title: Cas9 Day 10 +Dox

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
In order to evaluate the sequencing quality of amplicons and filter the low-quality sequencing data, Fastqc-0.11.3 and fastp-0.19.6 were used with default parameters for each sample
The clean sequencing reads of pair-ended segments were merged using FLASh-1.2.1 to obtain full-length reads. In order to obtain the amplified fragment reads of each surrogate reference sequence, BsmBI Linker was removed from the surrogate reference sequence. The BWA-MEM algorithm of bwa was used for local alignment, and the reads of all samples were divided into 12,000 independent libraries.
Due to the existence of sequencing or oligo synthesis introduced errors, each library was then filtered.
We adopt the following steps for data processing and filtering: 1) Obtain the sequence containing gRNA + scaffold fragment as dataset1. 2) Obtain the sequence containing GTTTGAAT in dataset1 as dataset2 (BsmBI linker fragments changed in orientation (GTTTGGAG-> GTTTGAAT)). 3) Extract the intermediate surrogate sequence from dataset2, which removed the length limit. In order to eliminate the interference of background noise before analyzing editing efficiency, all mutations or indels found in WT HEK293T cells group were removed.
Genome_build: synthetic DNA library
Supplementary_files_format_and_content: raw and filtered counts

source_name: HEK293T cells expressing SpCas9

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (LONZA) supplemented with 10 % fetal bovine serum (FBS) (Gibco), 1% GlutaMAX (Gibco), and penicillin/streptomycin (100 units penicillin and 0.1 mg streptomycin/mL) in a 37 °C incubator with 5% CO2 atmosphere and maximum humidity. Cells were passaged every 2-3 days when the confluence was approximately 80-90%.

extract_protocol:
Genomic DNA was extracted using the phenol-chloroform method. The genomic DNA were digested with RNase A (OMEGA) to remove RNA contamination (In this study, 50 µg RNase A worked well to digest the RNA contamination in 100～200 µg genomic DNA after incubating in 37 ℃ for 30 min).
PCR-free library was prepared using MGIeasy FS PCR-free DNA library Prep kit following the manufacturer’s instruction. Briefly, measure the concentration of purified PCR products using Qubit 4 TM fluorometer (Invitrogen) and dilute the concentration of each sample to 10 ng/µl. 10 µl diluted PCR product was mixed with an A-Tailing reaction which contained A-Tailing enzyme and buffer, incubated at 37°C for 30 minutes then 65°C for 15 min to inactive the enzyme. Then the A-Tailed sample was mixed with PCR Free index adapters (MGI.), T4 DNA Ligase and T4 ligase buffer to add index adapter at both 3’ and 5’ ends of PCR products.  The reaction was incubated at 23°C for 30 min and then purified with XP beads. Then denature the PCR products to be single-strand DNA (ssDNA) by incubating at 95 °C for 3 min and keep on 4 °C for the subsequent step. Transform the ssDNA to be circles using cyclase (MGI) at 37 °C for 30 min and then digested to remove linear DNA using Exo enzyme at 37 °C for 30 min. Purify the products again by XP beads and assay the concentration of library by Qubit 4 TM fluorometer.
Liraries were sequenced with pair-ended 150 bp deep-sequencing on a MGISEQ-2000 sequencing platform

treatment_protocol: Cells were transduction using a multiplicity of infection (MOI) of 0.3. from Day 2, cells were growth in selection medium (1 µg/mL puromycin). For Cas9 cells, overexpression of the Cas9 protein was induced with 1 µg/mL doxycycline.

value: HEK293T cells expressing SpCas9

tag: sample type

value: Surrogates sites amplified by PCR from transduced cells

tag: molecule subtype

value: PCR products


title: Bap1flfl_ring1b.suz12.XInput_OHT_rep2

status: Public on May 03 2021

type: SRA

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
BAP1ff_rsXInput_TAM_rep2_S16
processed data file:
mESC_BAP1ff_TAM_ring1b.suz12.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

library_source: genomic

data_processing:
For cChIP-seq, Bowtie 2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq for Polycomb factors and Pol II) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest (RING1B peaks for H2AK119ub1, H3K27me3, RING1B and SUZ12 cChIP-seq, TSS ± 2.5 kb for H3K27ac, H3K4me3 and H3K4me1 cChIP-seq, or gene bodies for total Pol II, Ser5P- and Ser2P-Pol II cChIP-seq) were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
For comparative box plot analysis, genomic regions of interest were annotated with read counts from merged spike-in normalised replicates using multiBamSummary from deeptools ( “--outRawCounts”).
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.
Supplementary_files_format_and_content: bed files containing genomic intervals that were defined as active promoters, active enhancers and intergenic active enhancers based on the high enrichment of ATAC-seq and H3K27ac cChIP-seq signal in untreated Bap1fl/fl cells and the overlap with a comprehensive set of gene annotations. H3K27ac-positive ATAC peaks overlapping with transcription start site (TSS) +/- 1 kb regions were considered to be active promoters, while H3K27ac-positive ATAC peaks located further than 1 kb away from TSS of genes were considered to be active enhancers. Active enhancers that didn't overlap with any gene bodies from our comprehensive set of gene annotations (intergenic active enhancers) were used for all the downstream analysis.
Supplementary_files_format_and_content: bed files containing coordinates for the mm10 genome segmentation using a 13-state ChromHMM model: *segments.bed is a BED4 file (chr, start, end, state name) used for read annotation and *dense.bed is a BED file used for visualisation in the UCSC Genome browser in the dense format (all genome annotations are shown on a single line with different states represented by different colors).

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), gDNA-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. ). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For RING1B and SUZ12 cChIP-seq, 5×107 mouse ESCs (untreated and OHT-treated) were crosslinked in 10 ml 1x PBS with 2 mM DSG (Thermo Scientific) for 45 minutes at 25°C, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Crosslinking was stopped by quenching with 125 mM glycine. Crosslinked ESCs were mixed with 2×106 human HEK293T cells, which have been similarly double-crosslinked, and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100, 1x PIC (Roche)) for 10 minutes at 4˚C. Released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x PIC (Roche)) for 5 minutes at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC (Roche)) and sonicated for 30 minutes using the BioRuptor Pico (Diagenode), shearing genomic DNA to an average size of 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%, followed by centrifugation at 20,000 g for 10 min at 4°C to collect the clear supernatant fraction. For cChIP-seq for Pol II and its phosphorylated forms, 5×107 ESCs (untreated and OHT-treated) were crosslinked in 10 ml 1x PBS with 1% formaldehyde (methanol-free, Thermo Scientific) for 10 min at 25°C and then quenched by addition of 125 mM glycine. Cross-linked ESCs were mixed with 2×106 human HEK293T cells, which have been similarly single-crosslinked, and then incubated in FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP40, 0.1% sodium deoxycholate, 0.1% SDS, 10 mM NaF, 1 mM AEBSF, 1×PIC) for 10 min at 4˚C. Chromatin was sonicated for 30 min using the BioRuptor Pico (Diagenode), followed by centrifugation at 20,000 g for 10 min at 4°C to collect the clear supernatant fraction.  For RING1B and SUZ12 ChIP, sonicated chromatin was diluted 10-fold with ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl, 1xPIC). For Pol II ChIP, 300 ug of chromatin per one IP was diluted in FA-lysis buffer up to a final volume of 1 ml. Diluted chromatin was pre-cleared for 1 hr using Protein A agarose beads (Repligen) that were pre-blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1 ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST, D22F2, 3 ul), anti-SUZ12 (CST, D39F6, 3 ul), anti-Rpb1-NTD (CST, D8L4Y, 15 μl) as a measure of total Pol II levels, anti-Rpb1-CTD-Ser5P (CST, D9N5I, 12.5 μl) and anti-Rpb1-CTD-Ser2P (CST, E1Z3G, 12.5 μl) as a measure of Pol II phosphorylation levels. To capture antibody-bound chromatin, ChIP reactions were incubated with pre-blocked protein A agarose beads (Repligen) for 2 hr (RING1B and SUZ12) or 3 hr (Pol II) at 4°C. For RING1B and SUZ12, ChIP washes were performed as described previously (Farcas et al. 2012). For Pol II, washes were performed with FA-Lysis buffer, FA-Lysis buffer containing 500 mM NaCl, DOC buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2 mM EDTA, 10 mM Tris-HCl pH 8), followed by two washes with TE buffer (pH 8). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-linking was reversed overnight at 65oC with 200 mM NaCl and 2 ul RNase A (Sigma). Matched input samples (10% of original ChIP reaction) were treated identically. The following day, ChIP samples and inputs were incubated with Proteinase K (Sigma) for at least 1.5 hr at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research).  For native cChIP-seq for H2AK119ub1, H3K27me3, H3K27ac, H3K4me3, and H3K4me1, 5×107 mouse ESCs (untreated and OHT-treated) were mixed with 2×107 Drosophila SG4 cells in 1x PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM sodium butyrate, and 5 mM N-ethylmaleimide). Nuclei were then washed and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, and 1x PIC (Roche)). Each sample was incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, and 1x PIC (Roche)) at 4°C for 1 hr, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with the corresponding S1 sample from above. Digestion to mostly mono-nucleosomes was confirmed by agarose gel electrophoresis of purified S1/S2 DNA.  For ChIP, S1/S2 nucleosomes were diluted 10-fold in Native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% TritonX-100, 10 mM sodium butyrate (for H3K27ac and H3K4me3 ChIPs), 10 mM N-ethylmaleimide, and 1xPIC (Roche)). Each ChIP reaction, 1 ml of diluted nucleosomes was incubated overnight at 4oC with the appropriate antibody, anti-H2AK119ub1 (CST, D27C4, 5 ul), anti-H3K27me3 (in-house, 5 ul), anti-H3K27ac (CST, D5E4, 3 μl), anti-H3K4me3 (in-house, 4 ul) or anti-H3K4me1 (CST, D1A9, 5 ul). Antibody-bound nucleosomes were captured for 1 hr at 4°C using protein A agarose (Repligen) beads, pre-blocked in Native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with TE buffer (pH 8). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3) for 30 min at room temperature, and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each ChIP sample, DNA from a matched input control (corresponding to 10% of original ChIP reaction) was purified in the same way.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

treatment_protocol: To induce conditional removal of BAP1, Bap1fl/fl mESCs were treated with 800 nM 4-hydroxytamoxifen (OHT) for 96 hr.

tag: cell line

tag: cell type

value: mouse embryonic stem cells (mESCs)

tag: genotype

value: Bap1fl/fl; Rosa26::ERT2-Cre

tag: clone

tag: strain

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 96 hr

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: ChIP

tag: antibody


title: PLASMA-S-KN-27-06-13

type: RNA

city: Rome

first: Silvia

last: Romano

address: Via di Grottarossa 1035

department: NESMOS

country: Italy

institute: University of Rome La Sapienza

description: miRNAs expression analysis

hyb_protocol: The arrays were stained in the Fluidics Station 450 and then scanned on the GeneChip® Scanner 3000 (Affymetrix, USA)

data_processing: MicroRNA probe outliers were defined from the manufacturer's instructions (Affymetrix), and further analysis included data summarization, normalization and quality control using the web-based miRNA QC Tool software (Affymetrix).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: PLASMA

label_protocol: Labeled RNA from each sample was analyzed by GeneChipmiRNA 2.0 Array (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Blood samples were obtained by venous punctures in EDTA-tubes for plasma preparation. Cell- and platelet-free plasma was prepared following a step centrifugation protocol: samples were centrifuged at 1.500 g for 15′ at 4 °C and supernatant will be stored at −80 °C. RNA was extracted using Plasma/Serum Circulating RNA purification Kit (NORGEN) following the manufacturer’s instructions.

extract_protocol: Cell- and platelet-free plasma was prepared following a step centrifugation protocol: samples were centrifuged at 1.500 g for 15′ at 4 °C and supernatant will be stored at −80 °C. RNA was extracted using Plasma/Serum Circulating RNA purification Kit (NORGEN) following the manufacturer’s instructions. RNA quality and purity were assessed with the use of the RNA 6000 Nano assay on Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: ex-vivo

tag: tissue

value: PLASMA

tag: disease state

value: schizophrenia


title: WT day 9

source_name: wildtype HEK293T cells

value: wildtype HEK293T cells


title: Cas9 Day 8 +Dox


title: PLASMA-SC-MC-20-06-13

description: miRNAs expression analysis

scan_protocol: The arrays were stained in the Fluidics Station 450 and then scanned on the GeneChip® Scanner 3000 (Affymetrix, USA)


title: Cas9 Day 10 -Dox


title: PLASMA-SH-PA-27-06-13

description: miRNAs expression analysis


title: PLASMA-SC-MA-20-06-13

description: miRNAs expression analysis


title: Bap1flfl_ring1b.suz12.XInput_OHT_rep1

description:
BAP1ff_rsXInput_TAM_rep1_S14
processed data file:
mESC_BAP1ff_TAM_ring1b.suz12.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: 12K oligos

source_name: synthetic oligos

value: a pool of 12K synthetic oligos

value: synthetic oligos


title: Bap1flfl_ring1b.suz12.XInput_UNT_rep1

description:
BAP1ff_rsXInput_UNT_rep1_S13
processed data file:
mESC_BAP1ff_UNT_ring1b.suz12.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, gDNA-seq

value: 0 hr


title: Bap1flfl_ring1b.suz12.XInput_UNT_rep2

description:
BAP1ff_rsXInput_UNT_rep2_S15
processed data file:
mESC_BAP1ff_UNT_ring1b.suz12.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: PLASMA-H-MST-27-06-13

description: miRNAs expression analysis

value: healthy


title: Bap1flfl_ring1b.suz12.XInput_UNT_rep3

description:
BAP1ff_rsXInput_UNT_rep3_S17
processed data file:
mESC_BAP1ff_UNT_ring1b.suz12.XInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Cas9 Day 8 -DOX


title: PLASMA-SC-CE-26-06-13

description: miRNAs expression analysis


title: Cas9 Day 2


title: PLASMA-H-MS-27-06-13

description: miRNAs expression analysis


title: PLASMA-HD-PB-20-06-13

description: miRNAs expression analysis


title: PLASMA-HD-RG-20-06-13

description: miRNAs expression analysis


title: WT day 2


title: WT day 8


title: PLASMA-HD-DV-26-06-13

description: miRNAs expression analysis


title: PLASMA-HD-MD-26-06-13

description: miRNAs expression analysis


title: PLASMA-HD-MN-20-06-13

description: miRNAs expression analysis


title: 12K plasmid

source_name: plasmids

value: a pool of 12K plasmids

value: plasmids


title: PLASMA-CH-VL-26-06-13

description: miRNAs expression analysis

value: Huntington disease


title: PRC1CPM_gDNAseq_OHT_rep2

data_processing:
For cnRNA-seq, first, paired-end reads were aligned using Bowtie 2 (with “--very-fast”, “--no-mixed” and “--no-discordant” options) against the concatenated mm10 and dm6 rDNA genomic sequence (GenBank: BK000964.3 and M21017.1) and reads mapping to rDNA were discarded. All unmapped reads were then aligned against the concatenated mm10 and dm6 genome sequences using STAR. Finally, reads that failed to map using STAR were aligned against the mm10+dm6 concatenated genome using Bowtie 2 (with “--sensitive-local”, “--no-mixed” and “--no-discordant” options) to improve mapping of introns. Uniquely aligned reads from the last two steps were combined for further analysis. PCR duplicates were removed using Sambamba. For the corresponding gDNA-seq experiments, paired-end reads were aligned to the concatenated mm10+dm6 genome using Bowtie 2 with the “--no-mixed” and “--no-discordant” options. Only uniquely mapped reads after removal of PCR duplicates with Sambamba were used for downstream analysis.
For visualisation of cnRNA-seq, uniquely aligned mouse reads were internally calibrated using dm6 spike-in as described previously (Fursova et al. 2019). Briefly, mm10 reads were randomly subsampled based on the total number of spike-in (dm6) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding gDNA-seq samples to correct the subsampling factors. After normalisation, read coverages across gene bodies were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates corelated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
For differential gene expression analysis, read counts from individual biological replicates prior to spike-in normalisation were obtained. A custom Perl script utilising SAMtools was used to annotate a custom-built non-redundant mm10 gene set (n = 20633) with read counts. The non-redundant gene set was derived from mm10 refGene genes by removing very short genes with poor sequence mappability and highly similar transcripts.
To identify significant gene expression changes, we used a custom R script that incorporates spike-in calibration into DESeq2 analysis as described previously (Fursova et al. 2019). Briefly, dm6 read counts were obtained for unique dm6 refGene genes to calculate DESeq2 size factors for normalisation of raw mm10 read counts for a custom non-redundant mm10 gene set. Prior to quantification, dm6 reads were pre-normalised using the dm6/mm10 total read ratio in the corresponding gDNA-seq samples in order to account for variations in spike-in cell mixing. For visualisation and ranking of the effect sizes, we performed shrinking of log2-fold changes using the original DESeq2 shrinkage estimator with an adaptive normal distribution as prior. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Genome_build: mm10; dm6
Supplementary_files_format_and_content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary_files_format_and_content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes, and statistical significance levels for a non-redundant set of mm10 refGene genes.

organism:
Drosophila melanogaster
Mus musculus

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (72hr OHT), gDNA-seq

extract_protocol:
For cnRNA-seq, 1×10^7 ESCs (untreated and OHT-treated) were mixed with 4×10^6 Drosophila SG4 cells in 1x PBS. Nuclei were isolated in 1 ml HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF, 3 mM DTT, 1xPIC (Roche)) for 1 min at room temperature, and then recovered by centrifugation at 1000 g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10 mM NaCl, 10 mM Tris pH 8, 3 mM MgCl2). Nuclei integrity was assessed using 0.4% Trypan Blue staining (ThermoScientific). Pelleted nuclei were resuspended in 1 ml of TRIzol reagent (ThermoScientific), and RNA was extracted according to the manufacturer’s protocol, followed by treatment with the TURBO DNA-free Kit (ThermoScientific) to remove any contaminating DNA. Quality of RNA was assessed using the 2100 Bioanalyzer RNA 6000 Pico kit (Agilent). RNA samples were depleted of rRNA with the NEBNext rRNA Depletion kit (NEB) prior to library prep. To quantitate the consistency of spike-in cell mixing for each individual sample, a small aliquot of nuclei was saved to isolate genomic DNA using phenol-chloroform extraction. This was followed by sonication of DNA for 15 min using the BioRuptor Pico (Diagenode), shearing genomic DNA to an average size of less than 1 kb.
cnRNA-seq libraries were prepared using the NEBNext Ultra (for Bap1fl/fl and PRC1CPM) or Ultra II (for PRC1CPM;Bap1fl/fl) Directional RNA Library Prep kit (NEB). Libraries from sonicated genomic DNA were constructed using NEBNext Ultra (for Bap1fl/fl and PRC1CPM) or Ultra II (for PRC1CPM;Bap1fl/fl) DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Both cnRNA-seq and gDNA-seq libraries were sequenced as 80 bp paired-end reads on the Illumina NextSeq 500 platform in biological triplicates.

treatment_protocol: To induce conditional removal of BAP1, on its own or in combination with PRC1 catalytic activity, Bap1fl/fl and PRC1CPM;Bap1fl/fl cells were treated with 800 nM 4-hydroxytamoxifen (OHT) for 96 hr. To induce conditional removal of PRC1 catalytic activity on its own, PRC1CPM cells were treated with 800 nM OHT for 72 hr.

value: 72 hr

value: Drosophila melanogaster


title: PRC1CPM_gDNAseq_OHT_rep1

value: mouse embryonic stem cells (mESCs)


title: PRC1CPM_gDNAseq_OHT_rep3


title: Bap1flfl_SUZ12_ChIPseq_OHT_rep3

description:
BAP1ff_SUZ12_TAM_rep3_S12
processed data file:
mESC_BAP1ff_TAM_SUZ12_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), SUZ12 ChIP-seq

value: Bap1fl/fl; Rosa26::ERT2-Cre

value: Cell Signaling Technology(# D39F6)


title: PRC1CPM_gDNAseq_UNT_rep3

source_name: mESCs with Drosophila spike-in, untreated control, gDNA-seq


title: PLASMA-HD-GG-26-06-13

description: miRNAs expression analysis


title: PRC1CPM_NucRNAseq_OHT_rep3

description:
PRC1_CPM_TAM_RNA_REP3_S19
processed data file:
mESC_PRC1CPM_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw

library_source: transcriptomic

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (72hr OHT), RNA-seq

value: tamoxifen (OHT)


title: PRC1CPM_gDNAseq_UNT_rep2


title: Bap1flfl_SUZ12_ChIPseq_OHT_rep2

description:
BAP1ff_SUZ12_TAM_rep2_S10
processed data file:
mESC_BAP1ff_TAM_SUZ12_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: 96 hr

value: Homo sapiens


title: Bap1flfl_SUZ12_ChIPseq_UNT_rep2

description:
BAP1ff_SUZ12_UNT_rep2_S9
processed data file:
mESC_BAP1ff_UNT_SUZ12_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, SUZ12 ChIP-seq


title: PLASMA-CH-SI-26-06-13

description: miRNAs expression analysis

value: PLASMA


title: PRC1CPM_NucRNAseq_OHT_rep2

description:
PRC1_CPM_TAM_RNA_REP2_S20
processed data file:
mESC_PRC1CPM_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: PRC1CPM_gDNAseq_UNT_rep1


title: Bap1flfl_SUZ12_ChIPseq_OHT_rep1

description:
BAP1ff_SUZ12_TAM_rep1_S8
processed data file:
mESC_BAP1ff_TAM_SUZ12_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: PRC1CPM_NucRNAseq_OHT_rep1

description:
PRC1_CPM_TAM_RNA_REP1_S21
processed data file:
mESC_PRC1CPM_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: PRC1CPM_NucRNAseq_UNT_rep3

description:
PRC1_CPM_UNT_RNA_REP3_S13
processed data file:
mESC_PRC1CPM_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw

source_name: mESCs with Drosophila spike-in, untreated control, RNA-seq


title: Bap1flfl_SUZ12_ChIPseq_UNT_rep1

description:
BAP1ff_SUZ12_UNT_rep1_S7
processed data file:
mESC_BAP1ff_UNT_SUZ12_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_SUZ12_ChIPseq_UNT_rep3

description:
BAP1ff_SUZ12_UNT_rep3_S11
processed data file:
mESC_BAP1ff_UNT_SUZ12_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: PRC1CPM_NucRNAseq_UNT_rep2

description:
PRC1_CPM_UNT_RNA_REP2_S14
processed data file:
mESC_PRC1CPM_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: Bap1flfl_RING1B_ChIPseq_OHT_rep3

description:
BAP1ff_RING1B_TAM_rep3_S10
processed data file:
mESC_BAP1ff_TAM_RING1B_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, tamoxifen-treated (96hr OHT), RING1B ChIP-seq

value: Cell Signaling Technology(# D22F2)


title: PRC1CPM_Bap1flfl_gDNAseq_OHT_rep3

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), gDNA-seq

value: Ring1aI50A/D53K; Ring1b(WT->I53A/D56K)fl/fl; Bap1fl/fl; Rosa26::ERT2-Cre


title: PRC1CPM_NucRNAseq_UNT_rep1

description:
PRC1_CPM_UNT_RNA_REP1_S15
processed data file:
mESC_PRC1CPM_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: Bap1flfl_RING1B_ChIPseq_OHT_rep2

description:
BAP1ff_RING1B_TAM_rep2_S1
processed data file:
mESC_BAP1ff_TAM_RING1B_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: PLASMA-CH-SV-20-06-13

description: miRNAs expression analysis


title: PRC1CPM_Bap1flfl_gDNAseq_UNT_rep3


title: PRC1CPM_Bap1flfl_gDNAseq_OHT_rep1


title: PLASMA-CH-RB-20-06-13

description: miRNAs expression analysis


title: MLO-Y4 cells - Control_rep3

city: Sapporo

first: Mari

last: Sato

address: Kita13 Nishi7 KIta ku

country: Japan

institute: Hokkaido University

description: Bone

data_processing:
Basecalling is performed using Illumina’s RTA version 1.18.64.
Demultiplexing was done using Bcl2fastq v1.8.3.
The sequencing reads were trimmed using Trimmomatic v0.36 with the following options: ILLUMINACLIP:TruSeq3-PE-2.fa:1:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:20:20 MINLEN:50.
Trimmed reads were aligned to the GRCm38 genome assembly using TopHat v2.1.0 and bowtie v2.2.6.0 with the following options: --microexon-search --library-type fr-firststrand.
Aligned reads were used as input for Cuffdiff in Cufflinks v2.1.1 to determine gene expression levels (FPKM) and differential expression. Cuffdiff2 options: --library-type fr-firststrand
Genome_build: GRCm38
Supplementary_files_format_and_content: LIPUS_vs_Control_gene_exp_diff.txt: Tab-delimited text file includes FPKM values and differential expression analysis results for each treatment condition calculated using Cuffdiff; Gene-level differential expression.

organism: Mus musculus

source_name: MLO-Y4 cells - Control

growth_protocol: Cells were maintained in α-modified essential medium (α-MEM) containing 10% fetal bovine serum (FBS) at 37℃ in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol:
Cells were harvested after LIPUS treatment and total RNA was extracted using the spin column kit (Zymo Research).
Libraries were prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit.

treatment_protocol: LIPUS stimulation was given (1.5 MHz, pulsed-wave mode intensity of 30 mW/cm2) for 20 minutes.

value: osteocyte-like cell line

tag: treatment

value: untreated


title: Bap1flfl_RING1B_ChIPseq_OHT_rep1

description:
BAP1ff_RING1B_TAM_rep1_S2
processed data file:
mESC_BAP1ff_TAM_RING1B_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: PLASMA-CH-QM-20-06-13

description: miRNAs expression analysis


title: PRC1CPM_Bap1flfl_NucRNAseq_OHT_rep3

description:
PRC1CPM_BAP1ff_NucRNAseq_Rep4_TAM_S6
processed data file:
mESC_PRC1CPM_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), RNA-seq


title: MLO-Y4 cells - Control_rep2

description: Bone


title: PRC1CPM_Bap1flfl_gDNAseq_UNT_rep1

value: 0 hr


title: PRC1CPM_Bap1flfl_NucRNAseq_OHT_rep2

description:
PRC1CPM_BAP1ff_NucRNAseq_Rep2_TAM_S4
processed data file:
mESC_PRC1CPM_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: PRC1CPM_Bap1flfl_NucRNAseq_OHT_rep1

description:
PRC1CPM_BAP1ff_NucRNAseq_Rep1_TAM_S2
processed data file:
mESC_PRC1CPM_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: PLASMA-CH-FP-27-06-13

description: miRNAs expression analysis


title: PRC1CPM_Bap1flfl_gDNAseq_OHT_rep2


title: MLO-Y4 cells - LIPUS - treated_rep3

description: Bone

source_name: MLO-Y4 cells - LIPUS - treated

value: treated with LIPUS


title: PLASMA-CH-CA-27-06-13

description: miRNAs expression analysis


title: PLASMA-CH-FA-27-06-13

description: miRNAs expression analysis


title: Bap1flfl_RING1B_ChIPseq_UNT_rep2

description:
BAP1ff_RING1B_UNT_rep2_S14
processed data file:
mESC_BAP1ff_UNT_RING1B_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with human HEK293T cells spike-in, untreated control, RING1B ChIP-seq


title: PRC1CPM_Bap1flfl_NucRNAseq_UNT_rep1

description:
PRC1CPM_BAP1ff_NucRNAseq_Rep1_UNT_S1
processed data file:
mESC_PRC1CPM_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: MLO-Y4 cells - Control_rep1

description: Bone


title: PRC1CPM_Bap1flfl_NucRNAseq_UNT_rep3

description:
PRC1CPM_BAP1ff_NucRNAseq_Rep4_UNT_S5
processed data file:
mESC_PRC1CPM_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: Bap1flfl_RING1B_ChIPseq_UNT_rep3

description:
BAP1ff_RING1B_UNT_rep3_S13
processed data file:
mESC_BAP1ff_UNT_RING1B_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_RING1B_ChIPseq_UNT_rep1

description:
BAP1ff_RING1B_UNT_rep1_S1
processed data file:
mESC_BAP1ff_UNT_RING1B_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: PRC1CPM_Bap1flfl_NucRNAseq_UNT_rep2

description:
PRC1CPM_BAP1ff_NucRNAseq_Rep2_UNT_S3
processed data file:
mESC_PRC1CPM_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_PRC1CPM_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: PRC1CPM_Bap1flfl_gDNAseq_UNT_rep2


title: PLASMA-CH-AG-26-06-13

description: miRNAs expression analysis

source_name: PLASMA


title: Bap1flfl_gDNAseq_OHT_rep3

description: 19lib_BAP1ff_rep6_TAM_gDNA_gDNA_NucRNAseq_S16


title: BAT preadipocyte differentiation day 8 EGCG replicate2

city: Xinyang

first: pengpeng

last: Zhang

state: Henan

address: No.237 Nanhu Road Shihe District

country: China

institute: Xinayang Normal University

data_processing:
Quality control of sequences was examined with FastQC version 0.11.9. The clean data were obtained using the Fastp version 0.20.1 to remove reads with adapters, reads containing ploy-N and reads with low quality.
The clean reads were subjected to mapping with Mus musculus mm9 reference genome by HISAT2 version 2.2.0.
The reads numbers mapped to each gene were counted by HTSeq v0.11. The normalized expression level of each gene was calculated by the fragments per kilobase of exon per million reads (FPKM)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BAT preadipocyte

growth_protocol: Primary WAT and BAT SVF cells were isolated using collagenase digestion as we previously described. Briefly, the inguinal WAT and interscapular BAT were collected from 6-week-old mice. Adipose tissue was cut into small pieces and digested with 1.5 mg ml-1 collagenase at 37 ℃ for 30-50 min. The digestions were terminated with DMEM containing 20% FBS, and filtered through 100-μm and 70-μm cells trainer to remove tissue debris. Cells were then centrifuged at 450g for 8 min and SVF cells pellet was resuspend. SVF cells were cultured in growth medium containing 20 % FBS, high glucose DMEM, at 37 ℃ with 5% CO2, culture medium was changed every 2 days. When the cells reached 90 % confluence, they were induced to adipogenic differentiation with induction medium, which contains DMEM, 10% FBS, 2.85 mM insulin, 0.3 mM dexamethasone and 0.63mM 3-isobutyl-methylxanthine for 4 days. Then the medium was switched to differentiation medium which contains DMEM, 10% FBS, 200 nM insulin and 10 nM T3 for another 4 days to induce the mature of adipocytes.

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’ instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EGCG or DMSO was added into the cell medium

value: BAT preadipocyte

tag: time

value: post differentiation day 8

value: EGCG incubation


title: MLO-Y4 cells - LIPUS - treated_rep2

description: Bone


title: MLO-Y4 cells - LIPUS - treated_rep1

description: Bone


title: Bap1flfl_gDNAseq_OHT_rep2

description: 16lib_BAP1ff_rep4_TAM_gDNA_gDNA_NucRNAseq_S18

value: Drosophila melanogaster


title: Bap1flfl_gDNAseq_OHT_rep1

description: 14lib_BAP1ff_rep2_TAM_gDNA_gDNA_NucRNAseq_S20

value: mouse embryonic stem cells (mESCs)


title: BAT preadipocyte differentiation day 8 EGCG replicate1


title: Bap1flfl_gDNAseq_UNT_rep3

description: 18lib_BAP1ff_rep6_UNT_gDNA_gDNA_NucRNAseq_S17

value: Bap1fl/fl; Rosa26::ERT2-Cre


title: Bap1flfl_gDNAseq_UNT_rep2

description: 15lib_BAP1ff_rep4_UNT_gDNA_gDNA_NucRNAseq_S19


title: RNA_10: Scramble_PIC

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

country: USA

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
Raw reads were mapped to human reference genome using STAR (v2.5.4b).
TPM values were calculated using RSEM (v1.2.22).
Genome_build: hg38
Supplementary_files_format_and_content: CSV files showing raw counts and TPM values per gene for each sample.

source_name: myeloid dendritic cells

growth_protocol: Nucleofected mDCs were cultured in RPMI medium (Thermo Fisher Scientific) without antibiotics and supplemented with 10% fetal bovine serum (FBS) (Sigma), 1% l-glutamine (Corning) and 1% HEPES buffer (Corning) for 48 hours.

extract_protocol:
Total RNA from isolated mDCs was extracted and purified using the PicoPure RNA Isolation Kit (Applied Biosystems).
Extracted total RNA were reverse trancribed using SuperScript III reverse transcriptase and amplified. The whole transcriptome amplification (WTA) and tagmentation-based library preparation were performed using Nextera XT (Illumina).

treatment_protocol: Knockdown of the lncRNA MIR4435-2HG was performed by nucleofecting isolated primary mDCs (program CM120, Amaxa 4D-Nucleofector, Lonza) with specific or scramble siRNAs (Horizon Dharmacon) according to the manufacturer’s instructions. Subsequently, the cells were either stimulated with 2µg/ml TLR3 ligand Poly(I:C) (Invivogen) or not given any stimulation (medium only as a negative control) for another 24 hours.

tag: participant

value: Healthy donor

tag: patient id

value: myeloid dendritic cells


title: BAT preadipocyte differentiation day 4 EGCG replicate1

tag: cell type

value: post differentiation day 4


title: Bap1flfl_NucRNAseq_OHT_rep3

description:
6lib_BAP1ff_rep6_TAM_NucRNAseq_S4
processed data file:
mESC_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw

tag: cell line

tag: genotype

value: tamoxifen (OHT)

value: 96 hr


title: BAT preadipocyte differentiation day 4 EGCG replicate2

tag: strain


title: Bap1flfl_gDNAseq_UNT_rep1

description: 13lib_BAP1ff_rep2_UNT_gDNA_gDNA_NucRNAseq_S21

tag: clone

tag: replicate


title: RNA_09: MIR4435-2HGsiRNA_PIC


title: Bap1flfl_NucRNAseq_OHT_rep2

description:
4lib_BAP1ff_rep4_TAM_NucRNAseq_S6
processed data file:
mESC_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw

tag: treatment agent

tag: treatment time point


title: BAT preadipocyte differentiation day 8 control replicate1

value: control


title: Bap1flfl_NucRNAseq_OHT_rep1

description:
2lib_BAP1ff_rep2_TAM_NucRNAseq_S8
processed data file:
mESC_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_BAP1ff_NucRNAseq_TAM_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw

tag: spike-in reference organism

tag: spike-in cell line


title: BAT preadipocyte differentiation day 8 control replicate2


title: Bap1flfl_NucRNAseq_UNT_rep3

description:
5lib_BAP1ff_rep6_UNT_NucRNAseq_S5
processed data file:
mESC_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: Bap1flfl_NucRNAseq_UNT_rep2

description:
3lib_BAP1ff_rep4_UNT_NucRNAseq_S7
processed data file:
mESC_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: Bap1flfl_ATAC.Input_OHT_rep4

description:
BAP1ff_Input_TAM_rep5_S16
processed data file:
mESC_BAP1ff_TAM_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw

data_processing:
For cATAC-seq and gDNA-seq, Bowtie 2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba. Reads mapping to the mitochondrial chromosome and other genomic regions with artificially high counts or low mappability, derived from the ENCODE blacklist, were also discarded.
For visualization of cATAC-seq, the data were internally calibrated using dm6 spike-in as described previously (Turberfield et al. 2019). Briefly, uniquely aligned mm10 reads after filtering were randomly subsampled based on the total number of spike-in (dm6) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding gDNA-seq samples to correct the subsampling factors. After normalisation, read coverages across TSS ± 2.5 kb genomic regions were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Genome_build: mm10; dm6
Supplementary_files_format_and_content: BigWig files were generated using the bamCoverage function from deeptools representing genome coverage of merged spike-in normalised biological replicates.

extract_protocol:
For cATAC-seq, 1×107 ESCs (untreated and OHT-treated) were mixed with 4×106 Drosophila SG4 cells in 1x PBS and then lysed in 1 ml HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF, 3 mM DTT, 1xPIC (Roche)) for 1 min at room temperature. Nuclei were recovered by centrifugation at 1000 g for 5 min at 4°C and washed three times in ice-cold RSB buffer (10 mM NaCl, 10 mM Tris pH 7.4, 3 mM MgCl2). The concentration and integrity of nuclei were assessed using 0.4% Trypan Blue staining (ThermoScientific). Next, 5×105 nuclei were resuspended in Tn5 reaction buffer (10 mM TAPS, 5 mM MgCl2, 10% dimethylformamide) and incubated with Tn5 transposase (25 µM, generated in house as previously described (King and Klose 2017)) for 30 min at 37°C. Tagmented DNA was purified using MinElute columns (QIAGEN) and eluted in 10 μl elution buffer. To control for the Tn5 transposase sequence bias and to determine the exact spike-in ratio for each individual sample, 50 ng of genomic DNA, isolated from the same nuclei preparation by phenol-chloroform extraction, was tagmented with Tn5 transposase (25 µM) for 30 min at 55°C and purified using MinElute columns (QIAGEN).
Libraries for cATAC-seq and gDNA-seq were prepared by PCR amplification using the NEBNext High-Fidelity 2X PCR Master Mix and custom-made Illumina barcodes (Buenrostro et al. 2015). Libraries were purified by two rounds of Agencourt AMPure XP bead cleanup (1.5× bead:sample ratio). The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced using the Illumina NextSeq 500 platform in biological quadruplicate using 80 bp paired-end reads.


title: Bap1flfl_NucRNAseq_UNT_rep1

description:
1lib_BAP1ff_rep2_UNT_NucRNAseq_S15
processed data file:
mESC_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw
mESC_BAP1ff_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw


title: RNA_08: Scramble_PIC


title: RNA_06: Scramble_PIC


title: Bap1flfl_ATAC.Input_OHT_rep2

description:
BAP1ff_Input_TAM_rep3_S12
processed data file:
mESC_BAP1ff_TAM_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: RNA_05: MIR4435-2HGsiRNA_PIC


title: Bap1flfl_ATAC.Input_OHT_rep3

description:
BAP1ff_Input_TAM_rep4_S14
processed data file:
mESC_BAP1ff_TAM_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: BAT preadipocyte differentiation day 4 control replicate1


title: RNA_04: Scramble_PIC


title: Bap1flfl_ATAC.Input_OHT_rep1

description:
BAP1ff_Input_TAM_rep2_S10
processed data file:
mESC_BAP1ff_TAM_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: Bap1flfl_ATAC.Input_UNT_rep4

description:
BAP1ff_Input_UNT_rep5_S15
processed data file:
mESC_BAP1ff_UNT_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: Bap1flfl_ATAC.Input_UNT_rep2

description:
BAP1ff_Input_UNT_rep3_S11
processed data file:
mESC_BAP1ff_UNT_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: WAT preadipocyte differentiation day8 EGCG replicate1

source_name: WAT preadipocyte

value: WAT preadipocyte


title: RNA_03: MIR4435-2HGsiRNA_PIC


title: WAT preadipocyte differentiation day 4 EGCG replicate2


title: Bap1flfl_ATAC.Input_UNT_rep1

description:
BAP1ff_Input_UNT_rep2_S9
processed data file:
mESC_BAP1ff_UNT_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: RNA_02: Scramble_PIC


title: WAT preadipocyte differentiation day8 EGCG replicate2


title: Bap1flfl_ATAC.Input_UNT_rep3

description:
BAP1ff_Input_UNT_rep4_S13
processed data file:
mESC_BAP1ff_UNT_ATAC.Input_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: BAT preadipocyte differentiation day 4 control replicate2


title: Bap1flfl_ATACseq_OHT_rep3

description:
BAP1ff_ATAC_TAM_rep4_S6
processed data file:
mESC_BAP1ff_TAM_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), ATAC-seq


title: WAT preadipocyte differentiation day 4 EGCG replicate1


title: RNA_07: MIR4435-2HGsiRNA_PIC


title: WAT preadipocyte differentiation day 8 control replicate2


title: Bap1flfl_ATACseq_OHT_rep1

description:
BAP1ff_ATAC_TAM_rep2_S2
processed data file:
mESC_BAP1ff_TAM_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: Bap1flfl_ATACseq_UNT_rep4

description:
BAP1ff_ATAC_UNT_rep5_S7
processed data file:
mESC_BAP1ff_UNT_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw

source_name: mESCs with Drosophila spike-in, untreated control, ATAC-seq


title: WAT preadipocyte differentiation day 8 control replicate1


title: ChIP_32: Healthy donor 09 mDC IgG

data_processing:
Library strategy: CUT&RUN
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (hg38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Genome_build: hg38

growth_protocol: The cells were not cultured.

extract_protocol:
Briefly, isolated mDCs from ECs and HIVNs were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac, H3K27me3 and H3K4me3 histone marks (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

treatment_protocol: The cells were not treated.

tag: chip antibody

value: IgG

tag: patient phenotype

tag: participant id


title: ChIP_31: Healthy donor 09 mDC H3K4me3

tag: tissue


title: Bap1flfl_ATACseq_UNT_rep2

description:
BAP1ff_ATAC_UNT_rep3_S3
processed data file:
mESC_BAP1ff_UNT_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: Bap1flfl_ATACseq_UNT_rep3

description:
BAP1ff_ATAC_UNT_rep4_S5
processed data file:
mESC_BAP1ff_UNT_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: WAT preadipocyte differentiation day 4 control replicate2

tag: time

tag: treatment


title: Bap1flfl_ATACseq_UNT_rep1

description:
BAP1ff_ATAC_UNT_rep2_S1
processed data file:
mESC_BAP1ff_UNT_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_OHT_rep4

description:
mESC_Bap1ff_TAM_input_rep4_S8
processed data file:
mESC_BAP1ff_TAM_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: ChIP

tag: antibody


title: ChIP_30: Healthy donor 09 mDC H3K27ac


title: WAT preadipocyte differentiation day 4 control replicate1

tag: cell type


title: ChIP_29: Healthy donor 09 mDC H3K27me3


title: ChIP_28: Healthy donor 08 mDC IgG


title: Bap1flfl_ATACseq_OHT_rep2

description:
BAP1ff_ATAC_TAM_rep3_S4
processed data file:
mESC_BAP1ff_TAM_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw

tag: cell line

tag: genotype


title: Hira_KO_rep3

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

data_processing:
FASTQ groomer tool  (https://usegalaxy.org)
BOWTIE2 v2.3.4.2  (https://usegalaxy.org)
featureCounts v1.6.3+galaxy2 (https://usegalaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 v2.11.40.6+galaxy1 (https://usegalaxy.org)

growth_protocol: C2C12 control and C2C12 Hira KO cell lines were collected when grown in high serum medium at low density (proliferating conditions)

extract_protocol:
C2C12 cells were collected for RNA extraction using Machery Nagel NucleoSpin RNA purification kit
Libraries were prepared with TruSeq Stranded Total RNA Sample preparation kit according to supplier recommendations. Briefly, the key stages of this protocol are successively, the removal of ribosomal RNA fraction from 1µg of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing

tag: strain source

value: skeletal muscle cell line

value: Hira -/-


title: Hira_KO_rep2


title: ChIP_27: Healthy donor 08 mDC H3K4me3


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_UNT_rep3

description:
mESC_Bap1ff_UNT_input_rep3_S3
processed data file:
mESC_BAP1ff_UNT_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: clone

tag: strain

tag: replicate

value: 0 hr


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_OHT_rep2

description:
mESC_Bap1ff_TAM_input_rep2_S6
processed data file:
mESC_BAP1ff_TAM_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: treatment agent

tag: treatment time point

tag: spike-in reference organism


title: Hira_KO_rep1


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_OHT_rep1

description:
mESC_Bap1ff_TAM_input_rep1_S5
processed data file:
mESC_BAP1ff_TAM_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: spike-in cell line


title: Bap1flfl_ATACseq_OHT_rep4

description:
BAP1ff_ATAC_TAM_rep5_S8
processed data file:
mESC_BAP1ff_TAM_ATAC_mm10.UniqMapped_sorted_rmdup_filtered_downsampled_MERGED.Coverage.bw


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_UNT_rep1

description:
mESC_Bap1ff_UNT_input_rep1_S1
processed data file:
mESC_BAP1ff_UNT_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_UNT_rep2

description:
mESC_Bap1ff_UNT_input_rep2_S2
processed data file:
mESC_BAP1ff_UNT_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_UNT_rep4

description:
mESC_Bap1ff_UNT_input_rep4_S4
processed data file:
mESC_BAP1ff_UNT_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: RNA_01: MIR4435-2HGsiRNA_PIC

tag: participant

tag: patient id


title: ChIP_26: Healthy donor 08 mDC H3K27ac

tag: chip antibody

tag: patient phenotype

tag: participant id

tag: tissue


title: Bap1flfl_H3K4me1_ChIPseq_OHT_rep4

description:
BAP1ff_TAM_Rep4_H3K4me1_ChIPseq_S8
processed data file:
mESC_BAP1ff_TAM_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), H3K4me1 ChIP-seq

tag: cell type

tag: ChIP

tag: antibody

value: Cell Signaling Technology(#D1A9)


title: Bap1flfl_H3K4me1_ChIPseq_OHT_rep2

description:
BAP1ff_TAM_Rep2_H3K4me1_ChIPseq_S4
processed data file:
mESC_BAP1ff_TAM_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: cell line

tag: genotype


title: Bap1flfl_H3K4me1_ChIPseq_OHT_rep3

description:
BAP1ff_TAM_Rep3_H3K4me1_ChIPseq_S6
processed data file:
mESC_BAP1ff_TAM_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: clone

tag: strain


title: ChIP_25: Healthy donor 08 mDC H3K27me3


title: Bap1flfl_H3K4me1_ChIPseq_UNT_rep4

description:
BAP1ff_UNT_Rep4_H3K4me1_ChIPseq_S7
processed data file:
mESC_BAP1ff_UNT_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, H3K4me1 ChIP-seq

tag: replicate

tag: treatment agent


title: ChIP_24: Elite controller 01 mDC IgG

value: Elite controller


title: Bap1flfl_k27ac.k4me3.k4me1.NInput_ChIPseq_OHT_rep3

description:
mESC_Bap1ff_TAM_input_rep3_S7
processed data file:
mESC_BAP1ff_TAM_k27ac.k4me3.k4me1.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: treatment time point

tag: spike-in reference organism


title: Bap1flfl_H3K4me1_ChIPseq_UNT_rep3

description:
BAP1ff_UNT_Rep3_H3K4me1_ChIPseq_S5
processed data file:
mESC_BAP1ff_UNT_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: spike-in cell line


title: Bap1flfl_H3K4me1_ChIPseq_OHT_rep1

description:
BAP1ff_TAM_Rep1_H3K4me1_ChIPseq_S2
processed data file:
mESC_BAP1ff_TAM_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: C2C12_rep1

tag: strain source

value: WT


title: Bap1flfl_H3K4me1_ChIPseq_UNT_rep2

description:
BAP1ff_UNT_Rep2_H3K4me1_ChIPseq_S3
processed data file:
mESC_BAP1ff_UNT_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: Drosophila melanogaster


title: Bap1flfl_H3K4me1_ChIPseq_UNT_rep1

description:
BAP1ff_UNT_Rep1_H3K4me1_ChIPseq_S1
processed data file:
mESC_BAP1ff_UNT_H3K4me1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: mouse embryonic stem cells (mESCs)


title: ChIP_23: Elite controller 01 mDC H3K4me3

tag: chip antibody


title: Hira_KO_input

data_processing:
FASTQ groomer tool  (https://usegalaxy.org)
BOWTIE2 v2.3.4.2  (https://usegalaxy.org)
MACS2 v2.1.1.2 using paired-end BAM files with the cutoff q-value 5-e2 and the broad region calling off, the input was used as control (https://usegalaxy.org)
ChIPseeker v1.18.0 (https://usegalaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 resulting bedgraph file was converted to bigwig format using the wig/bedgraph-to-bigwig converter v1.1.1 (https://usegalaxy.org)

extract_protocol:
Cells were subjected to nuclei isolation, chromatin fragmentation using Micrococcal Nuclease and nucleosome purification by Hydroxyapatite. Immunoprecipitation was performed overnight at 4°C with 6μg of chromatin and 5μg of antibody previously incubated with Protein-A- (for H3K27ac, H3K4me3, H3K27me3 antibodies) or Protein-G-coated (for H3.3 antibody) magnetic beads.
Library was prepared using KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (Roche, 07962363001) with IDT for Illumina TruSeq DNA-RNA UD 96 Indexes (UDI) (Illumina, 2023784) and quantified by RT-qPCR using NEBNext Library Quant Kit for Illumina (NEB, E7640AA). Sequencing was carried out on paired-end 50bp of Illumina HiSeq4000.


title: ChIP_22: Elite controller 01 mDC H3K27ac

tag: patient phenotype


title: Bap1flfl_H3K4me3_ChIPseq_OHT_rep3

description:
mESC_Bap1ff_TAM_H3K4me3_rep3_S11
processed data file:
mESC_BAP1ff_TAM_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), H3K4me3 ChIP-seq

value: Bap1fl/fl; Rosa26::ERT2-Cre

value: In house (Farcas, 2012)


title: Hira_KO_H3K27me3

value: H3K27me3, Cell Signalling, 9733, Lot 8


title: Bap1flfl_H3K4me3_ChIPseq_OHT_rep4

description:
mESC_Bap1ff_TAM_H3K4me3_rep4_S12
processed data file:
mESC_BAP1ff_TAM_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_H3K4me3_ChIPseq_OHT_rep1

description:
mESC_Bap1ff_TAM_H3K4me3_rep1_S9
processed data file:
mESC_BAP1ff_TAM_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: C2C12_rep3


title: Hira_KO_H3K27ac


title: ChIP_21: Elite controller 01 mDC H3K27me3

tag: participant id

value: myeloid dendritic cells


title: ChIP_20: Elite controller 04 mDC IgG

tag: tissue


title: Bap1flfl_H3K4me3_ChIPseq_OHT_rep2

description:
mESC_Bap1ff_TAM_H3K4me3_rep2_S10
processed data file:
mESC_BAP1ff_TAM_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: cell type

value: tamoxifen (OHT)


title: Bap1flfl_H3K4me3_ChIPseq_UNT_rep4

description:
mESC_Bap1ff_UNT_H3K4me3_rep4_S16
processed data file:
mESC_BAP1ff_UNT_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, H3K4me3 ChIP-seq

tag: ChIP


title: Bap1flfl_H3K4me3_ChIPseq_UNT_rep3

description:
mESC_Bap1ff_UNT_H3K4me3_rep3_S15
processed data file:
mESC_BAP1ff_UNT_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: antibody


title: C2C12_rep2

tag: cell line


title: Bap1flfl_H3K4me3_ChIPseq_UNT_rep1

description:
mESC_Bap1ff_UNT_H3K4me3_rep1_S13
processed data file:
mESC_BAP1ff_UNT_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: genotype


title: Hira_KO_H3.3

value: H3.3 (CosmoBio, CE-040B, Lot MA-002)


title: Bap1flfl_H3K4me3_ChIPseq_UNT_rep2

description:
mESC_Bap1ff_UNT_H3K4me3_rep2_S14
processed data file:
mESC_BAP1ff_UNT_H3K4me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: clone


title: Bap1flfl_H3K27ac_ChIPseq_OHT_rep4

description:
mESC_Bap1ff_TAM_H3K27Ac_rep4_S24
processed data file:
mESC_BAP1ff_TAM_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), H3K27ac ChIP-seq

tag: strain

value: 96 hr

value: Cell Signaling Technology(#D5E4)


title: C2C12_input


title: Bap1flfl_H3K27ac_ChIPseq_OHT_rep3

description:
mESC_Bap1ff_TAM_H3K27Ac_rep3_S23
processed data file:
mESC_BAP1ff_TAM_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: replicate


title: ChIP_18: Elite controller 04 mDC H3K27ac


title: C2C12_H3K27me3


title: ChIP_17: Elite controller 04 mDC H3K27me3


title: Hira_KO_H3K4me3

value: H3K4me3 (Merck Millipore, 07-473, Lot 3018770


title: ChIP_16: Healthy donor 06 mDC IgG

value: IgG

value: Healthy donor


title: Bap1flfl_H3K27ac_ChIPseq_OHT_rep2

description:
mESC_Bap1ff_TAM_H3K27Ac_rep2_S22
processed data file:
mESC_BAP1ff_TAM_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: treatment agent


title: Bap1flfl_H3K27ac_ChIPseq_OHT_rep1

description:
mESC_Bap1ff_TAM_H3K27Ac_rep1_S21
processed data file:
mESC_BAP1ff_TAM_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: treatment time point


title: C2C12_H3K4me3

value: skeletal muscle cell line


title: ChIP_15: Healthy donor 06 mDC H3K4me3


title: Bap1flfl_H3K27ac_ChIPseq_UNT_rep4

description:
mESC_Bap1ff_UNT_H3K27Ac_rep4_S20
processed data file:
mESC_BAP1ff_UNT_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, H3K27ac ChIP-seq

value: 0 hr

tag: spike-in reference organism


title: Bap1flfl_H3K27ac_ChIPseq_UNT_rep3

description:
mESC_Bap1ff_UNT_H3K27Ac_rep3_S19
processed data file:
mESC_BAP1ff_UNT_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: spike-in cell line


title: ChIP_19: Elite controller 04 mDC H3K4me3

value: Elite controller


title: ChIP_14: Healthy donor 06 mDC H3K27ac


title: Bap1flfl_H3K27ac_ChIPseq_UNT_rep1

description:
mESC_Bap1ff_UNT_H3K27Ac_rep1_S17
processed data file:
mESC_BAP1ff_UNT_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_k27me3.NInput_ChIPseq_OHT_rep4

description:
Lib22_Bap1_TAM_k27me3.NInput_Rep5_S17
processed data file:
mESC_BAP1ff_TAM_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT),gDNA-seq


title: Bap1flfl_k27me3.NInput_ChIPseq_OHT_rep3

description:
BAP1_TAM_k27me3.NInput_rep3_S11
processed data file:
mESC_BAP1ff_TAM_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_k27me3.NInput_ChIPseq_OHT_rep1

description:
BAP1_TAM_k27me3.NInput_rep1_S3
processed data file:
mESC_BAP1ff_TAM_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_k27me3.NInput_ChIPseq_OHT_rep2

description:
BAP1_TAM_k27me3.NInput_rep2_S7
processed data file:
mESC_BAP1ff_TAM_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: ChIP_13: Healthy donor 06 mDC H3K27me3


title: C2C12_H3.3

value: WT


title: ChIP_11: Healthy donor 07 mDC H3K4me3


title: Bap1flfl_k27me3.NInput_ChIPseq_UNT_rep4

description:
Lib20_Bap1_UNT_k27me3.NInput_Rep5_S15
processed data file:
mESC_BAP1ff_UNT_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control,gDNA-seq

value: Drosophila melanogaster


title: ChIP_12: Healthy donor 07 mDC IgG


title: C2C12_H3K27ac


title: Bap1flfl_k27me3.NInput_ChIPseq_UNT_rep3

description:
BAP1_UNT_k27me3.NInput_rep3_S9
processed data file:
mESC_BAP1ff_UNT_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: mouse embryonic stem cells (mESCs)


title: Bap1flfl_k27me3.NInput_ChIPseq_UNT_rep2

description:
BAP1_UNT_k27me3.NInput_rep2_S5
processed data file:
mESC_BAP1ff_UNT_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: Bap1fl/fl; Rosa26::ERT2-Cre


title: Bap1flfl_H3K27me3_ChIPseq_OHT_rep4

description:
Lib27_Bap1_TAM_K27_Rep5_S20
processed data file:
mESC_BAP1ff_TAM_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), H3K27me3 ChIP-seq

value: In house (Rose, 2016)


title: Bap1flfl_H3K27ac_ChIPseq_UNT_rep2

description:
mESC_Bap1ff_UNT_H3K27Ac_rep2_S18
processed data file:
mESC_BAP1ff_UNT_H3K27ac_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: ChIP_10: Healthy donor 07 mDC H3K27ac


title: Bap1flfl_H3K27me3_ChIPseq_OHT_rep3

description:
BAP1_TAM_H3K27me3_rep3_S18
processed data file:
mESC_BAP1ff_TAM_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Rep3_RenHSC_RNAseq.fastq.gz

city: Chicago

first: Megan

last: McNerney

state: IL

address: 900 E 57th St

department: Pathology

institute: The University of Chicago

data_processing:
RNAseq: FastQC was used for quality checking; the sequenced reads were aligned to the mouse genome (UCSC mm10) with STAR aligner (Dobin et al 2013), and alignments with a mapping quality <30 were removed.
RNAseq: Differential gene expression analysis was performed using DESeq2 (Love, Huber and Anders, 2014), and a negative binomial general linearized model fitting and Wald statistics were used to generate p values, with p values adjusted using the Benjamini Hochberg method
ChIP-seq: Sequencing reads were aligned to the human hg19 genome using BWA (version 0.7.12) (Li and Durbin, 2009) and low quality leads were removed using the SAMtools q30 filter (Li and Durbin, 2009)
ChIP-seq: Peaks were called using MACS2 (Zhang et al., 2008) with a q value threshold of 0.05
ChIP-seq: For differential peak calling, Diffbind (Stark and Brown, 2011) software was applied using an FDR cutoff of 0.10
ChIP-seq: The average read density from two biological replicates was normalized by RPKM in 50bp bins and visualized using the Deeptools software (Ramírez et al, 2016)
Genome_build: mm10, hg19
Supplementary_files_format_and_content: RNA-seq: DESeq2-generated rlog normalized read counts for each gene
Supplementary_files_format_and_content: CHIP-seq: bigWig files generated using bedGraphtoBigWig; peak text files

source_name: Bone Marrow HSCs (Lin-, Sca1+, Kit+, CD135-)

growth_protocol: K562 cells were single-cell cloned after knockdown of HPRT (control) or CUX1 as indicated, and CHIP-seq was performed. Mice were treated with doxycycline for five days, HSCs were sorted from the bone marrow and RNA was extracted.

extract_protocol:
RNA was isolated from bone marrow cells with Trizol and collected on RNeasy Micro columns
DNA after ChIP protocol was isolated using QIAquick PCR purification column (Qiagen)
RNA libraries were constructed using Illumina's TruSEQ kit; CHIP-seq libraries were constucted using Ovation Ultralow Library Kit (NuGEN)

treatment_protocol: Mice were treated for five days with doxycycline in vivo

tag: crispr guide

tag: shRNA

value: Renilla

tag: treatment

value: Five days of doxycycline


title: Rep2_RenHSC_RNAseq.fastq.gz


title: Rep3_LowHSC_RNAseq.fastq.gz


title: Bap1flfl_H3K27me3_ChIPseq_OHT_rep2

description:
BAP1_TAM_H3K27me3_rep2_S16
processed data file:
mESC_BAP1ff_TAM_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

value: tamoxifen (OHT)


title: Rep2_LowHSC_RNAseq.fastq.gz


title: ChIP_09: Healthy donor 07 mDC H3K27me3

tag: chip antibody

tag: patient phenotype

tag: participant id

value: myeloid dendritic cells


title: Bap1flfl_H3K27me3_ChIPseq_UNT_rep4

description:
Lib25_Bap1_UNT_K27_Rep5_S19
processed data file:
mESC_BAP1ff_UNT_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, H3K27me3 ChIP-seq

tag: cell type

tag: ChIP


title: Rep1_RenHSC_RNAseq.fastq.gz


title: Bap1flfl_H3K27me3_ChIPseq_UNT_rep2

description:
BAP1_UNT_H3K27me3_rep2_S15
processed data file:
mESC_BAP1ff_UNT_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: cell line

tag: antibody


title: ChIP_08: Elite controller 03 mDC IgG

tag: tissue


title: Bap1flfl_H3K27me3_ChIPseq_UNT_rep3

description:
BAP1_UNT_H3K27me3_rep3_S17
processed data file:
mESC_BAP1ff_UNT_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: genotype

tag: clone

tag: strain


title: Rep1_LowHSC_RNAseq.fastq.gz


title: ChIP_07: Elite controller 03 mDC H3K4me3


title: Bap1flfl_k27me3.NInput_ChIPseq_UNT_rep1

description:
BAP1_UNT_k27me3.NInput_rep1_S1
processed data file:
mESC_BAP1ff_UNT_k27me3.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: replicate

tag: treatment agent

tag: treatment time point


title: Bap1flfl_uH2A.NInput_OHT_rep2

description:
BAP1ff_TAM_Rep3_NativeInput_S10
processed data file:
mESC_BAP1ff_TAM_uH2A.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), gDNA-seq

value: 96 hr

tag: spike-in reference organism

tag: spike-in cell line


title: Bap1flfl_H3K27me3_ChIPseq_UNT_rep1

description:
BAP1_UNT_H3K27me3_rep1_S13
processed data file:
mESC_BAP1ff_UNT_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_uH2A.NInput_OHT_rep3

description:
BAP1ff_TAM_Rep4_NativeInput_S12
processed data file:
mESC_BAP1ff_TAM_uH2A.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: ChIP_06: Elite controller 03 mDC H3K27ac


title: Bap1flfl_uH2A.NInput_OHT_rep1

description:
BAP1ff_TAM_Rep1_NativeInput_S8
processed data file:
mESC_BAP1ff_TAM_uH2A.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: ChIP_05: Elite controller 03 mDC H3K27me3


title: Bap1flfl_uH2A.NInput_UNT_rep3

description:
BAP1ff_UNT_Rep4_NativeInput_S11
processed data file:
mESC_BAP1ff_UNT_uH2A.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, gDNA-seq


title: Bap1flfl_uH2A.NInput_UNT_rep2

description:
BAP1ff_UNT_Rep3_NativeInput_S9
processed data file:
mESC_BAP1ff_UNT_uH2A.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_H3K27me3_ChIPseq_OHT_rep1

description:
BAP1_TAM_H3K27me3_rep1_S14
processed data file:
mESC_BAP1ff_TAM_H3K27me3_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_H2AK119ub1_ChIPseq_OHT_rep3

description:
BAP1ff_TAM_Rep4_H2AK119ub1_ChIPseq_S6
processed data file:
mESC_BAP1ff_TAM_H2AK119ub1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, tamoxifen-treated (96hr OHT), H2AK119ub1 ChIP-seq

value: Cell Signaling Technology(#D27C4 )


title: Bap1flfl_H2AK119ub1_ChIPseq_OHT_rep1

description:
BAP1ff_TAM_Rep1_H2AK119ub1_ChIPseq_S2
processed data file:
mESC_BAP1ff_TAM_H2AK119ub1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_H2AK119ub1_ChIPseq_OHT_rep2

description:
BAP1ff_TAM_Rep3_H2AK119ub1_ChIPseq_S4
processed data file:
mESC_BAP1ff_TAM_H2AK119ub1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw


title: Bap1flfl_H2AK119ub1_ChIPseq_UNT_rep3

description:
BAP1ff_UNT_Rep4_H2AK119ub1_ChIPseq_S5
processed data file:
mESC_BAP1ff_UNT_H2AK119ub1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq


title: Dupuytren’s Disease 3

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Library strategy: scRNA-seq (10x)
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Quality control, normalisation, data integration, and downstream analysis using Seurat 3.2.3
Supplementary_files_format_and_content: fastq: fastq files of individual samples; mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample

source_name: Dupuytren's disease tissue

extract_protocol:
Enzymatic digestion followed by FACS of live (DAPI-) single cells
10x Genomics single cell 3' gene expression v2 / v3

tag: source

value: Dupuytren's disease tissue

tag: condition

value: Dupuytren's disease


title: Skoog’s Fascia 3

description: 10x Genomics single cell 3' gene expression v3

source_name: Skoog's fascia

value: Skoog's fascia

value: Healthy


title: ChIP_04: Elite controller 02 mDC IgG

source_name: myeloid dendritic cells

tag: chip antibody

value: IgG

tag: patient phenotype


title: Dupuytren’s Disease 2

description: 10x Genomics single cell 3' gene expression v2


title: Dupuytren’s Disease 1


title: ChIP_03: Elite controller 02 mDC H3K4me3

value: Elite controller

tag: participant id


title: ChIP_01: Elite controller 02 mDC H3K27me3


title: Skoog's Fascia 1


title: Bap1flfl_H2AK119ub1_ChIPseq_UNT_rep2

description:
BAP1ff_UNT_Rep3_H2AK119ub1_ChIPseq_S3
processed data file:
mESC_BAP1ff_UNT_H2AK119ub1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

tag: cell type

value: 0 hr

tag: ChIP


title: Neutrophils from healthy donor HD4

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

description:
HD4_neutros
mRNA-3' from neutrophils sorted from healthy donor

data_processing:
FASTQ polyA trimming
STAR alignment (version 2.7.3a): outFilterMismatchNmax 1, alignEndsType EndToEnd
Gene counts performed using quant3p
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix counts. Each column corresponds to gene counts for each generated BAM (after merging all resequenced samples and downsampled to 10 millions of reads for each one).

source_name: Neutrophils from peripheral blood

extract_protocol:
Cells were FACSorted in Lysis Binding Buffer and mRNA was extracted through Dynabeads polyT
RNA was sample-barcodad by a RT reaction. After, cDNA was purified with SPRIselect and amplified using the T7 promotor as template. RNA molecules were fragmented and purified again. Afterwards, a ssRNA adaptor was ligated to the 3’-end of the RNA fragments and, finally, cDNA was amplified.

tag: individual

value: healthy donor HD4

tag: covid status

value: Healthy donor

tag: gender

value: Female

tag: age

tag: hospitalization

value: No

tag: exitus

tag: haematological tumor

value: peripheral blood

value: Neutrophils

tag: number of cells


title: Sample_J1510_MODEL2_2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome mm10 by HISAT2 aligner (version 2.1.0)
Gene counts were quantified by htseq-count (version 0.11.2)
wig files were generated using Python
Genome_build: mm10
Supplementary_files_format_and_content: wig file, Gene counts file

source_name: mouse liver

growth_protocol: normal diet

extract_protocol:
RNA were extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the model 1 mice were co-expressed NFE2L2 G31A,CTNNB1 T41A  and sleeping beauty transponsa (20ug,20ug,1,6ug)  at 2 ml saline with hydradymanic tail vein injection, or the model 2 mice were co-expressed NFE2L2 T80K , CTNNB1 T41A(20ug,20ug)and sleeping beauty transponsa (20ug,20ug,1,6ug)  at 2  ml saline with hydradymanic tail vein injection

tag: model

value: MODEL2 (NFE2L2 T80K + CTNNB1 T41A)

value: 20 weeks

tag: strain

value: FVB

tag: Sex

value: male

tag: tissue

value: liver


title: Dermis 3

source_name: Healthy dermis

tag: source

value: Healthy dermis

tag: condition


title: Dermis 2


title: ChIP_02: Elite controller 02 mDC H3K27ac

tag: chip antibody

tag: patient phenotype

tag: participant id

value: myeloid dendritic cells


title: Neutrophils from healthy donor HD2

description:
HD2_neutros
mRNA-3' from neutrophils sorted from healthy donor

tag: individual

value: healthy donor HD2

value: Male

tag: cell type


title: Dermis 1

value: Healthy


title: Sample_J1509_MODEL2_1

value: 19 weeks


title: Sample_J1505_MODEL1_1

value: MODEL1 (NFE2L2 G31A + CTNNB1 T41A)

value: 18 weeks


title: Sample_J1506_MODEL1_2


title: Skoog’s Fascia 2

value: Skoog's fascia


title: Sample_FVbm17w_CTRL_3

value: CTRL

value: 17 weeks


title: UC4, Whole mucosa (colon)

city: Kiel

first: Celia

last: Escudero-Hernández

state: Schleswig-Holstein

address: Institute of Clinical Molecular Biology (IKMB), Am Bota

department: Dep. Cell Biology

country: Germany

institute: University Hospital Schleswig-Holstein

data_processing:
FASTQ files were generated using bcl2fastq software v2.18. Data was analyzed using the R Bioconductor software v3.5.1 (R Core Team 2018), including SARTools v1.6.6 and DESeq2 v1.22.1 packages
Differential gene expression (DGE) from RNA-seq data was determined with linear models using DESeq2 v1.22.1 and significance decided by Benjamini-Hochberg false discovery rate (FDR) adjusted p-values <0.05
Genome_build: Ensembl GRCh38 genome version, release 92
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole mucosa (colon)

extract_protocol:
Biopsies were homogenized in RLT buffer from RNeasy Mini Kit (Qiagen, Hilden, Germany) supplemented with 1% 2-mercaptoethanol using a T10 Ultra Turrax homogenizer (IKA, ThermoFisher Scientific). Total RNA from homogenized biopsy samples was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions
RNA sequencing libraries were constructed with SENSE totalRNA with Ribo cop rRNA depletion (Lexogene GmbH, Vienna, Austria), and single-read sequenced for 75 cycles to a depth of 25 million base reads on a HiSeq4000 instrument (Illumina, San Diego, CA), according to the manufacturer’s recommendations

value: colon

tag: disease activity

value: Active ulcerative colitis

tag: treatment

tag: gender

value: female


title: Neutrophils from healthy donor HD1

description:
HD1_neutros
mRNA-3' from neutrophils sorted from healthy donor

value: healthy donor HD1

tag: covid status

value: Healthy donor

value: Female

tag: age

tag: hospitalization

value: No

tag: exitus

value: peripheral blood

value: Neutrophils


title: UC3, Whole mucosa (colon)

value: male


title: Sample_J1512_MODEL2_3

tag: model

value: MODEL2 (NFE2L2 T80K + CTNNB1 T41A)

value: 22 weeks

tag: strain

value: FVB

value: liver


title: P56_Donor1_scRNA-seq

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: 10X single-nuclei

data_processing:
The Cell Ranger (v.3.0.2) pipeline from 10X Genomics was used.
"cellranger mkfastq" was used to demultiplex the raw base call files and create FASTQ files.
"celllranger count" was used to align, filter, and generate count matrices from the FASTQ files.
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab-delimited text file with columns as genes, rows as cells.

extract_protocol:
All hippocampal tissues in this study were obtained from patients with temporal lobe epilepsy with the informed consent of patients and approval of the UTSW Institutional Review Board (IRB).
Followed 10X Genomics kit manufacturer guidelines.

treatment_protocol: Surgically resected cortical tissue was homogenized using a glass Dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 500 μl of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich). Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer were first mixed in a 9:1 ratio. 500 μl of the resulting sucrose buffer was added to a 2 ml Eppendorf tube. 900 μl of the sucrose buffer was added to 500 μl of isolated nuclei in NSB. 1400 μl nuclei suspension was layered to the top of the sucrose buffer. This gradient was centrifuged at 13, 000 x g for 45 min at 4 °C. Nuclei pellet was resuspended and washed once in NSB. Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). A final concentration of 1000 nuclei/μl was adjusted with NSB.

tag: tissue

value: Posterior hippocampus

tag: age (yr)

tag: Sex

tag: race

value: White

tag: hemisphere

value: left

tag: epilepsy duration (yr)

tag: rin

tag: batch

tag: protocol

value: Protocol 1


title: aRCC9, Whole mucosa (colon)

value: colon

tag: disease activity

value: Active CC

tag: treatment


title: Neutrophils from healthy donor HD3

description:
HD3_neutros
mRNA-3' from neutrophils sorted from healthy donor

tag: individual

value: healthy donor HD3

tag: covid status

tag: gender

value: Male

tag: haematological tumor

tag: cell type

tag: number of cells


title: UC1, Whole mucosa (colon)

tag: tissue

value: Active ulcerative colitis

value: female

tag: age


title: P67_Donor3_scRNA-seq

description: 10X single-nuclei

tag: age (yr)

tag: Sex

value: African American

value: right


title: P57_Donor2_scRNA-seq

description: 10X single-nuclei

value: Female

tag: race

tag: hemisphere


title: UC2, Whole mucosa (colon)


title: A82_Donor5_scRNA-seq

description: 10X single-nuclei

value: Anterior hippocampus

tag: epilepsy duration (yr)

tag: rin


title: Non-classical monocytes from healthy donor HD3

description:
HD3_monosNC
mRNA-3' from non-classical monocytes sorted from healthy donor

source_name: Non-classical monocytes from peripheral blood

value: Healthy donor

tag: hospitalization

value: No

tag: exitus

value: peripheral blood

value: Non-classical monocytes


title: Sample_J1507_MODEL1_3

tag: model

value: MODEL1 (NFE2L2 G31A + CTNNB1 T41A)

value: 18 weeks

tag: strain

value: FVB

value: male

value: liver


title: aRCC8, Whole mucosa (colon)

value: colon

tag: disease activity

value: Active CC

tag: treatment


title: Classical monocytes from healthy donor HD3

description:
HD3_monos
mRNA-3' from classical monocytes sorted from healthy donor

source_name: Classical monocytes from peripheral blood

tag: individual

value: healthy donor HD3

tag: covid status

tag: gender

value: Male

tag: haematological tumor

value: Classical monocytes


title: A67_Donor3_scRNA-seq

description: 10X single-nuclei

tag: tissue

value: African American

value: right

tag: batch

tag: protocol

value: Protocol 1


title: Adult colony, Settling_polyps, Swimming larva scRNAseq

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

data_processing:
.Read_1 files were mapped into Stylophora genome assembly v1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_002571385.1/) using STARR, using default parameters. Read_1 files from adult sample were also map against Symbiodinium microadriaticum genome (http://smic.reefgenomics.org/), in order to detect symbiont expression in algal-bearing coral host cells.
.Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4). Pipeline can be found: http://compgenomics.weizmann.ac.il/tanay/?page_id=672

molecule: polyA RNA

organism: Stylophora pistillata

extract_protocol: .MARS-seq was performed as described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4)

tag: stage/cell type

value: Adult colony

value: Wild type


title: aRCC7, Whole mucosa (colon)

value: female

tag: age


title: Sample_FVbm13w-2_CTRL_2

value: CTRL

value: 13 weeks

tag: Sex


title: P76_Donor4_scRNA-seq

description: 10X single-nuclei

value: Posterior hippocampus

tag: age (yr)

tag: race

value: White

tag: hemisphere

value: left

tag: epilepsy duration (yr)

tag: rin


title: Sample_FVbm13w-1_CTRL_1

tag: model

tag: strain

value: FVB

value: male

value: liver


title: P82_Donor5_scRNA-seq

description: 10X single-nuclei

value: Female


title: Classical monocytes from healthy donor HD4

description:
HD4_monos
mRNA-3' from classical monocytes sorted from healthy donor

tag: individual

value: healthy donor HD4

value: Healthy donor

tag: hospitalization

value: No

tag: exitus

value: peripheral blood

tag: cell type

tag: number of cells


title: Classical monocytes from healthy donor HD1

description:
HD1_monos
mRNA-3' from classical monocytes sorted from healthy donor

value: healthy donor HD1

tag: covid status

tag: gender

tag: haematological tumor

tag: tissue

value: Classical monocytes


title: A57_Donor2_scRNA-seq

description: 10X single-nuclei

value: Anterior hippocampus

tag: Sex

tag: batch

tag: protocol

value: Protocol 1


title: A76_Donor4_scRNA-seq

description: 10X single-nuclei

tag: age (yr)

value: Male

tag: race

tag: hemisphere


title: Non-classical monocytes from healthy donor HD2

description:
HD2_monosNC
mRNA-3' from non-classical monocytes sorted from healthy donor

value: healthy donor HD2

tag: age

value: Non-classical monocytes


title: Non-classical monocytes from healthy donor HD4

description:
HD4_monosNC
mRNA-3' from non-classical monocytes sorted from healthy donor


title: A56_Donor1_scRNA-seq

description: 10X single-nuclei

value: White

tag: epilepsy duration (yr)

tag: rin


title: aRCC6, Whole mucosa (colon)

value: colon

tag: disease activity

value: Active CC

tag: treatment

value: female


title: aRCC5, Whole mucosa (colon)


title: SGC7901_oeNC_rep2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

description: miRNA-seq

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. Q20, Q30, and GC-content of the raw datas were calculated.
miRBase20.0 was used as reference, software mirDeep_star_v38 was used to obtain the potential miRNA and the miRNA counts.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and TPM values for each Sample

source_name: gastric cancer cell

growth_protocol: The human gastric cancer cell line SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell line was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with corresponding plasmids. After 36 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). After purification of microRNAs, the miRNA sequencing was performed according to the manufacturer’s instructions.

treatment_protocol: GC cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with corresponding plasmids by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 36 h post-transfection, cells were harvested for RNA sequencing.

tag: cell line

tag: cell type

value: gastric cancer

tag: transfection

value: empty plasmid (pcDNA3.1)


title: Bulk_Human_Donor010_Treg

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)

data_processing:
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Bulk_Human_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Bulk_Human_TPM.txt contains Transcript per Million normalized counts

source_name: Human cancer tissue

growth_protocol: Cell types were isolated from tissue samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were constructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads and on the NovaSeq6000 to obtain 50-bp paired end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

tag: cell type surface markers

value: Treg

tag: donor #


title: Myeloid dendritic cells from healthy donor HD3

description:
HD3_dendM
mRNA-3' from myeloid dendritic cells sorted from healthy donor

source_name: Myeloid dendritic cells from peripheral blood

tag: individual

value: healthy donor HD3

tag: covid status

value: Healthy donor

tag: gender

tag: hospitalization

tag: exitus

tag: haematological tumor

tag: tissue

value: Myeloid dendritic cells

tag: number of cells


title: Basophils from healthy donor HD2

description:
HD2_basos
mRNA-3' from basophils sorted from healthy donor

source_name: Basophils from peripheral blood

tag: age

value: No

value: peripheral blood

value: Basophils


title: Classical monocytes from healthy donor HD2

description:
HD2_monos
mRNA-3' from classical monocytes sorted from healthy donor

value: Classical monocytes


title: SGC7901_oeUBE2CP3_rep1

description: miRNA-seq

value: overexpression plasmid (pcDNA3.1)


title: SGC7901_oeUBE2CP3_rep2

description: miRNA-seq


title: Bulk_Human_Donor009_Treg


title: Non-classical monocytes from healthy donor HD1

description:
HD1_monosNC
mRNA-3' from non-classical monocytes sorted from healthy donor

value: healthy donor HD1

value: Female


title: aRCC3, Whole mucosa (colon)


title: aRCC2, Whole mucosa (colon)


title: Bulk_Human_Donor007_Treg


title: Bulk_Human_Donor008_Treg


title: Basophils from healthy donor HD3

description:
HD3_basos
mRNA-3' from basophils sorted from healthy donor

value: Male


title: Bulk_Mouse_036_Treg_PBS

data_processing:
Bulk RNA–seq data were mapped against the mouse mm10 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: mm10
Supplementary_files_format_and_content: Bulk_Mouse_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Bulk_Mouse_TPM.txt contains Transcript per Million normalized counts

source_name: murine infection model

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were constructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the NovaSeq6000 to obtain 50-bp paired end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

treatment_protocol: Mice were immunzied with either mock PBS or 100ug Ovalbumin with either Complete Freund's adjuvant or MPLA.

value: PBS


title: Myeloid dendritic cells from healthy donor HD2

description:
HD2_dendM
mRNA-3' from myeloid dendritic cells sorted from healthy donor

value: healthy donor HD2


title: Bulk_Mouse_033_Treg_PBS


title: SGC7901_oeNC_rep1

description: miRNA-seq


title: Bulk_Mouse_030_Treg_OC

value: OC


title: Bulk_Human_Donor006_Treg


title: Basophils from healthy donor HD4

description:
HD4_basos
mRNA-3' from basophils sorted from healthy donor

value: healthy donor HD4


title: Bulk_Human_Donor005_Treg


title: itCC8, Whole mucosa (colon)

description: paired with auCC8

value: colon

value: Inactive/Clinical remission CC

value: 6-9 mg/day budesonide

value: male


title: aRCC1, Whole mucosa (colon)

value: Active CC

value: female


title: itCC9, Whole mucosa (colon)

description: paired with auCC9


title: Bulk_Mouse_026_Treg_OC

value: Treg


title: Myeloid dendritic cells from healthy donor HD2 (resequenced)

description:
HD2_dendM_reseq420
mRNA-3' from myeloid dendritic cells sorted from healthy donor

value: Healthy donor

value: No

value: peripheral blood

value: Myeloid dendritic cells


title: aRCC4, Whole mucosa (colon)


title: Bulk_Human_Donor004_Treg


title: Bulk_Mouse_022_Treg_OC


title: itCC7, Whole mucosa (colon)

description: paired with auCC7


title: Myeloid dendritic cells from healthy donor HD4

description:
HD4_dendM
mRNA-3' from myeloid dendritic cells sorted from healthy donor

value: Female


title: Bulk_Mouse_018_Treg_OC


title: Bulk_Human_Donor002_Treg


title: Bulk_Human_Donor003_Treg


title: itCC5, Whole mucosa (colon)

description: paired with auCC5


title: itCC6, Whole mucosa (colon)

description: paired with auCC6


title: Myeloid dendritic cells from healthy donor HD1

description:
HD1_dendM
mRNA-3' from myeloid dendritic cells sorted from healthy donor

value: healthy donor HD1


title: Bulk_Mouse_010_Treg_MPLA

value: MPLA


title: itCC3, Whole mucosa (colon)

description: paired with auCC3


title: Bulk_Human_Donor010_Tfr

value: Tfr


title: itCC4, Whole mucosa (colon)

description: paired with auCC4


title: Bulk_Human_Donor008_Tfr


title: Plasmacytoid dendritic cells from healthy donor HD2

description:
HD2_dendP
mRNA-3' from plasmacytoid dendritic cells sorted from healthy donor

source_name: Plasmacytoid dendritic cells from peripheral blood

value: healthy donor HD2

value: Male

value: Plasmacytoid dendritic cells


title: Bulk_Human_Donor009_Tfr


title: Plasmacytoid dendritic cells from healthy donor HD4

description:
HD4_dendP
mRNA-3' from plasmacytoid dendritic cells sorted from healthy donor

value: healthy donor HD4


title: Myeloid dendritic cells from healthy donor HD1 (resequenced)

description:
HD1_dendM_reseq420
mRNA-3' from myeloid dendritic cells sorted from healthy donor


title: Bulk_Human_Donor007_Tfr


title: itCC2, Whole mucosa (colon)

description: paired with auCC2

value: colon

value: Inactive/Clinical remission CC

value: 6-9 mg/day budesonide


title: Bulk_Mouse_002_Treg_MPLA


title: itCC1, Whole mucosa (colon)

description: paired with auCC1

value: female


title: Bulk_Mouse_042_Tfr_PBS

value: PBS


title: Plasmacytoid dendritic cells from healthy donor HD3

description:
HD3_dendP
mRNA-3' from plasmacytoid dendritic cells sorted from healthy donor

value: healthy donor HD3

value: Healthy donor