of MDA-MB-231  replicate 2

description:
Library name: MDAMB231_RNAseq_rep2
RNA-seq of MDA-MB-231  replicate 2
counts_MCF10A_MDAMB231.txt


title: mESC, EED rescue 0h, MTF2KO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_MTF2KO_0h

value: E14 mESC

value: HA-EED rescue, MTF2KO background


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep2

description:
Library name: RNA-seq_chromatin_Adult_homecage_2
Adult_home_set1.bigwig

value: anterior dorsal cerebellar vermis


title: custom_chr21_genomic_control_FICO3_PHP

description: Library name: custome_chr21_genomic_control_FICO3_PHP.bam


title: mESC, EED rescue 0h, JARID2KO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_JARID2KO_0h

value: HA-EED rescue,JARID2KO background


title: mESC, EED rescue 0h, JARID2MTF2dKO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_JARID2MTF2dKO_0h

value: HA-EED rescue,JARID2MTF2dKO background


title: custom_chr21_Fico3_WT_Tau_with_Dox_rep2

description: Library name: custome_chr21_Fico3_WT_Tau_with_Dox_rep2.bam

value: iPSC


title: RNA-seq of MDA-MB-231  replicate 1

description:
Library name: MDAMB231_RNAseq_rep1
RNA-seq of MDA-MB-231  replicate 1
counts_MCF10A_MDAMB231.txt


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep4

description:
Library name: RNA-seq_chromatin_Adult_homecage_4
Adult_home_set1.bigwig

value: cerebellar cells

value: home cage control


title: custom_chr21_genomic_control_FICO3

description: Library name: custome_chr21_genomic_control_FICO3.bam


title: custom_chr21_Fico3_WT_Tau_rep2

description: Library name: custome_chr21_Fico3_WT_Tau_rep2.bam


title: mESC, EED rescue 0h, WT background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_WT_0h

value: HA-EED rescue, WT background


title: The BAT of mice housed at 6℃ for 24 h, replicate 5

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

description: Library name: FF5

data_processing:
The samples are sequenced on the machine to obtain image files, which are then converted by the sequencing platform's built-in software to generate raw data (FASTQ file)
The sequencing data were processed as follows: 1) using Fastp to remove adaptor sequences;2) removing reads with an average quality score below Q20;3) Removal of reads with an N-ratio greater than 20%;4) Discarding sequences less than 20 bp in length after adapter removal and quality trimming.
Use HISAT2 software to align the quality-controlled reads to the reference genome to obtain the localization information of the reads on the reference genome.  The comparison result is available in a BAM format file.
We use HTSeq statistics to compare the read count values of each gene with the original expression level of the gene. FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) is used for standardization as an indicator for measuring transcript or gene expression level.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: EXCEL file include raw counts for each sample
Supplementary files format and content: EXCEL include FPKM value for each sample

source_name: BAT

growth_protocol: C57BL/6J mice (male, 7-8 weeks) were housed in groups of 5 per cage with water and food provided ad libitum, in a specific‑pathogen‑free room with filtered air and controlled light/dark cycle (12/12 h), temperature (24±2˚C) and relative humidity (45‑65%).

extract_protocol:
Total RNA was extracted and the polyA RNA was purified with oligo(dT) beads
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols

treatment_protocol: Mice were exposed at 6˚C for 6h or 24 h

value: BAT

tag: strain

value: 6 °C


title: custom_chr21_Fico3_with_Dox_rep2

description: Library name: custome_chr21_Fico3_with_Dox_rep2.bam


title: RNA-seq ADCV, Adult nd1/2 dcKO, rep3

description:
Library name: RNA-seq_Adult_nd1-2dcKO_3
Adult_ND1-2cKO_RNA-Seq.bigwig

value: ND1/2 sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice

value: AAV injection


title: Nucleo-C of MDA-MB-231 replicate 1

description:
Library name: MDAMB231_NucleoC_rep1
Nucleo-C of MDA-MB-231 replicate 1
MDAMB231_NucleoC_rep1.allValidPairs.hic

value: Human triple negative breast cancer cell line


title: mESC, EED rescue 24h, WT background, HA-EED ChIP, Rep2

description: Library name: ChIPseq_HAEED_EEDrescue_WT_24h_Rep2


title: mESC, EED rescue 24h, MTF2KO background, HA-EED ChIP

description: Library name: ChIPseq_HAEED_EEDrescue_MTF2KO_24h


title: RNA-seq ADCV, Adult nd1/2 dcKO, rep2

description:
Library name: RNA-seq_Adult_nd1-2dcKO_2
Adult_ND1-2cKO_RNA-Seq.bigwig


title: RNA-seq ADCV, Adult nd1/2 dcKO, rep1

description:
Library name: RNA-seq_Adult_nd1-2dcKO_1
Adult_ND1-2cKO_RNA-Seq.bigwig


title: custom_chr21_Fico3_WT_Tau_with_Dox_rep1

description: Library name: custome_chr21_Fico3_WT_Tau_with_Dox_rep1.bam


title: RNA-seq of MCF10A  replicate 3

description:
Library name: MCF10A_RNAseq_rep3
RNA-seq of MCF10A  replicate 3
counts_MCF10A_MDAMB231.txt

value: Human mammary gland epithelial cell line

value: wild type


title: custom_chr21_Fico3_with_Dox_rep1

description: Library name: custome_chr21_Fico3_with_Dox_rep1.bam


title: The BAT of mice housed at 6℃ for 24 h, replicate 4

description: Library name: FF4


title: WGS input of MCF10A

description:
Library name: MCF10A_WGS
WGS input of MCF10A


title: Nucleo-C of MDA-MB-231 replicate 2

description:
Library name: MDAMB231_NucleoC_rep2
Nucleo-C of MDA-MB-231 replicate 2
MDAMB231_NucleoC_rep2.allValidPairs.hic


title: custom_chr21_Fico3_WT_Tau_rep1

description: Library name: custome_chr21_Fico3_WT_Tau_rep1.bam


title: RNA-seq ADCV, Adult nd2 cKO, rep3

description:
Library name: RNA-seq_Adult_nd2cKO_3
Adult_ND2cKO_RNA-Seq.bigwig

value: ND2 sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice


title: RNA-seq ADCV, chromatin fraction, Adult homecage, rep1

description:
Library name: RNA-seq_chromatin_Adult_homecage_1
Adult_home_set1.bigwig

value: Math1-Cre; ChR2YFP-GN


title: The BAT of mice housed at 6℃ for 24 h, replicate 1

description: Library name: FF1


title: The BAT of mice housed at 6℃ for 6 h, replicate 5

description: Library name: E5

value: 6 h


title: RNA-seq of MCF10A replicate 1

description:
Library name: MCF10A_RNAseq_rep1
RNA-seq of MCF10A replicate 1
counts_MCF10A_MDAMB231.txt


title: custom_chr21_Fico3_rep2

description: Library name: custome_chr21_Fico3_rep2.bam


title: The BAT of mice housed at 6℃ for 24 h, replicate 3

description: Library name: FF3


title: minimized Hi-C of MDA-MB-231

description:
Library name: MDAMB231_HiC
minimized Hi-C of MDA-MB-231
MDAMB231_HiC.allValidPairs.hic


title: RNA-seq ADCV, Adult nd1/2 dcKO, rep4

description:
Library name: RNA-seq_Adult_nd1-2dcKO_4
Adult_ND1-2cKO_RNA-Seq.bigwig

value: anterior dorsal cerebellar vermis


title: custom_chr21_Fico3_rep1

description: Library name: custome_chr21_Fico3_rep1.bam


title: The BAT of mice housed at 6℃ for 24 h, replicate 2

description: Library name: FF2


title: RNA-seq of MCF10A replicate 2

description:
Library name: MCF10A_RNAseq_rep2
RNA-seq of MCF10A replicate 2
counts_MCF10A_MDAMB231.txt


title: RNA-seq ADCV, Adult nd1 cKO, rep3

description:
Library name: RNA-seq_Adult_nd1cKO_3
Adult_ND1cKO_RNA-Seq.bigwig

value: ND1 sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice


title: The BAT of mice housed at 6℃ for 6 h, replicate 2

description: Library name: E2


title: custom_chr21_Fico3_PHP_with_Dox_rep1

description: Library name: custome_chr21_Fico3_PHP_with_Dox_rep1.bam


title: custom_chr21_Fico3_PHP_with_Dox_rep2

description: Library name: custome_chr21_Fico3_PHP_with_Dox_rep2.bam


title: The BAT of mice housed at 6℃ for 6 h, replicate 4

description: Library name: E4


title: T2T_aligned_genomic_control_FICO3_Tau

description: Library name: T2T_aligned_genomic_control_FICO3_Tau_CR_32_S32.sorted.dedup.bam


title: RNA-seq ADCV, Adult nd1 cKO, rep2

description:
Library name: RNA-seq_Adult_nd1cKO_2
Adult_ND1cKO_RNA-Seq.bigwig


title: Nucleo-seq of MCF10A in 5k nucleoli

description:
Library name: MCF10A_Nucleoseq_5k
Nucleo-seq of MCF10A in 5k nucleoli
MCF10A_5k_Nucleoseq_vs_input.bedgraph


title: The BAT of mice housed at 6℃ for 6 h, replicate 3

description: Library name: E3


title: T2T_aligned_genomic_control_FICO3_php

description: Library name: T2T_aligned_genomic_control_FICO3_php_CR_33_S33.sorted.dedup.bam


title: Nucleo-seq of MCF10A in 50k nucleoli

description:
Library name: MCF10A_Nucleoseq_50k
Nucleo-seq of MCF10A in 50k nucleoli
MCF10A_50k_Nucleoseq_vs_input.bedgraph


title: RNA-seq ADCV, Adult nd2 cKO, rep1

description:
Library name: RNA-seq_Adult_nd2cKO_1
Adult_ND2cKO_RNA-Seq.bigwig


title: Nucleo-seq of MCF10A in 1k nucleoli

description:
Library name: MCF10A_Nucleoseq_1k
Nucleo-seq of MCF10A in 1k nucleoli
MCF10A_1k_Nucleoseq_vs_input.bedgraph


title: T2T_aligned_Fico3_WT_Tau_with_Dox_rep2

description: Library name: T2T_aligned_Fico3_WT_Tau_with_Dox_rep2.bam


title: Nucleo-seq of MCF10A in 10k nucleoli

description:
Library name: MCF10A_Nucleoseq_10k
Nucleo-seq of MCF10A in 10k nucleoli
MCF10A_10k_Nucleoseq_vs_input.bedgraph


title: The BAT of mice housed at 6℃ for 6 h, replicate 1

description: Library name: E1


title: RNA-seq ADCV, Adult nd2 cKO, rep4

description:
Library name: RNA-seq_Adult_nd2cKO_4
Adult_ND2cKO_RNA-Seq.bigwig


title: custom_chr21_Fico3_PHP_rep2

description: Library name: custome_chr21_Fico3_PHP_rep2.bam


title: RNA-seq ADCV, Adult nd1 cKO, rep4

description:
Library name: RNA-seq_Adult_nd1cKO_4
Adult_ND1cKO_RNA-Seq.bigwig


title: RNA-seq ADCV, Adult ctrl, rep3

description:
Library name: RNA-seq_Adult_ctrl_3
Adult_ctrl_RNA-Seq.bigwig

value: ctrl sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice


title: RNA-seq ADCV, Adult nd2 cKO, rep2

description:
Library name: RNA-seq_Adult_nd2cKO_2
Adult_ND2cKO_RNA-Seq.bigwig


title: custom_chr21_Fico3_PHP_rep1

description: Library name: custome_chr21_Fico3_PHP_rep1.bam

value: iPSC


title: T2T_aligned_Fico3_WT_Tau_with_Dox_rep1

description: Library name: T2T_aligned_Fico3_WT_Tau_with_Dox_rep1.bam


title: RNA-seq ADCV, Adult ctrl, rep4

description:
Library name: RNA-seq_Adult_ctrl_4
Adult_ctrl_RNA-Seq.bigwig

value: cerebellar cells


title: The BAT of mice housed at 22℃, replicate 4

description: Library name: D4

value: 22 °C


title: RNA-seq ADCV, Adult ctrl, rep2

description:
Library name: RNA-seq_Adult_ctrl_2
Adult_ctrl_RNA-Seq.bigwig


title: T2T_aligned_Fico3_WT_Tau_rep2

description: Library name: T2T_aligned_Fico3_WT_Tau_rep2.bam


title: Nucleo-C of MCF10A replicate 1

description:
Library name: MCF10A_NucleoC_rep1
Nucleo-C of MCF10A replicate 1
MCF10A_NucleoC_rep1.allValidPairs.hic


title: NAD-seq of MCF10A

description:
Library name: MCF10A_NADseq
NAD-seq of MCF10A
MCF10A_NADseq_vs_input.bedgraph


title: minimized Hi-C of MCF10A

description:
Library name: MCF10A_HiC
minimized Hi-C of MCF10A
MCF10A_HiC.allValidPairs.hic


title: The BAT of mice housed at 22℃, replicate 5

description: Library name: D5


title: Nucleo-C of MCF10A replicate 2

description:
Library name: MCF10A_NucleoC_rep2
Nucleo-C of MCF10A replicate 2
MCF10A_NucleoC_rep2.allValidPairs.hic


title: The BAT of mice housed at 22℃, replicate 1

description: Library name: D1


title: The BAT of mice housed at 22℃, replicate 3

description: Library name: D3


title: Nucleo-seq of HeLa in 50k nucleoli

description:
Library name: HeLa_Nucleoseq_50k
Nucleo-seq of HeLa in 50k nucleoli
HeLa_50k_Nucleoseq_vs_input.bedgraph

source_name: HeLa

value: HeLa

value: Human cervical cancer cell line


title: T2T_aligned_Fico3_WT_Tau_rep1

description: Library name: T2T_aligned_Fico3_WT_Tau_rep1.bam


title: RNA-seq ADCV, Adult nd1 cKO, rep1

description:
Library name: RNA-seq_Adult_nd1cKO_1
Adult_ND1cKO_RNA-Seq.bigwig


title: T2T_aligned_genomic_control_FICO3

description: Library name: T2T_aligned_genomic_control_FICO3_CR_31_S31.sorted.dedup.bam


title: The iWAT of mice housed at 6℃ for 24 h, replicate 4

description: Library name: C4

source_name: iWAT

value: iWAT

value: 6 °C


title: Hi-C ADCV, Adult nd1/2 dcKO, rep2

description: Library name: Hi-C_Adult_nd1-2dcKO_2

data_processing:
Hi-C reads were aligned to the mm10 reference genome with Bowtie2 and HiC-Pro. Uniquely mapped paired-end reads were assigned to MboI restriction fragments and valid pairs with a minimum genomic distance of 1Kb were filtered for PCR duplicates. Interaction matrices were normalized using Knight-Ruiz (KR) matrix balancing and observed divided by expected (o/e) transformation and visualized using hic files in Juicebox
Assembly: mm10
Supplementary files format and content: hic files

extract_protocol:
Cerebella were removed and microdissected. The genomic DNA was digested with MboI and re-ligated after the biotin fill-in reaction, followed by sonication. The fragmented DNA was then subjected to biotin-IP.
Hi-C libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: 0.5 µl of AAV9-gRNA-mCherry (titer 1x10^13vg/ml) was delivered to the ADCV using a fine glass pipette connected to a microinjector system (Nanoinject II, Drummond) and mounted in the stereotaxic frame (Stoelting).

value: ND1/2 sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice

value: AAV injection


title: T2T_aligned_Fico3_with_Dox_rep2

description: Library name: T2T_aligned_Fico3_with_Dox_rep2.bam


title: Hi-C ADCV, Adult nd1/2 dcKO, rep1

description: Library name: Hi-C_Adult_nd1-2dcKO_1


title: Hi-C ADCV, Adult nd1/2 dcKO, rep3

description: Library name: Hi-C_Adult_nd1-2dcKO_3


title: Nucleo-C of HeLa

description:
Library name: HeLa_NucleoC_50k
Nucleo-C of HeLa
HeLa_NuceloC.allValidPairs.hic


title: The iWAT of mice housed at 6℃ for 24 h, replicate 3

description: Library name: C3


title: Hi-C ADCV, Adult ctrl, rep3

description: Library name: Hi-C_Adult_ctrl_3


title: T2T_aligned_Fico3_with_Dox_rep1

description: Library name: T2T_aligned_Fico3_with_Dox_rep1.bam


title: Hi-C ADCV, Adult ctrl, rep2

description: Library name: Hi-C_Adult_ctrl_2


title: Nucleo-seq of HeLa in 200k nucleoli

description:
Library name: HeLa_Nucleoseq_200k
Nucleo-seq of HeLa in 200k nucleoli
HeLa_200k_Nucleoseq_vs_input.bedgraph


title: The iWAT of mice housed at 6℃ for 24 h, replicate 1

description: Library name: C1


title: The iWAT of mice housed at 6℃ for 6 h, replicate 5

description: Library name: B5


title: RNA-seq of HCT116 replicate 3

description:
Library name: HCT116_RNAseq_rep3
RNA-seq of HCT116 replicate 3

value: Human colorectal epithelial-like cancer cell line


title: RNA-seq of HCT116 replicate 2

description:
Library name: HCT116_RNAseq_rep2
RNA-seq of HCT116 replicate 2

value: wild type


title: Nucleo-seq of HeLa in 20k nucleoli

description:
Library name: HeLa_Nucleoseq_20k
Nucleo-seq of HeLa in 20k nucleoli
HeLa_20k_Nucleoseq_vs_input.bedgraph


title: RNA-seq ADCV, Adult ctrl, rep1

description:
Library name: RNA-seq_Adult_ctrl_1
Adult_ctrl_RNA-Seq.bigwig


title: The BAT of mice housed at 22℃, replicate 2

description: Library name: D2

value: BAT


title: RNA-seq of HCT116 replicate 1

description:
Library name: HCT116_RNAseq_rep1
RNA-seq of HCT116 replicate 1


title: The iWAT of mice housed at 6℃ for 24 h, replicate 2

description: Library name: C2


title: WGS input of HeLa

description:
Library name: HeLa_WGS
WGS input of HeLa


title: NEUROD2 ChIP-seq cerebellum, rep1

description: Library name: NEUROD2_Adult_1

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome with Bowtie2 using the public server at https://usegalaxy.org/, normalized by library size, and visualized using bigwig files. Peak calling was performed using MACS2 and those overlapping with the ENCODE blacklist were removed. H3K27ac peaks >2 kb distal to H3K4me3-marked TSSs were considered as enhancers.
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: cerebellum

extract_protocol:
Cerebella were removed and microdissected. Lysates were sonicated, and protein-DNA complexes were isolated using the indicated antibodies.
ChIP-seq libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: For AAV injections, 0.5 µl of AAV9-gRNA-mCherry (titer 1x10^13vg/ml) was delivered to the ADCV using a fine glass pipette connected to a microinjector system (Nanoinject II, Drummond) and mounted in the stereotaxic frame (Stoelting).

value: cerebellum

value: mixed

tag: chip antibody

value: NEUROD2 (Abcam ab104430)


title: T2T_aligned_Fico3_rep2

description: Library name: T2T_aligned_Fico3_rep2.bam


title: The iWAT of mice housed at 6℃ for 24 h, replicate 5

description: Library name: C5


title: WGS input of HCT116

description:
Library name: HCT116_WGS
WGS input of HCT116


title: T2T_aligned_Fico3_PHP_with_Dox_rep1

description: Library name: T2T_aligned_Fico3_PHP_with_Dox_rep1.bam


title: T2T_aligned_Fico3_PHP_with_Dox_rep2

description: Library name: T2T_aligned_Fico3_PHP_with_Dox_rep2.bam


title: Hi-C ADCV, Adult ctrl, rep1

description: Library name: Hi-C_Adult_ctrl_1

value: anterior dorsal cerebellar vermis


title: T2T_aligned_Fico3_PHP_rep2

description: Library name: T2T_aligned_Fico3_PHP_rep2.bam


title: The iWAT of mice housed at 6℃ for 6 h, replicate 2

description: Library name: B2

value: 6 h


title: NAD-seq of HCT116

description:
Library name: HCT116_NADseq
NAD-seq of HCT116
HCT116_NADseq_vs_input.bedgraph


title: T2T_aligned_Fico3_rep1

description: Library name: T2T_aligned_Fico3_rep1.bam

value: iPSC


title: NEUROD2 ChIP-seq cerebellum, rep2

description: Library name: NEUROD2_Adult_2

value: cerebellar cells


title: NEUROD1 ChIP-seq cerebellum, rep2

description: Library name: NEUROD1_Adult_2

value: NEUROD1 (Cell Signaling Technology #4373)


title: The iWAT of mice housed at 6℃ for 6 h, replicate 3

description: Library name: B3


title: T2T_aligned_Fico3_PHP_rep1

description: Library name: T2T_aligned_Fico3_PHP_rep1.bam


title: NEUROD1 ChIP-seq cerebellum, rep1

description: Library name: NEUROD1_Adult_1


title: The iWAT of mice housed at 6℃ for 6 h, replicate 4

description: Library name: B4


title: Nucleo-seq of HCT116

description:
Library name: HCT116_Nucleoseq
Nucleo-seq of HCT116
HCT116_Nucleoseq_vs_input.bedgraph


title: aicda-/- 1 B cell, LPS activated, Replicate 2

description: Library name: B cell aicda-/- activated 2

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated using a copy number aware UMI deduplicator. Pipeline available at https://github.com/laurabiggins/TrAEL-seq Samples were imported into Seqmonk v1.49.1, truncated to a single base, then quantified either as total read count or as strand bias (R-F)/(R+F) equivalent to RFD. Assembly: GRCm38
Assembly: GRCm38
Supplementary files format and content: Replication Fork Direction and Read Count data in 50KB windows
Supplementary files format and content: b cell summaries.txt

source_name: Splenic B cell

growth_protocol: Single cell suspensions from spleens were prepared by passing the spleens through 70μm cell strainers in ice-cold RPMI-1640 with 2% FBS. B cells were isolated from the peripheral lymph nodes of mice using the B cell isolation kit (Miltenyi Biotec) and cultured in Dutch-modified RPMI-1640 media supplemented with 10% FBS, 50µM 2-mercaptoethanol, 100units/ml penicillin and 100μg/ml streptomycin (both ThermoFisher Scientific).

extract_protocol:
2x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl multiplexed TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: B-cells were cultured in 24-well plates at 0.8x106 cells per mL in Dutch-modified RPMI-1640 media supplemented with 10% FBS, 50µM 2-mercaptoethanol, 100units/ml penicillin and 100μg/ml streptomycin B- cell stimulation was achieved with 50μg/mL Lipopolysaccharide.

value: Splenic B cell

value: Lipopolysaccharide


title: The iWAT of mice housed at 6℃ for 6 h, replicate 1

description: Library name: B1

value: iWAT


title: H3K27ac ChIP-seq, Adult nd1/2 dcKO, rep1

description: Library name: H3K27ac_Adult_nd1-2dcKO_1

value: H3K27ac (Active Motif 39085)


title: WGS input of GM12878

description:
Library name: GM12878_WGS
WGS input of GM12878

value: Human lymphoblastoid cell line


title: The iWAT of mice housed at 22℃, replicate 5

description: Library name: A5

value: 22 °C


title: H3K27ac ChIP-seq, Adult nd1/2 dcKO, rep2

description: Library name: H3K27ac_Adult_nd1-2dcKO_2

value: ND1/2 sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice

value: AAV injection


title: The iWAT of mice housed at 22℃, replicate 4

description: Library name: A4


title: Nucleo-seq of GM12878 in 5k nucleoli

description:
Library name: GM12878_Nucleoseq_5k
Nucleo-seq of GM12878 in 5k nucleoli
GM12878_5k_Nucleoseq_vs_input.bedgraph

value: wild type


title: The iWAT of mice housed at 22℃, replicate 2

description: Library name: A2


title: aicda-/- 1 B cell, untreated, Replicate 1

description: Library name: B cell aicda-/- 1

value: untreated


title: Nucleo-seq of GM12878 in 1k nucleoli

description:
Library name: GM12878_Nucleoseq_1k
Nucleo-seq of GM12878 in 1k nucleoli
GM12878_1k_Nucleoseq_vs_input.bedgraph


title: H3K27ac ChIP-seq ADCV, Adult ctrl, rep2

description: Library name: H3K27ac_Adult_ctrl_2

value: ctrl sgRNAs in Math1-Cre; LSL-Cas9-EGFP mice


title: B cell, LPS activated, Replicate 1

description: Library name: B cell wild type activated 1


title: Nucleo-seq of GM12878 in 50k nucleoli

description:
Library name: GM12878_Nucleoseq_50k
Nucleo-seq of GM12878 in 50k nucleoli
GM12878_50k_Nucleoseq_vs_input.bedgraph


title: shACSL5+PA-3

city: Chongqing

first: Shaojie

last: Cheng

state: -- None selected --

address: No.1, Yi-Xue-Yuan Road, Yu-Zhong District

institute: Chongqing Medical University

description: Library name: Sample 12

data_processing:
Raw reads were firstly processed using fastp (v0.22.0) and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 (v2.1.0). FPKM of each gene was calculated and the read counts of each gene were obtained by featureCounts.
Assembly: GRCh38
Supplementary files format and content: File include Count values for each sample

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium (Gibco, USA) with 10% FBS and 1% penicillin/streptomycin. All cells were cultured in a 5% CO2 incubator at 37 °C.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions. 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: To investigate the role of ACSL5 mediate lung-tropic metastasis of breast tumors, Cancer cells were treated with or without palmitic acid. All cells were cultured in a 5% CO2 incubator at 37 °C.

value: breast cancer cell

value: ACSL5-knockdown, palmitic acid treated breast cancer cells derived from lung metastases


title: aicda-/- 1 B cell, LPS activated, Replicate 1

description: Library name: B cell aicda-/- activated 1


title: aicda-/- 1 B cell, untreated, Replicate 2

description: Library name: B cell aicda-/- 2


title: The iWAT of mice housed at 22℃, replicate 1

description: Library name: A1


title: Nucleo-seq of GM12878 in 10k nucleoli

description:
Library name: GM12878_Nucleoseq_10k
Nucleo-seq of GM12878 in 10k nucleoli
GM12878_10k_Nucleoseq_vs_input.bedgraph


title: B cell, LPS activated, Replicate 2

description: Library name: B cell wild type activated 2


title: The iWAT of mice housed at 22℃, replicate 3

description: Library name: A3


title: ZT18 Dex Rep1

city: Manchester

first: Robert

last: Maidstone

address: Michael Smith Building, Oxford Road

institute: University of Manchester

library_source: other

data_processing:
Reads were aligned to the mm10 genome using bowtie (v1.1.0)
sorted and indexed using Samtools (v1.2)
Peaks were called across ZT6 (from Array Express E-MTAB-10224)  and these ZT18 samples, separately for dexamethasone- and vehicle-treated , using MACS (v2.1.1),
Assembly: mm10
Supplementary files format and content: Peak list and reads for 4 samples deposited here, plus 4 samples previous deposited on Array Express E-MTAB-10224). Excel, 1 sheet per sample

molecule: protein

source_name: Liver

growth_protocol: Hnf4afl/flAlbCre+/- mice (aged 6-8 weeks), generated as described (Hayhurst et al., 2001). Male mice were used throughout. All animals had ad libitum access to standard laboratory chow and water, and were group-housed at room temperature (22°C) on 12hr:12hr light-dark cycles. Experimental mice (i.e. Cre transgene carriers) and floxed littermate controls were housed together, randomly assigned to cages at weaning, and then randomly assigned to treatment groups.

extract_protocol:
Tissue was collected after 1 hour. Chromatin was prepared from flash-frozen liver tissue using the Active Motif ChIP-IT High Sensitivity kit (Active Motif). 25μg of chromatin was incubated overnight at 4C with a GR antibody cocktail (ProteinTech 24050-1-A (lot 00044414) and Cell Signaling D8H2 (lot 2)). To permit direct comparison between samples, and to control for technical variation between ChIP reactions, a spike-in ChIP normalisation strategy was employed, with 30ng spike-in chromatin (53083, Active Motif) and 2μg spike-in antibody (61686, Active Motif (lot 34216004)) being included in each IP reaction. To obtain sufficient DNA for next-generation sequencing, three IP reactions were carried out for each sample, and then pooled for the pull-down step. Antibody was pulled down using washed magnetic protein G agarose beads (ReSyn Biosciences). Beads were washed five times with AM1 Wash Buffer (Active Motif) then DNA eluted as per ChIP-IT kit instructions. ChIP-seq DNA was purified with the MinElute PCR Purification kit (Qiagen).
Illumina TruSeq ChIP Library Preparation Kit, according to the manufacturer’s protocol
Sequenced paired end 76bp on HISEQ4000 at the Genomic Technologies Core Facility University of Manchester

treatment_protocol: Dexamethasone and vehicle treatment was carried out at the National Cancer Institute as previously described (Caratti et al., 2018). For acute treatment with dexamethasone, mice were injected by the intraperitoneal route with water-soluble dexamethasone (D2915 - Sigma-Aldrich) at a dose of 1mg/kg, dissolved in water for injection to a final dexamethasone concentration of 0.2mg/ml. Corresponding vehicle treatment was an equivalent mass of (2-hydroxypropyl)-beta-cyclodextrin (H107 - Sigma-Aldrich) dissolved in water for injection.

value: Liver

tag: Sex

value: male

value: Dex

tag: timepoint


title: ZT18 Vehicle Rep2

value: Vehicle


title: shACSL5+PA-1

description: Library name: Sample 10


title: ZT18 Dex Rep2


title: Ribose, DRG SCI 3dpi, rep3

city: London

first: Yayue

last: Song

address: Burlington Danes, Hammersmith Hospital, Imperial College London

institute: Imperial College London

description: Library name: Sample 12

data_processing:
Sequences were demultiplexed and adapters trimmed with bcl2fastq-v2.20 (Illumina) and read quality controls carried out using FastQC-v 0.12.1, trimming reads less than Phred33 quality score 20 and removing remaining adapters with Trim Galore-v- 0.6.10.
Assembly: Mus_musculus.GRCm38.100
Supplementary files format and content: csv file include FPKM values for each sample

source_name: Sciatic DRG neurons

extract_protocol:
RNA was harvested using RNeasy Micro kit (Qiagen)
Libraries were generated at Source Bioscience (Nottingham, UK) using the Kit for Illumina, NEBNext Ultra II Directional RNA Library Prep according to the recommended manufacturer protocol.

value: Sciatic DRG neurons


title: B cell, untreated, Replicate 2

description: Library name: B cell wild type 2

value: Splenic B cell


title: H3K27ac ChIP-seq ADCV, Adult ctrl, rep1

first: Yue

last: Yang

address: 2200 Campus Dr

institute: Northwestern University

description: Library name: H3K27ac_Adult_ctrl_1

value: anterior dorsal cerebellar vermis

value: cerebellar cells