title: F121 F2 ES Rep2, H3K9me3

city: Oxford

first: Mafalda

last: Almeida

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: nC0771_F121_F2_ES_H3K9me3

data_processing:
ChIP-sequencing analysis was performed using previously established pipelines45. For calibrated ChIP-seq experiments, raw fastq reads were mapped using Bowtie2 (v.2.3.5.1)67 to the 129S1xCast N-masked mm10 genome concatenated with the dm6 Drosophila genome using the following parameters: “--very-sensitive --no-discordant --no-mixed -X 2000”. Unmapped reads were then removed. PCR duplicates were identified and removed using picard-tools “MarkDuplicates” (Broad Institute) and remaining reads were then assigned to each allele using SNPsplit68. To calculate calibration factors, mm10 and dm6 mapped reads for each sample and input were counted using SAMtools (v.1.16)69. Calibration factors for cChIP-seq were then calculated according to the derived formula for occupancy ratio (ORi)70. In order to generate calibrated bigwig files for mouse chrX, bam files were initially filtered using the “intersect” function from BEDtools (v.2.30.0)71 to generate a bam file containing mouse chrX reads only. During the generation of the iXist-ChrXCast cell line using CRISPR-Cas9–facilitated homology-directed recombination, two SNPs (mm10, chrX:103482682 A/T and mm10, chrX:103482895 A/T) between the Cast and 129 alleles became uninformative, as both X alleles were converted to the 129 allele (T at both positions). Consequently, any reads spanning these two sites are no longer allele-specific as intended and were therefore removed from the allelic BAM files. BAM files were then sorted and indexed using SAMtools69 and bigWig files were finally generated using deepTools (v.3.5.1)72 bamCoverage per 10 million reads considering the calibration factors. BigWig files were then visualized using IGV (https://software.broadinstitute.org/software/igv/)73. To quantify the number of ChIP reads per kb over the Xist locus (chrX: 103460373-103483233), we used the function “bigWigAverageOverBed” from UCSCTools.
Assembly: mm10; dm6
Supplementary files format and content: bigWig

source_name: Parental of TsixStop cell line

growth_protocol: mESC were grown in ESC medium at 37oC in a 5% CO2 incubator and passaged onto 0.1% gelatin-coated plates in feeder-dependent conditions every 2-3 days using TrypLE Express (Life Technologies). Mitomycin C-inactivated SNLP (STO mouse fibroblasts expressing Neomycin and Puromycin resistance and Lif genes) were used as feeder cells. Cells were pre-plated and passaged at least twice to remove feeders prior to cell collection for genomic experiments. ESC medium consisted of Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS), 1x NEAA (Non-essential amino acids; Life Technologies), 2mM L-glutamine (Life Technologies), 1x Penicillin-Streptomycin (Life Technologies), 50µM b-mercaptoethanol (Life Technologies) and Leukemia Inhibitory Factor (LIF)-conditioned medium made in-house. Mouse embryonic stem cells were differentiated into NPC as previously described62,63. To obtain feederless mESC cell suspensions, mESC were collected using TrypLE and pre-plated four consecutive times for 40 min each. Cells were then washed in PBS twice to remove any traces of FBS and counted using a Countess® II FL Automated Cell Counter (Life Technologies). Cells were then resuspended in N2B27 medium (50% Neurobasal; 50% DMEM/F12 with 0.5x N2 and 0.25x B27, 1mM L-glutamine, 0.5x Penicillin-Streptomycin, 100μM b-mercaptoethanol, all from Life Technologies) supplemented with 1μg/mL of doxycycline to induce Xist expression simultaneously with the onset of differentiation, and plated at a density of 20,000 cells per cm2 in pre-gelatinized plates. Cells were fed daily from day 2 to day 7 of differentiation and fed also on day 1 for experiments in which this corresponded to the timepoint of 100 nM dTAG-13 addition. dTAG-13 treated NPC cultures were fed with media containing dTAG-13 from NPCd1 onwards until collection. On day 7, cells were dissociated by incubation with accutase (diluted 1:3 in PBS) (Merck Life Sciences) and counted. Three million cells were resuspended in N2B27 supplemented with doxycycline and 10 ng/mL EGF (cat# 315-09, Peprotech) and 10 ng/mL FGF2 (cat# 100-18B, Peprotech) and plated to grow in suspension in non-adherent bacterial petri dishes to promote embryoid body formation. On day 10, cells were recovered by centrifugation and plated onto pre-gelatinized dishes to expand more homogeneous neural stem cell cultures. At this point, neural stem cells were fed every other day and passaged as required using accutase (diluted 1:3 in PBS) (Merck Life Sciences) until the required timepoint. Cells were collected for different experiments at the appropriate timepoints (generally, NPCd1, d3 and d7 for ChIP experiments and multiple timepoints from NPCd1 to NPCd28 for chromatin-RNA) by washing with PBS and then incubating the cells at room temperature with accutase (diluted 1:3 in PBS) (Merck Life Sciences) until they were dissociated for collection.

extract_protocol:
Calibrated native ChIP-seq (cChIP-seq) was performed for H3K9me3 by collecting 5x107 mESCs or NPCs and spiking in 1 × 107 Drosophila Sg4 cells counted using a Countess II FL Automated Cell Counter (Life Technologies). Cells were pelleted by centrifugation and resuspended in 1mL of cold RSB (10mM Tris pH 8.0, 10mM NaCl, 3mM MgCl2) and lysed by addition of 14mL of cold RSB supplemented with 0.1% NP40 and gentle inversion. Nuclei were recovered by centrifugation at 1500 x g for 5 min at 4oC and washed in 4ml RSB with 0.25M sucrose and 3mM CaCl2 supplemented with protease inhibitors. Nuclei were recovered by centrifugation at 1500 x g for 5 min at 4oC and resuspended in 1mL of RSB with 0.25M sucrose and 3mM CaCl2 supplemented with protease inhibitors, which was transferred to a 1.5mL tube for MNase digestion (200U, Fermentas EN0181) of chromatin to mono- and di-nucleosomes at 37oC for 5 min with inversion every minute. The reaction was quenched by addition of 8µL 0.5M EDTA and spun at 5,000rpm for 5min at 4oC. The supernatant (S1) was collected into a new 1.5mL tube and kept on ice. The pellet was thoroughly resuspended in 300µL of Nucleosome Release Buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2mM EDTA) supplemented with protease inhibitors, and incubated for 1hour at 4oC with rotation. This suspension was passed five times through a 27G needle using a 1mL syringe and then spun at 5000rpm for 5min at 4oC. The supernatant (S2) was collected and combined with S1. The chromatin was centrifuged at 13000rpm for 5min to remove any precipitant, and supernatant was collected as chromatin, snap frozen and stored at -80oC until further processing. For immunoprecipitation (IP), chromatin was thawed on ice and 110µL were diluted in 1mL of native ChIP incubation buffer (70mM NaCl, 10mM Tris pH 7.5, 2mM MgCl2, 2mM EDTA, 0.1% Triton X-100) freshly supplemented with protease inhibitors.  100µL were transferred to a new 1.5mL tube and stored at 4oC to be used as input. The remaining diluted chromatin was incubated overnight with rotation with 5µg of H3K9me3 antibody (Abcam, ab8898) or H3K9me3 (Active Motif; AB2532132 Clone 0319; Cat #061013). Samples were then incubated for 90min with 45µL rProtein A Sepharose™ Fast Flow beads (Amersham) pre-blocked with 1mg/mL of yeast tRNA and 1mg/mL BSA. The beads were then washed five times for 10min with rotation at 4oC with Wash Buffer (20mM Tris pH 7.5, 2mM EDTA, 125mM NaCl, 0.1% Triton X-100) followed by one final wash in 1x TE. The DNA was then eluted from the beads by incubation at 25oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. DNA from the IP elutions and input samples was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions.
ChIP and input DNA was quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and submitted to library preparation using the the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and their length was estimated using the Bioanalyzer High Sensitivity DNA kit (Agilent) before pooling and subjected to paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

treatment_protocol: To induce Xist expression, medium was supplemented with 1µg/mL doxycycline. To induce protein degradation in lines expressing FKBP12F36V-tagged proteins, medium was supplemented with 100nM dTAG-13 (Tocris Bioscience).

tag: strain background

value: Cast x 129S

value: Parental of TsixStop cell line

value: mESC

tag: genotype

value: anti-H3K9me3 (Abcam, # ab8898)

tag: spike-in

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: Soldier nuclei, whole body

status: Public on Mar 12 2026

type: SRA

city: Sydney

first: Catherine

middle: Rose

last: Gatt

state: NSW

address: UNSW Sydney High St Kensington

department: School of Clinical Medicine

country: Australia

institute: University of New South Wales

description:
Library name: Soldier
10X Genomics
features.tsv.gz

library_source: transcriptomic single cell

data_processing:
Raw fastq reads from each caste (queen, king, soldier, worker) were aligned to the Z. nevadensis reference genome. A custom reference genome of Z. nevadensis was generated using Cell Ranger mkref v8.0.0 37. A cell count matrix of all the castes was then generated using Cell Ranger count v8.0.0 37 with default parameters.
A combined cell count matrix of all the castes was then generated using Cell Ranger aggr v8.0.0 37 with default parameters.
The Cell Ranger aggr v8.0.0 37 barcode and matrix output files were separated by sample (caste; king, queen, soldier, worker).
Automated cell type labels were obtained using SATURN-xfer. Cell type annotations were cross-referenced with curated marker genes from the D. melanogaster single-cell atlas.
Assembly: Liu, C. et al. Unravelling the evolution of wood-feeding in termites with 47 high-resolution genome assemblies. Nat. Commun. 16, 11154 (2025)
Supplementary files format and content: Cell Ranger output files: tab separated values files and matrix files.
Supplementary files format and content: znev_all_castes.h5ad: gene expression count matrix of all castes and nuclei, with annotated cell types.

molecule: nuclear RNA

organism: Zootermopsis nevadensis

source_name: whole body

extract_protocol:
Dissociation and isolation of single nuclei from the whole body of each sample was performed using an adapted version of a protocol established for Drosophila 36. Briefly, 100 μl of homogenisation buffer was dispensed into an DNA LoBind 1.5 ml tube (Eppendorf 022431021) and placed on ice. The homogenisation buffer consisted of nuclease free water, 250 mM nuclease free sucrose (FUJIFILM Wako Pure Chemical Industries, Ltd. 19-0001), 10 mM Tris (pH 8.0) (Nippon Gene 312-90061), 25 mM KCl (Cayman Chemical Company 600213), 5 mM MgCl2 (Serva 39772), 0.1% Triton-x 100 (FUJIFILM Wako Pure Chemical Industries, Ltd. 168-11805), 0.5% RNasin Plus (Promega N261B), 1× protease inhibitor (Promega G6521), and 0.1 mM DTT (Formedium Ltd. DTT005). Samples were placed into the homogenisation buffer and nuclei were released by approximately 20 gentle strokes of a plastic pestle (Violamo 1-2955-01) and an additional 900 μl of homogenisation buffer was added to the tube. Each sample was centrifuged (Eppendorf 5424R) at 1000 g for 10 minutes at 4°C, the supernatant was discarded, and the nuclei were resuspended in a 1000 μl of resuspension buffer on ice. The resuspension buffer consisted of 1× PBS (pH 7.4) (Thermo Fisher 2669978), 0.5% BSA (Wako Pure Chemical Industries, Ltd. 017-21273), and 0.5% RNasin Plus (Promega N261B). Each sample was then passed twice through a 100 µm cell strainer (As One 100-98-5) and placed into a 5 ml FACS tube (Falcon 352235) with a 35 µm cap for FACS sorting. Following dissociation, nuclei were stained with 1 μl of DAPI and were isolated from remaining debris with Fluorescence Activated Cell Sorting (FACS) using a BD FACSAria III. The worker sample was sorted into a 1.5 ml tube containing 400 μl of resuspension buffer. The queen, soldier, and king samples were sorted into 1.5 ml tubes containing 200 μl of resuspension buffer. Immediately after FACS sorting, nuclei were centrifuged at 1000 g for 10 minutes at 4°C and the 700 μl of supernatant was discarded. Nuclei were resuspended in the remaining 50-60 μl of supernatant, and the concentration of nuclei was calculated using a Thoma cell counting plate (Watson 177312C) with a ZEISS Axio Scope A.1 microscope.
Sequencing was performed as per the 10x Genomics User Guide (CG000315 Rev E). Gel Beads-in-emulsion (GEMs) were generated using the Chromium X Instrument (10x Genomics, Pleasanton, CA, USA), and scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Dual Index). The worker sample was loaded in the Chromium Next GEM Chip G with a target output of 10,000 nuclei, and the queen, soldier, and king samples were loaded in the Chromium Next GEM Chip G with a target output of 5,000 nuclei. All reactions were performed in the Eppendorf Mastercycler X50s with a 96-Deep Well Reaction Module. For both cDNA amplification and sample index PCR, 14 cycles were used across all samples.Sequencing was performed in-house on the NovaSeq 6000 platform

tag: tissue

value: whole body

tag: caste

value: Soldier


title: F121 F2 ES Rep2, Input

description: Library name: nC0770_F121_F2_ES_Input

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: treatment

tag: chip antibody


title: PGW11-5-5P-r0

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Slices were placed on Merscope slides (Vizgen, #10500102) and processed according to the manufacturer’s user guides

scan_protocol: Cell boundary staining, gel embedding, clearing, and probe hybridization steps were performed without modification from the fresh-frozen sample preparation guide. Samples were imaged on the MERSCOPE instrument using the 300-plex imaging kit.

data_processing: Data processing was done using the in-instrument software MERLIN pipeline provided by Vizgen.

molecule: total RNA

organism: Homo sapiens

source_name: human fetus

extract_protocol: Fresh frozen 14 μm coronal samples, cryosectioned using a CM3050 Leica cryostat, from the fronto-nasal region.

tag: developmental stage

tag: side

value: posterior section


title: NTS, leaf, WGBS deep, rep2

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

institute: University of Warwick

description: Library name: NTS_2_WGBS

data_processing:
Initial quality assessment of raw sequencing data was performed using FastQC (v0.11.5). Adapter trimming and quality filtering were conducted using fastp (v0.23.2) with parameters --cut_right --cut_window_size 4 --cut_mean_quality 20 --length_required 40. Post-trimming quality was reassessed with FastQC to ensure the effectiveness of trimming. MultiQC (v1.17) was used to aggregate quality reports.
Bismark (v0.22.3) was used for processing the BS-seq reads. The Tomato reference genome SL4.0 was bisulfite-converted and indexed using the bismark_genome_preparation command. Trimmed single-end reads were aligned to the indexed reference genome using bismark with the --non_directional flag. PCR duplicates were removed using deduplicate_bismark with default settings. Methylation extraction was performed using bismark_methylation_extractor with the parameters --cytosine_report and --CX to generate comprehensive cytosine reports for all contexts (CpG, CHG, CHH).
BigWig files representing methylation levels were generated using a custom script, CX_report2bigwig.sh, which converts CX reports into BigWigs for visualisation.
Assembly: SL4.0 (GCA_000188115.5)
Supplementary files format and content: Bigwig files (.bw) of CG methylation
Supplementary files format and content: Bigwig files (.bw) of CHG methylation
Supplementary files format and content: Bigwig files (.bw) of CHH methylation
Supplementary files format and content: Tab separated values (.tsv) containing the mC rate in 100 kbp windows for all samples in all contexts (CG, CHG, CHH)

organism: Solanum lycopersicum

source_name: expanded leaf

growth_protocol: Plants were grown in a glasshouse under long day conditions (16 hr light, 8 hr dark, 23°C, 42% humidity). Three weeks after germination seedlings were transferred to 3 litre pots and grown to maturity

extract_protocol:
Around 100 mg of the whole plant tissue were collected, snap frozen in liquid nitrogen and stored at -80oC. Tissue samples were ground using TissueLyser II (Qiagen) with sterile RNAse-free glass beads. DNA was extracted using a QIAGEN Plant DNeasy kit as manufacture’s manual. The quality of the DNA was assessed using a NanoDrop spectrophotometer and Qubit fluorometer.
Bisulfite libraries were prepared from 100 ng of genomic DNA using the TruSeq Nano kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions, with the following modification: after adapter ligation and clean-up, samples were treated with bisulfite using the Epitect Plus kit (Qiagen, Hilden, Germany). The thermal cycle incubation was repeated once before clean-up. DNA fragments were then amplified using the Kapa HiFi HotStart Uracil+ PCR mix in 14 cycles of PCR (Kapa Biosystems, Wilmington, MA, USA). Bisulfite libraries were sequenced on an Illumina HiSeq 3000 instrument, generating 150 bp paired-end reads.

value: expanded leaf

tag: line

value: A T1

value: Non Transgenic Sibling


title: TsixStop Rep2, H3K9me3, NPCd7

description: Library name: nC0769_TsixStop_NPCd7_H3K9me3_Rep2

source_name: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation

value: NPC


title: Untreated hiPSC-CM, biological replicate #3

city: Washington

first: Emilia

last: Entcheva

state: DC

address: 800 22nd Street NW SEH 5000

department: Biomedical Engineering

country: USA

institute: George Washington University

description: Library name: U1.BR3

library_source: transcriptomic

data_processing:
fastQC quality check, STAR alignment
FeatureCount for gene expression quantification, Deseq2 for differential gene expression
Assembly: GRCh38 reference genome
Supplementary files format and content: Processed data contains TPM counts for all samples. Zero-values have been removed. Ensembl gene accesssion numbers are provided in the first column.

molecule: polyA RNA

source_name: hiPSC-CM

growth_protocol: Commercially differentiated human induced pluripotent stem cell derived cardiomycytes (Fujifilm) were thawed and plated according to manufacturers instructions at 150,000 cells/well 48-well format. Maintenance media was exchanged every two days.

extract_protocol:
On cell culture day 7, samples were lysed using TRIzol Reagent (Invitrogen), according to manufacturer's protocol.
RNA-seq library preperation

treatment_protocol: On cell culture day 5, cells were treated small interfering RNAs (siRNA) targeting each individual HDAC or SIRT gene (or scrambled negative control siRNA). Note that siRNAs targeting HDAC10 and SIRT1 were not available to us at the time, thus were not included in this study. Transfection media was replaced with normal maintenance media on cell culture day 7.

value: hiPSC-CM

value: stem cell derived cardiomyocytes

tag: batch

value: A


title: TsixStop Rep2, H3K9me3, NPCd3

description: Library name: nC0767_TsixStop_NPCd3_H3K9me3_Rep2

value: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation


title: TsixStop Rep2, Input, NPCd7

description: Library name: nC0768_TsixStop_NPCd7_Input_Rep2


title: Untreated hiPSC-CM, biological replicate #2

description: Library name: U1.BR2


title: TsixStop Rep2, H3K9me3, mESC

description: Library name: nC0765_TsixStop_ES_H3K9me3_Rep2


title: Untreated hiPSC-CM, biological replicate #1

description: Library name: U1.BR1


title: NTS, leaf, WGBS deep, rep1

description: Library name: NTS_1_WGBS


title: F121 F2 ES, H3K9me3

description: Library name: nC0761_F121_F2_ES_H3K9me3


title: TsixStop Rep2, Input, mESC

description: Library name: nC0764_TsixStop_ES_Input_Rep2


title: F121 F2 ES, Input

description: Library name: nC0760_F121_F2_ES_Input


title: TET3, leaf, WGBS deep, rep2

description: Library name: TET3_2_WGBS


title: Negative siRNA in hiPSC-CM, biological replicate #6

description: Library name: N2.BR3

value: gene knockdown by short interfering RNA

value: B


title: FKBP-TASOR H4 ES, +dTAG+dox, H3K9me3

description: Library name: nC0731_dTTASORH4d_dTAG27hdox24h_H3K9me3_Rep2

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Cast x 129S

value: dTAG-13 for 27hours and doxycyline for 24hours


title: FKBP-TASOR H4 ES, +dTAG+dox, Input

description: Library name: nC0730_dTTASOH4d_dTAG27hdox24h_Input_Rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC


title: TET3, leaf, WGBS deep, rep1

description: Library name: TET3_1_WGBS


title: WT, leaf, WGBS deep, rep1

description: Library name: WT_1_WGBS

value: WT


title: WT, leaf, WGBS deep, rep2

description: Library name: WT_2_WGBS


title: FKBP-TASOR H4 ES, +dox, H3K9me3

description: Library name: nC0729_dTTASORH4d_dox24h_H3K9me3_Rep2

value: doxycycline for 24h

value: anti-H3K9me3 (Abcam, # ab8898)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: FKBP-TASOR H4 ES, +dox, Input

description: Library name: nC0728_dTTASORH4d_dox24h_Input_Rep2


title: FKBP-TASOR H4 ES, +dTAG, Input

description: Library name: nC0726_dTTASORH4d_dTAG27h_Input_Rep2

value: dTAG-13 for 27h


title: FKBP-TASOR H4 ES, Input

description: Library name: nC0724_dTTASORH4d_ES_Input_Rep2


title: Negative siRNA in hiPSC-CM, biological replicate #2

description: Library name: N1.BR2


title: Sub-library 7

city: Philadelphia

first: Laurence

last: Eisenlohr

state: PA

address: 3615 Civic Center Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description:
Library name: Sample 7
Parse Biosciences

data_processing:
All concatenated .fastq files were uploaded to Trailmaker for analysis (https://app.trailmaker.parsebiosciences.com/pipeline)
Assembly: GRCm39/mm10
Supplementary files format and content: tab-delimited csv files for gene lists and cell metadate
Supplementary files format and content: matrix file for raw count matrix across all samples

source_name: Popliteal lymph node

extract_protocol:
Lymph nodes were mechanically homogenized and flow sorted to isolate CD19- and CD19+ cells. Cells were then fixed according to Evercode Cell Fixation Kit
Libraries were prepared using the Evercode WT kit according to manufacturer instructions. Individual samples were barcoded and pooled into 8 sub-libraries.

treatment_protocol: 3000 pfu of corresponding virus via footpad injection

value: Popliteal lymph node

tag: age

value: 9 weeks

tag: Sex

value: female

value: ECTV (WT or ∆C15)


title: FKBP-TASOR H4 ES, H3K9me3

description: Library name: nC0725_dTTASORH4d_ES_H3K9me3_Rep2


title: Sub-library 8

description:
Library name: Sample 8
Parse Biosciences


title: FKBP-KAP1 A4C11 ES, +dox, H3K9me3

description: Library name: nC0721_dTKAP1A4C11d_dox24h_H3K9me3


title: FKBP-KAP1 A4C11 ES, +dTAG+dox, Input

description: Library name: nC0722_dTKAP1A4C11d_dTAG27hdox24h_Input


title: Negative siRNA in hiPSC-CM, biological replicate #4

description: Library name: N2.BR1

value: hiPSC-CM

value: stem cell derived cardiomyocytes


title: FKBP-KAP1 A4C11 ES, +dTAG+dox, H3K9me3

description: Library name: nC0723_dTKAP1A4C11d_dTAG27hdox24h_H3K9me3


title: Sub-library 6

description:
Library name: Sample 6
Parse Biosciences


title: HDAC11 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H11.BR3

value: gene knockdown by short interfering RNA

value: A


title: FKBP-KAP1 A4C11 ES, +dox, Input

description: Library name: nC0720_dTKAP1A4C11d_dox24h_Input

value: Cast x 129S


title: Negative siRNA in hiPSC-CM, biological replicate #5

description: Library name: N2.BR2

value: B


title: Negative siRNA in hiPSC-CM, biological replicate #3

description: Library name: N1.BR3


title: Sub-library 5

description:
Library name: Sample 5
Parse Biosciences


title: FKBP-TASOR H4 ES, +dTAG, H3K9me3

description: Library name: nC0727_dTTASORH4d_dTAG27h_H3K9me3_Rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: HDAC11 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H11.BR2


title: FKBP-KAP1 A4C11 ES, Input

description: Library name: nC0716_dTKAP1A4C11d_ES_Input

value: mESC


title: Sub-library 4

description:
Library name: Sample 4
Parse Biosciences


title: FKBP-KAP1 A4C11 ES, +dTAG, Input

description: Library name: nC0718_dTKAP1A4C11d_dTAG27h_Input


title: FKBP-KAP1 A4C11 ES, +dTAG, H3K9me3

description: Library name: nC0719_dTKAP1A4C11d_dTAG27h_H3K9me3


title: HDAC11 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H11.BR1


title: Negative siRNA in hiPSC-CM, biological replicate #1

description: Library name: N1.BR1


title: FKBP-KAP1 A4C11 ES, H3K9me3

description: Library name: nC0717_dTKAP1A4C11d_ES_H3K9me3


title: FKBP-MPP8 E10 ES, +dox, H3K9me3

description: Library name: nC0697_dTMPP8E10d_dox24h_H3K9me3_Rep2


title: FKBP-MPP8 E10 ES, +dTAG+dox, H3K9me3

description: Library name: nC0699_dTMPP8E10d_dTAG27hdox24h_H3K9me3_Rep2

value: dTAG-13 for 27hours and doxycyline for 24hours


title: FKBP-MPP8 E10 ES, +dTAG+dox, Input

description: Library name: nC0698_dTMPP8E10d_dTAG27hdox24h_Input_Rep2


title: FKBP-MPP8 E10 ES, +dox, Input

description: Library name: nC0696_dTMPP8E10d_dox24h_Input_Rep2

value: doxycycline for 24h


title: HDAC9 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H9.BR3


title: HDAC9 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H9.BR1


title: Sub-library 1

description:
Library name: Sample 1
Parse Biosciences


title: FKBP-MPP8 E10 ES, +dTAG, Input

description: Library name: nC0694_dTMPP8E10d_dTAG27h_Input_Rep2


title: HDAC9 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H9.BR2


title: FKBP-MPP8 E10 ES, +dTAG, H3K9me3

description: Library name: nC0695_dTMPP8E10d_dTAG27h_H3K9me3_Rep2

value: anti-H3K9me3 (Abcam, # ab8898)


title: FKBP-MPP8 E10 ES, Input

description: Library name: nC0692_dTMPP8E10d_ES_Input_Rep2

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: KO5 - CKDL250012225

description:
Library name: Sample 10
Raw counts KO5_dedup

data_processing:
umi_tools for UMI extraction from read 1 and assignment to read 2
UMI-tagged reads were trimmed to remove polyT tracts and Illumina adapter sequences
Trimmed, UMI-tagged reads were aligned against genome index (GRCm39) using STAR 2.7.10a
Count matrices were generated using featureCounts
Assembly: GRCm39/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using the TRI reagent, and purified with the Zymo Direct-zol RNA miniprep kit.
Zymo-seq SwitchFree 3' mRNA Library Kit


title: HDAC8 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H8.BR3


title: Sub-library 3

description:
Library name: Sample 3
Parse Biosciences


title: FKBP-KAP1 A4F3 ES, +dTAG+dox, Input

description: Library name: nC0682_dTKAP1A4F3d_dTAG27hdox24h_Input


title: KO4 - CKDL250012225

description:
Library name: Sample 9
Raw counts KO4_dedup


title: Sub-library 2

description:
Library name: Sample 2
Parse Biosciences


title: FKBP-MPP8 E10 ES, H3K9me3

description: Library name: nC0693_dTMPP8E10d_ES_H3K9me3_Rep2


title: FKBP-KAP1 A4F3 ES, +dox, Input

description: Library name: nC0680_dTKAP1A4F3d_dox24h_Input


title: HDAC8 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H8.BR2


title: FKBP-KAP1 A4F3 ES, +dox, H3K9me3

description: Library name: nC0681_dTKAP1A4F3d_dox24h_H3K9me3


title: KO2 - CKDL250012225

description:
Library name: Sample 7
Raw counts KO2_dedup


title: HDAC8 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H8.BR1


title: FKBP-KAP1 A4F3 ES, +dTAG, H3K9me3

description: Library name: nC0679_dTKAP1A4F3d_dTAG27h_H3K9me3

value: dTAG-13 for 27h


title: HDAC7 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H7.BR3


title: KO1 - CKDL250012225

description:
Library name: Sample 6
Raw counts KO1_dedup

value: Popliteal lymph node


title: FKBP-KAP1 A4F3 ES, +dTAG, Input

description: Library name: nC0678_dTKAP1A4F3d_dTAG27h_Input


title: FKBP-KAP1 A4F3 ES, H3K9me3

description: Library name: nC0677_dTKAP1A4F3d_ES_H3K9me3


title: KO3 - CKDL250012225

description:
Library name: Sample 8
Raw counts KO3_dedup

value: 9 weeks


title: FKBP-TASOR F8 ES, +dTAG+dox, H3K9me3

description: Library name: nC0667_dTTASORF8_dT27hdox24h_H3K9me3


title: HDAC7 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H7.BR2


title: FKBP-TASOR F8 ES, +dTAG+dox, Input

description: Library name: nC0666_dTTASORF8_dT27hdox24h_Input


title: FKBP-KAP1 A4F3 ES, +dTAG+dox, H3K9me3

description: Library name: nC0683_dTKAP1A4F3d_dTAG27hdox24h_H3K9me3


title: WT5 - CKDL250012225

description:
Library name: Sample 5
Raw counts WT5_dedup

value: female

value: WT ECTV


title: HDAC7 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H7.BR1

value: hiPSC-CM


title: FKBP-TASOR F8 ES, +dox, H3K9me3

description: Library name: nC0665_dTTASORF8_dox24h_H3K9me3


title: FKBP-KAP1 A4F3 ES, Input

description: Library name: nC0676_dTKAP1A4F3d_ES_Input


title: FKBP-TASOR F8 ES, +dox, Input

description: Library name: nC0664_dTTASORF8_dox24h_Input


title: WT4 - CKDL250012225

description:
Library name: Sample 4
Raw counts WT4_dedup


title: HDAC6 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H6.BR3

value: stem cell derived cardiomyocytes


title: FKBP-TASOR F8 ES, +dTAG, H3K9me3

description: Library name: nC0663_dTTASORF8_dT27h_H3K9me3


title: WT3 - CKDL250012225

description:
Library name: Sample 3
Raw counts WT3_dedup


title: FKBP-TASOR F8 ES, +dTAG, Input

description: Library name: nC0662_dTTASORF8_dT27h_Input


title: FKBP-TASOR F8 ES, Input

description: Library name: nC0660_dTTASORF8_ES_Input


title: HDAC6 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H6.BR2

value: gene knockdown by short interfering RNA


title: FKBP-TASOR F8 ES, H3K9me3

description: Library name: nC0661_dTTASORF8_ES_H3K9me3


title: WT1 - CKDL250012225

description:
Library name: Sample 1
Raw counts WT1_dedup


title: FKBP-MPP8 H1 ES, +dTAG+dox, Input

description: Library name: nC0658_dTMPP8H1_dT27hdox24h_Input


title: FKBP-MPP8 H1 ES, +dox, H3K9me3

description: Library name: nC0657_dTMPP8H1_dox24h_H3K9me3


title: FKBP-MPP8 H1 ES, +dTAG+dox, H3K9me3

description: Library name: nC0659_dTMPP8H1_dT27hdox24h_H3K9me3


title: HDAC6 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H6.BR1

value: A


title: HDAC5 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H5.BR2


title: CD8d10 KO4

description:
Library name: Sample 7
Raw counts KO4_dedup

source_name: Spleen

extract_protocol:
RNA was harvested using the TRI reagent, and purified with the Zymo Direct-zol RNA microprep kit.
Zymo-seq SwitchFree 3' mRNA Library Kit

value: Spleen

tag: age/sex

value: 9 weeks/female

value: CD8+ T cells


title: FKBP-MPP8 H1 ES, Input

description: Library name: nC0652_dTMPP8H1_ES_Input

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC


title: FKBP-MPP8 H1 ES, +dTAG, H3K9me3

description: Library name: nC0655_dTMPP8H1_dT27h_H3K9me3

value: anti-H3K9me3 (Abcam, # ab8898)


title: CD8d10 KO1

description:
Library name: Sample 5
Raw counts KO1_dedup


title: WT2 - CKDL250012225

description:
Library name: Sample 2
Raw counts WT2_dedup


title: HDAC5 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H5.BR1


title: FKBP-MPP8 H1 ES, H3K9me3

description: Library name: nC0653_dTMPP8H1_ES_H3K9me3

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: FKBP-MPP8 H1 ES, +dox, Input

description: Library name: nC0656_dTMPP8H1_dox24h_Input

value: doxycycline for 24h


title: FKBP-MPP8 H1 ES, +dTAG, Input

description: Library name: nC0654_dTMPP8H1_dT27h_Input

value: dTAG-13 for 27h


title: HDAC4 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H4.BR3


title: HDAC5 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H5.BR3


title: CD8d10 KO2

description:
Library name: Sample 6
Raw counts KO2_dedup


title: HDAC4 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H4.BR2


title: FKBP-SETDB1 A12A10 ES, +dTAG+dox, H3K9me3

description: Library name: nC0651_SetA12A10_dT27hdox24h_H3K9me3

value: dTAG-13 for 27hours and doxycyline for 24hours


title: CD8d10 WT5

description:
Library name: Sample 4
Raw counts WT5_dedup


title: CD8d10 KO5

description:
Library name: Sample 8
Raw counts KO5_dedup


title: FKBP-SETDB1 A12A10 ES, +dox, Input

description: Library name: nC0648_SetA12A10_dox24h_Input


title: FKBP-SETDB1 A12A10 ES, +dTAG+dox, Input

description: Library name: nC0650_SetA12A10_dT27hdox24h_Input


title: HDAC4 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H4.BR1


title: CD8d10 WT4

description:
Library name: Sample 3
Raw counts WT4_dedup


title: FKBP-SETDB1 A12A10 ES, +dTAG, H3K9me3

description: Library name: nC0647_SetA12A10_dT27h_H3K9me3


title: HDAC3 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H3.BR3


title: CD8d10 WT2


title: FKBP-SETDB1 A12A10 ES, +dox, H3K9me3

description: Library name: nC0649_SetA12A10_dox24h_H3K9me3


title: FKBP-SETDB1 A12A10 ES, Input

description: Library name: nC0644_SetA12A10_ES_Input


title: FKBP-SETDB1 A12A10 ES, +dTAG, Input

description: Library name: nC0646_SetA12A10_dT27h_Input


title: HDAC3 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H3.BR1


title: HDAC3 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H3.BR2


title: CD8d10 WT1

description:
Library name: Sample 1
Raw counts WT1_dedup


title: iXist-ChrX129, Control, H3K9me3AM, NPCd1

description: Library name: nC0613_A11B2_NPCd1_H3K9me3AM

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: NPC

value: doxycyline for 1 day coupled with differentiation

value: anti-H3K9me3 (Active Motif, # 061013)


title: iXist-ChrX129, Control, H3K9me3AM, NPCd3

description: Library name: nC0614_A11B2_NPCd3_H3K9me3AM

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: doxycyline for 3 days coupled with differentiation


title: iXist-ChrX129, Control, H3K9me3AM, mESC

description: Library name: nC0612_A11B2_ES_H3K9me3AM


title: iXist-ChrX129, Control, H3K9me3AM, NPCd7

description: Library name: nC0615_A11B2_NPCd7_H3K9me3AM

value: doxycyline for 7 days coupled with differentiation


title: FKBP-SETDB1 A12A10 ES, H3K9me3

description: Library name: nC0645_SetA12A10_ES_H3K9me3


title: TsixStop, H3K9me3, NPCd7

description: Library name: nC0254_TsixStopNPCd7d_proper_H3K9me3

value: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation


title: HDAC2 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H2.BR2

value: hiPSC-CM

value: stem cell derived cardiomyocytes

value: gene knockdown by short interfering RNA

value: A


title: TsixStop, Input, NPCd7

description: Library name: nC0253_TsixStopNPCd7d_proper_Input

value: Cast x 129S


title: TsixStop, H3K9me3, NPCd3

description: Library name: nC0252_TsixStopNPCd3d_proper_H3K9me3

value: anti-H3K9me3 (Abcam, # ab8898)


title: CD8d7KO4

description:
Library name: Sample 8
Raw counts KO4_dedup

value: Spleen

value: 9 weeks/female

value: CD8+ T cells


title: HDAC2 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H2.BR1


title: CD8d7KO3

description:
Library name: Sample 7
Raw counts KO3_dedup


title: TsixStop, H3K9me3, mESC

description: Library name: nC0250_TsixStopESd_proper_H3K9me3

value: mESC

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: TsixStop, Input, mESC

description: Library name: nC0249_TsixStopESd_proper_Input


title: CD8d7KO2

description:
Library name: Sample 6
Raw counts KO2_dedup


title: HDAC1 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H1.BR3


title: FKBP-SETDB1 P2F7 ES, +dTAG+dox, H3K9me3

description: Library name: nC0240_dTSetdb1P2F7d_dTAG27hdox24h_H3K9me3

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: dTAG-13 for 27hours and doxycyline for 24hours


title: CD8d7KO5

description:
Library name: Sample 9
Raw counts KO5_dedup


title: FKBP-SETDB1 P2F7 ES, +dTAG+dox, Input

description: Library name: nC0239_dTSetdb1P2F7d_dTAG27hdox24h_Input


title: HDAC2 knockdown in hiPSC-CM, biological replicate #3

description: Library name: H2.BR3


title: HDAC1 knockdown in hiPSC-CM, biological replicate #2

description: Library name: H1.BR2


title: TsixStop, Input, NPCd3

description: Library name: nC0251_TsixStopNPCd3d_proper_Input

value: NPC


title: FKBP-SETDB1 P2F7 ES, +dox, H3K9me3

description: Library name: nC0238_dTSetdb1P2F7d_dox24h_H3K9me3

value: doxycycline for 24h


title: FKBP-SETDB1 P2F7 ES, +dox, Input

description: Library name: nC0237_dTSetdb1P2F7d_dox24h_Input


title: HDAC1 knockdown in hiPSC-CM, biological replicate #1

description: Library name: H1.BR1


title: CD8d7WT3

description:
Library name: Sample 3
Raw counts WT3_dedup

value: WT ECTV


title: CD8d7WT5

description:
Library name: Sample 4
Raw counts WT5_dedup


title: FKBP-SETDB1 P2F7 ES, +dTAG, Input

description: Library name: nC0235_dTSetdb1P2F7d_dTAG27h_Input

value: dTAG-13 for 27h


title: FKBP-SETDB1 P2F7 ES, +dTAG, H3K9me3

description: Library name: nC0236_dTSetdb1P2F7d_dTAG27h_H3K9me3


title: CD8d7KO1

description:
Library name: Sample 5
Raw counts KO1_dedup


title: Thp3

city: Suzhou

first: Yixuan

last: Zhang

address: No.9 Chongwen Road

country: China

institute: Suzhou University

description: Library name: Sample 12

data_processing:
Clean data was obtained by using in-house perl scripts (Novogene America) to remove reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean reads were mapped to the human reference genome (GRCh38/hg38) using Hisat2 (v2.0.5), and transcript assembly was performed with StringTie (v1.3.3b).
Read indexing and mapping to the human reference genome (GRCh38/hg38) were performed using Hisat2 (v2.0.0).
Gene expression levels were quantified with FeatureCounts (v1.5.0-p3) and expressed as FPKM.
Assembly: GRCh38/hg38
Supplementary files format and content: CSV file includes gene counts for each sample
Supplementary files format and content: Additional supplementary files are DESeq2 output from Novogene. Only genes with p-adjusted value < 0.05 are included.

source_name: oral

growth_protocol: Cells were grown to maximum confluency prior to treatment.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme) and sequenced on the Illumina NovaSeq 6000 platform with a 150-bp paired-end sequencing strategy. Enrichment of mRNA, library construction, sequencing, and data analysis were performed on the Yunbios platform. Raw sequencing data were processed by Skewer (v0.2.2) and its quality was assessed with FastQC (v0.11.2). The sequencing reads had a length of 2×150 bp. Read indexing and mapping to the human reference genome (GRCh38/hg38) were performed using Hisat2 (v2.0.0), followed by transcriptome assembly using StringTie (v2.1.4). Gene expression levels were quantified using Fragments Per Kilobase of transcript per Million mapped reads (FPKM).

treatment_protocol: HaCaT and TIGK treated with 5 mM H₂O₂ for 3 h or left untreated (n = 3 per group, 12 samples in total).

value: oral

value: TIGK

value: keratinocytes

value: Add H2O4 to DermaLife K Keratinocyte Complete Medium


title: FKBP-SETDB1 P2F7 ES, Input

description: Library name: nC0233_dTSetdb1P2F7d_ES_Input

value: Cast x 129S


title: CD8d7WT2

description:
Library name: Sample 2
Raw counts WT2_dedup


title: FKBP-SETDB1 P2F7 ES, H3K9me3

description: Library name: nC0234_dTSetdb1P2F7d_ES_H3K9me3

value: anti-H3K9me3 (Abcam, # ab8898)


title: CD8d7WT1

description:
Library name: Sample 1
Raw counts WT1_dedup

value: Spleen


title: Thp1

description: Library name: Sample 10

value: Add H2O2 to DermaLife K Keratinocyte Complete Medium


title: KO5

description:
Library name: Sample 10
Raw counts KO5_dedup

value: 9 weeks/female

value: CD4+ T cells


title: FKBP-KAP1 A4A11 ES, +dTAG+dox, H3K9me3

description: Library name: nC0232_dTKAP1A4A11d_dTAG27hdox24h_H3K9me3

value: mESC

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: Tctrl3

description: Library name: Sample 9

value: DermaLife K Keratinocyte Complete Medium


title: FKBP-KAP1 A4A11 ES, +dTAG, H3K9me3

description: Library name: nC0228_dTKAP1A4A11d_dTAG27h_H3K9me3

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: FKBP-KAP1 A4A11 ES, +dTAG, Input

description: Library name: nC0227_dTKAP1A4A11d_dTAG27h_Input


title: Thp2

description: Library name: Sample 11

value: Add H2O3 to DermaLife K Keratinocyte Complete Medium


title: Tctrl2

description: Library name: Sample 8


title: FKBP-KAP1 A4A11 ES, Input

description: Library name: nC0225_dTKAP1A4A11d_ES_Input


title: KO3

description:
Library name: Sample 8
Raw counts KO3_dedup


title: Tctrl1

description: Library name: Sample 7


title: KO2

description:
Library name: Sample 7
Raw counts KO2_dedup


title: iXist-ChrXCast, Control, H3K9me3, NPCd7

description: Library name: nC0161_C7H8d_NPCd7_H3K9me3

value: NPC

value: doxycyline for 7 days coupled with differentiation


title: FKBP-KAP1 A4A11 ES, +dTAG+dox, Input

description: Library name: nC0231_dTKAP1A4A11d_dTAG27hdox24h_Input

value: dTAG-13 for 27hours and doxycyline for 24hours


title: FKBP-KAP1 A4A11 ES, +dox, H3K9me3

description: Library name: nC0230_dTKAP1A4A11d_dox24h_H3K9me3

value: doxycycline for 24h


title: KO4

description:
Library name: Sample 9
Raw counts KO4_dedup


title: FKBP-KAP1 A4A11 ES, H3K9me3

description: Library name: nC0226_dTKAP1A4A11d_ES_H3K9me3


title: iXist-ChrXCast, Control, H3K9me3, NPCd3

description: Library name: nC0156_C7H8d_NPCd3_H3K9me3

value: doxycyline for 3 days coupled with differentiation


title: FKBP-KAP1 A4A11 ES, +dox, Input

description: Library name: nC0229_dTKAP1A4A11d_dox24h_Input


title: Hhp3

description: Library name: Sample 6

source_name: skin

value: skin

value: HaCaT

value: keratinocytes

value: Add H2O4 to DermaLife K Keratinocyte Complete Medium


title: Hhp2

description: Library name: Sample 5


title: KO1

description:
Library name: Sample 6
Raw counts KO1_dedup

value: Spleen


title: iXist-ChrXCast, Control, Input, NPCd7

description: Library name: nC0160_C7H8d_NPCd7_Input

value: Cast x 129S


title: iXist-ChrXCast, Control, H3K9me3, NPCd1

description: Library name: nC0151_C7H8d_NPCd1_H3K9me3

value: doxycyline for 1 day coupled with differentiation

value: anti-H3K9me3 (Abcam, # ab8898)


title: iXist-ChrXCast, Control, Input, NPCd1

description: Library name: nC0150_C7H8d_NPCd1_Input

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: iXist-ChrXCast, Control, Input, mESC

description: Library name: nC0145_C7H8d_ES_Input

value: mESC


title: WT4

description:
Library name: Sample 4
Raw counts WT4_dedup

value: 9 weeks/female

value: CD4+ T cells

value: WT ECTV


title: iXist-ChrX129, Control, H3K9me3, NPCd7

description: Library name: nC0134_A11B2d_NPCd7_H3K9me3

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: NPC

value: doxycyline for 7 days coupled with differentiation


title: iXist-ChrXCast, Control, H3K9me3, mESC

description: Library name: nC0146_C7H8d_ES_H3K9me3

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: WT3

description:
Library name: Sample 3
Raw counts WT3_dedup


title: Hctrl3

description: Library name: Sample 3

value: skin

value: DermaLife K Keratinocyte Complete Medium


title: Hctrl2

description: Library name: Sample 2

value: HaCaT

value: keratinocytes


title: iXist-ChrXCast, Control, Input, NPCd3

description: Library name: nC0155_C7H8d_NPCd3_Input

value: doxycyline for 3 days coupled with differentiation


title: Hhp1

description: Library name: Sample 4

value: Add H2O2 to DermaLife K Keratinocyte Complete Medium


title: iXist-ChrX129, Control, Input, NPCd7

description: Library name: nC0133_A11B2d_NPCd7_Input

value: Cast x 129S


title: WT5

description:
Library name: Sample 5
Raw counts WT5_dedup

value: Spleen


title: iXist-ChrX129, Control, H3K9me3, NPCd3

description: Library name: nC0122_A11B2d_NPCd3_H3K9me3

value: anti-H3K9me3 (Abcam, # ab8898)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: iXist-ChrX129, Control, Input, NPCd3

description: Library name: nC0121_A11B2d_NPCd3_Input


title: WT2

description:
Library name: Sample 2
Raw counts WT2_dedup

value: 9 weeks/female


title: RS4;11 cells, shDNTTIP1, rep3

city: Harbin

first: Huitao

last: Fan

state: Heilongjiang

address: 23 Youzheng street

department: NHC Key Laboratory of Cell Transplantation

institute: The First Affiliated Hospital of Harbin Medical University

description:
Library name: shDNTTIP1.r3
shDNTTIP1.r3

data_processing:
Raw sequencing reads were quality-filtered using fastp (v.0.23.4) to remove adapter sequences and low-quality bases, followed by alignment to the GRCh38 human reference genome using STAR (v2.7.11) with default parameters. Gene-level read counts were quantified using featureCounts (v.2.0.6), and differential expression analysis was performed with the DESeq2 (v.1.40.2) package in R, where genes with P<0.05 were considered statistically significant.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

growth_protocol: Cell cultures were maintained at 37°C in a 5% CO2 humidified atmosphere. Cell line identity was confirmed via short tandem repeat (STR) analysis, and mycoplasma contamination was periodically tested, ensuring experimental reliability.

extract_protocol:
RNA was extracted using the RNA purification kit (TransGen Biotech, ER101-01). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.


title: RS4;11 cells, shDNTTIP1, rep2

description:
Library name: shDNTTIP1.r2
shDNTTIP1.r2


title: iXist-ChrX129, Control, Input, mESC

description: Library name: nC0097_A11B2d_ES_Input

value: mESC


title: con3

city: Chongqing

first: rui

last: wang

state: chongqing

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

institute: Chongqing Medical University

description:
Library name: sample 6
control+CD8+T group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: spleen

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: spleen

value: CD8+ T cell

value: control


title: con2

description:
Library name: sample 5
control+CD8+T group, replicate biosample 2


title: Mouse glioma sample, MR3 treatment, replicate 2

city: Palo Alto

first: Xinnan

last: Wang

state: CA

address: 1201 Welch Road, MSLS Building, Rm P151

department: Neurosurgery

institute: Stanford University

description:
Library name: Mouse_treated_rep2
Column name in Mouse_snRNA_seq.RDS: TN3

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (10x Genomics). Base calling, demultiplexing, and FASTQ file generation were performed using the Cell Ranger mkfastq pipeline.
Sequencing reads were aligned to the mouse reference genome (mm10; GENCODE vM23 / Ensembl 98) using the Cell Ranger count pipeline to generate gene-barcode expression matrices.
Quality control filtering was performed to remove low-quality nuclei. Nuclei with fewer than 200 detected genes, more than 5000 detected genes, or greater than 5% mitochondrial gene expression were excluded.
Genes expressed in fewer than three nuclei across the dataset were removed prior to downstream analysis.
Expression matrices were normalized and log-transformed using the Seurat pipeline. Highly variable genes were identified, and principal component analysis (PCA) was performed for downstream analyses.
Assembly: mm10 (GENCODE vM23 / Ensembl 98)
Supplementary files format and content: Processed data files include gene expression count matrices generated by the Cell Ranger pipeline and downstream processed Seurat objects. Matrices contain genes as rows and nuclei barcodes as columns, with integer values representing UMI counts per gene per nucleus.
Supplementary files format and content: Additional processed data include filtered gene expression matrices and cell metadata tables used for downstream single-nucleus RNA-seq analyses.

source_name: Glioma tumor

growth_protocol: Female C57BL/6J mice (6–8 weeks old) were obtained from The Jackson Laboratory and housed at the Stanford University Animal Facility under an approved IACUC protocol. To establish a syngeneic glioma model, mice were anesthetized with ketamine (100 mg/kg) and xylazine (10 mg/kg) via intraperitoneal injection. A midline incision was made to expose the skull and a burr hole was drilled over the left striatum (2 mm lateral and 2 mm posterior to the sagittal and coronal sutures). GL261-Luc cells (1.3 × 10^5 cells in 2 µL PBS) were stereotactically implanted at a depth of 3 mm from the cortical surface. Tumor growth was monitored on day 7 using an IVIS imaging system (Lago, Spectral Instrument Imaging) following intraperitoneal injection of D-luciferin (200 µL; 150 mg/kg for a 20 g mouse).

extract_protocol:
Nuclei were isolated from fresh-frozen mouse brain tissues using Dounce homogenization (D8938, Sigma-Aldrich) and the Nuclei EZ Prep Kit (Nuc101-1KT, Sigma-Aldrich) according to published protocols. Nuclei were centrifuged at 300 g for 10 minutes at 4°C and resuspended in FACS buffer (1% BSA in PBS) containing Recombinant RNase Inhibitor (2 U/mL; Takara) and anti-CD16/CD32 Fc block (BD Biosciences). After incubation for 5 minutes, nuclei were stained with NeuN antibody (ab190565, Abcam) and incubated on ice for 30 minutes with gentle shaking. Nuclei were centrifuged again at 300 g for 10 minutes at 4°C and resuspended in FACS buffer containing RNase inhibitor. Hoechst 33342 dye was added prior to sorting. NeuN-positive and NeuN-negative nuclei were sorted separately using fluorescence-activated cell sorting (FACS) into DNA LoBind tubes containing final buffer (200 µL UltraPure BSA, Thermo Fisher; 800 µL PBS; and 5 µL Protector RNase Inhibitor). Approximately 50,000 nuclei were collected per sample and adjusted to a concentration of ~1 × 10^6 nuclei/mL.
Single-nucleus RNA-seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics) following the manufacturer’s protocol. Nuclei suspensions were adjusted to target approximately 10,000 nuclei per sample and loaded onto the Chromium Controller (10x Genomics) to generate Gel Bead-in-Emulsions (GEMs). Reverse transcription, cDNA amplification, and library construction were performed according to the Chromium Single Cell 3′ Library Construction protocol v3.1. Library quality was assessed using an Agilent Bioanalyzer at the Stanford Protein and Nucleic Acid Facility. Multiplexed libraries were sequenced by Novogene (Sacramento, USA) on an Illumina NovaSeq S4 platform using paired-end 150 bp sequencing, targeting approximately 100 million reads per library.

treatment_protocol: Mice were assigned to control or treatment groups based on comparable tumor burden measured by bioluminescence imaging. Three mice received intracranial administration of MR3 (10 µM in 5 µL DMSO) at the tumor implantation site on days 11 and 18 post-implantation. Control mice received 5 µL DMSO using the same procedure. All intracranial injections followed the same surgical procedure used for tumor implantation. Mice were euthanized on day 22 post-implantation. Whole brains were snap-frozen in liquid nitrogen and stored at −80°C until processing. Only the bottom region of the left hemisphere, where the tumor was implanted, was used for snRNA-seq experiments.

value: Female

tag: strain

value: Glioma tumor

value: MR3 (10 µM in 5 µL DMSO) intracranial injection on days 11 and 18 post-implantation


title: iXist-ChrX129, Control, Input, NPCd1

description: Library name: nC0109_A11B2d_NPCd1_Input

tag: strain background

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: NPC

value: doxycyline for 1 day coupled with differentiation


title: RS4;11 cells, shDNTTIP1, rep1

description:
Library name: shDNTTIP1.r1
shDNTTIP1.r1

tag: genotype


title: iXist-ChrX129, Control, H3K9me3, mESC

description: Library name: nC0098_A11B2d_ES_H3K9me3

tag: spike-in


title: WT1

description:
Library name: Sample 1
Raw counts WT1_dedup

tag: tissue

value: CD4+ T cells

value: WT ECTV


title: Mouse glioma sample, DMSO treatment, replicate 3

description:
Library name: Mouse_control_rep3
Column name in Mouse_snRNA_seq.RDS: CN3

value: DMSO intracranial injection (5 µL) on days 11 and 18 post-implantation


title: Hctrl1

description: Library name: Sample 1

value: skin

value: HaCaT

value: keratinocytes

value: DermaLife K Keratinocyte Complete Medium


title: RS4;11 cells, shControl, rep3

description:
Library name: shControl.r3
shControl.r3

value: WT


title: Mouse glioma sample, DMSO treatment, replicate 2

description:
Library name: Mouse_control_rep2
Column name in Mouse_snRNA_seq.RDS: CN2


title: iXist-ChrX129, Control, H3K9me3, NPCd1

description: Library name: nC0110_A11B2d_NPCd1_H3K9me3

value: Cast x 129S

value: anti-H3K9me3 (Abcam, # ab8898)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: FKBP-SETDB1 P2F7, dTAGd1, Input, NPCd7

description: Library name: nC0085_SetP2F7d_NPCd7_dTAGd1_Input

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 7 days coupled with differentiation, dTAG-13 for 6 days


title: T_3

description:
Library name: sample 3
NET+CD8+T group, replicate biosample 3

value: spleen

value: CD8+ T cell


title: RS4;11 cells, shControl, rep2

description:
Library name: shControl.r2
shControl.r2


title: FKBP-SETDB1 P2F7, dTAGd1, H3K9me3, NPCd7

description: Library name: nC0086_SetP2F7d_NPCd7_dTAGd1_H3K9me3

value: NPC


title: Mouse glioma sample, MR3 treatment, replicate 1

description:
Library name: Mouse_treated_rep1
Column name in Mouse_snRNA_seq.RDS: TN2

value: Female

value: Glioma tumor

value: MR3 (10 µM in 5 µL DMSO) intracranial injection on days 11 and 18 post-implantation


title: Mouse glioma sample, DMSO treatment, replicate 1

description:
Library name: Mouse_control_rep1
Column name in Mouse_snRNA_seq.RDS: CN1

value: DMSO intracranial injection (5 µL) on days 11 and 18 post-implantation


title: FKBP-SETDB1 P2F7, Control, H3K9me3, NPCd7

description: Library name: nC0082_SetP2F7d_NPCd7_Control_H3K9me3

value: doxycyline for 7 days coupled with differentiation


title: con1

description:
Library name: sample 4
control+CD8+T group, replicate biosample 1

value: control


title: FKBP-SETDB1 P2F7, Control, Input, NPCd7

description: Library name: nC0081_SetP2F7d_NPCd7_Control_Input


title: RS4;11 cells, shControl, rep1

description:
Library name: shControl.r1
shControl.r1


title: T_1

description:
Library name: sample 1
NET+CD8+T group, replicate biosample 1


title: T_2

description:
Library name: sample 2
NET+CD8+T group, replicate biosample 2


title: RS4;11 cells, MS-275, rep3

description:
Library name: MS-275.r4
MS275_r3

treatment_protocol: RS4;11 cells treated with the HDAC inhibitor MS-275 (1 μM, 48 hours) versus DMSO control


title: FKBP-SETDB1 P2F7, dTAGd1, Input, NPCd3

description: Library name: nC0077_SetP2F7d_NPCd3_dTAGd1_Input

value: doxycyline for 3 days coupled with differentiation, dTAG-13 for 2 days


title: FKBP-SETDB1 P2F7, dTAGd1, H3K9me3, NPCd3

description: Library name: nC0078_SetP2F7d_NPCd3_dTAGd1_H3K9me3


title: RS4;11 cells, MS-275, rep2

description:
Library name: MS-275.r3
MS275_r2


title: NL3

description:
Library name: sample 9
Ly6Ghigh neutrophil group, replicate biosample 3

source_name: Ly6Ghigh neutrophil

value: Ly6Ghigh neutrophil

value: Ly6Ghigh neutrophils isolated from the lung tissue of BALB/c female mice


title: DSS_Inwax_MC_2

city: Urbana

first: Wenyan

last: Mei

state: Illinois

address: 2001 S. Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

description: Library name: DSS_Inwax_MC_2

data_processing:
Adaptor sequences and low-quality bases were removed from the raw sequencing data using Trimmomatic v0.39(PMID: 24695404). Transcript abundance was quantified using Kallisto v0.44.0(PMID: 27043002), aligning reads to the mouse transcriptome (GRCm39).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts and tpm for each Sample

source_name: middle colon

extract_protocol:
RNAs were extracted from the colons and spleens using PureLink RNA Mini Kit (Ambion, Cat. 12183025).
RNA-seq libraries were constructed and sequenced at the UIUC Biotechnology Center High-Throughput Sequencing Core.

value: middle colon


title: DSS_Inwax_MC_1

description: Library name: DSS_Inwax_MC_1


title: DSS_Inwax_MC_3

description: Library name: DSS_Inwax_MC_3


title: RS4;11 cells, MS-275, rep1

description:
Library name: MS-275.r1
MS275_r1

value: WT


title: DSS_cellulose_MC_3

description: Library name: DSS_Blank_MC_3


title: NL2

description:
Library name: sample 8
Ly6Ghigh neutrophil group, replicate biosample 2


title: FKBP-SETDB1 P2F7, Control, H3K9me3, NPCd3

description: Library name: nC0074_SetP2F7d_NPCd3_Control_H3K9me3

value: Cast x 129S

value: doxycyline for 3 days coupled with differentiation

value: anti-H3K9me3 (Abcam, # ab8898)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: NL1

description:
Library name: sample 7
Ly6Ghigh neutrophil group, replicate biosample 1


title: RS4;11 cells, DMSO, rep3

description:
Library name: DMSO.r4
DMSO_r3

value: DMSO


title: FKBP-SETDB1 P2F7, Control, Input, NPCd3

description: Library name: nC0073_SetP2F7d_NPCd3_Control_Input

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: NPC


title: Ly6Glow3

description:
Library name: sample 6
Ly6Glow neutrophil group, replicate biosample 3

source_name: Ly6Glow neutrophil

value: Ly6Glow neutrophil

value: Ly6Glow neutrophils isolated from the lung tissue of BALB/c female mice at the MACRO stage after orthotopic fat pad injection of 4T1-LM3


title: DSS_cellulose_MC_2

description: Library name: DSS_Blank_MC_2


title: RS4;11 cells, DMSO, rep2

description:
Library name: DMSO.r3
DMSO_r2


title: Ly6Glow2

description:
Library name: sample 5
Ly6Glow neutrophil group, replicate biosample 2


title: FKBP-SETDB1 P2F7, Control, Input, NPCd1

description: Library name: nC0069_SetP2F7d_NPCd1_Input

value: doxycyline for 1 day coupled with differentiation


title: Ly6Glow1

description:
Library name: sample 4
Ly6Glow neutrophil group, replicate biosample 1


title: Water_Inwax_DC_4

description: Library name: Water_Inwax_DC_4

source_name: distal colon

value: distal colon


title: FKBP-SETDB1 P2F7, Control, H3K9me3, mESC

description: Library name: nC0066_SetP2F7d_ES_H3K9me3

value: mESC


title: Water_Inwax_DC_2

description: Library name: Water_Inwax_DC_2


title: RS4;11 cells, HA-DNTTIP1_2, IgG

description:
Library name: HA-DNTTIP1-IgG_2
Column name in raw_counts_ALL Samples.txt:shControl

data_processing:
Raw FASTQ files underwent quality control with fastp (v.0.23.4), followed by alignment to the GRCh38 human genome using bowtie2 (v.2.5.4). Aligned reads (BAM format) were converted to bigWig coverage files using deeptools (v.3.5.5), and peaks were called with MACS3 (v.3.0.0) for differential analysis.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag assay was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD904, China). Cells were bound to ConA magnetic beads (10 min, RT) and incubated overnight at 4°C with primary antibodies (anti-HA/DNTTIP1). The next day, samples were sequentially incubated with secondary antibody (1 h, RT) and pA-Tn5 transposase complex (1 h, RT). After extensive washing, DNA was fragmented and eluted.
Libraries were prepared using the TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and sequenced on the Illumina NovaSeq 6000 platform (paired-end, 150 bp).

value: DNTTIP1 overexpression

value: HA-tagged DNTTIP1


title: Water_Inwax_DC_1

description: Library name: Water_Inwax_DC_1


title: FKBP-SETDB1 P2F7, Control, Input, mESC

description: Library name: nC0065_SetP2F7d_ES_Input


title: RS4;11 cells, HA-DNTTIP1_1, IgG

description:
Library name: HA-DNTTIP1-IgG_1
Column name in raw_counts_ALL Samples.txt:shControl


title: Ly6Ghi2

description:
Library name: sample 2
Ly6Ghigh neutrophil group, replicate biosample 2

value: Ly6Ghigh neutrophil

value: Ly6Ghigh neutrophils isolated from the lung tissue of BALB/c female mice at the MACRO stage after orthotopic fat pad injection of 4T1-LM3


title: RS4;11 cells, HA-DNTTIP1_2, HA

description:
Library name: HA-DNTTIP1-HA_2
Column name in raw_counts_ALL Samples.txt:shControl


title: Ly6Ghi3

description:
Library name: sample 3
Ly6Ghigh neutrophil group, replicate biosample 3


title: RS4;11 cells, HA-DNTTIP1_1, HA

description:
Library name: HA-DNTTIP1-HA_1
Column name in raw_counts_ALL Samples.txt:shControl


title: RS4;11 cells, DMSO, rep1

description:
Library name: DMSO.r1
DMSO_r1

value: WT


title: FKBP-SETDB1 P2F7, Control, H3K9me3, NPCd1

description: Library name: nC0070_SetP2F7d_NPCd1_H3K9me3

value: Cast x 129S


title: Ly6Ghi1

description:
Library name: sample 1
Ly6Ghigh neutrophil group, replicate biosample 1


title: Water_cellulose_DC_3

description: Library name: Water_Blank_DC_3


title: Water_cellulose_DC_4

description: Library name: Water_Blank_DC_4


title: RS4;11 cells, shDNTTIP1, IgG

description:
Library name: shDNTTIP1. IgG
Column name in raw counts_ALL Samples.txt:shDNTTIP1

extract_protocol:
CUT&Tag assay was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD904, China). Cells were bound to ConA magnetic beads (10 min, RT) and incubated overnight at 4°C with primary antibodies (anti-H3K27ac). The next day, samples were sequentially incubated with secondary antibody (1 h, RT) and pA-Tn5 transposase complex (1 h, RT). After extensive washing, DNA was fragmented and eluted.
Libraries were prepared using the TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and sequenced on the Illumina NovaSeq 6000 platform (paired-end, 150 bp).


title: FKBP-SETDB1 A12A10, Control, H3K9me3, NPCd7

description: Library name: nC0058_SetA12A10d_NPCd7_Control_H3K9me3

value: doxycyline for 7 days coupled with differentiation


title: sample1_JC001

city: NEW YORK

first: Joachim

last: Frank

state: NEW YORK

address: 630 WEST 168TH ST.

institute: Columbia University

description: Library name: sample1_JC001

data_processing:
Raw RNA-Seq FASTQ files were processed using the nf-core/rnaseq pipeline
Adapter trimming and the removal of low-quality bases are performed with Trim Galore
Assembly: OryCun2.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Ctenomys talarum

source_name: Fibroblast

extract_protocol:
Total RNA was extracted from tuco-tuco fibroblast cells (kit used ) and submitted to the JP Sulzberger Columbia Genome Center. RNA quality was assessed using a BioAnalyzer (Agilent Technologies; Instrument ID: DE72901373, Firmware: C.01.069, Type: G2939A) and yielded an RNA integrity number (RIN) of 7.7. Either this total RNA was used directly for library preparation, or poly-A selection was performed to enrich for mRNA.
Libraries were constructed using Illumina TrueSeq chemistry and sequenced using Illumina NovaSeq 6000. Base calling was performed by the Columbia Genome Center using Illumina’s Real-Time Analysis (RTA) software, and raw base call (BCL) files were converted to FASTQ format with adapter trimming using bcl2fastq2 (v2.20). Sequence reads were mapped to the Oryctolagus cuniculus (rabbit) genome using STAR (2.5.2b).

value: Fibroblast


title: sample2_JC002

description: Library name: sample2_JC002


title: RS4;11 cells, shControl, IgG

description:
Library name: shControl. IgG
Column name in raw_counts_ALL Samples.txt:shControl


title: FKBP-SETDB1 A12A10, dTAGd1, H3K9me3, NPCd7

description: Library name: nC0062_SetA12A10d_NPCd7_dTAGd1_H3K9me3

value: doxycyline for 7 days coupled with differentiation, dTAG-13 for 6 days

value: anti-H3K9me3 (Abcam, # ab8898)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: cmnor_6_3

city: Beijing

first: Jinfang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

description: Library name: cmnor_6_3

data_processing:
Illumina NovaSeq X
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM（Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Assembly: http://cucurbitgenomics.org/organism/18
Supplementary files format and content: text files include FPKM values for each Sample

organism: Citrullus lanatus

source_name: flesh

extract_protocol:
RNA was extracted from The homozygotes Cmnor; CmNOR/Cmnor heterozygotes and WT flesh were harveseted at 33 DAP,36 and 39 DAP  (days after pollination) and 6 days after storage with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed
The 36 libraries were built by TruseqTM RNA sample prep kit (Illumina, USA).

value: flesh

value: Cmnor homozygotes

value: 6 days after storage


title: DSS_Inwax_Spleen_3

description: Library name: DSS_Inwax_Spleen_3

value: spleen


title: DSS_Inwax_Spleen_2

description: Library name: DSS_Inwax_Spleen_2


title: RS4;11 cells, shDNTTIP1, H3K27ac

description:
Library name: shDNTTIP1. H3K27ac
Column name in raw counts_ALL Samples.txt:shDNTTIP1


title: FKBP-SETDB1 A12A10, dTAGd1, H3K9me3, NPCd3

description: Library name: nC0054_SetA12A10d_NPCd3_dTAGd1_H3K9me3

extract_protocol:
Calibrated native ChIP-seq (cChIP-seq) was performed for H3K9me3 by collecting 5x107 mESCs or NPCs and spiking in 1 × 107 Drosophila Sg4 cells counted using a Countess II FL Automated Cell Counter (Life Technologies). Cells were pelleted by centrifugation and resuspended in 1mL of cold RSB (10mM Tris pH 8.0, 10mM NaCl, 3mM MgCl2) and lysed by addition of 14mL of cold RSB supplemented with 0.1% NP40 and gentle inversion. Nuclei were recovered by centrifugation at 1500 x g for 5 min at 4oC and washed in 4ml RSB with 0.25M sucrose and 3mM CaCl2 supplemented with protease inhibitors. Nuclei were recovered by centrifugation at 1500 x g for 5 min at 4oC and resuspended in 1mL of RSB with 0.25M sucrose and 3mM CaCl2 supplemented with protease inhibitors, which was transferred to a 1.5mL tube for MNase digestion (200U, Fermentas EN0181) of chromatin to mono- and di-nucleosomes at 37oC for 5 min with inversion every minute. The reaction was quenched by addition of 8µL 0.5M EDTA and spun at 5,000rpm for 5min at 4oC. The supernatant (S1) was collected into a new 1.5mL tube and kept on ice. The pellet was thoroughly resuspended in 300µL of Nucleosome Release Buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2mM EDTA) supplemented with protease inhibitors, and incubated for 1hour at 4oC with rotation. This suspension was passed five times through a 27G needle using a 1mL syringe and then spun at 5000rpm for 5min at 4oC. The supernatant (S2) was collected and combined with S1. The chromatin was centrifuged at 13000rpm for 5min to remove any precipitant, and supernatant was collected as chromatin, snap frozen and stored at -80oC until further processing. For immunoprecipitation (IP), chromatin was thawed on ice and 110µL were diluted in 1mL of native ChIP incubation buffer (70mM NaCl, 10mM Tris pH 7.5, 2mM MgCl2, 2mM EDTA, 0.1% Triton X-100) freshly supplemented with protease inhibitors.  100µL were transferred to a new 1.5mL tube and stored at 4oC to be used as input. The remaining diluted chromatin was incubated overnight with rotation with 5µg of H3K9me3 antibody (Abcam, ab8898) or H3K9me3 (Active Motif; AB2532132 Clone 0319; Cat #061013). Samples were then incubated for 90min with 45µL rProtein A Sepharose™ Fast Flow beads (Amersham) pre-blocked with 1mg/mL of yeast tRNA and 1mg/mL BSA. The beads were then washed five times for 10min with rotation at 4oC with Wash Buffer (20mM Tris pH 7.5, 2mM EDTA, 125mM NaCl, 0.1% Triton X-100) followed by one final wash in 1x TE. The DNA was then eluted from the beads by incubation at 25oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. DNA from the IP elutions and input samples was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions.
ChIP and input DNA was quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and submitted to library preparation using the the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and their length was estimated using the Bioanalyzer High Sensitivity DNA kit (Agilent) before pooling and subjected to paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: NPC

value: doxycyline for 3 days coupled with differentiation, dTAG-13 for 2 days


title: RS4;11 cells, shControl, H3K27ac

description:
Library name: shControl. H3K27ac
Column name in raw_counts_ALL Samples.txt:shControl


title: DSS_Inwax_Spleen_1

description: Library name: DSS_Inwax_Spleen_1


title: cmnor_6_2

description: Library name: cmnor_6_2

growth_protocol: The homozygotes Cmnor; CmNOR/Cmnor heterozygotes and WT flesh were harveseted at 33 DAP,36 and 39 DAP  (days after pollination) and 6 days after storage


title: FKBP-SETDB1 A12A10, Control, Input, NPCd7

description: Library name: nC0057_SetA12A10d_NPCd7_Control_Input


title: FKBP-SETDB1 A12A10, dTAGd1, Input, NPCd3

description: Library name: nC0053_SetA12A10d_NPCd3_dTAGd1_Input


title: cmnor_6_1

description: Library name: cmnor_6_1


title: FKBP-SETDB1 A12A10, dTAGd1, Input, NPCd7

description: Library name: nC0061_SetA12A10d_NPCd7_dTAGd1_Input


title: FKBP-SETDB1 A12A10, Control, H3K9me3, NPCd3

description: Library name: nC0050_SetA12A10d_NPCd3_Control_H3K9me3

value: doxycyline for 3 days coupled with differentiation


title: RS4;11 cells, shDNTTIP1

description:
Library name: shDNTTIP1
Column name in raw counts_ALL Samples.txt:shDNTTIP1

data_processing:
raw sequencing data underwent quality control using fastp (v.0.23.4), followed by alignment to the human reference genome (hg38) with Bowtie2 (v.2.5.4). SAM-formatted alignment files were converted to BAM format using samtools (v.1.21), and PCR duplicates were removed via Picard MarkDuplicates function (v.3.4.0). Read coverage profiles (BigWig format) were generated using deeptools (v.3.5.5).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq assay was performed using the Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme, TD711, China). Transposed DNA was purified using magnetic DNA Extract Beads.
PCR-amplified with indexed primers, and processed into sequencing libraries using the TruePrep Index Kit V2 for Illumina (Vazyme, TD202, China). Libraries were sequenced on the Illumina NovaSeq 6000 platform.


title: DSS_cellulose_Spleen_2

description: Library name: DSS_Blank_Spleen_2


title: cmnorhe_6_3

description: Library name: cmnorhe_6_3

value: CmNOR/Cmnor heterozygotes


title: DSS_cellulose_Spleen_3

description: Library name: DSS_Blank_Spleen_3


title: cmnorhe_6_2

description: Library name: cmnorhe_6_2


title: RS4;11 cells, shControl

description:
Library name: shControl
Column name in raw_counts_ALL Samples.txt:shControl


title: ASHD5

city: Chuo

first: Yosuke

last: Watanabe

address: Shimokato 1110

department: Cardiology

country: Japan

institute: University of Yamanashi

description: Library name: Sample9

data_processing:
Quality control and adapter trimming were performed with fastQC and cutadapt on raw reads Fastq files.
Reads were aligned to reference human genome (hg38) and counted by HISAT2
Assembly: hg38
Supplementary files format and content: tsv file, countmatrix for all samples

source_name: Aortic valve

extract_protocol:
Aortic valve specimens excised during SAVR were immediately snap-frozen in liquid nitrogen and subsequently stored at –80 ℃ until further analysis.　Aortic valve specimens were cryogenically pulverized, and total RNA was extracted using the RNeasy Mini Kit (Qiagen, Tokyo, Japan) in accordance with the manufacturer's protocol.
RNA sequencing was perform using RNA sequencing was performed by macrogen JAPAN (Tokyo, Japan) using the NovaSeq 6000 platform (2×150 bp configuration). Poly(A) selection was used for mRNA enrichment, and raw FASTQ data were obtained for downstream gene expression analysis.

tag: condition

value: aortic stenosis (AS)

value: Aortic valve

value: hemodialysis (HD)


title: FKBP-SETDB1 A12A10, Control, Input, NPCd3

description: Library name: nC0049_SetA12A10d_NPCd3_Control_Input

data_processing:
ChIP-sequencing analysis was performed using previously established pipelines45. For calibrated ChIP-seq experiments, raw fastq reads were mapped using Bowtie2 (v.2.3.5.1)67 to the 129S1xCast N-masked mm10 genome concatenated with the dm6 Drosophila genome using the following parameters: “--very-sensitive --no-discordant --no-mixed -X 2000”. Unmapped reads were then removed. PCR duplicates were identified and removed using picard-tools “MarkDuplicates” (Broad Institute) and remaining reads were then assigned to each allele using SNPsplit68. To calculate calibration factors, mm10 and dm6 mapped reads for each sample and input were counted using SAMtools (v.1.16)69. Calibration factors for cChIP-seq were then calculated according to the derived formula for occupancy ratio (ORi)70. In order to generate calibrated bigwig files for mouse chrX, bam files were initially filtered using the “intersect” function from BEDtools (v.2.30.0)71 to generate a bam file containing mouse chrX reads only. During the generation of the iXist-ChrXCast cell line using CRISPR-Cas9–facilitated homology-directed recombination, two SNPs (mm10, chrX:103482682 A/T and mm10, chrX:103482895 A/T) between the Cast and 129 alleles became uninformative, as both X alleles were converted to the 129 allele (T at both positions). Consequently, any reads spanning these two sites are no longer allele-specific as intended and were therefore removed from the allelic BAM files. BAM files were then sorted and indexed using SAMtools69 and bigWig files were finally generated using deepTools (v.3.5.1)72 bamCoverage per 10 million reads considering the calibration factors. BigWig files were then visualized using IGV (https://software.broadinstitute.org/software/igv/)73. To quantify the number of ChIP reads per kb over the Xist locus (chrX: 103460373-103483233), we used the function “bigWigAverageOverBed” from UCSCTools.
Assembly: mm10; dm6
Supplementary files format and content: bigWig

value: Cast x 129S

tag: cell line


title: FKBP-SETDB1 A12A10, Control, H3K9me3, NPCd1

description: Library name: nC0046_SetA12A10d_NPCd1_H3K9me3

tag: cell type

value: doxycyline for 1 day coupled with differentiation


title: cmnorhe_6_1

description: Library name: cmnorhe_6_1

tag: treatment


title: DSS_cellulose_Spleen_1

description: Library name: DSS_Blank_Spleen_1


title: DSS_cellulose_MC_1

description: Library name: DSS_Blank_MC_1

value: middle colon


title: WT_6_3

description: Library name: WT_6_3

value: wild type


title: FKBP-SETDB1 A12A10, Control, Input, NPCd1

description: Library name: nC0045_SetA12A10d_NPCd1_Input

tag: chip antibody

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: RNA-seq of Melan-a BAP1 knockout clone 4 (biological replicate 1)

city: Singapore

first: Mona

middle: Meng

address: 20 College Rd, Singapore

country: Singapore

institute: Singaoire Eye Research Institute

description:
Library name: Melana_BAP1_KO_Clone_4_RNAseq_1
Bulk RNA-seq of Melan-a BAP1 knockout clone 4
MA5_18_3

data_processing:
Raw sequencing reads were demultiplexed and converted to FASTQ format. For bulk RNA-seq data, reads were quality controlled, trimmed if necessary, and aligned to the mouse reference genome, followed by gene-level quantification. For single-cell RNA-seq data, raw base call files were processed using the Cell Ranger pipeline for alignment, barcode processing, and generation of gene–cell count matrices. For WGS and WES data, reads were aligned to the mouse reference genome, followed by duplicate marking, base quality recalibration, and variant calling.
Somatic variants in BAP1 knockout clones were identified by comparison against the Melan-a wild-type reference. Variant annotation was performed using standard annotation tools. Quality control metrics were assessed for all datasets prior to downstream analysis.
Assembly: Mouse reference genome GRCm38 (mm10) was used for read alignment and downstream analyses.
Supplementary files format and content: For single-cell RNA sequencing data, base call files were processed using the Cell Ranger pipeline to perform alignment, barcode processing, and generation of filtered gene–cell count matrices.
Supplementary files format and content: For whole-genome sequencing, whole-exome sequencing, and bulk RNA-seq datasets, raw FASTQ files are provided without additional downstream processing.

source_name: cell

growth_protocol: Melan-a cells (BAP1 wild-type and CRISPR-engineered BAP1 knockout clones) and B16F10 cells were cultured under standard conditions in a humidified incubator at 37 °C with 5% CO₂ using recommended growth media. Primary murine ocular melanocytes were isolated from mouse ocular tissue and cultured under melanocyte-supporting conditions prior to DNA extraction. For in vivo experiments, Melan-a wild-type or BAP1 knockout cells were injected into syngeneic mice via ocular or subcutaneous routes, and tumors were harvested at defined endpoints for downstream analyses.

extract_protocol:
For bulk RNA-seq, total RNA was extracted from cultured cells using a column-based RNA isolation kit following the manufacturer’s instructions, including on-column DNase treatment. For whole-genome and whole-exome sequencing, genomic DNA was extracted using a standard phenol–chloroform or silica column–based method. For single-cell RNA sequencing, freshly isolated or fixed tumor tissues were mechanically and enzymatically dissociated into single-cell suspensions prior to library preparation according to the 10x Genomics fixed tissue workflow.
Bulk RNA-seq libraries were prepared from polyadenylated RNA using a stranded mRNA library preparation kit. Whole-genome sequencing libraries were prepared from genomic DNA using a PCR-free or low-cycle library preparation protocol. Whole-exome sequencing libraries were generated using a hybrid-capture–based exome enrichment kit. Single-cell RNA-seq libraries were constructed using the 10x Genomics Chromium platform following the manufacturer’s protocol for fixed tissue gene expression, generating barcoded single-cell cDNA libraries.

treatment_protocol: No drug or chemical treatments were applied. The primary experimental variables were BAP1 genotype (wild-type versus knockout) and tumor anatomical site (ocular versus subcutaneous).

value: cell

value: Melan-a

value: melanocyte cell line

value: BAP1 KO

value: No


title: RNA-seq of Melan-a BAP1 knockout clone 4 (biological replicate 2)

description:
Library name: Melana_BAP1_KO_Clone_4_RNAseq_2
Bulk RNA-seq of Melan-a BAP1 knockout clone 4
MA5_18_4


title: FKBP-SETDB1 A12A10, Control, H3K9me3, mESC

description: Library name: nC0042_SetA12A10d_ES_H3K9me3

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: anti-H3K9me3 (Abcam, # ab8898)


title: ASHD3

description: Library name: Sample7


title: WT_6_2

description: Library name: WT_6_2

value: flesh

value: 6 days after storage


title: ASHD4

description: Library name: Sample8

value: aortic stenosis (AS)

value: Aortic valve


title: RNA-seq of Melan-a BAP1 knockout clone 3 (biological replicate 2)

description:
Library name: Melana_BAP1_KO_Clone_3_RNAseq_2
Bulk RNA-seq of Melan-a BAP1 knockout clone 3
MA5_17_5


title: ASHD2

description: Library name: Sample6

value: hemodialysis (HD)


title: WT_6_1

description: Library name: WT_6_1


title: FKBP-SETDB1 A12A10, Control, Input, mESC

description: Library name: nC0041_SetA12A10d_ES_Input

value: Cast x 129S


title: ASHD1

description: Library name: Sample5


title: cmnor_39_3

description: Library name: cmnor_39_3

value: Cmnor homozygotes

value: 39 days after pollination


title: cmnor_39_2

description: Library name: cmnor_39_2


title: F121 F2 ES Rep2

description: Library name: 264_F121_F2_ES_Rep2

library_source: other

data_processing:
The data processing pipeline for ChrRNA-seq followed procedures similar to those described by Nesterova et al. 2019 Briefly, raw FASTQ files containing paired-end reads were first aligned to a custom rRNA reference using Bowtie2 (v2.3.5.1) to remove rRNA contaminants. Reads mapping to rRNA were discarded, and the remaining unmapped read pairs were subsequently aligned to the N-masked mouse genome (mm10) using STAR (v2.5.2b). STAR was run with the following parameters: “--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 1 --alignEndsType EndToEnd”. Only uniquely mapped reads were retained for downstream analyses. To distinguish allelic origin, alignments were split into Cast and 129S alleles using SNPsplit (v0.4.0dev, Babraham Institute)67 with the “--paired” option, based on annotated SNPs present bewteen the two strains. Allele-specific read counts were obtained using featureCounts (v1.5.2) with the parameters “-t transcript -g gene_id -s 2”. Alignments were sorted using Samtools (v1.16). For data visualisation, Bedtools (v2.30) was used to generate bigWig coverage tracks, which were then visualized using IGV (https://software.broadinstitute.org/software/igv/). Metagene profiles and heatmaps were created using deepTools (v3.5.2), supplemented with custom Python scripts. For biallelic (non-split) analyses, read counts were normalized to counts per million (CPM) mapped read pairs using the edgeR R package (v4.2.1). Only X-linked genes with at least 10 SNP-overlapping reads across all samples were considered for allelic ratio calculations. The allelic ratio was defined as Xi/(Xi + Xa), where Xi and Xa represent the inactive and active X chromosome alleles, respectively.
Assembly: mm10
Supplementary files format and content: txt

molecule: other

source_name: Parental of TsixStop cell line

extract_protocol:
Chromatin-RNA isolation and sequencing was as previously described. Briefly, cells were collected in a 15mL tube, washed with PBS and snap frozen immediately after PBS removal. Cells pellets were stored at -80oC until further processing. In order to purify chromatin-RNA, pellets were thawed on ice and resuspended in 800mL of hypotonic buffer HLBN (10mM NaCl, 2.5mM MgCl2, 10mM Tris pH 7.5, 0.1% NP40) and transferred to a 1.5mL tube. This solution was underlaid with a 480mL HLBN containing 24% sucrose to create a sucrose cushion for nuclear isolation by centrifugation at 1000g for 5min at 4oC. For fractionation, the nuclear pellet was then resuspended in 120mL NUN1 (20mM Tris pH8.0, 75mM NaCl, 0.5mM EDTA, 50% glycerol) freshly supplemented with 1mM DTT and protease inhibitors. After resuspension, 1200mL NUN2 (20mM HEPES pH7.6, 7.5mM MgCl2, 0.2mM EDTA, 0.3M NaCl, 1M urea, 1% NP40) freshly supplemented with 1mM DTT and protease inhibitors were added and mixed by gentle vortexing. Sample was incubated on ice for 15 min with occasional vortexing. After centrifugation for 10min at 15000rpm at 4oC, the supernatant containing the nucleoplasmic fraction was discarded and the chromatin pellet was resuspended in 200mL HSB (10mM Tris pH7.5, 500mM NaCl, 10mM MgCl2) supplemented with 2mL TURBO DNAse (Life Technologies) to digest the sample DNA by incubating at 37oC for at least 10min, shaking at 1400rpm. After this incubation, 2μL of 20% SDS and 4μL of proteinase K (20mg/ml) were added and the samples were incubated at 37oC for at least 30min for protein digestion. Chromatin-bound RNA was then purified using Trizol reagent according to manufacturer’s recommendations with addition of glycogen to aid precipitation of the RNA at -20oC overnight. Purified chromatin-RNA was subjected to a second round of TURBO DNAse treatment and a second round of Trizol reagent purification as previously described.
Chromatin-RNA concentrations were initially measured by Nanodrop to inform further dilution for quantification using Qubit HS RNA assay (Invitrogen) and quality control using RNA Pico 6000 Bioanalyser kit (Agilent). RNA Libraries were prepared for sequencing using the Illumina TruSeq stranded total RNA kit including the rRNA depletion according to the manufacturer’s instructions. Libraries were quantified and verified using Qubit High Sensitivity DNA (Invitrogen) and the Bioanalyser High Sensitivity DNA (Agilent) kits before pooling and paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

treatment_protocol: To induce Xist expression, medium was supplemented with 1µg/mL doxycycline. To induce protein degradation in lines expressing FKBP12F36V-tagged SETDB1, medium was supplemented with 100nM dTAG-13 (Tocris Bioscience).

value: Parental of TsixStop cell line


title: F121 F2 ES Rep1

description: Library name: 263_F121_F2_ES_Rep1


title: AS2

description: Library name: Sample2

value: non-dialysis


title: FKBP-KAP1 A4F3 ES, +dTAG+dox

description: Library name: 222_KAP1A4F3_27hdTAG24hdox_ES

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: dTAG-13 for 27hours and doxycyline for 24hours


title: cmnor_39_1

description: Library name: cmnor_39_1


title: RNA-seq of Melan-a BAP1 knockout clone 3 (biological replicate 1)

description:
Library name: Melana_BAP1_KO_Clone_3_RNAseq_1
Bulk RNA-seq of Melan-a BAP1 knockout clone 3
MA5_17_4

value: cell

value: Melan-a

value: melanocyte cell line


title: RNA-seq of Melan-a BAP1 knockout clone 2 (biological replicate 1)

description:
Library name: Melana_BAP1_KO_Clone_2_RNAseq_1
Bulk RNA-seq of Melan-a BAP1 knockout clone 2
MA4_3_3

value: BAP1 KO

value: No


title: AS4

description: Library name: Sample3


title: AS5

description: Library name: Sample4


title: AS1

description: Library name: Sample1


title: Primed Replicate 4

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: HD6m-IND4

data_processing:
Fastq files were processed using cellranger count  (v7.2.0)  with default parameters.
QC, filtering and integrated analysis was done using R v4.4.0 and Seurat v5.1.0
For further details please check article methods
Assembly: hg38
Supplementary files format and content: cellranger files outputs (.gz) and integrated Seurat object (.RDS)

source_name: Cell line

extract_protocol:
Parental and primed cell suspensions were counted and checked for viability using a Nexcelom K2 with AO/PI staining. 10X Genomics Chromium 3’v3.1 chemistry on a Chromium X controller targeting 10,000 cells per sample was used to capture cells
Gene expression profiling libraries were synthesized using manufacturer’s protocol without modification

value: T47D ATCC HTB-113

value: Goblet cells

value: 6 months after E2 depletion


title: RNA-seq of Melan-a BAP1 knockout clone 1 (biological replicate 1)

description:
Library name: Melana_BAP1_KO_Clone_1_RNAseq_1
Bulk RNA-seq of Melan-a BAP1 knockout clone 1
MA1_15_3


title: cmnorhe_39_2

description: Library name: cmnorhe_39_2

value: flesh

value: CmNOR/Cmnor heterozygotes


title: FKBP-KAP1 A4F3 ES, +dTAG

description: Library name: 220_KAP1A4F3_27hdTAG_ES

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: dTAG-13 for 27hours


title: FKBP-KAP1 A4F3 ES, +dox

description: Library name: 221_KAP1A4F3_24hdox_ES

value: Cast x 129S

value: doxycyline for 24hours


title: RNA-seq of Melan-a BAP1 knockout clone 2 (biological replicate 2)

description:
Library name: Melana_BAP1_KO_Clone_2_RNAseq_2
Bulk RNA-seq of Melan-a BAP1 knockout clone 2
MA4_3_4


title: cmnorhe_39_3

description: Library name: cmnorhe_39_3

value: 39 days after pollination


title: FKBP-KAP1 A4F3 ES

description: Library name: 219_KAP1A4F3_ES


title: Water_cellulose_DC_1

description: Library name: Water_Blank_DC_1

value: distal colon


title: cmnorhe_39_1

description: Library name: cmnorhe_39_1


title: RNA-seq of Melan-a BAP1 wild-type cells (biological replicate 2)

description:
Library name: Melana_WT_RNAseq_2
Bulk RNA-seq of Melan-a BAP1 wild-type cells
MA2WT

value: cell

value: BAP1 WT


title: FKBP-KAP1 A4C11 ES, +dTAG+dox

description: Library name: 218_KAP1A4C11_27hdTAG24hdox_ES

value: dTAG-13 for 27hours and doxycyline for 24hours


title: Primed Replicate 3

description: Library name: HD6m-IND3


title: RNA-seq of Melan-a BAP1 wild-type cells (biological replicate 1)

description:
Library name: Melana_WT_RNAseq_1
Bulk RNA-seq of Melan-a BAP1 wild-type cells
MA1WT

value: Melan-a

value: melanocyte cell line


title: WT_39_3

description: Library name: WT_39_3

value: wild type


title: Primed Replicate 2

description: Library name: HD6m-IND2

value: T47D ATCC HTB-113

value: Goblet cells


title: RNA-seq of Melan-a BAP1 knockout clone 1 (biological replicate 2)

description:
Library name: Melana_BAP1_KO_Clone_1_RNAseq_2
Bulk RNA-seq of Melan-a BAP1 knockout clone 1
MA1_15_4

value: BAP1 KO

value: No


title: WT_39_2

description: Library name: WT_39_2

value: flesh


title: Primed Replicate 1

description: Library name: HD6m-IND1

value: 6 months after E2 depletion


description:
Library name: Melana_BAP1_KO_Clone_4_WES
Whole-exome sequencing of Melan-a BAP1 knockout clone 4


description:
Library name: Melana_BAP1_KO_Clone_3_WES
Whole-exome sequencing of Melan-a BAP1 knockout clone 3


title: cmnor_36_3

description: Library name: cmnor_36_3

value: Cmnor homozygotes

value: 36 days after pollination


title: FKBP-KAP1 A4C11 ES

description: Library name: 215_KAP1A4C11_ES

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC


title: Parental Replicate 4

description: Library name: WT-IND4


description:
Library name: Melana_BAP1_KO_Clone_2_WES
Whole-exome sequencing of Melan-a BAP1 knockout clone 2

value: cell


title: Parental Replicate 3

description: Library name: WT-IND3


title: cmnor_36_1

description: Library name: cmnor_36_1


description:
Library name: Melana_BAP1_KO_Clone_1_WES
Whole-exome sequencing of Melan-a BAP1 knockout clone 1


title: cmnor_36_2

description: Library name: cmnor_36_2


description:
Library name: Melana_WT_WES
Whole-exome sequencing of Melan-a BAP1 wild-type cells

value: BAP1 WT


title: FKBP-MPP8 H1 ES, +dox

description: Library name: 213_MPP8H1_24hdox_ES

value: doxycyline for 24hours


title: Parental Replicate 2

description: Library name: WT-IND2


title: FKBP-MPP8 H1 ES, +dTAG

description: Library name: 212_MPP8H1_27hdTAG_ES

value: dTAG-13 for 27hours


title: WT_39_1

description: Library name: WT_39_1

value: 39 days after pollination


title: Parental Replicate 1

description: Library name: WT-IND1


title: FKBP-KAP1 A4C11 ES, +dTAG

description: Library name: 216_KAP1A4C11_27hdTAG_ES


description:
Library name: Primary_mice_melanocyte_WGS
Whole-genome sequencing of primary murine ocular melanocytes

source_name: Ocluar melanocytes

value: Ocluar melanocytes

value: primary melanocytes

value: WT


title: cmnorhe_36_3

description: Library name: cmnorhe_36_3

value: CmNOR/Cmnor heterozygotes


title: FKBP-KAP1 A4C11 ES, +dox

description: Library name: 217_KAP1A4C11_24hdox_ES


title: FKBP-TASOR F8 ES, +dTAG+dox

description: Library name: 210_TASORF8_27hdTAG24hdox_ES

value: dTAG-13 for 27hours and doxycyline for 24hours


title: FKBP-MPP8 H1 ES

description: Library name: 211_MPP8H1_ES


description:
Library name: Melana_WGS
Whole-genome sequencing of Melan-a murine melanocyte cell line

value: Melan-a

value: melanocyte cell line

value: No


description:
Library name: B16F10_WGS
Whole-genome sequencing of B16F10 murine melanoma cell line

value: melanoma cell line


title: FKBP-TASOR F8 ES, +dox

description: Library name: 209_TASORF8_24hdox_ES

value: Cast x 129S


title: cmnorhe_36_1

description: Library name: cmnorhe_36_1

value: flesh

value: 36 days after pollination


title: FKBP-MPP8 H1 ES, +dTAG+dox

description: Library name: 214_MPP8H1_27hdTAG24hdox_ES

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC