title: delC2_opaque_3

description:
Library name: MAD12
3' end seq

value: yeast cell

value: opaque


title: Ribo_Mettl18_KO1

status: Public on Feb 17 2026

type: SRA

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

description: Library name: Sample 4

library_source: transcriptomic

data_processing:
Basecalling with Illumina Casava 1.8 software
Quality filtering and 3' adapter trimming by Fastp 0.21.0
Library sorting based on sample barcode sequence by cutadapt 3.7
UMI extraction by UMI-tools 1.1.2
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Deduplication using UMI by UMI-tools 1.1.2
Read quantitation using custom scripts
Assembly: mm10
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribo-Seq

molecule: total RNA

organism: Mus musculus

source_name: pancreatic acinar cell 266-6

growth_protocol: WT and Mettl18 KO 266-6 cells were transfected with the plasmid for Reg1-FLAG, cultured for 48 h on 0.1% gelatin-coated dish in DMEM supplemented with 10% FBS and Penicillin-Streptomycin (Gibco, 10 U/mL).

extract_protocol:
Cells were lysed in lysis buffer containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl₂, 1 mM DTT, 1% Triton X-100, and 100 μg/ml cycloheximide, and subsequently cleared by centrifugation at 20,000 × g for 10 minutes at 4°C.
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, ligation of preadenylated linker, rRNA depeletion by riboPOOL for mouse (siTOOLs), reverse transcription, circligation and PCR amplification.

tag: cell line

value: pancreatic acinar cell 266-6

tag: genotype

value: Mettl18 KO


title: KO5

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: CPM-RibotagEndo.txt

data_processing:
Data quality was checked by FastQC software (v0.11.9).
Reads were trimmed by Trimmomatic (v0.39) (Bolger et al., 2014) and ribosomic RNAs were depleted by SortMeRNA tool (v2.1) (Kopylova et al., 2012).
Remaining reads were mapped to murine genome sequence (GRCm38 from Genome Reference Consortium) by HiSAT2 (v2.1.0) (Kim et al., 2019).
Counts per million (CPMs) were obtained by the edgeR package (v3.32.0) (Robinson et al., 2010) in R language (v4.0.2) for those raw reads counts higher than 10 in at least 50% of the samples in at least one group.
Genome_build: Mouse reference genome mm10
Supplementary_files_format_and_content: txt file containing all the gene expressions (CPM) for all the samples. Each column is a sample. Each row is a gene.

source_name: Endothelial cells residing in white adipose tissue (WAT)

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and food

extract_protocol:
WAT samples (50-100mg) were ice-cold homogenized in 1mL of homogenization buffer (50mM Tris, 100mM KCl, 12mM MgCl2, 1% Nonidet P-40, 1% Triton X-100, 0.1% SDS, 1% Sodium Deoxycolate, 1mM DTT, 200U/mL Promega RNasin, 1mg/mL heparin, 100μg/mL cycloheximide, Sigma protease inhibitor mixture at pH 7.4) using a glass Dounce. After clearing, 25μL of the homogenate was separated and frozen as INPUT sample. The remaining homogenate (approximately 800μL) was mixed with 4μL of a mouse monoclonal anti-HA antibody (HA.11 clone 16B12, Biolegend) and placed on a gentle spinner in a cold room for 2h. Afterwards, the antibody-tissue homogenates were mixed with 100μL of Dynabeads protein G magnetic beads (#10004D, Life Technologies) and incubated over-night on a spinner at 4°C. Samples containing bead-antibody-tissue homogenates were placed in a magnetic rack on ice. Immunoprecipitates were washed 3 times for 10 min with 800μL of high-salt buffer (50mM Tris, 300mM KCl, 12mM MgCl2, 1% Nonidet P-40, 1mM DTT, 100μg/mL cycloheximide at pH 7.4) at 4°C in a cold room on a rotator. Immediately after the last wash, 350μL of lysis buffer was added to each sample and vortexed for 30s to break apart the antibody-bead protein bond and placed in a magnetic stand for separation from beads. Total RNA was purified using a RNeasy Plus Micro Kit (#74034, Qiagen). Final RNA was diluted in 20μL of RNase-free water and quantified using a Quant-iT RiboGreen RNA assay kit (#R11490, Thermo Fisher). RNA integrity was assessed on a 2100 Bioanalyzer device (Agilent Technologies) using the RNA 6000 Pico kit (Agilent Technologies).
cDNA was synthetized from 2 to 5ng RNA with the SMARTer Ultra Low Input RNA kit v4  (Clontech). Sequencing libraries were prepared with the NexteraXT kit (Illumina).

tag: strain

tag: tissue

tag: biological replicate

tag: mfn2 presence in endothelial cells

value: Absent


title: mESC R70H, Jarid2_2 , Replicate 2

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

country: USA

institute: Sylvester Comprehensive Cancer Center

description:
Library name: 112_JARID2_2_Rep2
with spike in - human T47D (genome: hg38_encode)

library_source: genomic

data_processing:
Sequenced reads (FASTQ files) were processed with nf-core pipelines (PMID: 32055031) for read trimming, QC and alignment. Nf-core/chipseq v2.2.0 ( https://github.com/nf-core/chipseq/tree/2.0.0)
BAM files without spikein were used in ENCODE pipeline 2 v2.2.1 to  generate signal over noise bigwigs as well as to call peaks (spp for transcription factors; macs2 for broad markers) and IDR for optimal peak calling consistency between replicates. BAM files with spikein were used in Nf-core/chipseq v2.2.0 to generate bigwigs with spinke-in normalization (check methods for details) as well as to call peaks (macs2 for broad markers) and macs for optimal peak calling consistency between replicates
Assembly: mm10
Supplementary files format and content: Bigwig files signal over noise from pooled replicates for samples w/o spike-in. For samples with spike-in, normalized by spike-in bigwigs for each replicate

molecule: genomic DNA

source_name: Mouse embryonic stem cells (mESCs)

growth_protocol: mESCs were cultured in ESC+2i media, while mNPCs were differentiated using a three-stage protocol: 4 days in ESC media, followed by 4 days in EB media, and a final 4 days in EB media supplemented with 5 μM of RA.

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 11% solution containing formaldehyde (Thermo Fisher #28908), 50mM HEPES-KOH(pH 7.5), 100mM Nacl, 0.5M EDTA, 0.5M EGTA for 10 min. 1/20 of the plates volume equivalent of freshly prepared Glycine 2.5M(stock) was added to quench the reaction for 5min . The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers . Cells were pelleted at 2950 x g for 10 min at 4°C, washed 1x with 10 ml cold PBS, and pelleted once more. Cell pellets were flash freeze in liquid nitrogen and store at -80°C until processing day. Cell pellet collected from 6 plates of cells was resuspended in 5 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 5 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and then transfer to 15ml sonication tubes (Diagenode cat# C01020031). Cells were sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 50µl of sonicated samples was transferred to a new microtube with 50µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H20. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples. 2ug of Antibody (see Key Resources table for list of antibodies) was bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), previously washed with 1 ml of 0.5% BSA in 1x PBS three times, and rotated end-to-end overnight at 4°C (Eppendorf cat# 0030108051). After binding of the antibodies, beads were washed with 1 ml of 0.5% BSA in 1x PBS three times. 10ug of chromatin was added to 1.5ml LoBind tube (Eppendorf cat# 0030108051) containing pre-bound antibodies beads and brought up to 500µl final volume with Lysis Buffer and rotated end-to-end overnight at 4°C. 5 µl was removed as input material (1%) and placed in a separate microtube at 4°C completing the volume to 50uL with Lysis Buffer 3. Beads were washed 6 times with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and 150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 960xg at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample and input, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H2O and quantified by Qubit
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370L. Lot: 10193454) following the manufacturer’s instructions.

tag: cell type

value: Mouse embryonic stem cells (mESCs)

tag: antibody

value: JARID2, CST (Cat #13594)10ul


title: delC2_opaque_2

city: Providence

first: Corey

last: Frazer

state: Rhode Island

address: 171 Meeting Street, Rm573 BioMed GG

department: Molecular Microbiology and Immunology

institute: Brown University

description:
Library name: MAD11
3' end seq

data_processing:
BBDuk  version 38.23
STAR Aligner version 2.7.10b
EdgeR
Assembly: C. albicans sc5314 Assembly 21
Supplementary files format and content: Raw read counts
Supplementary files format and content: Normalised read counts

molecule: polyA RNA

organism: Candida albicans

growth_protocol: Cells were grown in synthetic complete dextrose (SCD) liquid media to mid log (1OD/ml) at 24C

extract_protocol:
RiboPure Yeast Kit
Lexogen QuantSeq 3' mRNA-Seq Library Prep

tag: phenotype


title: KO4

description: CPM-RibotagEndo.txt

value: Endothelial cells residing in white adipose tissue (WAT)


title: DNA methylation profile for 203991450163_R03C01

type: genomic

city: Exeter

first: Gregory

last: Wheildon

address: Stocker Road

department: CBS

country: United Kingdom

institute: University of Exeter

description: DNA methylation profile from healthy control

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3 and Cy5

organism: Homo sapiens

source_name: Brain

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from ~100 mg of each dissected brain region  using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

value: Brain

tag: brain region

value: Striatum

tag: Sex

value: Male

tag: age

tag: disease state

value: Control

tag: brain bank

value: London

tag: bisulfite conversion batch

tag: neuronal proportion


title: KO3

description: CPM-RibotagEndo.txt


title: KO1

description: CPM-RibotagEndo.txt


title: Ribo_Mettl18_WT3

description: Library name: Sample 3

value: WT


title: KO2

description: CPM-RibotagEndo.txt


title: DNA methylation profile for 203976760024_R07C01

value: Entorhinal cortex

value: Female


title: WT4

description: CPM-RibotagEndo.txt

value: Present


title: WT2

description: CPM-RibotagEndo.txt


title: DNA methylation profile for 203991450165_R04C01

value: Cerebellum


title: Ribo_Mettl18_WT2

description: Library name: Sample 2


title: WT3

description: CPM-RibotagEndo.txt


title: Ribo_Mettl18_WT1

description: Library name: Sample 1


title: WT1

description: CPM-RibotagEndo.txt


title: DNA methylation profile for 203976760022_R02C01


title: DNA methylation profile for 203977000013_R05C01


title: CVS_HEKGT_Lipofectamine3000_EnvA_384wellvs15cm-15cm

city: San Francisco

first: David

last: Shin

state: CA

address: 1651 4th Street Room 521A

department: Neurosurgery

institute: University of California, San Francisco

library_source: other

data_processing:
Output fastqs from sequenced rabies barcode libraries were filtered and processed using the custom script barcode_processing.sh. The bbduk (v39.01) package (BBMap, Bushnell B.; sourceforge.net/projects/bbmap/) was used to discard any reads with average quality (maq) below 20. Reads were then trimmed down to individual RVdG barcodes, UMIs, and cell barcodes (for transcriptome-matched datasets). RVdG barcodes were aligned to a custom reference white list (Supplementary Table 1) with bowtie2, allowing for one base pair mismatch. After sorting output files with samtools, the RVdG barcodes, UMIs, and cell barcodes were merged on read IDs. The command line package UMI-tools (v1.1.2) was then used to quantify the number of UMIs per cell barcode and rabies barcode combination. A UMI collapsing threshold was set at 1 to collapse any UMIs with only one base pair difference into a single UMI count.
Assembly: Barcode whitelist in Supplemental Figure 1 in the associated manuscript
Supplementary files format and content: TSV format. Contains STICR barcode sequence and UMI-reduced read abundance.

molecule: other

organism: Lyssavirus rabies

source_name: rescued in HEKGT and pseudotyped in BHK21

extract_protocol:
phenol-chloroform extraction to extract viral RNA genomes; gigaprep to extract plasmid DNA
To quantify plasmid barcode library diversity, 50 ng of plasmid DNA was tagmented using seqWell’s Tagify UMI reagent, in order to tag each barcode-containing plasmid DNA fragment with a UMI and partial Illumina Read1 adapter. Tagmented fragments were purified using a 1× left-sided size selection using SPRIselect beads according to the manufacturer’s protocol. Sample indexing PCR was subsequently performed using custom sample index primers that bind to the BFP primer site sequence immediately proximal to the barcode sequence and to the TruSeq P5 PCR handle generated during Tn5 tagmentation (Primers 3 and 4, Key Resource Table). The library was sequenced using a target of 100 million reads. To quantify viral barcode library diversity, EnvA-pseudotyped barcoded RVdG was concentrated by ultracentrifugation as described above and RNA was isolated by phenol-chloroform extraction, the procedure for which is described as follows. The viral pellet was resuspended in 1 mL of Trizol (Invitrogen 15596026), and incubated at room temperature for five minutes to permit dissociation of rabies proteins from viral RNA. Subsequently, 200 μL of chloroform (Fisher 60047878) was added and vortexed for 30 seconds, followed by spin at 12000xg for 15 minutes at 4°C. 600 μL of the upper aqueous phase was collected and RNA was precipitated by mixing with 500 μL of isopropanol and 1 μL of Glycoblue (Invitrogen AM9515) and incubating for 10 minutes. Precipitated RNA was pelleted by centrifugation at 12000xg for 10 minutes at 4°C, washed twice with 80% ethanol, air dried for 2 minutes, and resuspended in 10 μL of nuclease-free water. Reverse transcription was performed on 1-5 μg of RNA using SuperScript IV (ThermoFisher 18090010) and 1 μL of 50 mM custom RT primer targeting a sequence distal to the barcode relative to the negative stranded viral genome, in order to generate cDNA containing barcodes from viral genome RNA but not from contaminant mRNA. RT primer also contained an overhanging sequence carrying an 8 bp randomer, which functions as a UMI to correct for PCR amplification bias after sequencing, and a binding site for Illumina sample index primer. The resulting cDNA (5 uL, or 25% of the RT reaction) was amplified using 10-12 cycles of PCR with KAPA HotStart PCR ReadyMix (Roche KK2601) and custom sample index primers, one of which is specific to an overhang introduced by the RT primer to facilitate viral genome-specific amplification. Each library was sequenced using at least 10 million reads.

value: G-deleted Rabies Virus

value: CVS N2c


title: DNA methylation profile for 203977000019_R03C01


title: DNA methylation profile for 203991460065_R06C01

description: DNA methylation profile from Huntington's disease patient

value: Huntington's disease


title: SMC1, β3-AR-stimulated control BAs-rep1

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: SMC1_plusCL_rep1

data_processing:
The raw reads of ChIP-seq data were preprocessed by the CHIPs pipeline[https://doi.org/10.12688/f1000research.52878.1], which includes read trimming, read mapping to the mouse genome (mm10), read level quality control, and peak level quality control.
The BigWig files were generated by deepTools bamCoverage software (version 3.3.1) with --normalizeUsing CPM --binSize 10 --ignoreDuplicates --extendReads based on uniquely mapped reads in BAM files produced by CHIPs pipeline
Assembly: mm10
Supplementary files format and content: BigWig

growth_protocol: WT-1 cells were cultured in high-glucose DMEM with 10% FBS. To induce differentiation, WT-1 cells were allowed to reach confluency and treated with induction medium supplemented with 10% FBS, 20 nM insulin, 1 nM Triiodothyronine (T3), 0.125 mM indomethacin, 5 µM dexamethasone, and 0.5 mM IBMX for 2 days. Subsequently, cells were maintained in differentiation medium supplemented with 2% FBS, 20 nM insulin, 1 nM T3 for an additional 4 days. During the differentiation process, the medium was changed every other day.

extract_protocol:
For CTCF ChIP, adipocytes on 10 cm plates were crosslinked with 1% formaldehyde at room temperature for 10 minutes, quenched with glycine, and washed twice with ice-cold PBS. For SMC1 and MED1 ChIP, an additional crosslinking step was performed with 2 mM freshly prepared DSG at room temperature for 45 minutes before formaldehyde fixation. Crosslinked adipocytes were scraped in PBS supplemented with 1mM PMSF, pelleted at 3,000 g for 5 minutes at 4°C, and suspended in 300 μl lysis buffer (50 mM Tris pH 7.5, 1% SDS, 0.25% sodium deoxycholate, and 1X protease inhibitor cocktail), followed by incubation on ice for 10 minutes. The volume was then increased to 1.2 ml by adding 900 μl of ChIP dilution buffer (50 mM Tris pH 7.5, 0.1% SDS, 150 mM NaCl, 1.84% Triton X-100, and 1x protease inhibitor cocktail). Chromatin was sonicated using a Branson Sonifier SFX250 (50% amplitude, 3.5 minutes). After centrifugation at 13,000 rpm for 10 minutes, the supernatant was transferred to a new tube and mixed with 1.8 ml ChIP dilution buffer. For each ChIP reaction 1.5 ml lysate was incubated overnight at 4°C with 5 μg of the indicated antibodies (CTCF (Cell Signaling, 3418S), SMC1 (ThermoFisher Scientific, A300-055A), a MED1 (Invitrogen, PA5-36114)).On the next day, 20 μl of DynabeadsTM Protein G beads were added and incubated for additional 2 hours at 4°C. The beads were washed twice with ice-cold ChIP buffer with 0.1% SDS, washed twice with ice-cold High-salt wash buffer (50 mM Tris pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM EDTA, 0.1% SDS), washed twice with ice-cold LiCl buffer (10 mM Tris pH 8.0, 0.25 M LiCl, 0.5% Triton X-100, 0.5% sodium deoxycholate, 1 mM EDTA), and washed once with ice-cold TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). The protein-DNA complex was eluted from beads by adding 100 μl of freshly prepared elution buffer (10 mM Tris pH 8.0, 0.1% SDS, 150 mM NaCl, 5 mM DTT) and incubated at 65°C in a thermomixer set at 600 rpm for 1 hour. Then, reverse crosslinking was carried out by adding 2 μl of RNaseA (10 mg/ml, ThermoFisher Scientific, EN0531) and incubating at 37°C for 1 hour, followed by supplementation with 3 μl of Proteinase K (20 mg/ml, ThermoFisher Scientific, 25530049) and incubation at 65°C for 3 hours or overnight. Genomic DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and dissolved in 20 μl H2O.
ChIP library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacturer’s protocol. 5 ng ChIP DNA was used for library preparation.

treatment_protocol: Gene knockdown was conducted in day 6 mature adipocytes. Mature adipocytes were transduced with lentivirus expressing either a non-targeting shRNA or an shRNA targeting H2A.Z, generating control or H2A.Z knockdown (KD) adipocytes. To activate β3-AR signaling, day11 control or H2A.Z KD adipocytes were treated with either vehicle or β3-AR agonist, CL316,243, for 4 hours.

value: brown adipocytes

value: H2A.Z KD

tag: treatment

value: Beta3-AR agonist


title: CVS_HEKGT_Lipofectamine3000_EnvA_384wellvs15cm-384well

tag: cell line

value: rescued in HEKGT and pseudotyped in BHK21


title: N2c_HEKGT_Lipofectamine3000_Gpseudotyped_15cm-3

source_name: rescued in HEK293T

tag: genotype

value: rescued in HEK293T


title: SMC1, vehicle-treated control BAs-rep1

description: Library name: SMC1_minusCL_rep1


title: SMC1, β3-AR-stimulated control BAs-rep2

description: Library name: SMC1_plusCL_rep2


title: DNA methylation profile for 203977090035_R06C01

value: Brain


title: N2c_HEKGT_Lipofectamine3000_Gpseudotyped_15cm-4


title: SADB19_HighComplexityViralLibrary-2


title: CVSN2c_HighComplexityViralLibrary-1


title: SMC1, vehicle-treated control BAs-rep2

description: Library name: SMC1_minusCL_rep2


title: N2c_HEKGT_Lipofectamine3000_Gpseudotyped_15cm-2


title: SADB19_HighComplexityViralLibrary-1


title: N2c_HEKGT_Lipofectamine3000_Gpseudotyped_15cm-1


title: MED1, β3-AR-stimulated control BAs-rep2

description: Library name: MED1_plusCL_rep2


title: DNA methylation profile for 203991450165_R03C01

value: Striatum

value: Male


title: N2c_293T_Lipofectamine3000_Gpseudotyped_15cm-4


title: N2c_293T_Lipofectamine3000_Gpseudotyped_15cm-3


title: MED1, β3-AR-stimulated control BAs-rep1

description: Library name: MED1_plusCL_rep1

value: Control

value: vehicle


title: DNA methylation profile for 203968030088_R01C01

value: Entorhinal cortex

value: London


title: DNA methylation profile for 203991450165_R05C01


title: N2c_293T_Lipofectamine3000_Gpseudotyped_15cm-2


title: N2c_293T_Lipofectamine3000_Gpseudotyped_15cm-1


title: N2c_293T_Lipofectamine2000_Gpseudotyped_15cm-4


title: MED1, vehicle-treated control BAs-rep1

description: Library name: MED1_minusCL_rep1


title: N2c_293T_Lipofectamine2000_Gpseudotyped_15cm-3


title: DNA methylation profile for 203991460065_R03C01

value: Female


title: DNA methylation profile for 203968030088_R08C01

value: Cerebellum


title: MED1, vehicle-treated control BAs-rep2

description: Library name: MED1_minusCL_rep2


title: CVSN2c_Genome_Plasmid_Library

description: I2 file contains UMI; R2 contains barcode

source_name: propagated in MegaX DH10B

value: G-deleted Rabies Virus

value: propagated in MegaX DH10B


title: CVSN2c_HighComplexityViralLibrary-2

value: CVS N2c


title: N2c_293T_Lipofectamine2000_Gpseudotyped_15cm-1


title: PMC, Rep8, Day7

city: Rochester

first: Ruoqiao

last: Wang

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester Medical Center

description:
Library name: S105_PMC_1_100_NC200_1_Day7
Illumina Stranded mRNA

data_processing:
Raw read counts were normalized using the regularized logarithm (rlog) transformation.
Assembly: GRCh38
Supplementary files format and content: count in txt file

source_name: PBMCs

extract_protocol:
Monocyte isolation: Fresh whole blood was obtained from an ongoing study at the University of Rochester Medical Center (n=8). Blood collected in 8 mL ACD tubes was layered over Ficoll Histopaque and centrifuged at 2000 RPM for 25 minutes (4/3 brake). The plasma layer was partially removed, and the PBMC ring was collected into a 50 mL conical tube and centrifuged at 500 ×g for 5 minutes (9/9 brake). Monocytes were isolated using CD14+ MicroBeads following the manufacturer’s instructions, resuspended, and cultured in 10% RPMI (with 1% PSG) for downstream assays. Platelet isolation: Fresh whole blood in 8 mL ACD tubes was centrifuged at 250 ×g for 15 minutes (2/2 brake). The plasma layer was gently transferred to a 50 mL conical tube, PGI2 was added to 1 μg/mL, and samples were centrifuged at 1000 ×g for 10 minutes (5/5 brake). Plasma was removed, and platelet pellets were slowly resuspended in Tyrode’s solution supplemented with 10% ACD (v/v) and 1 μg/mL PGI2. Platelets were washed by repeating the centrifugation step and resuspended in 1.5 mL Tyrode’s solution. Platelets were activated with 1 μg/mL collagen for 20 minutes at 37◦C prior to coculture with monocytes.Platelet-monocyte co-cultures and RNA extraction:Monocytes were cultured alone or with autologous platelets at a monocyte-to-platelet ratio of  1:100, at a final concentration of 0.3 ×10^6 monocytes/mL in RPMI supplemented with 10% FBS. Monocytes were collected at 24 h and 6 days. Cells were centrifuged at 500 ×g for 5 minutes, the supernatant was removed, and pellets were resuspended in 80 μL MACS buffer (0.5% BSA + 2 mM EDTA in 1X DPBS) with 20 μL Anti–HLA-DR MicroBeads. Samples were incubated for 20 minutes at 4◦C in the dark, washed with 1 mL MACS buffer by centrifugation (500 ×g, 5 minutes, 9/9 brake), and resuspended in 500 μL MACS buffer. Monocytes were positively selected using MS columns on a MACS Manual Separator according to the manufacturer’s protocol. Recovered cells were pelleted and lysed in 500 μL TRIzol™. Chloroform (100 μL) was added, mixed, and incubated for 5 minutes at room temperature. Lysates were centrifuged at 12,000 ×g for 15 minutes at 4◦C, and the aqueous phase was collected. An equal volume of 100% ethanol was added, and RNA was purified using the Qiagen RNeasy Mini Kit per the manufacturer’s instructions.
Libraries were prepared using the Illumina Stranded mRNA Library Prep Kit and sequenced as paired-end 150 bp reads on a NovaSeq X 10B flow cell.

value: PBMCs

value: monocytes

tag: condition

tag: group

value: PMC

tag: monocyte-platelet ratio

tag: day

value: day 7


title: Input for SMC1 and MED1, β3-AR-stimulated control BAs-rep2

description: Library name: Input_for_SMC1_MED1_plusCL_rep2

tag: cell type

value: brown adipocytes

value: Beta3-AR agonist


title: DNA methylation profile for 203977000075_R05C01

tag: tissue

value: Brain

value: Striatum


title: N2c_293T_Lipofectamine2000_Gpseudotyped_15cm-2

value: rescued in HEK293T


title: Input for SMC1 and MED1, β3-AR-stimulated control BAs-rep1

description: Library name: Input_for_SMC1_MED1_plusCL_rep1

value: Control


title: DNA methylation profile for 203991460065_R04C01

value: Male

value: Huntington's disease


title: SADB19_Genome_Plasmid_Library

description: R2 contains barcode


title: Input for SMC1 and MED1, vehicle-treated control BAs-rep2

description: Library name: Input_for_SMC1_MED1_minusCL_rep2


title: DNA methylation profile for 203976760023_R05C01

value: London


title: H2A.Z, β3-AR-stimulated  BAs, rep3

data_processing:
The raw reads of ChIP-seq data were preprocessed by the CHIPs pipeline[https://doi.org/10.12688/f1000research.52878.1], which includes read trimming, read mapping to the mouse genome (mm10), read level quality control, and peak level quality control.
For H2AZ ChIP-seq, the BAM files with deduplicated reads were imported into the DANPOS2 for genome-wide peak identification.
The BigWig files were generated by deepTools bamCoverage software (version 3.3.1) with --normalizeUsing CPM --binSize 10 --ignoreDuplicates --extendReads based on uniquely mapped reads in BAM files produced by CHIPs pipeline
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: XLS files for identified ChIP-seq peaks when compared to IgG background (except for IgG samples)
Supplementary files format and content: XLS files for identified ChIP-seq peaks when compared to Input background (only for vehicle_H3K4me3, b3AR stim_H3K4me3, vehicle_H3K27ac, and b3AR stim_H3K27ac samples)

extract_protocol:
Adipocytes on plates were crosslinked with 1% formaldehyde at room temperature for 10 minutes, quenched with glycine, and washed twice with ice-cold PBS. Crosslinked adipocytes were then scraped down in PBS supplemented with 0.1% Triton X-100 and 1x protease inhibitor cocktail, followed by incubation on ice for 10 minutes. After centrifugation, the cells were resuspended in PBS supplemented with 0.1% Triton X-100, 1x protease inhibitor cocktail, and 1 mM CaCl2. An appropriate amount of MNase was added to the cell suspension, and MNase digestion was carried out at 37°C for 10 minutes with gentle shaking in a thermomixer. The reaction was quenched by placing the samples on ice, adding 5 mM EDTA and 5 mM EGTA, and centrifuging at 13,000 rpm for 10 minutes at 4°C. The chromatin digestion profile was determined by electrophoresis, and the optimal digestion condition resulted in around 70% of mono-nucleosome. The chromatin was resuspended in ChIP buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM EDTA, 1mM PMSF, 1x protease inhibitor cocktail), rotated at 4°C for 2 hours, and centrifuged at 13,000 rpm for 10 minutes at 4°C. The supernatants containing mono-nucleosomes were collected, and the 5 μg of the indicated antibodies (H2A.Z, H3K4me3, H3K27ac, Ribbit IgG) were individually added. Chromatin with each antibody was incubated overnight at 4°C. On the next day, 20 μl DynabeadsTM Protein G beads (ThermoFisher Scientific) were added and incubated for 2 hours at 4°C. The beads were washed twice with ice-cold ChIP buffer with 0.1% SDS, washed twice with ice-cold High-salt wash buffer (50 mM Tris pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM EDTA, 0.1% SDS), washed twice with ice-cold LiCl buffer (10 mM Tris pH 8.0, 0.25 M LiCl, 0.5% Triton X-100, 0.5% sodium deoxycholate, 1 mM EDTA), and washed once with ice-cold TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). The protein-DNA complex was eluted from beads by adding 100 μl freshly prepared elution buffer (10 mM Tris pH 8.0, 0.1% SDS, 150 mM NaCl, 5 mM DTT) and incubated at 65°C in a thermomixer set at 600 rpm for 1 hour. Then, reverse crosslinking was carried out by adding 2 μl RNaseA (10 mg/ml, ThermoFisher Scientific) and incubating at 37°C for 1 hour, followed by supplementation with 3 μl Proteinase K (20 mg/ml, ThermoFisher Scientific) and incubation at 65°C for 3 hours or overnight. Genomic DNA was purified using AMPure XP beads (Beckman Coulter) and dissolved in 20 μl H2O for ChIP-seq.
ChIP library preparation was performed using Ovation Ultralow System V2 (Tecan Life Sciences) according to the manufacturer’s protocol. 2 ng ChIP DNA was used for library preparation.

tag: chip antibody

value: H2A.Z (Abcam, #ab4174)

value: WT


title: IgG for H2A.Z rep1


title: DNA methylation profile for 203976760022_R07C01

tag: brain region

value: Entorhinal cortex


title: IgG for H2A.Z rep3


title: nonPMC, Rep8, Day7

description:
Library name: S103_Non_PMC_NC200_1_Day7
Illumina Stranded mRNA

value: nonPMC


title: IgG for H2A.Z rep2


title: PMC, Rep7, Day2

description:
Library name: S101_PMC_1_100_NC200_1_Day2
Illumina Stranded mRNA

value: PBMCs

value: day 2


title: H2A.Z, β3-AR-stimulated  BAs, rep2


title: DNA methylation profile for 203991450165_R06C01

value: Cerebellum

tag: Sex

value: Female


title: MED1, β3-AR-stimulated H2A.Z KD BAs-rep2

description: Library name: MED1_KD_plusCL_rep2

value: brown adipocytes

value: H2A.Z KD


title: Input for MED1, β3-AR-stimulated H2A.Z KD BAs-rep2

description: Library name: Input_for_MED1_KD_plusCL_rep2

value: vehicle


title: MED1, β3-AR-stimulated H2A.Z KD BAs-rep1

description: Library name: MED1_KD_plusCL_rep1

value: Beta3-AR agonist


title: DNA methylation profile for 203968030089_R07C01

value: Brain

tag: age


title: Input for SMC1 and MED1, vehicle-treated control BAs-rep1

description: Library name: Input_for_SMC1_MED1_minusCL_rep1

value: Control


title: DNA methylation profile for 203977000013_R07C01

value: Striatum

tag: disease state


title: H2A.Z, β3-AR-stimulated BAs, rep1


title: H456 top quartile

city: Portland

first: Braden

last: Lobingier

state: Oregon

address: 3181 SW Sam Jackson Park Road, Mail Code L-334

department: Chemical Physiology and Biochemistry

institute: Oregon Health and Sciences University

description: Library name: H456B

data_processing:
Raw sequencing reads from next-generation sequencing were cropped and aligned to reference files using Python where counts per guide were found with  the ScreenProcessing pipeline (https://github.com/mhorlbeck/ScreenProcessing)
Assembly: hCRISPRi-v2
Supplementary files format and content: .counts files are lists of counts of sgRNAs found within each library, only searching sublibrary transfected in that sample

source_name: cell line

growth_protocol: HEK293 FLP-In and HEK293T-LentiX cells were obtained from ThermoFisher and Takara Biosciences, respectively and grown at 37C, 5% CO2 in Dulbecco's Modified Eagle Medium (4.5 g/L glucose and L-glutamine, no pyruvate), with 10% fetal bovine serum supplemented. Stable expression of pUBC-SSF-DORmct-APEX2 was acheived with FRT mediated recombination into FLP-In cells, and dCas-KRAB-BFP was lentivirally transduced into these stables. Fluorescence activated cell sorting on a BD FACS Aria II for BFP and DORmct (as assayed by M1-antiFLAG-AF647) was used to sort for cells expressing dCas and clonal populations were expanded and tested for highly efficacious dCas9 dependent knockdown.

extract_protocol:
Sorted cells were pellet and frozen. Once all samples were collected, the QiaAmp Blood Mini kit was used to extract genomic DNA from samples. PCR amplification of integraded guide sequences was performed with Q5 high-fidelity and barcoding primers for 27 cycles, purified on QIAquick PCR purification columns, and loaded onto 20% polyacrylamide/TBE gels for excision and extraction of a ~270 bp band. Extracted DNA was quantified by Bioanalyzer and sequenced on an Illumina HiSeq-4000 with custom primers
See Horlbeck 2016

treatment_protocol: Libraries of single guides (hCRISPRi-v2-top5, Horlbeck 2016) targetting the entire human genome split across seven sublibraries (H1-H7) were combined into three sublibraries (H17,H23,H456) and transfected into HEK293T-LentiX cells for production of libraries of virus. Virus was used to transduce cells stably expressing pUBC-SSF-DORmct-APEX2 & dCas9-KRAB-BFP at a low MOI (~0.2) such that each cell did not recieve more than one guide. Two days after transduction, cells were selected for integration of virus with 0.75 ug/ml puromycin for 3 days and grown for a total of 8 days before assaying. Day of assay, cells were stimulated with 10 uM DADLE for 90 minutes before lifting with TrypLE and performing the APEX/AUR intact cell assay (cells were resuspended in PBS, 100 uM Amplex UltraRed added and cells incubated for 15 minutes total. PBS/4% BSA/50 uM H2O2 was added to initiate reaction  and after one minute 1 mM sodium azide added to quench. Cells were washed twice with PBS/2% BSA before resuspending in PBS/1% BSA). Reacted cells were then subject to fluorescence activated cell sorting on a BD FACS Aria II, where they were first gated for cells and singlets, then for being BFP-positive, and binned based on fluorescence in the APC channel, and top and bottom quartiles were sorted into separate tubes.

value: cell line

value: HEK293 FLP In


title: DNA methylation profile for 203977090035_R07C01

value: Huntington's disease

tag: brain bank

value: London


title: Input for CTCF, β3-AR-stimulated control BAs, rep2

description: Library name: Input_for_CTCF_plusCL_rep2


title: PMC, Rep7, Day7

description:
Library name: S97_PMC_1_100_NC220_1_Day7
Illumina Stranded mRNA

value: monocytes

value: PMC

value: day 7


title: H456 bottom quartile

description: Library name: H456T


title: nonPMC, Rep7, Day2

description:
Library name: S99_Non_PMC_NC200_1_Day2
Illumina Stranded mRNA

value: PBMCs

value: nonPMC

value: day 2


title: DNA methylation profile for 203976760024_R08C01

value: Entorhinal cortex

value: Female

tag: bisulfite conversion batch


title: PMC, Rep6, Day2

description:
Library name: S93_PMC_1_100_NC220_1_Day2
Illumina Stranded mRNA


title: H23 top quartile

description: Library name: H23B


title: nonPMC, Rep7, Day7

description:
Library name: S95_Non_PMC_NC220_1_Day7
Illumina Stranded mRNA


title: Input for MED1, β3-AR-stimulated H2A.Z KD BAs-rep1

description: Library name: Input_for_MED1_KD_plusCL_rep1

value: brown adipocytes

value: vehicle


title: Input for CTCF, vehicle-treated control BAs-rep2

description: Library name: Input_for_CTCF_minusCL_rep2


title: DNA methylation profile for 203991460019_R04C01

description: DNA methylation profile from healthy control

value: Brain

value: Cerebellum

tag: neuronal proportion


title: DNA methylation profile for 203968030088_R02C01

description: DNA methylation profile from Huntington's disease patient

value: Striatum


title: Input for CTCF, β3-AR-stimulated control BAs, rep1

description: Library name: Input_for_CTCF_plusCL_rep1

value: Control

tag: treatment

value: Beta3-AR agonist


title: nonPMC, Rep6, Day2

description:
Library name: S91_Non_PMC_NC220_1_Day2
Illumina Stranded mRNA


title: PMC, Rep6, Day7

description:
Library name: S89_PMC_1_100_NC184_1_Day7
Illumina Stranded mRNA


title: Input for CTCF, vehicle-treated control BAs-rep1

description: Library name: Input_for_CTCF_minusCL_rep1

tag: cell line


title: H17 top quartile

description: Library name: H17B

value: cell line

value: HEK293 FLP In

tag: genotype


title: H23 bottom quartile

description: Library name: H23T


title: CTCF, β3-AR-stimulated control BAs, rep1

description: Library name: CTCF_plusCL_rep1


title: DNA methylation profile for 203976760024_R05C01

value: London


title: PMC, Rep5, Day7

description:
Library name: S81_PMC_1_100_NC187_1_Day7
Illumina Stranded mRNA

value: monocytes

tag: condition

value: PMC


title: nonPMC, Rep6, Day7

description:
Library name: S87_Non_PMC_NC184_1_Day7
Illumina Stranded mRNA

value: PBMCs

tag: group

value: day 7


title: CTCF, β3-AR-stimulated control BAs, rep2

description: Library name: CTCF_plusCL_rep2


title: DNA methylation profile for 203977000010_R05C01


title: H17 bottom quartile

description: Library name: H17T


title: U2OS_mock_control_siRNA_biolrep_4

city: London

first: Pradeep

last: Ramagiri

state: Greater London

address: 15 Cotswold Rd

department: Cancer Therapeutics

institute: The Institute of Cancer Research

description: Library name: U2OS_DHX8_Untreated_D

data_processing:
Raw FastQ files were processed using nf-core/rnaseq pipeline (version 21.04.3) which comprises the following software:  1. Read QC (FastQC v0.11.9 and MultiQC v1.12) 2. Alignment to the reference genome (GRCh38) using STAR aligner (v.2.7.6a) 3. Sort and index alignments (SAMtools) 4. Duplicate read marking (picard MarkDuplicates)
Once the reads were aligned, HTSeq-count (HTSeq v0.12.4) was used to count the number of reads mapping unambiguously to genomic features in each sample.
Differential expression analysis of the count data was performed in R using the Bioconductor package DESeq2 (v1.20.0). For differential splicing analysis, 1st pass and 2nd pass BAM files were created by mapping raw reads to reference genome (GRCh38) using STAR (v.2.7.6a). Differential local splicing variations (LSV) were detected and quantified using MAJIQ (v2.2-e25c4ac). Pathway and Gene Set Enrichment Analysis was carried out in R using package fgsea (v1.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Bone

growth_protocol: Human cell lines were obtained from ATCC and identity confirmed by short tandem repeat profiling. Cells were cultured in DMEM supplemented with 10% FCS, 2 mM glutamine and non-essential amino acids. All cell lines were maintained at 37 °C, 5% CO2 and tested negative for mycoplasma.

extract_protocol:
RNA extracted using an automated Magnapure (Roche) workstation according to the manufacturer’s instructions and RNA quality assessed using an Agilent bioanalyzer (Agilent)
RNA libraries for RNA-seq were prepared using Novogene NGS Stranded RNA Library Prep Set (PT044)* and sequenced in NovaSeq X Plus.

treatment_protocol: H1299 dTAG cells were treated for 6 hours with 250 nM dTAG-V1. U2OS, HCT116 and H1229 cells were reverse transfected with DHX8 or negative control siRNA using Hiperfect cationic lipid for 72 hours. HCT116 cells transfected with DHX8 or scramble control siRNA were treated +/- doxycyline to induce exogenous wild-type or mutant DHX8. U2OS cells were transfected with DHX8-O5 (GCAGUGGGUUCUUCCGUAA), DHX8-O2 (GGAAUAAAGUGAAGUCUAG) or AllStars negative control siRNA (Quagen).

value: Bone

value: Osteosarcoma

value: WT

value: Mock control

tag: time

value: 72 hours


title: DNA methylation profile for 203976760024_R02C01

value: Brain

value: Female

value: Huntington's disease


title: nonPMC, Rep5, Day7

description:
Library name: S79_Non_PMC_NC187_1_Day7
Illumina Stranded mRNA

value: nonPMC

tag: monocyte-platelet ratio

tag: day


title: PMC, Rep5, Day2

description:
Library name: S73_PMC_1_100_NC187_1_Day2
Illumina Stranded mRNA

tag: tissue

tag: cell type

value: day 2


title: U2OS_mock_control_siRNA_biolrep_2

description: Library name: U2OS_DHX8_Untreated_B


title: nonPMC, Rep5, Day2

description:
Library name: S71_Non_PMC_NC187_1_Day2
Illumina Stranded mRNA


title: β3-AR-stimulated H2A.Z KD BAs, rep2

description: Library name: KD_plusCL_rep2

data_processing:
Read pairs were trimmed using cutadapt 1.14 to remove adapter sequences. Bowtie2 was used to map reads to reference genome mm10
Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl)
All custom scripts described herein are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts)
Assembly: mm10
Supplementary files format and content: TXT file includes differential expression result in β3-AR-stimulated control versus vehicle control
Supplementary files format and content: TXT file includes differential expression result in β3-AR-stimulated H2A.Z KD versus  β3-AR-stimulated control
Supplementary files format and content: BigWig
Library strategy: PRO-Seq

molecule: nuclear RNA

extract_protocol:
Mouse brown adipocytes from a 10 cm dish were washed twice with ice-cold PBS and incubated on ice for 5 minutes in 10 ml swelling buffer (10 mM Tris HCl pH8.0, 2 mM MgCl2, 3mM CaCl2). Cells were then scraped, suspended, filtered through a 100 μm strainer. The cell pellets were resuspended in 250 μl of buffer W (10 mM Tris HCl pH8.0, 5 mM MgCl2, 10 mM KCl, 250 mM sucrose, 1 mM EGTA, 10% (v/v) Glycerol with freshly added 0.5 mM DTT and 0.2 μl/ml RNase inhibitor (SUPERase-In, Invitrogen)). Lysis was performed by adding 10 mL of lysis buffer (buffer W supplemented with 0.5% NP-40 and 0.05% Tween-20), followed by incubation on ice for 5 minutes. The cell suspension was filtered again through a 40 μm strainer, centrifuged, and washed with 10 mL of buffer W. The pelleted cells were then resuspended in freezing buffer (50 mM Tris-HCl, pH 8.0, 40% (v/v) glycerol, 5 mM MgCl₂, 1.1 mM EDTA) supplemented freshly with 0.5 mM DTT and 1 μL/mL RNase inhibitor. Cell permeability was assessed using trypan blue staining. A total of 1–2 million permeabilized cells were snap-frozen in 200 μL of freezing buffer using liquid nitrogen and stored at -80°C. All subsequent steps were performed by the Nascent Transcriptomics Core at Harvard Medical School (Boston, MA). Briefly, run-on reactions were conducted at 37°C. The adenylated 3' adapter was prepared using the 5' DNA Adenylation Kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB), following the manufacturer's instructions with a final concentration of 15% PEG-8000. The reaction was incubated at 16°C overnight. To block unligated adapters, 180 μL of betaine blocking buffer containing 0.6 μM blocking oligo was added to the ligation mixture, followed by incubation at 65°C for 5 minutes and on ice for 2 minutes before streptavidin bead capture. After T4 polynucleotide kinase treatment, the beads were sequentially washed with high-salt, low-salt, and blocking oligo wash buffers before resuspension in the 5' adapter mix.
Reverse transcription was performed using SuperScript IV Reverse Transcriptase (ThermoFisher) with 25 pmol of the Illumina TruSeq RP1 primer. The RT product was eluted from the beads and used for library preparation. Libraries were prepared by Nascent Transcriptomics Core at Harvard.

value: brown adipocytes

value: H2A.Z KD

value: β3-AR agonist


title: DNA methylation profile for 203977000010_R08C01

tag: brain region

value: Entorhinal cortex

value: Control

value: London


title: U2OS_mock_control_siRNA_biolrep_1

description: Library name: U2OS_DHX8_Untreated_A


title: DNA methylation profile for 203977000075_R02C01

tag: Sex


title: U2OS_scramble_control_siRNA_biolrep_4

description: Library name: U2OS_DHX8_NEG_CON_D

value: DMSO control


title: DNA methylation profile for 203976760023_R02C01

value: Striatum

tag: age


title: PMC, Rep4, Day7

description:
Library name: S69_PMC_1_100_NC040_3_Day7
Illumina Stranded mRNA

value: PBMCs

value: monocytes

value: PMC

value: day 7


title: CTCF, vehicle-treated control BAs-rep2

description: Library name: CTCF_minusCL_rep2

value: vehicle


title: U2OS_scramble_control_siRNA_biolrep_3

description: Library name: U2OS_DHX8_NEG_CON_C

value: Bone

value: Osteosarcoma

value: WT

value: 72 hours


title: DNA methylation profile for 203976760023_R06C01

value: Brain

value: Cerebellum

value: Male

tag: disease state

value: Huntington's disease

value: Oxford


title: nonPMC, Rep4, Day7

description:
Library name: S67_Non_PMC_NC040_3_Day7
Illumina Stranded mRNA

value: nonPMC


title: U2OS_scramble_control_siRNA_biolrep_2

description: Library name: U2OS_DHX8_NEG_CON_B

value: DMSO control


title: DNA methylation profile for 203976760022_R01C01

value: Entorhinal cortex

tag: brain bank


title: β3-AR-stimulated control BAs, rep2

description: Library name: plusCL_rep2

value: brown adipocytes

value: Control

value: β3-AR agonist


title: vehicle control BAs, rep2

description: Library name: minusCL_rep2


title: nonPMC, Rep4, Day2

description:
Library name: S59_Non_PMC_NC040_3_Day2
Illumina Stranded mRNA

value: PBMCs

value: monocytes

value: day 2


title: CTCF, vehicle-treated control BAs-rep1

description: Library name: CTCF_minusCL_rep1

value: vehicle


title: U2OS_mock_control_siRNA_biolrep_3

description: Library name: U2OS_DHX8_Untreated_C

value: Bone

value: Osteosarcoma

value: WT

value: Mock control


title: PMC, Rep3, Day7

description:
Library name: S57_PMC_1_100_NC053_3_Day7
Illumina Stranded mRNA

value: PMC

value: day 7


title: U2OS_scramble_control_siRNA_biolrep_1

description: Library name: U2OS_DHX8_NEG_CON_A

value: 72 hours


title: DNA methylation profile for 203977000075_R03C01

value: Brain

value: Striatum

value: Female

value: London

tag: bisulfite conversion batch


title: β3-AR-stimulated control BAs, rep1

description: Library name: plusCL_rep1

value: brown adipocytes

value: Control


title: β3-AR-stimulated H2A.Z KD BAs, rep1

description: Library name: KD_plusCL_rep1

value: H2A.Z KD

value: β3-AR agonist


title: DNA methylation profile for 203977000075_R01C01

value: Male

value: Huntington's disease

value: Oxford

tag: neuronal proportion


title: PMC, Rep4, Day2

description:
Library name: S61_PMC_1_100_NC040_3_Day2
Illumina Stranded mRNA

value: PBMCs

value: monocytes

value: day 2


title: U2OS_DHX8_siRNA_O5_biolrep_4

description: Library name: U2OS_DHX8_siRNA_O5_D

value: Bone

value: Osteosarcoma

value: WT

tag: treatment

value: DHX8 siRNA


title: vehicle control BAs, rep1

description: Library name: minusCL_rep1

tag: cell line

value: vehicle


title: nonPMC, Rep3, Day7

description:
Library name: S55_Non_PMC_NC053_3_Day7
Illumina Stranded mRNA

value: nonPMC

value: day 7


title: WT mNPC, 16d, Replicate 2

description:
Library name: WT_mNPC_16d_REP2
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cell ranger software v7.2.0; Further QC filtering and analysis were done loading cellranger results in R v4.4.0 with Read10X function from Seurat package.
Assembly: mm10
Supplementary files format and content: Seurat object (RDS), barcodes, matrices and features from cellranger count output.

source_name: Mouse Neural progenitor cells (mNPCs)

extract_protocol: Please check manuscript

value: Mouse Neural progenitor cells (mNPCs)

tag: genotype

value: 16d Differentiated NPCs


title: WT mNPC, 16d, Replicate 1

description:
Library name: WT_mNPC_16d_REP1
10x Genomics


title: DNA methylation profile for 203976760022_R05C01

description: DNA methylation profile from Huntington's disease patient

value: Brain

value: Cerebellum

value: Female


title: DNA methylation profile for 203991460019_R08C01

value: Entorhinal cortex

value: Huntington's disease


title: PMC, Rep3, Day2

description:
Library name: S49_PMC_1_100_NC053_3_Day2
Illumina Stranded mRNA

value: PBMCs

tag: condition

value: PMC


title: R70H, Clone2, mNPC, 16d, Replicate 2

description:
Library name: R70H_Clone2_mNPC_16d_REP2
10x Genomics


title: U2OS_DHX8_siRNA_O5_biolrep_3

description: Library name: U2OS_DHX8_siRNA_O5_C

value: 72 hours


title: DNA methylation profile for 203977090035_R01C01

description: DNA methylation profile from healthy control

value: Male

value: Control

value: Oxford


title: U2OS_DHX8_siRNA_O2_biolrep_4

description: Library name: U2OS_DHX8_siRNA_O2_D

value: Bone

value: Osteosarcoma

value: WT

value: DHX8 siRNA


title: R70H, Clone1, mNPC, 16d, Replicate 2

description:
Library name: R70H_Clone1_mNPC_16d_REP2
10x Genomics

value: Mouse Neural progenitor cells (mNPCs)


title: nonPMC, Rep2, Day7

description:
Library name: S43_Non_PMC_NC032_3_Day7
Illumina Stranded mRNA

value: monocytes

tag: group

value: nonPMC

value: day 7


title: DNA methylation profile for 203977000019_R07C01

value: Brain

value: Cerebellum


title: U2OS_DHX8_siRNA_O2_biolrep_3

description: Library name: U2OS_DHX8_siRNA_O2_C

tag: time


title: DNA methylation profile for 203991460065_R05C01

value: Entorhinal cortex


title: R70H, Clone1, mNPC, 16d, Replicate 1

description:
Library name: R70H_Clone1_mNPC_16d_REP1
10x Genomics

value: 16d Differentiated NPCs


title: PMC, Rep2, Day2

description:
Library name: S37_PMC_1_100_NC032_3_Day2
Illumina Stranded mRNA

value: PBMCs

value: PMC

tag: monocyte-platelet ratio

value: day 2


title: nonPMC, Rep2, Day2

description:
Library name: S35_Non_PMC_NC032_3_Day2
Illumina Stranded mRNA

tag: day


title: U2OS_DHX8_siRNA_O2_biolrep_2

description: Library name: U2OS_DHX8_siRNA_O2_B

tag: tissue

value: 72 hours


title: U2OS_DHX8_siRNA_O5_biolrep_2

description: Library name: U2OS_DHX8_siRNA_O5_B

tag: cell type


title: WT, mNPC, Histone H2B ubiquitination, Replicate 2

description: Library name: WT_mNPC_Ub_W_REP2

data_processing:
Sequenced reads (FASTQ files) were processed with nf-core pipelines (PMID: 32055031) for read trimming, QC and alignment algainst mm10 using nf-core/cutandrun v3.2.2 (https://github.com/nf-core/cutandrun/tree/3.2.2)  with additional ‘--aligner bowtie2 --read_length 150 --trim_nextseq 20 --blacklist [BED]’
Assembly: mm10, GRCh38
Supplementary files format and content: Bigwig files with average (normalized) signal from replicates and/or alleles (WT/M)
Library strategy: Cut&Run

source_name: WT mESC

extract_protocol:
CUT&RUN assays were performed using the CUTANA kit following the manufacturer's protocol (EpiCypher, 14-1048). Briefly, mESCs Ring1B WT and R70H mutants were trypsinized (0.05%) to obtain a single-cell suspension followed by mild crosslinking with 0.1% formaldehyde for 1 minute. A total of 2 × 10⁵ cells were incubated with ConA beads, followed by overnight incubation with antibodies against HA (EpiCypher, 13-2010), Flag (EpiCypher, 13-2031), H3K27me3 (Active Motif, 39155), H2AK119ub (Cell Signaling D27C4), and IgG (EpiCypher, 13-0042).
E. coli was used as a spike-in control for all samples. Additionally, the SNAP-CUTANA™ K-MetStat Panel (EpiCypher, 19-1002) was included as an additional spike-in control for IgG and H3K27me3. Two biological replicates were used per condition.

treatment_protocol: there was no additional treatments

value: WT mESC

tag: antibody


title: DNA methylation profile for 203991450163_R08C01

tag: brain region

tag: Sex

value: Male

value: Control

value: Oxford


title: R70H, Clone2, mNPC, 16d, Replicate 1

description:
Library name: R70H_Clone2_mNPC_16d_REP1
10x Genomics


title: PMC, Rep2, Day7

description:
Library name: S45_PMC_1_100_NC032_3_Day7
Illumina Stranded mRNA


title: nonPMC, Rep3, Day2

description:
Library name: S47_Non_PMC_NC053_3_Day2
Illumina Stranded mRNA


title: HCT116_DHX8wild-type_scramble_control_siRNA_biolrep_4

description: Library name: HCT116_wtDHX8_noDOX_SCRM_4

source_name: Large intestine; Colon

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: WT

value: Scramble control siRNA


title: PMC, Rep1, Day7

description:
Library name: S33_PMC_1_100_NC051_3_Day7
Illumina Stranded mRNA

value: monocytes

value: day 7


title: nonPMC, Rep1, Day7

description:
Library name: S31_Non_PMC_NC051_3_Day7
Illumina Stranded mRNA

value: nonPMC


title: DNA methylation profile for 203976760024_R04C01

value: Brain

value: Striatum

tag: age

tag: disease state

value: Huntington's disease


title: U2OS_DHX8_siRNA_O2_biolrep_1

description: Library name: U2OS_DHX8_siRNA_O2_A

value: Bone

value: Osteosarcoma

value: DHX8 siRNA


title: WT, mNPC, allelW, HA, Replicate 2

description: Library name: WT_mNPC_allelW_HA_W_REP2

value: WT mESC

value: Mouse Neural progenitor cells (mNPCs)

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug


title: HCT116_DHX8wild-type_scramble_control_siRNA_biolrep_3

description: Library name: HCT116_wtDHX8_noDOX_SCRM_3

value: 72 hours


title: WT, mNPC, allelW, HA, Replicate 1

description: Library name: WT_mNPC_allelW_HA_W_REP1


title: B0_112_017_T1

city: Stanford

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

description:
Library name: B0_112_017_T1
Bulk RNAseq

data_processing:
FASTQ files were quasi-aligned to Gencode version 27, and Salmon was used to obtain expression levels.
After restricting to protein coding genes, expression levels per gene were normalized to TPM.
Assembly: GRCh38.
Supplementary files format and content: Tab-delimited text files with TPM for each sample.

source_name: Tumor

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

value: Tumor

tag: timepoint

value: T1 (baseline)


title: PMC, Rep1, Day2

description:
Library name: S25_PMC_1_100_NC051_3_Day2
Illumina Stranded mRNA

value: PBMCs

value: PMC

value: day 2


title: B0_112_017_T4

description:
Library name: B0_112_017_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (2 doses), nivolumab (1 dose)


title: WT, mNPC, allelW, FL, Replicate 2

description: Library name: WT_mNPC_allelW_FL_W_REP2

value: Flag(DYKDDDDK-Tag)

value: WT


title: WT, mNPC, H3K27me3, Replicate 2

description: Library name: WT_mNPC_k27me3_W_REP2

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: HCT116_DHX8wild-type_scramble_control_siRNA_biolrep_2

description: Library name: HCT116_wtDHX8_noDOX_SCRM_2

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: Scramble control siRNA


title: nonPMC, Rep1, Day2

description:
Library name: S23_Non_PMC_NC051_3_Day2
Illumina Stranded mRNA

value: monocytes

value: nonPMC


title: HCT116_DHX8wild-type_scramble_control_siRNA_biolrep_1

description: Library name: HCT116_wtDHX8_noDOX_SCRM_1


title: B0_112_016_T2

description:
Library name: B0_112_016_T2
Bulk RNAseq

value: T2b (post-RT/pre-BO112 #2)

value: RT (6 Ggy x 5), BO-112 (1 dose)


title: WT, mESC, H3K27me3, Replicate 2

description: Library name: WT_mESC_k27me3_W_REP2

value: WT mESC

value: Mouse embryonic stem cells (mESCs)


title: RPE1 ATAC-seq rep 2

first: Jessica

middle: A

last: Downs

address: 237 Fulham Road

description: Library name: RPE1 ATAC-seq rep 2

data_processing:
Fastq reads were trimmed using TrimGalore (v0.6.6) (Krueger F, Trimgalore (2023), GitHub repository, https://github.com/FelixKrueger/TrimGalore) using the options --trim-n --paired.
Trimmed reads were mapped to the human CHM13-T2Tv1.1 genome (GenBank GCA_009914755.3) using Bowtie2 (v2.4.2) (Langmead and Salzberg, 2012) using the parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --soft-clipped-unmapped-tlen --non-deterministic --phred33 -I 50 -X 1000.
Reads with more than 3 mismatches were removed with Sambamba (v0.5.0) (Tarasov et al., 2015), and their corresponding mates were removed with Picard tools (v2.23.8) (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute).
Sam files were converted to bam with SAMtools (v1.11) (Danecek et al., 2021).
Reads mapped to chrM were removed using SAMtools, and duplicate reads were removed using Picard.
Bigwig files were generated using deepTools bamCoverage and normalised using total number of mapped reads after filtering, de-deduplication, and chrM removal (Ramirez et al., 2014).
Peaks were called using MACS2 (v2.2.7.1) (Zhang et al., 2008) callpeak with filtered bam files as input and options -g 3054832041 -f BAMPE -q 0.01.
Bedtools (Quinlan and Hall, 2010) multiiner was used to identify peaks present in 2 out of 2 biological replicates.
Assembly: T2T-CHM13v1.1
Supplementary files format and content: Bigwig files showing ATAC-seq read coverage for reads mapped to the T2T-CHM13v1.1 reference genome, aftering filtering, de-duplication, and chrM removal.
Supplementary files format and content: NarrowPeak files showing ATAC-seq peaks called using MACS2 for each biological replicate.
Supplementary files format and content: Bed file showing consensus ATAC-seq peaks present in 2 out of 2 biological replicates.

source_name: Retina

growth_protocol: hTERT-RPE1 cells were cultured in Dulbecco Modified Minimal Essential Medium (DMEM)/F-12 (Sigma) supplemented with 10% FBS (Gibco), 200µM glutamax (Gibco), 0.26% sodium bicarbonate (Gibco), and 1% penicillin/streptomycin (P/S)(Sigma). Cells were maintained at 37oC in a humified incubator with 5% CO2

extract_protocol:
ATAC-seq (Assay for Transposase-Accessible Chromatin by Sequencing) was performed according to the Omni-ATAC protocol (Corces et al., 2017). Briefly, 100,000 cells were collected per experiment and nuclei were extracted. Nuclei were incubated with Tn5 on ice for 30 minutes. DNA was purified using the Qiagen MinElute reaction cleanup kit (Qiagen).
DNA extracted from ATAC-seq was amplified using the NEBNext high-fidelity PCR master mix (New England Biolabs) and Illumina Nextera DNA indexes (Illumina). Libraries were purified using AMPure XP beads (Beckman Coulter), then profiled using the Agilent TapeStation D1000 high sensitivity ScreenTape on the Agilent 4150 TapeStation System, and sequenced on the Illumina Novaseq X Plus with 150 x 150 bp reads by Novogene (Novogene Corporation Inc. UK).

value: Retina

value: Retinal pigment epithelial


title: HCT116_DHX8-wildtype_DHX8_siRNA_biolrep_4

description: Library name: HCT116_wtDHX8_noDOX_DHX8kd_4

value: DHX8 siRNA

value: 72 hours


title: WT, mESC, Histone H2B ubiquitination, Replicate 2

description: Library name: WT_mESC_Ub_W_REP2


title: B0_112_016_T1

description:
Library name: B0_112_016_T1
Bulk RNAseq

value: Tumor

value: T1 (baseline)


title: RPE1 ATAC-seq rep 1

description: Library name: RPE1 ATAC-seq rep 1

value: WT


title: WT, mESC, IgG, Replicate 2

description: Library name: WT_mESC_G_W_REP2

value: IgG, EpiCypher (Cat #13-0042)1ug


title: HCT116_DHX8-wildtype_DHX8_siRNA_biolrep_2

description: Library name: HCT116_wtDHX8_noDOX_DHX8kd_2

value: Large intestine; Colon


title: WT, mESC, IgG, Replicate 1

description: Library name: WT_mESC_G_W_REP1


title: FSK-treated H2A.Z KD human BAs, rep4

description: Library name: KD_plusFSK_rep4

data_processing:
The raw reads of Micro-C sequencing data were trimmed to remove any sequencing indexes or adaptors using the Trim Galore software (version 0.6.6).
The trimmed reads were mapped to the human genome (hg38) using the BWA MEM algorithm (version 0.7.17-r1188)
BAM files produced by BWA MEM were imported into the pairtools software to generate read pairs representing valid contacts of two chromatin regions, following the sorting, deduplication, and splitting procedures.
Any read pairs with a read mapping quality score of less than five or a genomic distance of less than 100bp were excluded from our study due to the low mapping quality and potential random ligation
The resulting high-quality read pairs were converted into a contact matrix in multiple genomic resolutions in each condition. The contact matrix was stored in HDF5 format as a COOL file using the COOLER package (version 0.9.1) [PMID: 31290943] or a HIC file using the JUICER software (version 1.22.01)
Contact matrices were then normalized using iterative correction in COOL files or Knight–Ruiz in HIC files.
Assembly: hg38
Supplementary files format and content: HIC file, contact matrix in multiple genomics resolution data generated by jucier

source_name: Primary human brown adipocytes

growth_protocol: Primary human brown preadipocytes were isolated from the deep neck region of a lean and metabolically healthy donor. To initiate differentiation, preadipocytes were allowed to reach confluency and treated with DMEM/F-12 medium supplemented with 10% FBS, 33 μM biotin, 0.5 μM human insulin, 17 μM pantothenate, 0.1 μM dexamethasone, 2 nM T3, 500 μM IBMX, 30 μM indomethacin, 10 μg/ml Transferrin, and 1 μM Rosiglitazone for 21 days. Throughout the differentiation process, the medium was changed every three days.

extract_protocol:
Micro-C was performed using  DovetailTM Micro-C kit (Dovetail GENOMICS) according to the manufacturer’s protocol. Vehicle-treated control, FSK-treated control, and FSK-treated H2A.Z KD human brown adipocytes were washed twice with PBS and then the nuclei were isolated by incubating the cells with lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 1 mM MgCl2, 0.1% NP40, and 1x protease inhibitor cocktail) for 10 minutes on ice. The cell suspension was filtered through a 40 μm strainer, centrifuged at 1,000g for 5 minutes, and washed twice with ice-cold PBS. The nuclei were counted and diluted with PBS to 1 million/ml, followed by fixation with 3 mM DSG at room temperature for 35 minutes and 1% formaldehyde at room temperature for 10 minutes with rotation. The fixation was quenched by adding Tris-HCl, pH7.5 to a final concentration of 375 mM. Nuclei were collected with a spin at 2,000 g for 5 minutes and washed twice with ice-cold PBS. Nuclei pellet was resuspended with MNase digestion buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP40, and 1x protease inhibitor cocktail) and appropriate amount of MNase was added to digest genomic DNA at 37°C for 20 minutes in an agitating thermal mixer set at 1,000 rpm. The MNase reaction was inactivated by adding 0.5 M EGTA to a final concentration of 4 mM, followed by incubation at 65°C for 10 minutes in an agitating thermal mixer set at 1,000 rpm. The fragment size distribution was assessed using a Bioanalyzer or Tapestation HS DNA chip. The optimal digestion condition resulted in 40-70% of mono-nucleosomes. MNase-digested chromatin was then subjected to proximity ligation, library preparation, ligation capture and amplification according to the manufacturer’s protocol.
Library preparation, ligation capture and amplification were performed using the DovetailTM Micro-C kit (Dovetail GENOMICS) according to the manufacturer’s protocol.

treatment_protocol: H2A.Z knockdown was conducted in primary human brown adipocytes on day 21. Mature adipocytes were transduced with lentivirus expressing either a non-targeting shRNA or an shRNA targeting H2A.Z, generating control or H2A.Z knockdown (KD) adipocytes. To activate β3-AR signaling, day26 control or H2A.Z KD adipocytes were treated with either vehicle or forskolin (FSK) for 4 hours.

value: Primary human brown adipocytes

value: brown adipocytes

value: H2A.Z knckdown

value: FSK


title: B0_112_016_T4

description:
Library name: B0_112_016_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (2 doses), nivolumab (1 dose)


title: FSK-treated H2A.Z KD human BAs, rep3

description: Library name: KD_plusFSK_rep3


title: B0_112_015_T4

description:
Library name: B0_112_015_T4
Bulk RNAseq


title: HCT116_DHX8-wildtype_DHX8_siRNA_biolrep_1

description: Library name: HCT116_wtDHX8_noDOX_DHX8kd_1

value: Colorectal adenocarcinoma


title: B0_112_015_T1

description:
Library name: B0_112_015_T1
Bulk RNAseq


title: HCT116_DHX8-wildtype_DHX8_siRNA_biolrep_3

description: Library name: HCT116_wtDHX8_noDOX_DHX8kd_3


title: B0_112_014_T4

description:
Library name: B0_112_014_T4
Bulk RNAseq


title: FSK-treated H2A.Z KD human BAs, rep2

description: Library name: KD_plusFSK_rep2


title: HCT116_DHX8wild-type_scramble_control_siRNA_plusDoxycyclin_biolrep_4

description: Library name: HCT116_wtDHX8_DOX_SCRM_4

value: Scramble control siRNA plus doxycycline


title: WT, mESC, allelW, FL, Replicate 2

description: Library name: WT_mESC_allelW_FL_W_REP2

value: WT mESC

value: Mouse embryonic stem cells (mESCs)

value: Flag(DYKDDDDK-Tag)


title: HCT116_DHX8wild-type_scramble_control_siRNA_plusDoxycyclin_biolrep_3

description: Library name: HCT116_wtDHX8_DOX_SCRM_3

value: 72 hours


title: FSK-treated control human BAs, rep4

description: Library name: plusFSK_rep4

value: Control


title: B0_112_014_T1

description:
Library name: B0_112_014_T1
Bulk RNAseq

value: Tumor

value: T1 (baseline)


title: WT mNPC, IgG, Replicate 2

description: Library name: mNPC_IgG_W_REP2

value: Mouse Neural progenitor cells (mNPCs)

value: IgG, EpiCypher (Cat #13-0042)1ug

value: WT


title: FSK-treated control human BAs, rep3

description: Library name: plusFSK_rep3

value: Primary human brown adipocytes

value: brown adipocytes


title: B0_112_014_T2

description:
Library name: B0_112_014_T2
Bulk RNAseq

value: T2b (post-RT/pre-BO112 #2)

value: RT (6 Ggy x 5), BO-112 (1 dose)


title: FSK-treated H2A.Z KD human BAs, rep1

description: Library name: KD_plusFSK_rep1

value: H2A.Z knckdown

value: FSK


title: B0_112_013_T4

description:
Library name: B0_112_013_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (3 doses)


title: HCT116_DHX8wild-type_scramble_control_siRNA_plusDoxycyclin_biolrep_2

description: Library name: HCT116_wtDHX8_DOX_SCRM_2

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: Scramble control siRNA plus doxycycline


title: HCT116_DHX8wild-type_scramble_control_siRNA_plusDoxycyclin_biolrep_1

description: Library name: HCT116_wtDHX8_DOX_SCRM_1

value: 72 hours


title: WT mNPC, IgG, Replicate 1

description: Library name: mNPC_IgG_W_REP1

value: WT mESC


title: WT, mESC, allelW, HA, Replicate 1

description: Library name: WT_mESC_allelW_HA_W_REP1

value: Mouse embryonic stem cells (mESCs)

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug


title: B0_112_013_T3

description:
Library name: B0_112_013_T3
Bulk RNAseq

value: Tumor

value: T3 (post-RT/pre-BO112 #3)

value: RT (6 Gy x 5), BO-112 (2 doses)


title: HCT116_DHX8-wildtype_DHX8_siRNA_plusDoxycyclin_biolrep_4

description: Library name: HCT116_wtDHX8_DOX_DHX8kd_4

value: WT

value: DHX8 siRNA plus doxycycline


title: FSK-treated control human BAs, rep2

description: Library name: plusFSK_rep2

value: Primary human brown adipocytes

value: brown adipocytes

value: Control


title: R70H mNPC, IgG, MB, Replicate 2

description: Library name: mNPC_IgG_MB_REP2

value: Mouse Neural progenitor cells (mNPCs)

value: IgG, EpiCypher (Cat #13-0042)1ug

value: RNF2 R70H/WT


title: R70H mNPC, IgG, MB, Replicate 1

description: Library name: mNPC_IgG_MB_REP1


title: FSK-treated control human BAs, rep1

description: Library name: plusFSK_rep1

value: FSK


title: vehicle-treated control human BAs, rep4

description: Library name: minusFSK_rep4

value: vehicle


title: HCT116_DHX8-wildtype_DHX8_siRNA_plusDoxycyclin_biolrep_3

description: Library name: HCT116_wtDHX8_DOX_DHX8kd_3

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: 72 hours


title: DNA methylation profile for 203976760022_R06C01

description: DNA methylation profile from Huntington's disease patient

value: Brain

value: Cerebellum

value: Male

value: Huntington's disease

tag: brain bank

value: Oxford

tag: bisulfite conversion batch

tag: neuronal proportion


title: B0_112_013_T1

description:
Library name: B0_112_013_T1
Bulk RNAseq

value: Tumor

value: T1 (baseline)

tag: treatment


title: B0_112_013_T2

description:
Library name: B0_112_013_T2
Bulk RNAseq

value: T2 (pre-RT/pre-BO112 #2)


title: vehicle-treated control human BAs, rep3

description: Library name: minusFSK_rep3

tag: cell line

value: Primary human brown adipocytes

value: brown adipocytes

tag: genotype

value: Control


title: HCT116_DHX8-wildtype_DHX8_siRNA_plusDoxycyclin_biolrep_2

description: Library name: HCT116_wtDHX8_DOX_DHX8kd_2

value: WT

value: DHX8 siRNA plus doxycycline

tag: time


title: B0_112_012_T4

description:
Library name: B0_112_012_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (3 doses)


title: R70H mNPC, IgG, MA, Replicate 1

description: Library name: mNPC_IgG_MA_REP1

value: Mouse Neural progenitor cells (mNPCs)

value: IgG, EpiCypher (Cat #13-0042)1ug

value: RNF2 R70H/WT


title: HCT116_DHX8-wildtype_DHX8_siRNA_plusDoxycyclin_biolrep_1

description: Library name: HCT116_wtDHX8_DOX_DHX8kd_1

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: 72 hours


title: R70H mNPC, IgG, MA, Replicate 2

description: Library name: mNPC_IgG_MA_REP2


title: B0_112_012_T1

description:
Library name: B0_112_012_T1
Bulk RNAseq


title: R70H mNPC, Histone H2B ubiquitination, MB, Replicate 2

description: Library name: 112_mNPC_Ub_MB_REP2


title: vehicle-treated control human BAs, rep1

description: Library name: minusFSK_rep1

value: vehicle


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_biolrep_4

description: Library name: HCT116_mutDHX8_RNA_noDOX_SCRM_4

value: DHX8-R647G/F648G mutant

value: Scramble control siRNA


title: H2A.Z, FSK-treated control human BAs-rep2

description: Library name: H2AZ_plusFSK_rep2

data_processing:
The raw reads of ChIP-seq data were preprocessed by the CHIPs pipeline[https://doi.org/10.12688/f1000research.52878.1], which includes read trimming, read mapping to the human genome (hg38), read level quality control, and peak level quality control.
For H2AZ ChIP-seq, the BAM files with deduplicated reads were imported into the DANPOS2 for genome-wide peak identification.
The BigWig files were generated by deepTools bamCoverage software (version 3.3.1) with --normalizeUsing CPM --binSize 10 --ignoreDuplicates --extendReads based on uniquely mapped reads in BAM files produced by CHIPs pipeline
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: XLS files for identified ChIP-seq peaks when compared to Input background (except for input samples)

extract_protocol:
For H2A.Z and H3K27ac ChIP-seq in primary human brown adipocytes, cells were washed twice with PBS and then the nuclei were isolated by incubating the cells with lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 1 mM MgCl2, 0.1% NP40, and 1x protease inhibitor cocktail) for 10 minutes on ice. The cell suspension was filtered through a 40 μm strainer, centrifuged at 1,000g for 5 minutes, and washed twice with ice-cold PBS. The nuclei were counted and diluted with PBS to 1 million/ml, then fixed with 1% formaldehyde at room temperature for 10 minutes, quenched with glycine, and washed twice with ice-cold PBS. Crosslinked adipocytes were scraped in PBS supplemented with 1mM PMSF, pelleted at 3,000 g for 5 minutes at 4°C, and suspended in 300 μl lysis buffer (50 mM Tris pH 7.5, 1% SDS, 0.25% sodium deoxycholate, and 1X protease inhibitor cocktail), followed by incubation on ice for 10 minutes. The volume was then increased to 1.2 ml by adding 900 μl of ChIP dilution buffer (50 mM Tris pH 7.5, 0.1% SDS, 150 mM NaCl, 1.84% Triton X-100, and 1x protease inhibitor cocktail). Chromatin was sonicated using a Branson Sonifier SFX250 (50% amplitude, 3.5 minutes). After centrifugation at 13,000 rpm for 10 minutes, the supernatant was transferred to a new tube and mixed with 1.8 ml ChIP dilution buffer. For each ChIP reaction 1.5 ml lysate was incubated overnight at 4°C with 5 μg of the indicated antibodies antibodies (H2A.Z (Active Motif, 39943), H3K27ac (Active Motif, 39133)).On the next day, 20 μl of DynabeadsTM Protein G beads were added and incubated for additional 2 hours at 4°C. The beads were washed twice with ice-cold ChIP buffer with 0.1% SDS, washed twice with ice-cold High-salt wash buffer (50 mM Tris pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM EDTA, 0.1% SDS), washed twice with ice-cold LiCl buffer (10 mM Tris pH 8.0, 0.25 M LiCl, 0.5% Triton X-100, 0.5% sodium deoxycholate, 1 mM EDTA), and washed once with ice-cold TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). The protein-DNA complex was eluted from beads by adding 100 μl of freshly prepared elution buffer (10 mM Tris pH 8.0, 0.1% SDS, 150 mM NaCl, 5 mM DTT) and incubated at 65°C in a thermomixer set at 600 rpm for 1 hour. Then, reverse crosslinking was carried out by adding 2 μl of RNaseA (10 mg/ml, ThermoFisher Scientific, EN0531) and incubating at 37°C for 1 hour, followed by supplementation with 3 μl of Proteinase K (20 mg/ml, ThermoFisher Scientific, 25530049) and incubation at 65°C for 3 hours or overnight. Genomic DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and dissolved in 20 μl H2O.
ChIP library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacturer’s protocol. 5 ng ChIP DNA was used for library preparation.

treatment_protocol: D21 primary human brown adipocytes  were transduced with lentivirus expressing a non-targeting shRNA, generating control  adipocytes. To activate β3-AR signaling, day26 control adipocytes were treated with either vehicle or forskolin (FSK) for 4 hours.

value: FSK


title: R70H mNPC, Histone H2B ubiquitination, MA, Replicate 2

description: Library name: 112_mNPC_Ub_MA_REP2


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_biolrep_2

description: Library name: HCT116_mutDHX8_RNA_noDOX_SCRM_2


title: vehicle-treated control human BAs, rep2

description: Library name: minusFSK_rep2

value: Primary human brown adipocytes


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_biolrep_3

description: Library name: HCT116_mutDHX8_RNA_noDOX_SCRM_3


title: B0_112_011_T2

description:
Library name: B0_112_011_T2
Bulk RNAseq

value: Tumor

value: T2 (pre-RT/pre-BO112 #2)


title: B0_112_010_T3

description:
Library name: B0_112_010_T3
Bulk RNAseq

value: T3 (post-RT/pre-BO112 #3)

value: RT (6 Gy x 5), BO-112 (2 doses)


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_biolrep_1

description: Library name: HCT116_mutDHX8_RNA_noDOX_SCRM_1


title: H3K27ac, FSK-treated control human BAs-rep2

description: Library name: H3K27ac_plusFSK_rep2

value: brown adipocytes

value: Control


title: R70H mNPC, H3K27me3, MB, Replicate 2

description: Library name: 112_mNPC_k27me3_MB_REP2

value: Mouse Neural progenitor cells (mNPCs)

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: B0_112_011_T1

description:
Library name: B0_112_011_T1
Bulk RNAseq

value: T1 (baseline)


title: R70H mNPC, allelW, HA, MB, Replicate 2

description: Library name: 112_mNPC_allelW_HA_MB_REP2

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug

value: RNF2 R70H/WT


title: R70H mNPC, H3K27me3, MA, Replicate 2

description: Library name: 112_mNPC_k27me3_MA_REP2


title: B0_112_010_T2

description:
Library name: B0_112_010_T2
Bulk RNAseq


title: R70H mNPC, allelW, HA, MB, Replicate 1

description: Library name: 112_mNPC_allelW_HA_MB_REP1


title: H2A.Z, FSK-treated control human BAs-rep1

description: Library name: H2AZ_plusFSK_rep1


title: H3K27ac, FSK-treated control human BAs-rep1

description: Library name: H3K27ac_plusFSK_rep1


title: Input, FSK-treated control human BAs-rep2

description: Library name: Input_plusFSK_rep2


title: B0_112_010_T1

description:
Library name: B0_112_010_T1
Bulk RNAseq


title: B0_112_011_T4

description:
Library name: B0_112_011_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (3 doses)


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_3

description: Library name: HCT116_mutDHX8_RNA_DOX_SCRM_3

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: DHX8-R647G/F648G mutant

value: Scramble control siRNA plus doxycycline

value: 72 hours


title: Input, FSK-treated control human BAs-rep1

description: Library name: Input_plusFSK_rep1

value: Primary human brown adipocytes

value: FSK


title: R70H mNPC, allelM, FL, MB, Replicate 2

description: Library name: 112_mNPC_allelM_FL_MB_REP2

value: Flag(DYKDDDDK-Tag)


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_1

description: Library name: HCT116_mutDHX8_RNA_DOX_SCRM_1


title: B0_112_009_T4

description:
Library name: B0_112_009_T4
Bulk RNAseq

value: Tumor


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_4

description: Library name: HCT116_mutDHX8_RNA_DOX_SCRM_4


title: R70H mNPC, allelM, HA, MA, Replicate 1

description: Library name: 112_mNPC_allelM_HA_MA_REP1


title: R70H mNPC, allelW, FL, MA, Replicate 2

description: Library name: 112_mNPC_allelW_FL_MA_REP2


title: B0_112_009_T1

description:
Library name: B0_112_009_T1
Bulk RNAseq


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_2

description: Library name: HCT116_mutDHX8_RNA_DOX_SCRM_2


title: R70H mESC, Histone H2B ubiquitination, MB, Replicate 2

description: Library name: 112_mESC_Ub_MB_REP2

value: Mouse embryonic stem cells (mESCs)


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_3

description: Library name: HCT116_mutDHX8_RNA_DOX_DHX8kd_3

value: DHX8 siRNA plus doxycycline


title: H3K27ac, vehicle-treated control human BAs-rep1

description: Library name: H3K27ac_minusFSK_rep1

value: brown adipocytes

value: Control

value: vehicle


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_2

description: Library name: HCT116_mutDHX8_RNA_DOX_DHX8kd_2


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_4

description: Library name: HCT116_mutDHX8_RNA_DOX_DHX8kd_4


title: Input, vehicle-treated control human BAs-rep2

description: Library name: Input_minusFSK_rep2


title: B0_112_007_T4

description:
Library name: B0_112_007_T4
Bulk RNAseq


title: B0_112_007_T2

description:
Library name: B0_112_007_T2
Bulk RNAseq

value: T2 (pre-RT/pre-BO112 #2)


title: Input, vehicle-treated control human BAs-rep1

description: Library name: Input_minusFSK_rep1


title: B0_112_009_T2

description:
Library name: B0_112_009_T2
Bulk RNAseq


title: FSK-treated H2A.Z KD human BAs, rep3

description: Library name: KD_plusFSK_rep3

data_processing:
The raw reads of RNA sequencing data were trimmed to remove any sequencing indexes or adaptors using the Trim Galore software (version 0.6.6).
The STAR (version 2.7.9a) was used to map the trimmed reads to the mouse genome (mm10) and generate a gene-level read count matrix based on GENCODE gene annotation (version vM23).
The deepTools bamCoverage software (version 3.3.1) was used to generate BigWig files with --normalizeUsing RPKM based on BAM files produced by the STAR
The gene-level read count matrix was imported into the R package DESeq2 (version 1.32.0) for differential expression analysis with paired comparisons for three replicates.
Assembly: hg38
Supplementary files format and content: TSV file includes raw counts for each sample
Supplementary files format and content: TSV file includes differential expression result in treated control versus vehicle control
Supplementary files format and content: TSV file includes differential expression result in FSK treated H2A.Z KD versus  FSK treated control
Supplementary files format and content: BigWig

extract_protocol:
Total RNAs from vehicle-treated control, FSK-treated control, and FSK-treated H2A.Z KD primary human brown adipocytes were isolated using Direct-zol RNA Miniprep kits (Zymo Research, Irvine, CA).
Poly A-enriched mRNA libraries were prepared by Novogene

value: H2A.Z knckdown


title: HCT116_DHX8-R647G_F648G_RNAbinding_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_1

description: Library name: HCT116_mutDHX8_RNA_DOX_DHX8kd_1


title: B0_112_007_T1

description:
Library name: B0_112_007_T1
Bulk RNAseq

value: T1 (baseline)


title: FSK-treated H2A.Z KD human BAs, rep2

description: Library name: KD_plusFSK_rep2


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_biolrep_4

description: Library name: HCT116_mutDHX8_ATPase_noDOX_SCRM_4

value: Large intestine; Colon

value: DHX8-K549E mutant

value: Scramble control siRNA


title: R70H mESC, H3K27me3, MB, Replicate 2

description: Library name: 112_mESC_k27me3_MB_REP2

value: H3K27me3, EpiCypher (Cat #13-0055)1ug

value: RNF2 R70H/WT


title: R70H mESC, H3K27me3, MA, Replicate 2

description: Library name: 112_mESC_k27me3_MA_REP2


title: R70H mESC, Histone H2B ubiquitination, MA, Replicate 2

description: Library name: 112_mESC_Ub_MA_REP2


title: H3K27ac, vehicle-treated control human BAs-rep2

description: Library name: H3K27ac_minusFSK_rep2

value: Primary human brown adipocytes


title: R70H mESC, IgG, MB, Replicate 2

description: Library name: 112_mESC_G_MB_REP2

value: IgG, EpiCypher (Cat #13-0042)1ug


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_biolrep_3

description: Library name: HCT116_mutDHX8_ATPase_noDOX_SCRM_3

value: Colorectal adenocarcinoma

value: 72 hours


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_biolrep_2

description: Library name: HCT116_mutDHX8_ATPase_noDOX_SCRM_2


title: FSK-treated control human BAs, rep3

description: Library name: plusFSK_rep3

value: FSK


title: B0_112_004_T1

description:
Library name: B0_112_004_T1
Bulk RNAseq

value: Tumor


title: R70H mESC, IgG, MB, Replicate 1

description: Library name: 112_mESC_G_MB_REP1

value: Mouse embryonic stem cells (mESCs)


title: B0_112_004_T3

description:
Library name: B0_112_004_T3
Bulk RNAseq

value: T3 (post-RT/pre-BO112 #3)

value: RT (6 Gy x 5), BO-112 (2 doses)


title: R70H mESC, IgG, MA, Replicate 2

description: Library name: 112_mESC_G_MA_REP2


title: B0_112_003_T4

description:
Library name: B0_112_003_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (3 doses), nivolumab (2 doses)


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_4

description: Library name: HCT116_mutDHX8_ATPase_DOX_SCRM_4

value: Scramble control siRNA plus doxycycline


title: R70H mESC, IgG, MA, Replicate 1

description: Library name: 112_mESC_G_MA_REP1


title: R70H mESC, allelW, HA, MB, Replicate 2

description: Library name: 112_mESC_allelW_HA_MB_REP2

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_biolrep_1

description: Library name: HCT116_mutDHX8_ATPase_noDOX_SCRM_1

value: Large intestine; Colon

value: DHX8-K549E mutant


title: B0_112_003_T3

description:
Library name: B0_112_003_T3
Bulk RNAseq

value: RT (6 Gy x 5), BO-112 (2 doses), nivolumab (1 dose)


title: B0_112_004_T2

description:
Library name: B0_112_004_T2
Bulk RNAseq

value: T2 (pre-RT/pre-BO112 #2)


title: FSK-treated H2A.Z KD human BAs, rep1

description: Library name: KD_plusFSK_rep1

value: Primary human brown adipocytes

value: brown adipocytes

value: H2A.Z knckdown


title: vehicle-treated control human BAs, rep3

description: Library name: minusFSK_rep3

value: Control

value: vehicle


title: B0_112_003_T1

description:
Library name: B0_112_003_T1
Bulk RNAseq

value: Tumor

value: T1 (baseline)


title: FSK-treated control human BAs, rep2

description: Library name: plusFSK_rep2

value: FSK


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_3

description: Library name: HCT116_mutDHX8_ATPase_DOX_SCRM_3

value: Colorectal adenocarcinoma

value: 72 hours


title: R70H mESC, allelW, HA, MB, Replicate 1

description: Library name: 112_mESC_allelW_HA_MB_REP1

value: Mouse embryonic stem cells (mESCs)

value: RNF2 R70H/WT


title: vehicle-treated control human BAs, rep2

description: Library name: minusFSK_rep2


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_2

description: Library name: HCT116_mutDHX8_ATPase_DOX_SCRM_2

value: Scramble control siRNA plus doxycycline


title: HCT116_DHX8-K549E_ATPase_mutant_scramble_control_siRNA_plusDoxycyclin_biolrep_1

description: Library name: HCT116_mutDHX8_ATPase_DOX_SCRM_1

value: Large intestine; Colon


title: B0_112_002_T4

description:
Library name: B0_112_002_T4
Bulk RNAseq

value: T4 (surgery)

value: RT (6 Gy x 5), BO-112 (3 doses), nivolumab (2 doses)


title: R70H mESC, allelW, FL, MA, Replicate 2

description: Library name: 112_mESC_allelW_FL_MA_REP2

value: Flag(DYKDDDDK-Tag)


title: FSK-treated control human BAs, rep1

description: Library name: plusFSK_rep1

value: Primary human brown adipocytes


title: B0_112_002_T3

description:
Library name: B0_112_002_T3
Bulk RNAseq

value: T3 (post-RT/pre-BO112 #3)

value: RT (6 Gy x 5), BO-112 (2 doses), nivolumab (1 dose)


title: HCT116_DHX8-K549E_ATPase_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_4

description: Library name: HCT116_mutDHX8_ATPase_DOX_DHX8kd_4

value: DHX8-K549E mutant

value: DHX8 siRNA plus doxycycline


title: vehicle-treated control human BAs, rep1

description: Library name: minusFSK_rep1

value: brown adipocytes

value: Control

value: vehicle


title: R70H mESC, allelM, HA, MA, Replicate 2

description: Library name: 112_mESC_allelM_HA_MA_REP2

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug


title: B0_112_002_T2

description:
Library name: B0_112_002_T2
Bulk RNAseq

value: Tumor

value: T2 (pre-RT/pre-BO112 #2)


title: H1299_DHX8dtag_cl1A_CON_6H_biolrep_4

description: Library name: H1299_DHX8dtag_cl1A_CON_6H_4

source_name: Lung

value: Lung

value: Non-small cell lung cancer

value: WT

value: DMSO control

value: 6 hours


title: HCT116_DHX8-K549E_ATPase_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_3

description: Library name: HCT116_mutDHX8_ATPase_DOX_DHX8kd_3

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: 72 hours


title: H1299_DHX8dtag_cl1A_CON_6H_biolrep_3

description: Library name: H1299_DHX8dtag_cl1A_CON_6H_3


title: HCT116_DHX8-K549E_ATPase_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_2

description: Library name: HCT116_mutDHX8_ATPase_DOX_DHX8kd_2


title: R70H mESC, allelM, FL, MB, Replicate 1

description: Library name: 112_mESC_allelM_FL_MB_REP1

value: Mouse embryonic stem cells (mESCs)

value: Flag(DYKDDDDK-Tag)

value: RNF2 R70H/WT


title: R70H mESC, allelM, FL, MB, Replicate 2

description: Library name: 112_mESC_allelM_FL_MB_REP2


title: B0_112_002_T1

description:
Library name: B0_112_002_T1
Bulk RNAseq

value: T1 (baseline)


title: H1299_DHX8dtag_cl1A_CON_6H_biolrep_2

description: Library name: H1299_DHX8dtag_cl1A_CON_6H_2


title: HCT116_DHX8-K549E_ATPase_mutant_DHX8_siRNA_plusDoxycyclin_biolrep_1

description: Library name: HCT116_mutDHX8_ATPase_DOX_DHX8kd_1

value: DHX8-K549E mutant

value: DHX8 siRNA plus doxycycline


title: B0_112_001_T3

description:
Library name: B0_112_001_T3
Bulk RNAseq

value: T3 (post-RT/pre-BO112 #3)

value: RT (6 Gy x 5), BO-112 (2 doses), nivolumab (1 dose)


title: HCT116_Mock_control_biolrep_4

description: Library name: HCT116_MOCK_4

value: Mock control


title: WT, mNPC, H3K27me3, Replicate 1

description:
Library name: WT_mNPC_k27me3_W_REP1
Merged Signal of k27me3 WT mNPC Replicates

value: WT mESC

value: Mouse Neural progenitor cells (mNPCs)

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: HCT116_Mock_control_biolrep_3

description: Library name: HCT116_MOCK_3

value: WT


title: B0_112_001_T2

description:
Library name: B0_112_001_T2
Bulk RNAseq

value: Tumor

value: T2 (pre-RT/pre-BO112 #2)


title: WT, mNPC, allelW, FL, Replicate 1

description:
Library name: WT_mNPC_allelW_FL_W_REP1
Merged Signal of all RING1B mNPC WT alleles and replicates


title: H1299_DHX8dtag_cl1A_CON_6H_biolrep_1

description: Library name: H1299_DHX8dtag_cl1A_CON_6H_1

value: Lung

value: Non-small cell lung cancer

value: DMSO control

value: 6 hours


title: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_biolrep_4

description: Library name: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_4

value: 250 nM dTAG-V1


title: WT, mNPC, Histone H2B ubiquitination, Replicate 1

description:
Library name: WT_mNPC_Ub_W_REP1
Merged Signal of k27me3 WT mNPC Replicates


title: RNA-seq of TWIST1 KD LoVo cells (Rep 3)

city: DALLAS

first: ZHUAN

last: ZHOU

state: TX

address: 7430 W Northwest Hwy APT 1, Dallas, TX 75225, USA

department: Surgery

institute: University if Texas Southwestern Medical Center

description: Library name: LoVo_SR_3

data_processing:
[ChIP-seq] Raw reads were quality trimmed using Trim Galore, aligned to hg38 using Bowtie 2 (v.2.4.5), and converted to BAM format using samtools (v.1.6).
[ChIP-seq] Sorted BAM files were used as input for MACS2 (v.2.2.7.1) for peak calling (p-value < 0.05). Significant peaks were annotated by CHIPpeakAnno (v.3.30.1).
[RNA-seq] Raw reads were quality trimmed using Trim Galore (v0.6.6) and mapped to hg38 using HISAT2 (v.2.1.0). Mapped reads were converted to BAM format using samtools (v.1.6).
[RNA-seq] Sorted BAM files were used as input for featureCounts (v.2.0.0) to count the mapped reads to the gene coordinates reported in the GTF annotation file (GENCODE v.43).
Assembly: hg38
Supplementary files format and content: [ChIP-seq] MACS2 output files (.narrowPeak) containing genomic coordinates, peak boundaries, and statistical significance. [RNA-seq] Tab-delimited text files containing raw read counts per gene.

source_name: colon

growth_protocol: DMEM plus 10% FBS, 37oC, 5% CO2

extract_protocol:
[For ChIP-seq] Cells were cultured, fixed with formaldehyde, lysed, and sonicated. TWIST1 antibody (Abcam ab50887) was used for immunoprecipitation. [For RNA-seq] RNA was isolated using the Qiagen RNeasy Mini Kit. mRNA was purified from total RNA using oligo-dT magnetic beads.
[For ChIP-seq] Paired-end libraries were generated using Illumina protocols. Libraries were sequenced on the Illumina NextSeq 500 platform (150-bp paired-end). [For RNA-seq] After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis using dUTP. Libraries were sequenced on the Illumina NovaSeq 6000.

treatment_protocol: WIST1 knockout was generated using CRISPR-Cas9. TWIST1 knockdown was generated using shRNA.

value: colon

value: LoVo

value: TWIST1 knockdown

value: TWIST1 shRNA


title: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_biolrep_3

description: Library name: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_3


title: WT, mESC, Histone H2B ubiquitination, Replicate 1

description:
Library name: WT_mESC_Ub_W_REP1
Merged Signal of Histone H2B ubiquitination mESC WT replicates

value: Mouse embryonic stem cells (mESCs)


title: HCT116_Mock_control_biolrep_2

description: Library name: HCT116_MOCK_2

value: Large intestine; Colon

value: Colorectal adenocarcinoma

value: Mock control

value: 72 hours


title: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_biolrep_2

description: Library name: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_2

value: WT


title: RNA-seq of TWIST1 KD LoVo cells (Rep 2)

description: Library name: LoVo_SR_2


title: HCT116_Mock_control_biolrep_1

description: Library name: HCT116_MOCK_1


title: WT, mESC, H3K27me3, Replicate 1

description:
Library name: WT_mESC_k27me3_W_REP1
Merged Signal of all k27me3 mESC WT replicates

value: WT mESC

value: H3K27me3, EpiCypher (Cat #13-0055)1ug


title: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_biolrep_1

description: Library name: H1299_DHX8dtag_cl1A_250nM_6H_dTAGv1_1

value: Lung


title: B0_112_001_T1

description:
Library name: B0_112_001_T1
Bulk RNAseq

value: Tumor

value: T1 (baseline)


title: RNA-seq of TWIST1 KD LoVo cells (Rep 1)

description: Library name: LoVo_SR_1


title: LPS1

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

country: China

institute: Fudan University

description: Library name: sample1

data_processing:
The original sequencing data were analyzed by using FastQC software. 10X Chromium single cell transcriptome sequencing can be divided into three regions near the polyA and five regions near the transcriptional initiation site. Among them, 5-terminal transcript sequencing is usually performed together with T cell and B cell receptor gene TCR/BCR sequences for sequencing analysis. Different kits (including 3-terminal vs 5-terminal, and different versions) have slightly different library structures: For example, for a sample processed by a 10X single-cell 3-terminal V2 kit, Read 1 consists of a 16bp 10X Cell Barcode and a 10bp UMI sequence; The sample processed by the V3 kit, Read 1, consisted of 16 bp 10X Cell Barcode and 12 bp UMI sequence. In the analysis, 10X Cell Barcode in Read1 was used to separate individual cells, and UMI was used to remove PCR amplification bias and distinguish between transcripts. Read2 is a 151 bp cDNA sequence, and the first 91 bp is generally used for downstream analysis of Cell Ranger.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: Matrix table wuth raw gene counts for every gene and every cell

source_name: spleen

extract_protocol:
For the inspection and counting of single-cell suspension, the survival rate of cells is generally required to be above 85%, and the qualified cells are prepared by washing and re-suspension into a suitable cell concentration of 700~1200 cells/µl
According to the expected number of target cells, Gel Bead in Emulsion was constructed for single cell separation. After the normal formation of GEMs, GEMs were collected for reverse transcription in PCR instrument to realize labeling. For GEMs oil breaking treatment, a strand of cDNA was purified and enriched with magnetic beads, then cDNA amplification and quality inspection were carried out. The qualified cDNA was constructed by the second generation sequencing library, and the quantitative quality of the library was finally tested through the experimental processes of fragmentation, connecting sequencing joints, and sample Index PCR.

value: spleen

value: adult

value: male

value: cecal ligation and puncture (CLP)-induced AKI mode


title: WT, mESC, allelW, FL, Replicate 1

description:
Library name: WT_mESC_allelW_FL_W_REP1
Merged Signal of all RING1B mESC WT alleles and replicates

value: Flag(DYKDDDDK-Tag)


title: RNA-seq of Control LoVo cells (Rep C)

description: Library name: LoVo_C1_C

value: colon

value: LoVo

value: wild type

value: shRNA control


title: RNA-seq of Control LoVo cells (Rep B)

description: Library name: LoVo_C1_B


title: R70H mNPC, Histone H2B ubiquitination, MB, Replicate 1

description:
Library name: 112_mNPC_Ub_MB_REP1
Merged Signal of Histone H2B ubiquitination R70H mNPC Reps MB

value: Mouse Neural progenitor cells (mNPCs)

value: RNF2 R70H/WT


title: DKO RING1B, R70H, GSK3431uM, 48h, H3k27me3, Replicate 1

description: Library name: DKO_RING1B_R70H_GSK3431uM_48h_H3k27me3_REP1

value: Human embryo kidney tissue