title: Patient 34 post chemotherapy sample take during debulking surgery

city: Aurora

first: Benjamin

last: Bitler

state: Colorado

address: CU Anschutz Research Complex II  12700 East 19th Avenue  3400D

department: Cancer Biology

institute: University of Colorado-Anschutz

hyb_protocol: 5μL (100-300ng) of each RNA sample was mixed with 8μL of the Master Mix (reporter codeSet and hybridization buffer). 2μL of the capture probeSet was added; the solution was mixed and spun down. It was placed in a 65°C thermocycler (Bio-Rad Laboratories Inc, Hercules, California, USA) for 16 hours (maximum hybridization time should not exceed 48 hours).

scan_protocol: The samples were transferred to the preparation station (NanoString Technologies, Seattle, WA) with prepared nCounter Master Kit and a cartridge. The samples binding to the cartridge. The preparation station 12 lanes per run in approximately 2.5 to 3 hours. The cartridges were transferred to the Digital Analyzer (NanoString Technologies, Seattle, WA) for analysis. Cartridges were then scanned on the Digital Analyzer at 555 fields of view.

data_processing: Performed using nSolver Analysis Software version 4.0 using the nSolver advanced analysis tool. Background thresholding (or subtraction) according to the mean of negative control counts. Positive control normalization with geometric mean. Reference/housekeeping normalization using the geometric mean of housekeeping genes annotated in the RLF.

source_name: Primary high grade serous ovarian cancer

label_protocol: Not applicable.

growth_protocol: Not applicable. Specimens were collected from formalin-fixed paraffin embedded high grade serous ovarian cancer tumors.

extract_protocol: RNA was extracted using the High Pure FFPE RNA Isolation kit (Roche). RNA quantity and quality were assessed using an RNA Screentape on a TapeStation 4150 (Agilent). RNA concentration was determined by comparison to the RNA ladder and the percentage of RNA fragments greater than 200 bp was calculated (average 70.6%, all samples > 55%)

treatment_protocol: patient samples were obtained from native tumors during biopsy (pre) and interval debilking surgery following NACT (post)

tag: source

value: CU Anschutz, unpublished

tag: age

tag: Stage

value: IIIC

tag: pfs (months)

tag: recurrence

value: Yes

tag: chemoherapy status

value: Chemoresistant

tag: life status

value: Died


title: Patient 35 post chemotherapy sample take during debulking surgery

status: Public on Feb 17 2026

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

value: IV

value: No

value: Too soon

value: Alive


title: All Stars siRNA negative control treated with 17-AAG 72 hours replicate 3

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

hyb_protocol: The resulting cRNA was co-hybridised with Cy5 labelled Universal Human Reference RNA (Stratagene, CA) to the 4x44K Agilent human gene expression array (G4112F-014850, Agilent).

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C US84300231

data_processing: The images were feature-extracted to generate raw data files using Agilent feature extraction version 10.5.1.1 and extraction protocol GE2_105_Jan09 and grid file 014850_D_F_20090416. Background subtracted data for sample and reference were entered in the Genespring analysis software (Agilent) and Lowess normalization was applied to the samples.

label_protocol: The Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol v 5.7 was used. Briefly, 1 microgram of RNA was labelled with Cy3 using the Agilent Quick Amp kit according to manufacturer’s instructions.

growth_protocol: U2-OS cells were obtained from the ATCC. 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 was extracted using the ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems, CA) according to the manufacturer’s instructions, from at least three independent cell cultures. RNA quality was assessed using the bioanalyzer (Agilent, CA).

treatment_protocol: The HiPerFect (Qiagen) reverse transfection protocol was used as standard for U2OS transfection using 50 nM siRNA for 48 or 72h. 250 nM17-AAG, or the equivalent volume of DMSO, was added on the final day of the experiment so a 6h treatment would coincide with either 48 or 72h siRNA knock-down

tag: cell line

tag: sirna

value: All Stars

tag: tissue

value: Osteosarcoma

tag: treatment

tag: time (hours)

source_name: Universal Human Reference RNA (Stratagene)

tag: sample type

value: Reference sample


title: Patient 28 post chemotherapy sample take during debulking surgery


title: Mock transfected DMSO vehicle control 48 hours replicate 2

value: Mock

value: DMSO


title: Patient 32 post chemotherapy sample take during debulking surgery


title: HSF1 knock-down DMSO vehicle control 48 hours replicate 3


title: Patient 33 post chemotherapy sample take during debulking surgery

value: Chemosensitive


title: Patient 31 post chemotherapy sample take during debulking surgery


title: Patient 26 post chemotherapy sample take during debulking surgery

value: IIB


title: All Stars siRNA negative control treated with 17-AAG 48 hours replicate 3


title: All Stars siRNA negative control treated with 17-AAG 72 hours replicate 2


title: non transfected control media control 72 hours replicate 2


title: HSF1 knock-down treated with 17-AAG 72 hours replicate 2


title: Mock transfected media control 48 hours replicate 3

source_name: Mock transfected media control 48 hours


title: Patient 24 post chemotherapy sample take during debulking surgery

value: IIIB

value: Chemorefractory


title: Patient 30 post chemotherapy sample take during debulking surgery

value: CU Anschutz, unpublished

value: IVB


title: DHX8 knock-down media control 72 hours replicate 3

source_name: DHX8 knock-down media control 72 hours


title: Patient 21 post chemotherapy sample take during debulking surgery

value: IIIC

value: Yes

value: Chemoresistant


title: Patient 29 post chemotherapy sample take during debulking surgery


title: Mock transfected treated with 17-AAG 48 hours replicate 3


title: Patient 19 post chemotherapy sample take during debulking surgery

value: Died


title: Patient 18 post chemotherapy sample take during debulking surgery

value: IV

value: No

value: Lost to follow-up 3/2014


title: All Stars siRNA negative control media control 48 hours replicate 2

value: All Stars

value: Osteosarcoma


title: Patient 27 post chemotherapy sample take during debulking surgery

value: IIA


title: HSF1 knock-down media control 72 hours replicate 2

source_name: HSF1 knock-down media control 72 hours

value: Reference sample


title: All Stars siRNA negative control DMSO vehicle control 48 hours replicate 3

value: DMSO


title: DHX8 knock-down treated with 17-AAG 48 hours replicate 3


title: HSF1 knock-down media control 48 hours replicate 3

source_name: HSF1 knock-down media control 48 hours


title: Mock transfected treated with 17-AAG 72 hours replicate 2

value: Mock


title: Patient 15 post chemotherapy sample take during debulking surgery

value: Alive


title: Patient 25 post chemotherapy sample take during debulking surgery

value: Chemosensitive


title: All Stars siRNA negative control media control 48 hours replicate 3


title: Patient 14 post chemotherapy sample take during debulking surgery

value: CU Anschutz, unpublished

value: IIIB

value: Lost to follow-up 1/2020


title: Patient 22 post chemotherapy sample take during debulking surgery

value: IIB


title: Patient 23 post chemotherapy sample take during debulking surgery

value: IIIC

value: Yes


title: Patient 20 post chemotherapy sample take during debulking surgery


title: HSF1 knock-down DMSO vehicle control 72 hours replicate 2


title: Patient 13 post chemotherapy sample take during debulking surgery

value: Chemoresistant

value: Died


title: HSF1 knock-down DMSO vehicle control 72 hours replicate 3


title: All Stars siRNA negative control media control 72 hours replicate 2


title: DHX8 knock-down media control 48 hours replicate 2

source_name: DHX8 knock-down media control 48 hours


title: Patient 10 post chemotherapy sample take during debulking surgery


title: Patient 17 post chemotherapy sample take during debulking surgery


title: DHX8 knock-down DMSO vehicle control 72 hours replicate 3


title: Patient 12 post chemotherapy sample take during debulking surgery


title: Patient 9 post chemotherapy sample take during debulking surgery

value: IVB


title: Patient 16 post chemotherapy sample take during debulking surgery

value: Chemorefractory


title: All Stars siRNA negative control DMSO vehicle control 72 hours replicate 3

value: All Stars

value: Osteosarcoma


title: Patient 11 post chemotherapy sample take during debulking surgery

value: IVA


title: HSF1 knock-down media control 72 hours replicate 3

value: Reference sample


title: Mock transfected treated with 17-AAG 48 hours replicate 2

value: Mock


title: DHX8 knock-down DMSO vehicle control 48 hours replicate 3

value: DMSO


title: HSF1 knock-down treated with 17-AAG 72 hours replicate 3


title: Patient 6 post chemotherapy sample take during debulking surgery

value: Chemosensitive


title: HSF1 knock-down media control 48 hours replicate 2


title: Patient 5 post chemotherapy sample take during debulking surgery


title: HSF1 knock-down DMSO vehicle control 48 hours replicate 2


title: Mock transfected treated with 17-AAG 72 hours replicate 3


title: DHX8 knock-down DMSO vehicle control 72 hours replicate 2


title: All Stars siRNA negative control DMSO vehicle control 48 hours replicate 2


title: Mock transfected DMSO vehicle control 72 hours replicate 3


title: Patient 7 post chemotherapy sample take during debulking surgery

value: CU Anschutz, unpublished

value: Alive


title: Patient 35 pre chemotherapy biopsy sample

value: IV

value: No

value: Too soon


title: Patient 3 post chemotherapy sample take during debulking surgery

value: IIIC

value: Yes


title: Patient 2 post chemotherapy sample take during debulking surgery


title: DHX8 knock-down treated with 17-AAG 48 hours replicate 2


title: Patient 8 post chemotherapy sample take during debulking surgery

value: Died


title: Patient 4 post chemotherapy sample take during debulking surgery

value: Chemoresistant


title: HSF1 knock-down treated with 17-AAG 48 hours replicate 2


title: Mock transfected media control 72 hours replicate 2

source_name: Mock transfected media control 72 hours


title: Patient 1 post chemotherapy sample take during debulking surgery

value: IVB


title: Patient 33 pre chemotherapy biopsy sample


title: Patient 34 pre chemotherapy biopsy sample


title: Patient 32 pre chemotherapy biopsy sample


title: Patient 31 pre chemotherapy biopsy sample


title: DHX8 knock-down media control 72 hours replicate 2


title: DHX8 knock-down treated with 17-AAG 72 hours replicate 2


title: non transfected control media control 72 hours replicate 3


title: Patient 30 pre chemotherapy biopsy sample


title: Patient 29 pre chemotherapy biopsy sample


title: DHX8 knock-down DMSO vehicle control 48 hours replicate 2


title: All Stars siRNA negative control treated with 17-AAG 48 hours replicate 2

value: All Stars


title: Mock transfected media control 72 hours replicate 3

value: Osteosarcoma


title: DHX8 knock-down media control 48 hours replicate 3


title: Patient 27 pre chemotherapy biopsy sample

value: IIA


title: Patient 26 pre chemotherapy biopsy sample

value: IIB


title: Patient 20 pre chemotherapy biopsy sample


title: Mock transfected DMSO vehicle control 48 hours replicate 3

value: Mock

value: Reference sample


title: HSF1 knock-down media control 48 hours replicate 1


title: Mock transfected media control 48 hours replicate 2


title: Patient 28 pre chemotherapy biopsy sample


title: Patient 25 pre chemotherapy biopsy sample

value: Chemosensitive


title: All Stars siRNA negative control media control 72 hours replicate 3


title: non transfected control media control 48 hours replicate 3


title: Patient 24 pre chemotherapy biopsy sample

value: CU Anschutz, unpublished

value: IIIB

value: Chemorefractory


title: All Stars siRNA negative control treated with 17-AAG 72 hours replicate 1


title: DHX8 knock-down treated with 17-AAG 72 hours replicate 1


title: Patient 21 pre chemotherapy biopsy sample


title: Patient 22 pre chemotherapy biopsy sample

value: No

value: Alive


title: Patient 23 pre chemotherapy biopsy sample

value: IIIC


title: Patient 18 pre chemotherapy biopsy sample

value: IV

value: Lost to follow-up 3/2014


title: Mock transfected DMSO vehicle control 72 hours replicate 2

value: DMSO


title: Patient 19 pre chemotherapy biopsy sample

value: Yes

value: Chemoresistant

value: Died


title: Patient 17 pre chemotherapy biopsy sample


title: Mock transfected media control 48 hours replicate 1

value: Osteosarcoma


title: HSF1 knock-down DMSO vehicle control 72 hours replicate 1


title: DHX8 knock-down DMSO vehicle control 72 hours replicate 1


title: DHX8 knock-down DMSO vehicle control 48 hours replicate 1


title: Patient 16 pre chemotherapy biopsy sample


title: Patient 15 pre chemotherapy biopsy sample


title: Mock transfected media control 72 hours replicate 1


title: All Stars siRNA negative control DMSO vehicle control 48 hours replicate 1

value: All Stars


title: All Stars siRNA negative control DMSO vehicle control 72 hours replicate 1


title: non transfected control media control 48 hours replicate 1


title: DHX8 knock-down treated with 17-AAG 48 hours replicate 1


title: non transfected control media control 72 hours replicate 1


title: Patient 12 pre chemotherapy biopsy sample


title: Patient 9 pre chemotherapy biopsy sample

value: IVB


title: Patient 10 pre chemotherapy biopsy sample


title: Patient 13 pre chemotherapy biopsy sample


title: Patient 11 pre chemotherapy biopsy sample

value: IVA


title: Patient 8 pre chemotherapy biopsy sample

value: Chemosensitive


title: Patient 7 pre chemotherapy biopsy sample

value: CU Anschutz, unpublished


title: Patient 5 pre chemotherapy biopsy sample

value: IIIB


title: HSF1 knock-down DMSO vehicle control 48 hours replicate 1

value: Reference sample


title: Patient 4 pre chemotherapy biopsy sample


title: Patient 14 pre chemotherapy biopsy sample

value: No

value: Lost to follow-up 1/2020


title: Patient 6 pre chemotherapy biopsy sample

value: IIIC


title: All Stars siRNA negative control media control 48 hours replicate 1


title: All Stars siRNA negative control media control 72 hours replicate 1


title: Patient 3 pre chemotherapy biopsy sample

value: Chemorefractory


title: HSF1 knock-down media control 72 hours replicate 1


title: HSF1 knock-down treated with 17-AAG 72 hours replicate 1


title: All Stars siRNA negative control treated with 17-AAG 48 hours replicate 1


title: Patient 1 pre chemotherapy biopsy sample


title: Mock transfected treated with 17-AAG 72 hours replicate 1

value: Mock


title: Mock transfected DMSO vehicle control 72 hours replicate 1

value: DMSO


title: ChIP-seq-H3K4me3-shKDM5C2-MCF7

type: SRA

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

country: China

institute: Gannan Medical University

description:
Library name: Sample 9
CS_HS_MCF7_shKDM5C2_H3K4me3

library_source: genomic

data_processing:
Basecalling and demultiplexing were performed using MGI DNBSEQ-T7 Sequencer Control Software and ZebraCall version 2.1.
Reads were aligned to the hg19 genome assembly using Bowtie version 2.4.1.
The bigwig files were generated by using Homer v4.11, in which the total tags are normalized to 1.00e+08.
Peaks are called by using Homer findPeaks script
Assembly: Homo sapiens genome Ensembl GRCh37 (hg19)
Supplementary files format and content: bigWig files for each Sample

molecule: genomic DNA

growth_protocol: MCF7 breast cancer cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained in a humidified incubator with 5% CO₂ at 37 °C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine. Crosslinked chromatin was sonicated to an average size of 200–500 bp in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 7.8, and protease inhibitors), diluted in dilution buffer, and immunoprecipitated overnight with specific antibodies. The complexes were collected using Protein A/G magnetic beads, sequentially washed with TSEI, TSEII, and TE buffers, and reverse crosslinked at 65 °C overnight. DNA was purified using a spin column-based DNA purification kit and used for library preparation.
DNA libraries for ChIP seq were prepared using the NEBNext® Ultra II DNA Library Prep Kit for Illumina following the manufacturer’s protocols.

tag: cell type

value: breast cancer cells

tag: genotype

value: KDM5C knockdown


title: ChIP-seq-H3K4me3-shKDM5C1-MCF7

description:
Library name: Sample 8
CS_HS_MCF7_shKDM5C1_H3K4me3


title: Patient 2 pre chemotherapy biopsy sample

value: Yes

value: Alive


title: DHX8 knock-down media control 72 hours replicate 1

value: Osteosarcoma


title: HSF1 knock-down treated with 17-AAG 48 hours replicate 1


title: DHX8 knock-down media control 48 hours replicate 1


title: ChIP-seq-H3K4me3-shCTL-MCF7

description:
Library name: Sample 5
CS_HS_MCF7_shCTL_H3K4me3

value: Control knockdown


title: Mock transfected treated with 17-AAG 48 hours replicate 1


title: ChIP-seq-H3K4me3-shESRRA1-MCF7

description:
Library name: Sample 6
CS_HS_MCF7_shESRRA1_H3K4me3

value: ESRRA knockdown


title: ChIP-seq-H3K4me3-shESRRA2-MCF7

description:
Library name: Sample 7
CS_HS_MCF7_shESRRA2_H3K4me3


title: RNA immunoprecipitation with DHX8 antibody replicate 5

extract_protocol: RNA was immunoprecipitated with an antibody to DHX8 and mouse IgG  as control using the EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to the manufacturer’s instructions, from at least five independent cell cultures. RNA quality was assessed using the bioanalyzer (Agilent, CA).

treatment_protocol: U2-OS cells were cultured and harvested in the exponential growth phase

tag: antibody


title: RNA immunoprecipitation with mouse IgG replicate 3

source_name: RNA immunoprecipitation with mouse IgG

value: Mouse IgG control


title: K2

city: Nanjing

first: Qingyuan

last: Wang

state: Jiangsu

address: No. 300 Guangzhou Road

department: The First Clinical Medical College

institute: Nanjing medical university

description:
Library name: K2
Fresh frozen Spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
Raw reads were trimmed and quality-filtered with fastp (default parameters).
Clean reads were aligned to the human genome (GRCh38, Ensembl 104) using SpaceRanger v2.1.0 to generate feature-barcode matrices."
Assembly: human genome (GRCh38, Ensembl 104)
Supplementary files format and content: K1.rds, Seurat objects
Supplementary files format and content: K2.rds, Seurat objects
Library strategy: Spatial Transcriptomics

source_name: Gastric cancer and matched normal gastric mucosa tissues

extract_protocol:
Tissues were surgically excised, embedded in optimal cutting temperature (OCT) compound (SAKURA), rapidly frozen on dry ice, and stored at −80 °C until cryosectioning. Samples with an RNA integrity number (RIN) ≥ 7 were sectioned at 10 μm thickness using a cryostat (Leica CM1950) and subsequently subjected to fixation, staining, imaging, pre-permeabilization, and permeabilization.
After cDNA transfer from the slides, barcoded cDNA was purified, amplified, fragmented, A-tailed, adaptor-ligated, and index PCR–amplified. Final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and assessed for size distribution with a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.


title: RNA immunoprecipitation with mouse IgG replicate 4


title: Mock transfected DMSO vehicle control 48 hours replicate 1


title: K1

description:
Library name: K1
Fresh frozen Spatial transcriptome sequencing

value: Gastric cancer and matched normal gastric mucosa tissues


title: RNA immunoprecipitation with DHX8 antibody replicate 2


title: RNA immunoprecipitation with mouse IgG replicate 5


title: RNA immunoprecipitation with DHX8 antibody replicate 3


title: ChIP-seq-Input-MCF7

description:
Library name: Sample 4
CS_HS_MCF7_shCTL_Input


title: Transcriptome-wide SHAPE-MaP analysis of MTX-treated cells, 2A3 probed, Replicate 2

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Library name: SHAPE-MaP_MTX_2A3_rep2

data_processing:
Paired-end reads were clipped of sequencing adapters using Cutadapt v4.478 (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 50:50 -O 1) and merged using PEAR v0.9.1179 (parameters: -n 50 -q 20 -u 0 -e -y 15G -z). Merged reads were then combined with R1 and the reverse-complemented R2 for read pairs that could not be merged, and mapped to the hg38 assembly of the human reference genome using STAR v2.7.10b (parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 2 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.15 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignEndsType Local --outFilterScoreMinOverLread 0.15 --outFilterMatchNminOverLread 0.15 --outSAMprimaryFlag AllBestScore --outSAMattributes All). Genome-level mutation counts and coverage (RC files) were obtained from BAM alignments using the rf-count-genome module of the RNA Framework (parameters: -ls second -m -ds 50 -rd -me 0.1 -ncl). Transcriptome-level counts and coverage were then extracted from genome-level RC files through the extract function of the rf-rctools utility of the RNA Framework, using the MANE v1.4 gene annotation. For reactivity normalization, cross-experiment transcriptome-wide normalization factors were derived using the rf-normfactor utility of the RNA Framework (parameters: -sm 3 -nm 3 -mc 1000) and provided to the rf-norm utility via the -nf parameter. Only bases with a coverage ≥ 1,000X were retained for downstream analyses.
Supplementary files format and content: Wiggle files of raw SHAPE-MaP mutation frequencies

molecule: polyA RNA

growth_protocol: Human MDA-MB-231 cells were cultured in high glucose DMEM medium (cat. L0104, Biowest), supplemented with 10% fetal bovine serum (FBS) (cat. H1138, Merck), 25 U/mL penicillin and 25 μg/mL streptomycin, at 37°C and 5% CO2. Culture plates were pre-coated with 0.001% poly-L-lysine (cat. P8920, Merck) to ensure that cells would remain attached during probing.

extract_protocol: RNA samples in TRIzol™ were mixed with 0.2 volumes chloroform (cat. 319988, Merck) by vigorous vortexing for 15 sec, after which samples were allowed to sit at room temperature for 2 min, before centrifugation at 12,500g for 15 min (4°C). After phase separation, the upper aqueous phase was transferred to a clean 2 mL tube and mixed with 1 volume 2-propanol (cat. 190764, Merck) by vigorous vortexing for 15 sec. Samples were allowed to sit at room temperature for 10 min, before centrifugation at 17,000g for 10 min (4°C). Supernatant was discarded and the RNA pellet was washed twice in 75% ethanol. The RNA pellet was then allowed to air-dry for 10 min, before resuspension in nuclease-free water, pre-warmed at 70°C. Residual gDNA was removed by digestion with TURBO DNase I at 37°C for 30 min.

treatment_protocol: For drug treatment, cells were first washed once with PBS, prewarmed at 37°C. Then, Mitoxantrone (MTX) from a 10 mM stock in DMSO was mixed with fresh complete medium, prewarmed at 37°C, to achieve a final concentration of 10 μM, and the medium added to the cells. For control experiments, medium was mixed with an equivalent amount of neat DMSO. Cells were then incubated for 30 min at 37°C. For SHAPE probing, cells were washed twice in PBS, prewarmed at 37°C, to remove any traces of serum. 2A3 (or an equivalent volume of neat DMSO, for control experiments) was then mixed with fresh PBS, prewarmed at 37°C, and added to the cells. Cells were incubated at 37°C for 7.5 min. Reactions were then quenched by addition of 1 volume ice-cold 1 M DTT in PBS, after which the supernatant was aspired, cells were washed once in PBS, and then lysed by direct addition of 2 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific).


title: RNA immunoprecipitation with mouse IgG replicate 2


title: Transcriptome-wide SHAPE-MaP analysis of DMSO-treated cells, 2A3 probed, Replicate 2

description: Library name: SHAPE-MaP_DMSO_2A3_rep2


title: RNAseq in MEFs treated with a hairpin shSetdb1.6

city: Parkville

first: Andrew

last: Keniry

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

description: Library name: Setdb1_6.fq

data_processing:
Basecalls performed using CASAVA version 1.4
Assembly: mm10
Supplementary files format and content: log2RPM

organism: Mus musculus

source_name: cell line

growth_protocol: Mouse embryonic fibroblasts were obtained from E13.5 embryos. Cells were cultured in DMEM with 10% (v/v) FBS at 37°C and 10% (v/v) CO2.

extract_protocol:
RNA was extracted using Qiagen RNA prep kit
Illumina TruSeq RNA

treatment_protocol: Primary XXist∆A/XPGK MEFs were transduced with retroviruses and selected with puromycin after 24 h. Three days after transduction, cells were cultured with or without 5-azacytidine for 24 h and harvested for RNA 7 days post-transduction

value: MEF


title: RNA immunoprecipitation with DHX8 antibody replicate 4

value: Reference sample


title: Whole retina single cell suspension, collected at 96 hours post DMSO treatment

city: Moscow

first: Sarah

last: Hendricks

state: ID

address: 685 S. Line Street, IRIC 210

institute: University of Idaho

description:
Library name: DMSO
10X Genomics

library_source: transcriptomic single cell

data_processing:
The sequences were aligned to the zebrafish reference genome (GCA_000002035.4_GRCz11), annotated, and quality controlled using the Illumina DRAGEN Single Cell application.
Assembly: GCA_000002035.4_GRCz11
Supplementary files format and content: Tab-separated value files and matrix file

organism: Danio rerio

source_name: Whole retinas

extract_protocol:
Whole retinas were dissected from DMSO- or Mtz-treated adult zebrafish at specified time points (DMSO 96HPT, MTZ 96HPT, MTZ 120HPT), and dissociated into single-cell suspensions. Eyes were enucleated from euthanized zebrafish, transferred to L-15 medium, and dissected to isolate the retina with RPE intact. Retinas were pooled per fish, placed in L-15:EBSS, and digested with papain solution (containing DNase I and RNase inhibitor) at 28°C with cycles of trituration. Digestion was quenched with 0.1% BSA, and cells were centrifuged, washed, and resuspended. Cell counts and viability (93.75–96.5%) were assessed via trypan blue. Final suspensions were adjusted to 1000 cells/μL for downstream applications.
The single cell samples were loaded onto the 10X Genomics fluidics platform. Single cell cDNA libraries were prepared using Chromium iX system and a GEM-X Single Cell 3’ v4 kit (10X Genomics) following manufacturer instructions. Briefly, GEM-X kit reagents, cell suspensions, and gel beads were loaded onto the Chromium iX microfluidic chip for partitioning into Gel Beads-in Emulsion (GEMs) so that a single cell would be contained in each microdroplet alongside the barcode containing gel bead. The cDNA was generated and barcoded within the GEM so that the transcripts from each cell had a unique identifier. Subsequently the cDNAs were processed in bulk for library preparation including fragmentation, amplification, and addition of adaptors for sequencing. cDNA and libraries were subjected to quality control using Fragment Bioanalyzer. Libraries were sequenced using Illumina Next Seq 2000.

value: Whole retinas

value: retinal cells


title: Whole retina single cell suspension, collected at 120 hours post Mtz treatment

description:
Library name: MTZ 120HPT
10X Genomics

value: retina cells

value: Mtz


title: Transcriptome-wide SHAPE-MaP analysis of MTX-treated cells, 2A3 probed, Replicate 1

description: Library name: SHAPE-MaP_MTX_2A3_rep1


title: Whole retina single cell suspension, collected at 96 hours post Mtz treatment

description:
Library name: MTZ 96HPT
10X Genomics


title: Transcriptome-wide SHAPE-MaP analysis of untreated cells, DMSO control, Replicate 1

description: Library name: SHAPE-MaP_Untreated_DMSO_rep1


title: Transcriptome-wide SHAPE-MaP analysis of DMSO-treated cells, 2A3 probed, Replicate 1

description: Library name: SHAPE-MaP_DMSO_2A3_rep1


title: Transcriptome-wide SHAPE-MaP analysis of untreated cells, DMSO control, Replicate 2

description: Library name: SHAPE-MaP_Untreated_DMSO_rep2


title: SYNIR gRNA 3 Untreated

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: Biomedical Sciences Building First Floor, Red Hill Road

department: MCD

institute: UC Santa Cruz

description:
Library name: SYNIR_NT_gRNA3
DEG_SYNIR-KO_NT.tsv

data_processing:
Reads were quantified with Salmon quant(--validateMappings --gcBias --seqBias) against Gencode vM31
Transcript-level abundance estimates were summarized to gene level using tximport with length-scaled TPM counts (countsFromAbundance = "lengthScaledTPM").
Differential expression was performed with DESeq2 using default parameters and a two-factor design comparing samples with targeting- and non-targeting-gRNAs
Assembly: mm39
Supplementary files format and content: DEG_SEMR-KO_LPS.tsv: differential gene expression, SEMR vs negative ctrl gRNAs under LPS stimulus
Supplementary files format and content: DEG_SEMR-KO_NT.tsv: differential gene expression, SEMR vs negative ctrl gRNAs in untreated samples
Supplementary files format and content: DEG_SYNIR-KO_LPS.tsv: differential gene expression, SYNIR vs negative ctrl gRNAs under LPS stimulus
Supplementary files format and content: DEG_SYNIR-KO_NT.tsv: differential gene expression, SYNIR vs negative ctrl gRNAs in untreated samples

source_name: marrow

growth_protocol: Cells were maintained at 60-70% confluence in DMEM supplemented with 10% Fetal Calf Serum and Penicillin/Streptomycin.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (SigmaAldrich, T9424) and Direct-zol RNA Miniprep Plus kit (Zymo Research, R2072), following manufacturer’s instructions. RNA samples were sent to Novogene for 150x150 bp stranded library preparation.
Following RNA extraction, samples were sent to Novogene for stranded RNA-seq.

treatment_protocol: Complementary oligos were ordered from IDT, reconstituted and ligated into pU6 expression vector. The vector also contained a puromycin resistance cassette and mCherry reporter. Lentivirus was prepared as described above and iBMDM samples were each infected with a single gRNA. Infected cells were puromycin-selected for 7 days when the mCherry population reach >90%. Each gRNA-iBMDM line was treated with 200ng/ml LPS for 6 h and samples were collected for RNA processing.

value: marrow

value: Immortalized bone marrow derived macrophage

value: Bone marrow derived macrophage

value: No treatment


title: RNAseq in MEFs treated with a hairpin shSetdb1.4 and 5-azacytadine replicate B

description: Library name: Setdb1_4b_5aza.fq


title: SYNIR gRNA 1 Untreated

description:
Library name: SYNIR_NT_gRNA1
DEG_SYNIR-KO_NT.tsv


title: SYNIR gRNA 2 Untreated

description:
Library name: SYNIR_NT_gRNA2
DEG_SYNIR-KO_NT.tsv


title: RNA immunoprecipitation with DHX8 antibody replicate 1


title: RNAseq in MEFs treated with a hairpin shSetdb1.6 and 5-azacytadine

description: Library name: Setdb1_6_5aza.fq


title: RNAseq in MEFs treated with a hairpin shSetdb1.4 replicate A

description: Library name: Setdb1_4a.fq


title: RNAseq in MEFs treated with a hairpin shSetdb1.4 replicate B

description: Library name: Setdb1_4b.fq


title: SYNIR gRNA 3 +LPS

description:
Library name: SYNIR_LPS_gRNA3
DEG_SYNIR-KO_LPS.tsv

value: LPS


title: RNAseq in MEFs treated with a hairpin shSetdb1.4 and 5-azacytadine replicate A

description: Library name: Setdb1_4a_5aza.fq


title: RNA immunoprecipitation with mouse IgG replicate 1


title: RNAseq in MEFs treated with  5-azacytadine

description: Library name: PGK_5aza.fq


title: SYNIR gRNA 1 +LPS

description:
Library name: SYNIR_LPS_gRNA1
DEG_SYNIR-KO_LPS.tsv


title: SEMR gRNA 3 Untreated

description:
Library name: SEMR_NT_gRNA3
DEG_SEMR-KO_NT.tsv


title: RNAseq in MEFs treated with a non-silensing hairpin replicate B

description: Library name: Nons_b.fq


title: SEMR gRNA 2 Untreated

description:
Library name: SEMR_NT_gRNA2
DEG_SEMR-KO_NT.tsv


title: RNAseq in MEFs treated with a non-silensing hairpin and 5-azacytadine replicate A

description: Library name: Nons_a_5aza.fq


title: SYNIR gRNA 2 +LPS

description:
Library name: SYNIR_LPS_gRNA2
DEG_SYNIR-KO_LPS.tsv


title: RNAseq in MEFs treated with a non-silensing hairpin and 5-azacytadine replicate B

description: Library name: Nons_b_5aza.fq


title: SEMR gRNA 1 Untreated

description:
Library name: SEMR_NT_gRNA1
DEG_SEMR-KO_NT.tsv


title: RNAseq in MEFs treated with a hairpin against Luciferase

description: Library name: Luc.fq


title: RNAseq in MEFs treated with a non-silensing hairpin replicate A

description: Library name: Nons_a.fq


title: Negative control gRNA 2 Untreated

description:
Library name: negctrl_NT_gRNA2
DEG_SEMR-KO_NT.tsv
DEG_SYNIR-KO_NT.tsv


title: RNAseq in MEFs treated with a hairpin against Luciferase and 5-azacytadine

description: Library name: Luc_5aza.fq


title: Negative control gRNA 3 Untreated

description:
Library name: negctrl_NT_gRNA3
DEG_SEMR-KO_NT.tsv
DEG_SYNIR-KO_NT.tsv


title: SEMR gRNA 3 +LPS

description:
Library name: SEMR_LPS_gRNA3
DEG_SEMR-KO_LPS.tsv


title: Negative control gRNA 3 +LPS

description:
Library name: negctrl_LPS_gRNA3
DEG_SEMR-KO_LPS.tsv
DEG_SYNIR-KO_LPS.tsv


title: SEMR gRNA 2 +LPS

description:
Library name: SEMR_LPS_gRNA2
DEG_SEMR-KO_LPS.tsv


title: Day 14, clone 3

description: Library name: clone3_day_14

library_source: other

data_processing:
mageck count -l  grna_library.tsv --fastq Plasmid_Pool.fastq.gz  <remaining fastq.gz> --sample-label Plasmid_Pool  <remaining samples>--unmapped-to-file --trim-5 1 --sgrna-len 19
Assembly: mm39
Supplementary files format and content: gRNA_counts.tsv: tab delimted, raw counts for each guideRNA x sample
Supplementary files format and content: grna_library.tsv: tab delimted, gRNA library sequences
Library strategy: CRISPR Screen

molecule: other

extract_protocol:
Flow cytometry and PCR amplification of genomic sgRNA sequences were conducted as previously described in detail in https://doi.org/10.1016/j.celrep.2020.108541.
Up to 10 gRNAs were designed for each noncanocial coding sequence (CDS) with CRISPRware. Six gRNAs were chosen against canonical CDSs with CRISPick. 1,500 non-targeting were also included, and up to 8 gRNAs targeting long noncoding RNA regions outside of targeted ORF. GRNAs wer cloned into pU6 lentivirus and transduced at multiplicity of infection <0.3

treatment_protocol: Library infected and puromycin selected iBMDM, +NFkB-EGFP +CRISPR-sgRNA cells were expanded to 2000X coverage. Cells were stimulated with PAM3CSK4 (200 ng/mL) for 24 h to induce expression of NFkB-EGFP.


title: SEMR gRNA 1 +LPS

description:
Library name: SEMR_LPS_gRNA1
DEG_SEMR-KO_LPS.tsv


title: WT LLC 6

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

data_processing:
Fastq files were analyzed with RSEM v. 1.3.1 in order to obtain normalized counts of expressed genes in TPM. RSEM has been launched using STAR aligner 2.7.1a
Reads were aligned against the mouse mm10 reference genome (Ensembl_database)
RSEM was launched with the following parameters –paired-end --sort-bam-by-coordinate  –strandedness reverse --calc-ci --ci-memory 12288 --estimate-rspd --append-names –star –output-genome-bam –sort-bam-memory-per-thread 4G –time
Assembly: Mouse GRCm38 annotated with Mus_musculus.GRCm38.100.chr.gtf (Ensembl_database)
Supplementary files format and content: data.matrix.TPM.xlsx = File containing the normalized counts expressed in TPM in all samples.

source_name: Lewis lung carcinoma-injected wild type mouse

growth_protocol: Lewis lung carcinoma (LLC) cells were cultured in DMEM containing 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, and 0.25 μg/mL antimycotic in a humidified 5% CO2 incubator at 37° C.

extract_protocol:
Gastrocnemii were removed, flash frozen on liquid nitrogen, and RNA was extracted from about 20 mg of tissue using the Reliaprep RNA tissue miniprep system kit (Promega, Milan, Italy).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3-month-old WT and GC-KO mice were  injected on the back with 10^6 Lewis lung carcinoma (LLC) cells resuspended in 100 μl of saline. Controls were injected with the same volume of saline. Tissues were harvested 23 days post-injection.

tag: strain

value: Gastrocnemius

value: wild type

value: Lewis lung carcinoma-injected


title: Gc-KO LLC 1

source_name: Lewis lung carcinoma-injected Gc-KO mouse

value: Gc-KO


title: Gc-KO LLC 4


title: Gc-KO LLC 6


title: Day 14, clone 1

description: Library name: clone1_day_14


title: Gc-KO LLC 3


title: Day 0, clone 2

description: Library name: clone2_day_0


title: WT LLC 3


title: Day 0, clone 1

description: Library name: clone1_day_0


title: Gc-KO SAL 3

source_name: Saline-injected Gc-KO mouse

value: SALINE


title: Gc-KO LLC 5


title: Negative control gRNA 1 Untreated

description:
Library name: negctrl_NT_gRNA1
DEG_SEMR-KO_NT.tsv
DEG_SYNIR-KO_NT.tsv


title: Gc-KO SAL 2


title: Negative control gRNA 2 +LPS

description:
Library name: negctrl_LPS_gRNA2
DEG_SEMR-KO_LPS.tsv
DEG_SYNIR-KO_LPS.tsv


title: Gc-KO LLC 2


title: WT LLC 7


title: Gc-KO SAL 1


title: Negative control gRNA 1 +LPS

description:
Library name: negctrl_LPS_gRNA1
DEG_SEMR-KO_LPS.tsv
DEG_SYNIR-KO_LPS.tsv


title: WT LLC 2


title: WT LLC 5


title: GFP High, clone 3

description: Library name: clone3_GFP_high

value: 24h Pam3CSK4


title: WT LLC 4


title: KD_plusCL_β3-AR-stimulated H2A.Z KD BAs, replicate1

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

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 mouse genome (mm10) 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: mm10
Supplementary files format and content: HIC file, contact matrix in multiple genomics resolution data generated by jucier
Library strategy: Micro-C

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:
Micro-C was performed using  DovetailTM Micro-C kit (Dovetail GENOMICS) according to the manufacturer’s protocol. Vehicle-treated control, β3-AR-stimulated control, and β3-AR-stimulated H2A.Z KD brown adipocytes were washed twice with room temperature PBS and then scraped down in 1 ml PBS per well of a 6-well plate. The suspended adipocytes were crosslinked with 0.3 M DSG at room temperature for 10 minutes with rotation, followed by 1% formaldehyde at room temperature for 10 minutes with rotation. Adipocytes were collected with a spin at 3,000 g for 5 minutes and washed with 1x Wash buffer twice. Crosslinked adipocytes from a well of a 6-well plate were resuspended in 200 μl 1x Nuclease Digest buffer and divided into 4 tubes to determine the appropriate amount of Micrococcal nuclear (MNase) by incubating at 22°C for 15 minutes in an agitating thermal mixer set at 1,250 rpm. The MNase reaction was inactivated by adding 5 μl of 0.5M EGTA and 3 μl of 20% SDS, followed by incubation at 22°C for 5 minutes in an agitating thermal mixer set at 1,250 rpm. The fragment size distribution was assessed using a Bioanalyzer HS DNA chip. The optimal digestion condition resulted in 40-70% of mono-nucleosome. MNase-digested chromatin was then subjected to proximity ligation.
Library preparation, ligation capture and amplification were performed using the DovetailTM Micro-C kit (Dovetail GENOMICS) according to the manufacturer’s protocol.

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 knckdown

value: Beta3-AR agonist


title: shNT_plusCL_β3-AR-stimulated control BAs, replicate2

value: Control


title: Day 0, clone 3

description: Library name: clone3_day_0


title: Day 14, clone 2

description: Library name: clone2_day_14


title: KD_plusCL_β3-AR-stimulated H2A.Z KD BAs, replicate3


title: shNT_plusCL_β3-AR-stimulated control BAs, replicate4


title: shNT_plusCL_β3-AR-stimulated control BAs, replicate3


title: WT LLC 1


title: WT SAL 3

source_name: Saline-injected wild type mouse


title: GFP High, clone 1

description: Library name: clone1_GFP_high


title: shNT_plusCL_β3-AR-stimulated control BAs, replicate1


title: KD_plusCL_β3-AR-stimulated H2A.Z KD BAs, replicate2


title: GFP Low, clone 1

description: Library name: clone1_GFP_low


title: GFP Low, clone 3

description: Library name: clone3_GFP_low


title: KD_plusCL_β3-AR-stimulated H2A.Z KD BAs, replicate4


title: GFP Low, clone 2

description: Library name: clone2_GFP_low


title: WT SAL 1


title: shNT_minusCL_vehicle control BAs, replicate3

value: vehicle


title: WT SAL 2


title: shNT_minusCL_vehicle control BAs, replicate4


title: GFP High, clone 2

description: Library name: clone2_GFP_high


title: TM54_shRNA_CDC14A-4

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

description: Library name: 4423

data_processing:
The nf-core/rnaseq v3.21.0 (https://nf-co.re/rnaseq) pipeline was used to process the data.
The pipeline was executed with nf-core tools v3.3.2 and Nextflow v25.04.6.
STAR v2.7.10a alignment and RSEM v1.3.1 transcript quantification were performed.
Assembly: GRCm39 (GENCODE Mouse Release M37)
Supplementary files format and content: tab-delimited text file includes expected raw counts for each sample

source_name: Heart

growth_protocol: Wildtype and TM54 mice were housed to 12 weeks old for RNA extraction from heart

extract_protocol:
Total RNA extracted  via RNeasy mini kit (Qiagen #74104)
The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) was utilized according to the manufacturer's recommendations. ERCC RNA Spike-In Mix (ThermoFisher, #4456740) was added to normalized total RNA prior to library preparation following manufacturer’s protocol.

treatment_protocol: 1-2 day old wildtype and TM54 mice were injected with AAV9sc.shControl or AAV9sc.shCDC14A

value: Heart

value: FVB/N

value: heart tissue

tag: batch


title: shNT_minusCL_vehicle control BAs, replicate2


title: β3-AR-stimulated H2A.Z KD BAs, replicate4, pilot


title: DNA methylation profile for 203977000016_R04C01

type: genomic

city: Exeter

first: Gregory

last: Wheildon

address: Stocker Road

department: CBS

institute: University of Exeter

description: DNA methylation profile from Huntington's disease patient

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

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: Entorhinal cortex

tag: Sex

value: Male

tag: age

tag: disease state

value: Huntington's disease

tag: brain bank

value: Manchester

tag: bisulfite conversion batch

tag: neuronal proportion


title: DNA methylation profile for 203991450163_R02C01

value: Striatum


title: DNA methylation profile for 203977000010_R06C01

value: Cerebellum


title: TM54_shRNA_CDC14A-1

description: Library name: 4480

tag: cell line


title: β3-AR-stimulated control BAs, replicate4, pilot


title: shNT_minusCL_vehicle control BAs, replicate1


title: TM54_shRNA_CDC14A-3

description: Library name: 4429

tag: tissue


title: DNA methylation profile for 203991460065_R08C01


title: β3-AR-stimulated H2A.Z KD BAs, replicate1, pilot

tag: treatment


title: vehicle control BAs, replicate2, pilot


title: DNA methylation profile for 203977000013_R01C01


title: vehicle control BAs, replicate1, pilot


title: TM54_shRNA_Control-4

description: Library name: 4468


title: TM54_shRNA_Control-6

description: Library name: 4474


title: DNA methylation profile for 203977000016_R07C01

value: Female


title: β3-AR-stimulated H2A.Z KD BAs, replicate2, pilot


title: DNA methylation profile for 203968030089_R03C01


title: β3-AR-stimulated control BAs, replicate3, pilot


title: β3-AR-stimulated H2A.Z KD BAs, replicate3, pilot


title: vehicle control BAs, replicate3, pilot


title: β3-AR-stimulated control BAs, replicate2, pilot


title: β3-AR-stimulated control BAs, replicate1, pilot


title: TM54_shRNA_CDC14A-2

description: Library name: 4226


title: β3-AR-stimulated H2A.Z KD BAs, replicate2

description:
KD_plusCL_rep2
count_matrix.tsv
b3AR_stim_KD_vs_Control_protein_DEG_DESeq2.tsv

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: mm10
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 β3-AR-stimulated control versus vehicle control
Supplementary files format and content: TSV file includes differential expression result in β3-AR-stimulated H2A.Z KD versus  β3-AR-stimulated control
Supplementary files format and content: BigWig

extract_protocol:
Total RNAs from vehicle-treated control, β3-AR-stimulated control, and β3-AR-stimulated H2A.Z KD brown adipocytes were isolated using Direct-zol RNA Miniprep kits (Zymo Research, Irvine, CA). Ribosome RNA (rRNA) depletion was carried out using RiboCap rRNA Depletion Kit for Human/Mouse/Rat (LEXOGEN).
The rRNA-depleted RNAs were then utilized for cDNA library preparation with the CORALL RNA-Seq V2 Library Prep Kit (LEXOGEN).


title: vehicle control BAs, replicate4, pilot


title: TM54_shRNA_Control-5

description: Library name: 4470


title: DNA methylation profile for 203991460019_R03C01


title: TM54_shRNA_Control-3

description: Library name: 4432


title: β3-AR-stimulated H2A.Z KD BAs, replicate3

description:
KD_plusCL_rep3
count_matrix.tsv
b3AR_stim_KD_vs_Control_protein_DEG_DESeq2.tsv


title: DNA methylation profile for 203991450163_R05C01


title: β3-AR-stimulated H2A.Z KD BAs, replicate1

description:
KD_plusCL_rep1
count_matrix.tsv
b3AR_stim_KD_vs_Control_protein_DEG_DESeq2.tsv


title: DNA methylation profile for 203977000019_R02C01


title: TM54_shRNA_Control-1

description: Library name: 4473


title: β3-AR-stimulated control BAs, replicate2

description:
shNT_plusCL_rep2
count_matrix.tsv
Control_b3AR_stim_vs_vehicle_protein_DEG_DESeq2.tsv
b3AR_stim_KD_vs_Control_protein_DEG_DESeq2.tsv


title: TM54_shRNA_Control-2

description: Library name: 4289


title: NTG_shRNA_CDC14A-3

description: Library name: 4479

value: wildtype


title: β3-AR-stimulated control BAs, replicate3

description:
shNT_plusCL_rep3
count_matrix.tsv
Control_b3AR_stim_vs_vehicle_protein_DEG_DESeq2.tsv
b3AR_stim_KD_vs_Control_protein_DEG_DESeq2.tsv

value: brown adipocytes


title: DNA methylation profile for 203968030089_R05C01


title: vehicle control BAs, replicate3

description:
shNT_minusCL_rep3
count_matrix.tsv
Control_b3AR_stim_vs_vehicle_protein_DEG_DESeq2.tsv


title: vehicle control BAs, replicate1

description:
shNT_minusCL_rep1
count_matrix.tsv
Control_b3AR_stim_vs_vehicle_protein_DEG_DESeq2.tsv


title: DNA methylation profile for 203977000016_R02C01

value: Cambridge


title: vehicle control BAs, replicate2

description:
shNT_minusCL_rep2
count_matrix.tsv
Control_b3AR_stim_vs_vehicle_protein_DEG_DESeq2.tsv


title: NTG_shRNA_CDC14A-1

description: Library name: 4425


title: H3K27ac, β3-AR-stimulated H2A.Z KD BAs, 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 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: H3K27ac (Active Motif, #39133)

value: H2A.Z knckdown

value: Beta3-AR agonist


title: H3K4me3, β3-AR-stimulated H2A.Z KD BAs, rep1

value: H3K4me3 (Millipore Sigma, #07-473)


title: DNA methylation profile for 203977090035_R08C01


title: DNA methylation profile for 203976760023_R07C01


title: NTG_shRNA_CDC14A-2

description: Library name: 4477

value: Heart

value: FVB/N


title: NTG_shRNA_CDC14A-4

description: Library name: 4481

value: heart tissue


title: NTG_shRNA_Control-2

description: Library name: 4469


title: H3K4me3, β3-AR-stimulated H2A.Z KD BAs, rep2


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


title: H3K4me3, β3-AR-stimulated control BAs, rep2

value: Control


title: β3-AR-stimulated control BAs, replicate1

description:
shNT_plusCL_rep1
count_matrix.tsv
Control_b3AR_stim_vs_vehicle_protein_DEG_DESeq2.tsv
b3AR_stim_KD_vs_Control_protein_DEG_DESeq2.tsv


title: H3K4me3, β3-AR-stimulated control BAs, rep1


title: IgG, β3-AR-stimulated control BAs


title: DNA methylation profile for 203977000010_R01C01

value: Brain


title: H3K27ac, β3-AR-stimulated H2A.Z KD BAs, rep1


title: DNA methylation profile for 203977000019_R06C01

value: Entorhinal cortex

value: Huntington's disease


title: NTG_shRNA_Control-3

description: Library name: 4476


title: NTG_shRNA_Control -1

description: Library name: 4454


title: H3K27ac, β3-AR-stimulated control BAs, rep2


title: DNA methylation profile for 203991450165_R01C01

value: Striatum

value: Manchester


title: H3K27ac, β3-AR-stimulated control BAs, rep1


title: H3K27ac, β3-AR-stimulated BAs

value: WT


title: RN2_seBE_Rap biol rep3

city: Philadelphia

first: Diqiu

last: Ren

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description: Library name: C6

data_processing:
Raw FASTQ files were filtered and adapter-trimmed with fastp (v1.0.1) using parameters: --trim_tail1 5 --trim_tail2 5 --detect_adapter_for_pe --length_required 100. Trimmed reads were aligned to the mouse reference genome (GRCm39) using STAR (v2.7.1a) in two-pass mode (--twopassMode Basic). Alignments used --outFilterMismatchNmax 5, --outFilterMultimapNmax 10, and were written as coordinate-sorted BAM with standard tags (NH HI AS nM MD NM XS) and MAPQ 60 for unique alignments (--outSAMmapqUnique 60). STAR was run with --quantMode GeneCounts TranscriptomeSAM to generate per-gene counts and transcriptome-mapped reads. BAM files were indexed with samtools (v1.9). Primary gene-level quantification was performed with featureCounts (Subread v2.0.3) using -t exon -g gene_id -p --countReadPairs -B -Q 20 -s 2 (reverse-stranded) against the matched composite GTF. Count matrices were imported to R, and differential expression was performed with DESeq2 using the specified experimental design.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes gene-level raw read counts per gene generated from coordinate-sorted BAM files using featureCounts (Subread v2.0.3) with GRCm39 gene annotation.

source_name: AML cell line

growth_protocol: Mouse RN2 acute myeloid leukemia cell line was grown in RPMI-1640 (GIBCO) with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from about 1 million cells using the Direct-zol RNA Miniprep Plus kit (ZYMO) with DNase I treatment.
RNA-seq libraries were prepared by Novogene using directional mRNA library preparation protocol (poly A enrichment)

treatment_protocol: RN2 cells transduced with intact BE, Cas9 nickase, evoA1 catalytic mutant, or seBE constructs were sorted on day 5 after transduction. RN2 intact BE and seBE+ cells were treated with 1 nM rapamycin or vehicle 24 hours before sorting.

value: AML cell line

value: MLL-AF9 / NrasG12D AML cells

value: treated with 1nM rapamycin for 24h


title: RN2_seBE_Veh biol rep3

description: Library name: C5

value: treated with vehicle for 24h


title: DNA methylation profile for 203991450163_R01C01

value: Male


title: DNA methylation profile for 203977000019_R01C01

value: Cerebellum


title: H3K4me3, β3-AR-stimulated  BAs

value: brown adipocytes

value: H3K4me3 (Millipore Sigma, #07-473)

value: Beta3-AR agonist


title: RN2_catalytic_mutant biol rep3

description: Library name: C4


title: DNA methylation profile for 203991460019_R07C01


title: input, β3-AR-stimulated BAs


title: IgG, vehicle BAs

value: vehicle


title: input, vehicle BAs


title: DNA methylation profile for 203977000075_R04C01


title: IgG, β3-AR-stimulated  BAs


title: RN2_nCas9 biol rep3

description: Library name: C3


title: H3K27ac, vehicle BAs

value: H3K27ac (Active Motif, #39133)


title: RN2_intact_BE_Veh biol rep3

description: Library name: C1


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

data_processing:
The raw reads of ATAC-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 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 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: tab-delimited XLS file includes identified peaks by DANPOS2

extract_protocol:
ATAC-seq was performed using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s protocol. Murine brown preadipocytes were seeded in a 6-well plate and differentiated into mature adipocytes. Half an hour prior to performing ATAC-seq in adipocytes treated with vehicle or 1 μM CL316,243 for 4 hours, 200 U/ml DNase I was added to culture medium to eliminate free DNA. Adipocytes on the plate were washed three times with ice-cold PBS, scraped down in 1ml PBS, and counted. A total of 50,000 cells were transferred into a new tube and centrifuged at 500 g for 5 minutes at 4°C. Cell pellets were resuspended with 100 μl ice-cold ATAC lysis buffer and centrifuged at 500 g for 10 minutes at 4°C. Cell pellets were resuspended with 50 μl Tagmentation Master Mix and incubated at 37°C for 30 minutes in a thermomixer set at 800 rpm. The reaction was quenched by adding 250 μl DNA Purification Binding Buffer and 5 μl 3 M sodium acetate. The labeled DNA was purified using DNA purification columns and eluted with 35 μl DNA Purification Elution Buffer.
The purified DNA was subjected to library preparation using ATAC-Seq Kit (Active Motif) according to the manufacturer’s protocol.

value: H2A.Z knckdown


title: RN2_intact_BE_Rap biol rep3

description: Library name: C2


title: DNA methylation profile for 203977000016_R06C01

value: Brain

value: Entorhinal cortex


title: H3K4me3, vehicle BAs


title: DNA methylation profile for 203977000013_R02C01

value: Striatum

value: Huntington's disease


title: β3-AR-stimulated control BAs, rep2

value: Control


title: β3-AR-stimulated control BAs, rep1


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


title: RN2_seBE_Rap biol rep2

description: Library name: B6

value: AML cell line

value: WT


title: vehicle control BAs, rep1


title: DNA methylation profile for 203977090035_R03C01

value: Manchester


title: vehicle control BAs, rep2


title: RN2_seBE_Veh biol rep2

description: Library name: B5

value: MLL-AF9 / NrasG12D AML cells

value: treated with vehicle for 24h


title: DNA methylation profile for 203977000075_R07C01

value: Male


title: ssn6KO_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: MAD80
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

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

value: yeast cell

tag: phenotype

value: opaque


title: ssn6KO_3

description:
Library name: MAD81
3' end seq

tag: cell type


title: RN2_catalytic_mutant biol rep2

description: Library name: B4

tag: genotype


title: het_opaque_2

description:
Library name: MAD77
3' end seq


title: DNA methylation profile for 203991460019_R02C01

value: Cerebellum

value: London


title: het_opaque_3

description:
Library name: MAD78
3' end seq


title: RN2_nCas9 biol rep2

description: Library name: B3


title: het_white_2

description:
Library name: MAD74
3' end seq

value: white


title: DNA methylation profile for 203977090035_R04C01


title: het_opaque_1

description:
Library name: MAD76
3' end seq


title: RN2_intact_BE_Veh biol rep2

description: Library name: B1


title: DNA methylation profile for 203977000019_R04C01


title: het_white_1

description:
Library name: MAD73
3' end seq


title: het_white_3

description:
Library name: MAD75
3' end seq


title: delM2_opaque_3

description:
Library name: MAD72
3' end seq


title: delM2_opaque_1

description:
Library name: MAD70
3' end seq


title: DNA methylation profile for 203977000013_R06C01


title: RN2_seBE_Veh biol rep1

description: Library name: A5


title: delM2_white_2

description:
Library name: MAD68
3' end seq


title: delM2_white_3

description:
Library name: MAD69
3' end seq


title: DNA methylation profile for 203976760022_R08C01

description: DNA methylation profile from healthy control

value: Female


title: delM2_white_1

description:
Library name: MAD67
3' end seq


title: ssn6KO_1

description:
Library name: MAD79
3' end seq


title: RN2_intact_BE_Rap biol rep2

description: Library name: B2

value: treated with 1nM rapamycin for 24h


title: RN2_seBE_Rap biol rep1

description: Library name: A6


title: RN2_catalytic_mutant biol rep1

description: Library name: A4


title: DNA methylation profile for 203977000075_R08C01

value: Brain


title: delM1_opaque_3

description:
Library name: MAD66
3' end seq


title: DNA methylation profile for 203991450165_R07C01


title: RN2_nCas9 biol rep1

description: Library name: A3


title: delM1_opaque_1

description:
Library name: MAD64
3' end seq


title: delM1_opaque_2

description:
Library name: MAD65
3' end seq


title: DNA methylation profile for 203977000016_R05C01


title: DNA methylation profile for 203968030088_R04C01

value: Entorhinal cortex


title: delM1_white_3

description:
Library name: MAD63
3' end seq


title: RN2_intact_BE_Veh biol rep1

description: Library name: A1


title: delM1_white_2

description:
Library name: MAD62
3' end seq


title: delM1_white_1

description:
Library name: MAD61
3' end seq


title: delN2_opaque_2

description:
Library name: MAD59
3' end seq


title: mPFC R70H M Sample 526 GEX

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: Sylvester Comprehensive Cancer Center

description:
Library name: mPFC_R70H_M_526_GEX
mPFC WT Male Single-Nucleus Multiome ATAC + RNA

data_processing:
Data Processing and Quality Control (QC): FASTQ files generated from snATAC+RNA profiling of mouse hippocampus (mHC) and prefrontal cortex (mPFC) were processed using Cell Ranger ARC v2.0.2 (count function) with the mm39 reference genome. This pipeline performed read alignment, barcode filtering, peak calling, and quantification of both ATAC and gene expression (GEX) features. The resulting output was imported into R (v4.4.0) using the Read10X function from Seurat (v5.3.0), creating a Seurat object. Chromatin accessibility data were incorporated using CreateChromatinAssay from the Signac package (v1.14.0). Initial QC was conducted by inspection of key metrics, including mitochondrial content (percent.mt ≤ 3%), RNA feature counts (nFeature_RNA ≥ 1000 and ≤ 15,000), ATAC fragment counts (nCount_ATAC ≥ 1000), RNA molecule counts (nCount_RNA ≤ 30,000), and transcription start site (TSS) enrichment (≥ 0.5). Doublets were identified and removed using DoubletFinder, with optimal pK values determined via parameter sweep and bimodality coefficient analysis.
Assembly: mm39
Supplementary files format and content: RDS file of integrated samples and replicates filtered and annotated

molecule: nuclear RNA

source_name: Prefrontal Cortex

extract_protocol:
Brain regions were dissected according to the Allen Brain Reference. Nuclei were isolated following the Miltenyi Biotec “Reliable nuclei extraction and enrichment” protocol. Dissected tissues were transferred to gentleMACS™ C Tubes with 2 mL ice-cold lysis buffer and dissociated using program 4C_nuclei_1. The suspension was filtered through a 70-μm strainer, rinsed with 2 mL lysis buffer, and centrifuged (300 × g, 5 min, 4 °C). Pellets were resuspended in resuspension buffer, passed through a 30-μm strainer, and centrifuged again (300 × g, 5 min). Nuclei were resuspended in 450 μL nuclei separation buffer per 10⁶ nuclei, mixed with 50 μL Anti-Nucleus MicroBeads, and incubated for 15 min at 4 °C. After adding 2 mL separation buffer, samples were subjected to magnetic separation. MS columns were placed on a MACS® Separator and equilibrated with 3 mL separation buffer. Labeled nuclei were loaded onto the column and washed twice with 1 mL separation buffer. Columns were removed from the magnet, placed in collection tubes, and the nuclei were eluted by adding separation buffer and pushing the plunger.
10x Chromium Single Cell Multiome ATAC + GEX library construction protocol recommended by manufacturer

value: Prefrontal Cortex

value: Single-Nucleus Multiome ATAC + RNA

value: Heterozigous WT Rnf2 R70H

tag: library type

value: mRNA


title: delN2_opaque_1

description:
Library name: MAD58
3' end seq


title: RN2_intact_BE_Rap biol rep1

description: Library name: A2

value: AML cell line

value: WT


title: delM2_opaque_2

description:
Library name: MAD71
3' end seq


title: delN2_opaque_3

description:
Library name: MAD60
3' end seq


title: delN2_white_1

description:
Library name: MAD55
3' end seq


title: DNA methylation profile for 203968030088_R07C01

value: Striatum

value: Control


title: delN2_white_3

description:
Library name: MAD57
3' end seq

value: yeast cell


title: DNA methylation profile for 203968030088_R05C01


title: delN1_opaque_2

description:
Library name: MAD53
3' end seq

value: opaque


title: delN2_white_2

description:
Library name: MAD56
3' end seq


title: delN1_opaque_3

description:
Library name: MAD54
3' end seq


title: DNA methylation profile for 203991450165_R02C01

value: Cerebellum

value: Male


title: mPFC R70H M Sample 526 ATAC

description:
Library name: mPFC_R70H_M_526_ATAC
mPFC WT Male Single-Nucleus Multiome ATAC + RNA

library_source: genomic single cell

value: ATAC


title: mPFC R70H F Sample 521 ATAC

description:
Library name: mPFC_R70H_F_521_ATAC
mPFC R70H Female Single-Nucleus Multiome ATAC + RNA


title: delN1_white_2

description:
Library name: MAD50
3' end seq

value: white


title: mPFC WT M Sample 524 GEX

description:
Library name: mPFC_WT_M_524_GEX
mPFC WT Male Single-Nucleus Multiome ATAC + RNA


title: delN1_opaque_1

description:
Library name: MAD52
3' end seq


title: delN1_white_3

description:
Library name: MAD51
3' end seq


title: mPFC WT M Sample 524 ATAC

description:
Library name: mPFC_WT_M_524_ATAC
mPFC WT Male Single-Nucleus Multiome ATAC + RNA


title: DNA methylation profile for 203977000016_R01C01

value: London


title: delT2_3

description:
Library name: MAD48
3' end seq


title: delN1_white_1

description:
Library name: MAD49
3' end seq


title: DNA methylation profile for 203976760023_R01C01

value: Brain

value: Huntington's disease


title: delT2_2

description:
Library name: MAD47
3' end seq


title: DNA methylation profile for 203968030089_R04C01

value: Female


title: mPFC R70H F Sample 521 GEX

description:
Library name: mPFC_R70H_F_521_GEX
mPFC R70H Female Single-Nucleus Multiome ATAC + RNA

value: Prefrontal Cortex

value: Single-Nucleus Multiome ATAC + RNA


title: DNA methylation profile for 203977000016_R08C01

description: DNA methylation profile from Huntington's disease patient

value: Entorhinal cortex


title: mPFC WT M Sample 525 GEX

description:
Library name: mPFC_WT_M_525_GEX
mPFC WT Male Single-Nucleus Multiome ATAC + RNA

value: mRNA


title: delT2_1

description:
Library name: MAD46
3' end seq


title: DNA methylation profile for 203968030089_R01C01


title: mPFC WT M Sample 525 ATAC

description:
Library name: mPFC_WT_M_525_ATAC
mPFC WT Male Single-Nucleus Multiome ATAC + RNA

value: WT


title: delT1_2

description:
Library name: MAD44
3' end seq


title: delT1_3

description:
Library name: MAD45
3' end seq


title: delT1_1

description:
Library name: MAD43
3' end seq


title: mPFC WT F Sample 520 GEX

description:
Library name: mPFC_WT_F_520_GEX
mPFC WT Female Single-Nucleus Multiome ATAC + RNA


title: WT_opaque_3

description:
Library name: MAD42
3' end seq


title: DNA methylation profile for 203977090035_R05C01


title: WT_opaque_1

description:
Library name: MAD40
3' end seq


title: DNA methylation profile for 203977000019_R05C01

value: Striatum


title: mPFC WT F Sample 520 ATAC

description:
Library name: mPFC_WT_F_520_ATAC
mPFC WT Female Single-Nucleus Multiome ATAC + RNA


title: DNA methylation profile for 203976760023_R04C01

value: Control


title: WT_white_2

description:
Library name: MAD38
3' end seq

value: yeast cell


title: WT_white_1

description:
Library name: MAD37
3' end seq


title: WT_opaque_2

description:
Library name: MAD41
3' end seq

value: opaque


title: DNA methylation profile for 203976760023_R03C01

value: Cerebellum


title: DNA methylation profile for 203977090035_R02C01

value: Male


title: delNM2_opaque_3

description:
Library name: MAD36
3' end seq


title: mHC WT M Sample 525 ATAC

description:
Library name: mHC_WT_M_525_ATAC
mHC WT Male Single-Nucleus Multiome ATAC + RNA

source_name: Hippocampus

value: Hippocampus

value: ATAC


title: mHC WT M Sample 525 GEX

description:
Library name: mHC_WT_M_525_GEX
mHC WT Male Single-Nucleus Multiome ATAC + RNA


title: mHC WT M Sample 524 GEX

description:
Library name: mHC_WT_M_524_GEX
mHC WT Male Single-Nucleus Multiome ATAC + RNA


title: delNM2_opaque_1

description:
Library name: MAD34
3' end seq


title: DNA methylation profile for 203991460019_R01C01

value: London


title: WT_white_3

description:
Library name: MAD39
3' end seq

value: white


title: delNM2_opaque_2

description:
Library name: MAD35
3' end seq


title: delNM2_white_2

description:
Library name: MAD32
3' end seq


title: DNA methylation profile for 203977000013_R08C01

value: Brain

value: Huntington's disease


title: DNA methylation profile for 203977000010_R07C01


title: mHC WT F Sample 520 GEX

description:
Library name: mHC_WT_F_520_GEX
mHC WT Female Single-Nucleus Multiome ATAC + RNA


title: delNM1_opaque_3

description:
Library name: MAD30
3' end seq


title: mHC WT M Sample 524 ATAC

description:
Library name: mHC_WT_M_524_ATAC
mHC WT Male Single-Nucleus Multiome ATAC + RNA


title: delNM2_white_3

description:
Library name: MAD33
3' end seq


title: delNM2_white_1

description:
Library name: MAD31
3' end seq


title: mHC WT F Sample 520 ATAC

description:
Library name: mHC_WT_F_520_ATAC
mHC WT Female Single-Nucleus Multiome ATAC + RNA


title: DNA methylation profile for 203977000013_R03C01

description: DNA methylation profile from healthy control


title: delNM1_opaque_1

description:
Library name: MAD28
3' end seq


title: delNM1_white_3

description:
Library name: MAD27
3' end seq


title: delNM1_opaque_2

description:
Library name: MAD29
3' end seq


title: mHC R70H M Sample 526 ATAC

description:
Library name: mHC_R70H_M_526_ATAC
mHC R70H Male Single-Nucleus Multiome ATAC + RNA

value: Heterozigous WT Rnf2 R70H


title: DNA methylation profile for 203976760023_R08C01

value: Female


title: delNM1_white_2

description:
Library name: MAD26
3' end seq


title: DNA methylation profile for 203977000016_R03C01


title: mHC R70H M Sample 526 GEX

description:
Library name: mHC_R70H_M_526_GEX
mHC R70H Male Single-Nucleus Multiome ATAC + RNA

value: Single-Nucleus Multiome ATAC + RNA


title: DNA methylation profile for 203976760024_R03C01

value: Entorhinal cortex


title: DNA methylation profile for 203968030089_R02C01


title: ab2_opaque_2

description:
Library name: MAD23
3' end seq


title: ab2_white_1

description:
Library name: MAD19
3' end seq


title: mHC R70H M Sample 523 ATAC

description:
Library name: mHC_R70H_M_523_ATAC
mHC R70H Male Single-Nucleus Multiome ATAC + RNA


title: ab2_opaque_3

description:
Library name: MAD24
3' end seq


title: ab2_white_2

description:
Library name: MAD20
3' end seq


title: ab1_opaque_3

description:
Library name: MAD18
3' end seq


title: DNA methylation profile for 203977000075_R06C01


title: ab2_white_3

description:
Library name: MAD21
3' end seq


title: ab1_white_3

description:
Library name: MAD15
3' end seq


title: ab2_opaque_1

description:
Library name: MAD22
3' end seq


title: mHC R70H F Sample 521 GEX

description:
Library name: mHC_R70H_F_521_GEX
mHC R70H Female Single-Nucleus Multiome ATAC + RNA

value: mRNA


title: ab1_opaque_1

description:
Library name: MAD16
3' end seq


title: DNA methylation profile for 203968030088_R03C01


title: mHC R70H F Sample 521 ATAC

description:
Library name: mHC_R70H_F_521_ATAC
mHC R70H Female Single-Nucleus Multiome ATAC + RNA


title: mESC R70H, Mtf2, Replicate 2

description:
Library name: 112_MTF2_Rep2
with spike in - human T47D (genome: hg38_encode)

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

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.

value: Mouse embryonic stem cells (mESCs)

tag: antibody

value: MTF2 Polyclonal antibody, PROTEINTECH (Cat #16208-1-AP )


title: mHC R70H M Sample 523 GEX

description:
Library name: mHC_R70H_M_523_GEX
mHC R70H Male Single-Nucleus Multiome ATAC + RNA


title: ab1_opaque_2

description:
Library name: MAD17
3' end seq

value: yeast cell


title: delNM1_white_1

description:
Library name: MAD25
3' end seq


title: DNA methylation profile for 203977000010_R02C01

value: Striatum

value: Control


title: ab1_white_2

description:
Library name: MAD14
3' end seq


title: DNA methylation profile for 203968030088_R06C01

value: Male


title: delC2_opaque_1

description:
Library name: MAD10
3' end seq

value: opaque


title: mESC R70H, Jarid2_2, Replicate 1

description:
Library name: 112_JARID2_2_Rep1
with spike in - human T47D (genome: hg38_encode)

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


title: mESC R70H, Mtf2, Replicate 1

description:
Library name: 112_MTF2_Rep1
with spike in - human T47D (genome: hg38_encode)


title: delC2_white_2

description:
Library name: MAD08
3' end seq


title: DNA methylation profile for 203991450163_R04C01

value: London


title: ab1_white_1

description:
Library name: MAD13
3' end seq

value: white


title: delC2_white_1

description:
Library name: MAD07
3' end seq


title: delC1_white_1

description:
Library name: MAD01
3' end seq


title: mESC WT, Mtf2, Replicate 2

description:
Library name: WT_MTF2_Rep2
with spike in - human T47D (genome: hg38_encode)

value: WT


title: delC2_white_3

description:
Library name: MAD09
3' end seq


title: delC1_opaque_3

description:
Library name: MAD06
3' end seq


title: DNA methylation profile for 203977000019_R08C01

value: Brain


title: DNA methylation profile for 203977000010_R04C01

description: DNA methylation profile from Huntington's disease patient

value: Cerebellum

value: Huntington's disease


title: delC1_white_3

description:
Library name: MAD03
3' end seq


title: delC1_opaque_1

description:
Library name: MAD04
3' end seq


title: delC1_opaque_2

description:
Library name: MAD05
3' end seq


title: DNA methylation profile for 203977000013_R04C01


title: mESC WT, Jarid2_2, Replicate 2

description:
Library name: WT_JARID2_2_Rep2
with spike in - human T47D (genome: hg38_encode)


title: delC1_white_2

description:
Library name: MAD02
3' end seq


title: DNA methylation profile for 203977000010_R03C01


title: mESC WT, Jarid2_2, Replicate 1

description:
Library name: WT_JARID2_2_Rep1
with spike in - human T47D (genome: hg38_encode)


title: Control1(M.tb H37Rv)_replicate

city: Chandigarh

first: Indu

last: Verma

state: Chandigarh

address: Lab 310, Research Block A, 3rd Floor

department: Biochemistry

country: India

institute: Post Graduate Institute of Medical Education and Research

description: SG17044571_252632310048_S001_GE1_1200_Jun14_2_4

hyb_protocol: For hybridization, array slide was assembled into hybridization chamber and loaded into the oven rotator rack set at rotation 10 rpm at 65°C for 17 hours.

scan_protocol: Slides were scanned using microarray scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters and M.tb whole genome microarray data was analyzed using GeneSpring (15 day trial version)

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis Culture (M.tb H37Rv) RNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. For transcription and cRNA labeling, nuclease-free water, 5×transcription buffer, 0.1 M DTT, NTP mix, T7 RNA polymerase blend, Cyanine 3- CTP were added to sample tubes and incubated at 40°C for 2 hours in water bath. Further purification of amplified cRNA samples was performed by using RNeasy mini kit and cRNA quantitation was performed using nanodrop (ND-1000 UV-VIS spectrophotometer) to detect Cyanine 3 dye concentration (pmol/μL), RNA absorbance ratio (260 nm/280 nm), cRNA concentration (ng/μL). cRNA yield and specific activity for each sample was calculated. Next for the fragmentation of labeled cRNA for each sample, 10×gene expression blocking agent, nuclease-free water and 25×fragmentation buffer were added to 1.2 µg of Cyanine 3-labeled and linearly amplified cRNA and tubes were incubated at 60°C for 30 minutes and then immediately placed on ice for one minute followed by addition of 2×Hi-RPM hybridization buffer to stop the fragmentation reaction. Then sample tubes were centrifuged at 13,000 rpm for 1 minute at room temperature and were loaded onto the array slide.

growth_protocol: M.tb H37Rv (NCTC 7416) was cultured in Soutan‘s media containing 2% glycerol and 0.05% Tween-80 under shaking conditions at 200rpm. Logarithmically growing cultures were used for M.tb RNA isolation by TRIzolTM.

extract_protocol: RNA from biopsy samples and M.tb H37Rv culture were initially purified using Mini Elute Clean-up kit (Qiagen) as per manufacturer‘s instructions. The amount, purity and RNA integrity were determined by using nanodrop and Agilent 2100 bioanalyzer. Input RNA (200ng) from TBP biopsy samples (Test) and M.tb H37Rv (Control) were added to 1.5mL microcentrifuge tube and incubated at 65oC in water bath for 10 minutes to denature the template followed by incubation at ice for 5 minutes. For cDNA synthesis, 5×first strand buffer, 0.1 M DTT, 10 mM dNTP mix and affinity script RNase block mix were added and tubes were first incubated in water bath at 40°C for 2 hours and then at 70°C for 15 minutes. After completion of incubation steps, sample tubes were shifted to ice for 5 minutes.

treatment_protocol: Pleural biopsy samples were collected in RNA later. To remove RNA later, 1 mL phosphate buffer saline (PBS) was added to biopsy samples and were centrifuged at 3000g for 15 minutes at 4 degree C. Supernatant was removed and the biopsy samples were resuspended in PBS and washed twice at 5000g for 15 minutes at 4 degree C. After washing, supernatant was removed and biopsy samples were homogenised. To remove eukaryotic RNA, cell pellet from biopsy samples were treated with 4M guanidinium thiocyanate solution (GTC). Samples were mixed well until suspension became clear and cell lysate was centrifuged at 5000g for 20 minutes at 4 degree C. Supernatant was discarded and cell pellets from biopsy samples were further used for RNA isolation using TRIzol.

value: M.tb H37Rv culture

tag: gender


title: DNA methylation profile for 203991460019_R05C01

tag: brain region

value: Entorhinal cortex


title: mESC WT, Mtf2, Replicate 1

description:
Library name: WT_MTF2_Rep1
with spike in - human T47D (genome: hg38_encode)


title: TBP3_replicate

description: SG17044571_252632310048_S001_GE1_1200_Jun14_2_3 (1)

source_name: TBP biopsy RNA

value: Biopsy


title: DNA methylation profile for 203977090036_R01C01

description: DNA methylation profile from healthy control

tag: Sex


title: TBP2

description: SG17044571_252632310048_S001_GE1_1200_Jun14_1_2

tag: age


title: TBP4

description: SG17044571_252632310048_S001_GE1_1200_Jun14_1_4 (1)


title: mESC WT, Input2, Replicate 2

description:
Library name: WT_input2_Rep2
with spike in - human T47D (genome: hg38_encode)

value: Mouse embryonic stem cells (mESCs)


title: TBP1

description: SG17044571_252632310048_S001_GE1_1200_Jun14_1_1


title: DNA methylation profile for 203991460065_R07C01

value: Female

tag: disease state


title: DNA methylation profile for 203991450163_R07C01

tag: brain bank


title: mESC R70H, Input2, Replicate 1

description:
Library name: 112_input2_Rep1
with spike in - human T47D (genome: hg38_encode)


title: mESC R70H, Input2, Replicate 2

description:
Library name: 112_input2_Rep2
with spike in - human T47D (genome: hg38_encode)


title: TBP1_replicate

description: SG17044571_252632310048_S001_GE1_1200_Jun14_2_2


title: TBP3

description: SG17044571_252632310048_S001_GE1_1200_Jun14_1_3


title: Control1(M.tb H37Rv)

description: SG17044571_252632310048_S001_GE1_1200_Jun14_2_1


title: Input control for LoVo ChIP

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_Input

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: wild type


title: Ribo_Mettl18_KO3

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 6

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

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.

value: pancreatic acinar cell 266-6

value: Mettl18 KO


title: DNA methylation profile for 203976760022_R03C01

value: Control

tag: bisulfite conversion batch


title: DNA methylation profile for 203991450163_R06C01

value: Striatum

value: London

tag: neuronal proportion


title: Gro-seq-MCF7

description:
Library name: Sample 10
GS_HS_MCF7_siCTL

data_processing:
Library strategy: Gro-seq
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 2.00e+09.
Assembly: Homo sapiens genome Ensembl GRCh37 (hg19)
Supplementary files format and content: bigWig files for each Sample

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
MCF7 cells were washed 3 times with cold 1X phosphate buffered saline (PBS) buffer and then incubated in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min on ice and harvested. Cells were first re-suspended and lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100ml of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase In, 1% sarkosyl, 500mM ATP, GTP, and Br-UTP, 2mM CTP) and incubated for 5 min at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. NRO-RNA was then subjected to base hydrolysis on ice for 40 min and followed by treatment with DNase I and antarctic phosphatase. To purify the Br-UTP labeled nascent RNA, the NRO-RNA was immunoprecipitated with an anti-BrdU agarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween-20) for 1h at 4°C while rotating. To repair the end, the immunoprecipitated BrU-RNA was re-suspended in 50mL reaction (43mL DEPC water, 5.2mL T4 PNK buffer, 1mL SUPERase In and 1mL T4 PNK (New England BioLabs)) and incubated at 37°C for 1h. RNA was then extracted, precipitated using acidic phenol-chloroform (Ambion) and subjected to poly-A tailing reaction by using poly-A polymerase (New England BioLabs) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223- primers (5’- pGATCGTCGGACTGTAGAACTCT; CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’) where the p indicates 5’ phosphorylation, ‘;’ indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. Specifically, tailed RNA (8.0mL) was subjected to reverse transcription using superscript III (Invitrogen), after which the cDNA products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product (100-500bp) was excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (New England BioLabs). Re-linearized single strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. Primers oNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and oNTI201 (5’- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to generate DNAs for deep sequencing.
GRO-seq libraries were generated from nascent RNA labeled by BrUTP during nuclear run-on transcription in MCF-7 cells, followed by BrU-based immunoprecipitation, enzymatic end-repair, polyadenylation, reverse transcription, circularization, relinearization, size selection, and PCR amplification prior to sequencing.

tag: cell line

value: breast cancer cells

value: control knockdown


title: Input control for MDST8 ChIP

description: Library name: MDST8_Input

tag: tissue


title: DNA methylation profile for 203991460065_R01C01

value: Brain

value: Male


title: mESC WT, Input2, Replicate 1

description:
Library name: WT_input2_Rep1
with spike in - human T47D (genome: hg38_encode)

value: WT


title: TWIST1 ChIP-seq in LoVo cells

description: Library name: LoVo_TWIST1_ChIP


title: TWIST1 ChIP-seq in MDST8 cells

description: Library name: MDST8_TWIST1_ChIP


title: Ribo_Mettl18_KO2

description: Library name: Sample 5