title: RNAseq_MCF10A_withDox_withOHT_rep3

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

data_processing:
Base calling was performed using Illumina's CASAVA software or FASTQ generation software v1.0.0 and the quality of the generated FASTQ files was analyzed with FastQC.
For mRNA sequencing, Fastq-files were imported to the Galaxy Web-based anaylsis portal and mapped to the human genome (hg19) using the aligner HISAT2. Differential expression analysis was done with featureCounts and limma.
Following the generation of a count-table for all analyzed conditions, DAVID was used to identify enriched GO-terms and gene-set enrichment analysis (GSEA) was used to determine enriched gene sets.
Assembly: hg19
Supplementary files format and content: One tab-delimited text file that contains the raw-counts for all 12 individual MCF10A samples in a single table and a second tab-delimited text file that contains the raw-counts for all 9 individual 92-1 samples. These count-tables were used to carry out all further data-processing steps as outlined above.

growth_protocol: Human uveal melanoma cells (92-1), expressing MY-COMP or a control, were grown in RPMI-1640 medium supplemented with 10% FCS and 1% penicillin/ streptomycin. The human breast cancer cells (MCF10A), containing a doxycyline inducible MY-COMP construct and an OHT-inducible ER-YAP2SA construct, were cultured in DMEM/F-12 medium supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin. All cells were cultured at 37C at 5% CO2.

extract_protocol:
For RNA sequencing, cells were harvested and total RNA was extracted with RNeasy MiniKit (Qiagen) according to manufacturer's instructions. On-column Dnase I digestion was performed followed by mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB).
Library preparation was done with the NEBNext Ultra II Directional RNA Library Prep for Illumina (NEB) following the manufacturer's manual. Libraries were size-selected using SPRIselect beads (Backman-Coulter) after PCR-amplification using the NEBNext Multiplex Oligos for Illumina Kit (NEB). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single read mode on a NextSeq500 platform (Illumina).

treatment_protocol: In the MCF10A cells, the indcution of MY-COMP expression was done by adding 0.5 µg/ml doxycycline and the stabilization of ER-YAP2SA was achieved by adding 4-OHT for 14 hours. Transfection of 92-1 cells was done with 30-90 nM of either siCtrl or siYAP/TAZ using RNAiMAX reagent.

value: Breast Cancer

tag: dox-treatment (expression of my-comp)

value: induced (expression of MY-COMP)

tag: 4-oht treatment (activation of yap-mutant)

value: induced (stabilization of ER-YAP2SA)

tag: constitutive expression

value: not applicable

tag: transfection with sirna

tag: biological replicate


title: CTRL_A_2_IFN

status: Public on Mar 06 2024

type: SRA

city: Cambridge

first: Jay

last: Penney

state: MA

address: 77 Massachusetts Avenue

department: Picower Institute

country: USA

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome reference GRCh38/hg38 using the R software package Rsubread
Mapped reads were converted to gene level counts using the featureCounts function of Rsubread with “strandSpecific” parameter set to 0
Differential analysis was performed using DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: Excel file contains raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: iPSC

growth_protocol: iPSCs were differentiated to iPSC-microglia per McQuade et al., 2018 and grown in iMBM media supplemented with 25 ng/mL mCSF and 100 ng/mL IL34.

extract_protocol:
RNA was extracted using the QIAGEN Rneasy Plus mini kit.
Libraries for RNA-seq were generated using NEB Ultra II kit following manufacturers protocols.

treatment_protocol: Initial RNA-seq was performed on untreated cells. Inflammatory treatments were performed with either 50 ng/mL IFNgamma or 100 ng/mL LPS for 2 hours before collection of RNA for sequencing.

tag: cell line

value: iPSC

tag: cell type

value: iPSC-microglia

tag: genotype

value: WT

tag: treatment

value: 50 ng/mL IFNg, 2 hrs


title: CTRL_B_1_IFN


title: mPFC, RES, 2

city: Seoul

first: Sihwan

last: Seol

address: 84, Heukseok-ro

country: South Korea

institute: Chung-Ang University

data_processing:
Preprocessing was performed to eliminate artifacts (low quality, adapter sequence, contaminated DNA, or PCR duplicates) from sequenced raw reads by using Trimmomatic (version 0.38).
The preprocessed reads were mapped to the reference genome (mm10) by using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.1.0) program, which can handle spliced reads through Bowtie2 aligner, to generate aligned reads.
StringTie (version 1.3.4d) was used for transcript assembly and quantification.
Assembly: mm10
Supplementary files format and content: a csv file include normalized values, FPKM values, read counts for each sample

organism: Mus musculus

source_name: brain

extract_protocol:
The RNA was isolated with the RNeasy Micro kit (74004, QIAGEN, Hilden, Germany)
Total RNA was transformed into cDNA libraries by using the TruSeq Stranded Total RNA LT Sample Prep Gold kit in accordance with the manufacturer’s instructions (Illumina, USA).

tag: tissue

value: brain

tag: strain

tag: age

tag: Sex

value: male

tag: treatment (phenotype)

value: chronic unpredictable stress (resilient)

tag: group

value: RES


title: U20990

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were aligned to hg19 using STAR aligner
Reads were annotated to transcripts using Gencode v18 annotation
Assembly: Gencode v18 annotation
Supplementary files format and content: CSV file includes raw counts for each samples

source_name: Periperal blood

extract_protocol:
Blood was collected from all study participants using RNA Paxgene vacutainer tubes. PAXgene blood tubes were thawed quickly and brought to room temperature prior to total RNA isolation according to the manufacturer’s instructions, and Globin mRNA was removed using GLOBINclear (Invitrogen/Ambion).
RNA samples were subject to Ribo-zero depletion, and libraries prepared using the Illumina Truseq library preparation kit and sequenced on the Illumina HiSeq 2500 (2 x 50), generating a mean of 48 million reads per sample.

value: Periperal blood

value: F

tag: diagnosis

value: MDD

tag: suicide attempt

value: N

tag: si group

value: High SI


title: U20981

value: M

value: No SI


title: mPFC, RES, 1


title: DPSC-EV_rep1

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Single-end RNA sequencing reads were aligned to the GRCh37 version of the human genome using STAR.
Gene expression was quantified using featureCounts, using GRCh37 gene annotation obtained from Ensembl (vep_95_GRCh37).
Differential gene expression analysis was performed using R/Bioconductor packages limma-voom and edgeR. Significance was set at a false discovery rate (FDR) <0.05 and differentially expressed genes (DEGs) were selected using a log2 fold change (logFC) > +2/-2
Functional enrichment analysis of DEGs was performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases and Molecular Signatures Database (MSigDB) v7.1.
Assembly: GRCh37.75
Supplementary files format and content: Tab-delimited text file

source_name: Dental pulp

extract_protocol:
RNA was extracted from cells using the PureLink™ RNA Mini Kit (Invitrogen). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Universal Plus™ mRNA-Seq Library Preparation Kit (NuGEN Technologies Inc.) following manufacturer’s protocols.
mRNA-seq single end

value: Dental pulp

value: Dental pulp stem cells

value: control

value: empty lentiviral transduction and neural induction


title: RNAseq_MCF10A_withDox_withOHT_rep2

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

value: Breast Cancer

tag: dox-treatment (expression of my-comp)

value: induced (expression of MY-COMP)

tag: 4-oht treatment (activation of yap-mutant)

value: induced (stabilization of ER-YAP2SA)

value: not applicable


title: CTRL_A_1_IFN

value: iPSC

value: iPSC-microglia

value: WT

value: 50 ng/mL IFNg, 2 hrs


title: U21134

value: Periperal blood

value: F

value: MDD

value: Low SI


title: U20939

value: N

value: No SI


title: RNAseq_MCF10A_withDox_withOHT_rep1

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

tag: constitutive expression

tag: transfection with sirna


title: mPFC, CTRL, 3

value: brain

value: male

value: CTRL


title: CTRL_B_1_UNTR

tag: cell line


title: mPFC, CTRL, 2


title: RNAseq_MCF10A_withDox_noOHT_rep3

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

tag: cell type

value: Breast Cancer

value: uninduced (unstable ER-YAP2SA)

tag: biological replicate


title: U20755

value: Y


title: RNAseq_MCF10A_withDox_noOHT_rep2

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

value: induced (expression of MY-COMP)

value: not applicable


title: mPFC, SUS, 2

value: chronic unpredictable stress (susceptible)

value: SUS


title: U20662

value: M

value: Healthy control


title: U20726

value: Periperal blood


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), health control [Control_2]

city: Shanghai

first: Wang

last: yaodong

address: Wanyuan Road

country: China

institute: Children's hospital of fudan university

data_processing:
Fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Mus musculus Ensembl v101
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: Mus musculus Ensembl v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Primary bone marrow cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: Mice in CLP groups were accepted cecal ligation and puncture (ref.19131954). To establish intra-abdominal infection and approximate the clinical conditions of human sepsis where there is a delay between the onset of sepsis and the delivery of therapy, mice were intraperitoneal injected with antibiotic (Imipenem; 25 mg kg-1 body weight) at 8 and 16 hours after surgery.

value: Primary bone marrow cells

tag: genotype

value: WT

tag: treatment

value: health control


title: mPFC, CTRL, 1

tag: tissue

tag: strain


title: CTRL_A_1_UNTR

value: iPSC

value: iPSC-microglia


title: CTRL_A_2_UNTR


title: RNAseq_MCF10A_withDox_noOHT_rep1

description:
RNA-seq
RNAseq_MCF10A_countdata.txt


title: U20558

tag: age

tag: Sex

value: N

value: No SI


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), health control [Control_1]


title: 22Rv1 THZ531 treated replica 3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: hg19
Supplementary files format and content: Gene expression values normalized by DESeq2 unsing FAST DB v2018_1 annotations

growth_protocol: 22Rv1 cells were grown in RPMI medium (Euroclone), supplemented with 10% fetal bovine serum, Sodium Pyruvate, HEPES, penicillin and streptomycin (GIBCO, Life Technologies) and glucose (Thermo Fisher)

extract_protocol:
total RNA was extracted and DNAse treated using the RNEasy mini kit (Qiagen) according to manufacturer’s instruction
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand).

treatment_protocol: 24hrs post-seeding 22Rv1 cells were treated with Indisulam (3.3µM, 12hrs), or Pladienolide B (10nM, 6hrs) or THZ531 (200Nm, 6hrs) or DMSO, as control.

value: prostate cancer cell line

tag: time

value: 6 hrs


title: U20323

value: F

tag: diagnosis


title: RNAseq_MCF10A_noDox_withOHT_rep2

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

value: Breast Cancer

value: uninduced (no expression of MY-COMP)

value: induced (stabilization of ER-YAP2SA)


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), 6 day after CLP [CLP_d6_2]

value: 6 day after CLP


title: U20470

tag: suicide attempt


title: 22Rv1 Pladienolide B treated replica 3

value: Pladienolide B 10 nM


title: RNAseq_MCF10A_noDox_withOHT_rep3

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

value: not applicable


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), 6 day after CLP [CLP_d6_1]


title: CTRL_B_2_UNTR


title: RNAseq_MCF10A_noDox_withOHT_rep1

description:
RNA-seq
RNAseq_MCF10A_countdata.txt


title: U20238

value: Periperal blood

value: Healthy control

tag: si group


title: 22Rv1 Indisulam treated replica 3

value: Indisulam 3.3µM

value: 12 hrs


title: U20111

value: MDD

value: High SI


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), 3 day after CLP [CLP_d3_2]

value: Primary bone marrow cells

value: WT

value: 3 day after CLP


title: 22Rv1 DMSO treated replica 3

value: prostate cancer cell line

value: DMSO


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), 3 day after CLP [CLP_d3_1]


title: RNAseq_MCF10A_noDox_noOHT_rep3

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

value: Breast Cancer

tag: dox-treatment (expression of my-comp)

value: uninduced (unstable ER-YAP2SA)


title: RNAseq_MCF10A_noDox_noOHT_rep2

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

value: uninduced (no expression of MY-COMP)

tag: 4-oht treatment (activation of yap-mutant)


title: RNAseq_MCF10A_noDox_noOHT_rep1

description:
RNA-seq
RNAseq_MCF10A_countdata.txt

tag: constitutive expression


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), 1 day after CLP [CLP_d1_2]

value: 1 day after CLP


title: 22Rv1 Pladienolide B treated replica 2

value: Pladienolide B 10 nM

value: 6 hrs


title: U20070

value: Periperal blood

value: M

value: N

value: No SI


title: U20106

value: F

value: MDD

value: Low SI


title: 22Rv1 THZ531 treated replica 2


title: Bone marrow cells of 6-8 week C57BL/6 mice (male), 1 day after CLP [CLP_d1_1]

value: Primary bone marrow cells

value: WT


title: RNAseq_92_1_MY_COMP_rep3

description:
RNA-seq
RNAseq_92_1_countdata.txt

value: Uveal Melanoma

value: not applicable

value: MY-COMP

tag: transfection with sirna

value: siCtrl


title: 82025


title: 22Rv1 Indisulam treated replica 2

tag: cell line

value: prostate cancer cell line

value: Indisulam 3.3µM

value: 12 hrs


title: RNAseq_92_1_MY_COMP_rep2

description:
RNA-seq
RNAseq_92_1_countdata.txt

tag: cell type


title: 22Rv1 DMSO treated replica 2

value: DMSO


title: Ezh2_Y641F iMEFs PRC2i 0.250µM H3K27me3 rep2 [D387C165]

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie

library_source: genomic

data_processing:
library strategy: Cut&Run
Adapters and low‐quality bases (<Q20) were removed from Cut&Run-Seq reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were mapped to the mouse reference genome mm10 with Bowtie2 (v2.2.5) using default parameters. PCR duplicates were with with Picard Tools MarkDuplicates (v1.97).
BigWig files were created using DeepTools bamCoverage (v3.0.2) with the following parameters: --normalizeUsingRPKM –ignoreForNormalization chrX chrY –samFlagInclude 64 –extendReads. Reads overlapping problematic, blacklisted regions (mm10-blacklist.v2.bed) were excluded from the computation of coverage with the option --blackListFileName.
In addition to scaling by library size, in order to remove any composition biases, we calculated a normalizing factor using the BioconductoR csaw::normFactors function. The normalization factor was passed onto DeepTools bamCoverage with the parameter --scaleFactor.
Processing of ChIP-Seq reads was done similarly to Cut&Run-Seq reads. Reads were however mapped to the human reference genome assembly hg19.
Assembly: mm10 for Cut&Run-Seq libraries; hg19 for ChIP-Seq libraries
Supplementary files format and content: BigWig files of genome-wide enrichment of the probed histone modification.

molecule: genomic DNA

source_name: iMEFs

growth_protocol: iMEFs were grown in Dulbecco’s Modified Eagle Medium (DMEM) high-glucose (4.5 g/L) supplemented with 10% fetal calf serum, nonessential amino acids and 2 mM L-glutamine at 37°C with 5% CO2 and 98% humidity.

extract_protocol:
Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018).
In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes.
In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes.
Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction.
Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100).

value: iMEFs

tag: antibody


title: 22Rv1 Pladienolide B treated replica 1

value: Pladienolide B 10 nM

value: 6 hrs


title: 4961

value: Periperal blood

value: M

value: N

value: No SI


title: RNAseq_92_1_siYAP_rep3

description:
RNA-seq
RNAseq_92_1_countdata.txt

value: control (GFP)

value: siYAP/TAZ

tag: biological replicate


title: Ezh2_Y641F iMEFs PRC2i ctrl H3K27me3 rep2 [D387C163]

tag: genotype

tag: treatment

value: UNC2400 (ctrl for UNC1999)


title: RNAseq_92_1_MY_COMP_rep1

description:
RNA-seq
RNAseq_92_1_countdata.txt

value: Uveal Melanoma

value: not applicable


title: 71236

tag: tissue

value: F

value: MDD

value: Y

value: High SI


title: PRC2 WT iMEFs PRC2i 0.250µM H3K27me3 rep2 [D387C162]

value: WT


title: 45516

tag: age

value: Healthy control


title: 22Rv1 THZ531 treated replica 1

value: prostate cancer cell line


title: PRC2 WT iMEFs PRC2i 0.125µM H3K27me3 rep2 [D387C161]

value: iMEFs


title: RNAseq_92_1_siYAP_rep1

description:
RNA-seq
RNAseq_92_1_countdata.txt


title: 22Rv1 Indisulam treated replica 1

value: Indisulam 3.3µM

value: 12 hrs


title: 22Rv1 DMSO treated replica 1

value: DMSO


title: 4437164

value: Periperal blood

tag: Sex

value: M

value: N

value: No SI


title: 4434208


title: Treg, ppx [Pool9_CKDL210006264-1a-N711-N502]

city: Stanford

first: Cameron

middle: Scott

last: Bader

state: California

address: 269 Campus Drive, CCSR Room 2250

department: BMT and Cell Therapy

institute: Stanford University

data_processing:
Raw reads were aligned using STAR v2.6.1
Aligned .bam files were parsed using RSEM to generate raw expected reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file for all samples with raw read counts.

source_name: Treg, ppx

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (Zymo).
RNA libraries for RNA-seq were prepared using KAPA HyperPlus Kit following manufacturer's protocols.

value: CD4+ Treg

value: Single-agent prophylaxis


title: RNAseq_92_1_siCtrl_rep3

description:
RNA-seq
RNAseq_92_1_countdata.txt

value: Uveal Melanoma

value: not applicable

value: control (GFP)

value: siCtrl


title: RNAseq_92_1_siCtrl_rep2

description:
RNA-seq
RNAseq_92_1_countdata.txt


title: 4434190

value: F

value: MDD

value: High SI


title: Ezh2_Y641F iMEFs PRC2i 0.250µM H3K27me3 rep1 [D387C158]

value: iMEFs


title: Treg, ppx [Pool7_CKDL210006264-1a-N707-N502]


title: Ezh2_Y641F iMEFs PRC2i 0.125µM H3K27me3 rep2 [D387C164]


title: 4429195


title: 4426148

value: Healthy control


title: Ezh2_Y641F iMEFs PRC2i ctrl H3K27me3 rep1 [D387C156]

value: UNC2400 (ctrl for UNC1999)


title: CnR4_H3K4me1

description:
CUT&RUN-seq
merge of files from re-sequenced sample
Illumina NextSeq500/2000

data_processing:
Base calling was performed using Illumina's CASAVA software or FASTQ generation software v1.0.0 and the quality of the generated FASTQ files was analyzed with FastQC.
For Cut&Run sequencing, fastq-files were imported to the Galaxy web-based analysis portal and reads were aligned to the human genome (hg19) using Bowtie2. All paired CUT&RUN reads were filtered by using a Phred score cutoff of 30 and mitochondrial reads were removed. Peaks were called with MACS2.
DeepTools 2 was used to create CUT&RUN profiles. First, normalized bigWig files were created using bamcoverage with a bin size of 10 and normalizing to counts per million reads mapped (CPM). BigWig files were used to compute reads centered on YAP-seq peak summits (called with MACS2) using computeMatrix. Profiles were created with plotProfile tools. CUT&RUN data were visualized with the Integrated Genome Viewer.
Assembly: hg19
Supplementary files format and content: For CUT&RUN-seq, the provided processed files are bigwig files for data display in a genome browser.
Library strategy: CUT&RUN

growth_protocol: Uveal melanoma cells (92.1) were maintained in RPMI-1640 medium supplemented with with 10% FCS and 1% penicillin/ streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
For Cut&Run sequencing, cells were washed twice and then coupled to ConA-coated magentic beads (Polysciences Europe). Cells were resuspended with antibody buffer (0.005% digitonin and 2 mM EDTA). Then cells were incubated with the antibody (see for details above) for 2 hours at RT. Cells were then washed in the presence of digitonin and 700 ng/ml MNase was added per sample for 1 hour at 4°C, followed by two more washes.
Following the initial washes, the MNase treated cells were washed once in low salt rinse buffer and then incubated in buffer containing CaCl2 and digitonin to activate the protein A-MNase. The DNA was digested for 30 min on ice and the Mnase activity was then stoped in the presence of 50 µg/ml Rnase A. DNA fragments were released at 37°C for 30 min and the decrosslinking was done for 1 hour at 50°C in the presence of Proteinase K. DNA was extracted wit phenol-chloroform and DNA was precipitated with ethanol and resuspended in TE buffer.
In some cases (Cut&Run samples where antibodies were used for H3K4me1, H3K4me3, H3K27ac and H4ac), a 1 min crosslinking with 1% formaldehyde was performed. In these cases, all buffers were used without digitonin and instead 0.05% SDS and 0.1% Triton X-100 were added to the wash buffer.
The DNA libraries were prepared with 6 ng of CUT&RUN DNA fragments, using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. The libraries were PCR-amplified with 15 PCR cycles using the NEBNext Multiplex Oligos for Illumina Kit. The libraries were purified using Agencourt AMPure XP beads (Beckman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
followed by sequencing.

treatment_protocol: The 92-1 cells were not specifically treated for the Cut&Run experiment.

tag: cell cycle synchronization

value: unsynchronized

tag: specifics for sample preparation

tag: spike-in

tag: chip/cut&run antibody

value: H3K4me1 (ab8895; Abcam)


title: 4424163

value: Periperal blood

tag: diagnosis

tag: suicide attempt

tag: si group


title: PRC2 WT iMEFs PRC2i 0.250µM H3K27me3 rep1 [D387C155]

value: WT


title: RNAseq_92_1_siYAP_rep2

description:
RNA-seq
RNAseq_92_1_countdata.txt

tag: dox-treatment (expression of my-comp)

tag: 4-oht treatment (activation of yap-mutant)

tag: constitutive expression

tag: transfection with sirna

value: siYAP/TAZ


title: CnR4_IgG

description:
CUT&RUN-seq
n/a

tag: cell line

tag: cell type

value: IgG (control)


title: Treg, noppx [Pool5_CKDL210006264-1a-N705-N502]

source_name: Treg, noppx

value: CD4+ Treg

tag: treatment

value: No prophylaxis


title: 4423176

tag: tissue

value: N

value: No SI


title: PRC2 WT iMEFs PRC2i 0.125µM H3K27me3 rep1 [D387C154]

tag: genotype

tag: antibody


title: CnR3_H3K4me3

description:
CUT&RUN-seq
n/a

value: Uveal Melanoma

tag: cell cycle synchronization

value: not applicable

value: H3K4me3 (ab8580; Abcam)


title: PRC2 WT iMEFs PRC2i ctrl H3K27me3 rep2 [D387C160]


title: Treg, noppx [Pool4_CKDL210006264-1a-N704-N502]


title: PRC2 WT iMEFs PRC2i ctrl H3K27me3 rep1 [D387C153]


title: 4421197

tag: age

tag: Sex

value: M

value: MDD

value: Y

value: High SI


title: 4417130

value: Healthy control


title: RNAseq_92_1_siCtrl_rep1

description:
RNA-seq
RNAseq_92_1_countdata.txt

value: control (GFP)

value: siCtrl

tag: biological replicate


title: CnR3_IgG

description:
CUT&RUN-seq
n/a

value: unsynchronized

tag: specifics for sample preparation

tag: spike-in

tag: chip/cut&run antibody


title: Ezh2_Y641F iMEFs PRC2i 0.125µM H3K27me3 rep1 [D387C157]

value: iMEFs


title: Butyrate + IL-13 3

city: Cincinnati

first: Theresa

last: Alenghat

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were aligned to the mm10 genome using the Illumina sequence analysis pipeline.
Differentially expressed genes between Untreated and IL-13 groups were identified using DSeq2.
Supplementary files format and content: mm10
Supplementary files format and content: text files with DSeq2 output for each sample.

source_name: intestinal organoid

growth_protocol: Organoids were dervied from the ileum (enteroids) of WT C57Bl/6 and maintained at 37C, 5% CO2, in organoid culture media.

extract_protocol:
Enteroids were harvested and RNA was isolated using the RNeasy Kit (Qiagen) according to manufacturer's instructions
Directional polyA RNAseq according to standard Illumina protocols

treatment_protocol: Organoids were treated with 1mM Butyrate for 48hrs and/or 20 ng/mL IL-13 for 72 hrs.

value: intestinal organoid

value: Intestinal epithelial cells

value: 1 mM Butyrate + 20 ng/mL IL-13


title: Treg, SOC [Pool36_CKDL210006264-1a-AK1572-N504]

source_name: Treg, SOC

value: CD4+ Treg

value: SOC


title: Eed_KO iMEFs H3K36me3 rep2 [D387C130]


title: Eed_KO iMEFs H3K36me3 rep1 [D387C129]


title: 4416213

value: Periperal blood

tag: diagnosis

tag: suicide attempt

value: N

tag: si group

value: Low SI


title: CD4, SOC [Pool31_CKDL210006264-1a-N707-N504]

source_name: CD4, SOC

value: CD4+ Tcon


title: 4416160

value: M

value: No SI


title: Treg, ppx [Pool6_CKDL210006264-1a-N706-N502]

value: Single-agent prophylaxis


title: Treg, ppx [Pool8_CKDL210006264-1a-N710-N502]


title: H3.3K27M iMEFs H3K36me3 rep2 [D387C128]


title: H3.3K27M iMEFs H3K36me3 rep1 [D387C127]


title: Butyrate + IL-13 2


title: 4415140

value: F

value: Healthy control


title: CD4, SOC [Pool28_CKDL210006264-1a-N704-N504]


title: Ezh2_Y641F iMEFs H3K36me3 rep2 [D387C126]


title: 4412200


title: IL-13 3

value: 20 ng/mL IL-13


title: Butyrate + IL-13 1


title: IL-13 2


title: CD4, ppx [Pool27_CKDL210006264-1a-N703-N504]

source_name: CD4, ppx


title: Ezh2_Y641F iMEFs H3K36me3 rep1 [D387C125]


title: CD4, SOC [Pool37_CKDL210006264-1a-N701-AK415]


title: Treg, noppx [Pool3_CKDL210006264-1a-N703-N502]

value: No prophylaxis


title: CD4, ppx [Pool26_CKDL210006264-1a-N702-N504]


title: 4320


title: 28117

value: MDD

value: High SI


title: Ezh2_KO iMEFs H3K36me3 rep2 [D387C124]

value: iMEFs


title: CD4, ppx [Pool25_CKDL210006264-1a-N701-N504]


title: Ezh2_KO iMEFs H3K36me3 rep1 [D387C123]


title: 28101

value: Y


title: 28084


title: CD4, ppx [Pool24_CKDL210006264-1a-AK1572-N503]


title: Untreated 3

value: intestinal organoid

value: Intestinal epithelial cells

value: Untreated


title: CD4, ppx [Pool23_CKDL210006264-1a-AK1568-N503]


title: Butyrate 2

value: 1 mM Butyrate


title: Butyrate 1


title: 28067

value: Periperal blood


title: CD4, noppx [Pool21_CKDL210006264-1a-N711-N503]

source_name: CD4, noppx

value: CD4+ Tcon


title: iPSC-derived osteoblast, sample 60

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and then mapped to the human GENCODE V29 reference genome using STAR_2.5.3a with parameters --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outSAMstrandField intronMotif --runThreadN 12 --twopassMode Basic --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNoverReadLmax 0.04 --outStd SAM --outSAMmode Full --outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within –quantMode TranscriptomeSAM GeneCounts --outWigType bedGraph --outWigNorm RPM --outWigStrand Unstranded --outFileNamePrefix  Raw counts per gene model (GENCODE M22) were extracted with featureCounts v1.6.4
Assembly: human GENCODE V29 reference genome
Supplementary files format and content: Tab delimited featurecounts output file with the following columns: GENCODE V29 gene ID, Chr, Start, End, Strand, Length, total_read_count

growth_protocol: iPSCs to MSCs differentiaiton was carried out as the follow steps. iPSC colonies were harvested with Accutase (Innovative Cell Technologies, AT-104) and seeded as single cells on Matrigel-coated plate in mTeSR1 and supplemented with 2uM Thiazovivin. The next day, TeSR1 medium was replaced with STEMdiff mesoderm induction medium (MIM) (Stem Cell Technologies, 05221) when cells were at approximately 20 - 50% confluence. Cells were then fed daily and cultured in STEMdiff MIM for four days. On day 5, the culture medium was switched to MesenCult-ACF medium (Stem Cell Technologies, 05440/8) for the rest of the MSC induction duration. For passage two or above, cells were subcultured on MesenCult-ACF attachment substrate. After three weeks of differentiation, the cells were sorted for the CD105 (BD biosciences, 561443, 1/20) positive and CD45 (BD Biosciences, 555483, 1/5) negative MSC population, and then expanded in MSC medium consisting of low-glucose DMEM (Gibco, 10567022) containing 10% FBS (Sotiropoulou et al., 2006). The iPSC-derived MSCs were then plated in a 6-well plate at a density of 3X103 /cm2 in MSC medium. After 3 days, culture medium was switched to osteogenic differentiation medium (α MEM (Thermo Fisher Scientific, A1049001) supplemented with 10% FBS, 1% non-essential amino acids, 0.1 uM dexamethasone (MilliporeSigma, D4902), 10 mM β-glycerophosphate (MilliporeSigma, G9422), and 200 uM ascorbic acid (MilliporeSigma, A4544)) and maintained in this medium for 21 days. The culture medium was changed every 2-3 days.

extract_protocol:
Cells were washed with PBS and harvested for RNA extraction using miRNeasy mini kit (QIAGEN, 217004) according to the manufacture’s instruction.
Following RNA extraction, ribosomal depleted RNA was converted to cDNA and Illumina’s TruSeq Stranded Sample Prep kit was used to generate libraries.

value: osteoblast

tag: time

value: differentiation day21


title: Untreated 2


title: PRC2 WT iMEFs H3K36me3 rep1 [D387C121]

tag: cell line

value: WT


title: Eed_KO iMEFs H3K27Ac rep2 [D127C72]


title: PRC2 WT iMEFs H3K36me3 rep2 [D387C122]


title: iPSC-derived preosteoblast, sample 59

tag: cell type

value: preosteoblast

value: differentiation day 7


title: CD4, ppx [Pool22_CKDL210006264-1a-N712-N503]

tag: treatment

value: Single-agent prophylaxis


title: CD4, noppx [Pool20_CKDL210006264-1a-N710-N503]

value: No prophylaxis


title: Treg, noppx [Pool2_CKDL210006264-1a-N702-N502]

value: CD4+ Treg


title: iPSC-derived MSC, sample 58

value: mesenchymal stem cell

value: differentiation day 0


title: Eed_KO iMEFs H3K27Ac rep1 [D127C71]

value: iMEFs


title: Ezh2_Y641F iMEFs rep1 [A988T05 RNA-seq]

data_processing:
To analyze the iMEFs RNA-Seq libraries, adapters and low‐quality bases (<Q20) were removed from single- and paired-end reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were then mapped to the mouse reference genome mm10 using the STAR (v2.7.0a) aligner and the corresponding gene annotation from GENCODE: release 23/GRCm38.p6. The following parameters were used for mapping of RNA-seq reads against the reference genome: --seedSearchStartLmax 20 --outSAMattributes NH HI NM MD --alignEndsType EndToEnd.
Gene counts were generated using FeatureCounts (Subread v1.5.1). Since iMEFs RNA-seq data include SE50 and PE100 datasets, we removed any potential batch effects with the removeBatchEffect function of the BioconductoR limma package prior to conducting the differential expression analysis with DESeq2.
Processing of FL RNA-Seq libraries was done similarly to that of iMEFs libraries, but reads were aligned to the human reference genome hg19 and annotated with the corresponding gene annotation from GENCODE (release 19/GRCh37.p13).
Assembly: mm10 for iMEFs libraries, hg19 for FL libraries
Supplementary files format and content: Processed data files include raw gene counts.

extract_protocol:
To isolate RNA from MEFs, cells of all experimental conditions were grown simultaneously and RNA was extracted 3 days after plating 200,000 cells. Total RNA was isolated using Trizol-Chloroform extraction and isopropanol precipitation. cDNA was further obtained using the High Capacity cDNA RT kit.
RNA from FL samples was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed on an automated Tapestation 4200 platform. RNA Integrity Numbers (RINs) were used to evaluate the integrity of RNA samples with > 7.0 considered intact and < 7.0 considered degraded.
iMEFs RNA-Seq libraries were prepared using the Swift Biosciences RNA library kit. FL RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit.


title: Butyrate 3

tag: tissue

value: intestinal organoid


title: Untreated 1

value: Intestinal epithelial cells

tag: genotype


title: CD4, noppx [Pool19_CKDL210006264-1a-N707-N503]


title: Ezh2_Y641F iMEFs rep2 [A988T06 RNA-seq]


title: Ezh2_Y641F iMEFs H3K27Ac rep2 [D127C68]

tag: antibody


title: iPSC-derived osteoblast, sample 57


title: Eed_KO iMEFs rep2 [A988T14 RNA-seq]


title: iPSC-derived preosteoblast, sample 56


title: iPSC-derived osteoblast, sample 54


title: CD4, noppx [Pool17_CKDL210006264-1a-N705-N503]


title: Ezh2_Y641F iMEFs H3K27Ac rep1 [D127C67]


title: iPSC-derived MSC, sample 55


title: Treg, noppx [Pool16_CKDL210006264-1a-N704-N503]


title: H3.3K27M Ezh2_KO iMEFs rep2 [A988T12 RNA-seq]

value: H3.3K27M Ezh2_KO


title: iPSC-derived preosteoblast, sample 53


title: H3.3K27M iMEFs H3K27Ac rep1 [D127C69]


title: Ezh2_KO iMEFs H3K27Ac rep1 [D127C65]


title: PRC2 WT iMEFs H3K27Ac rep2 [D127C64]


title: H3.3K27M Ezh2_KO iMEFs rep1 [A988T11 RNA-seq]


title: H3.3K27M iMEFs rep2 [A988T10 RNA-seq]


title: iPSC-derived MSC, sample 52


title: Treg, SOC [Pool15_CKDL210006264-1a-N703-N503]

value: SOC


title: iPSC-derived osteoblast, sample 51


title: IL-13 1

value: 20 ng/mL IL-13


title: PRC2 WT iMEFs H3K27Ac rep1 [D127C63]


title: CD4, noppx [Pool18_CKDL210006264-1a-N706-N503]

value: CD4+ Tcon


title: Treg, ppx [Pool11_CKDL210006264-1a-AK1568-N502]


title: H3.3K27M iMEFs rep1 [A988T09 RNA-seq]


title: iPSC-derived preosteoblast, sample 50


title: Treg, ppx [Pool10_CKDL210006264-1a-N712-N502]


title: iPSC-derived MSC, sample 49


title: Ezh2_KO iMEFs rep2 [A988T04 RNA-seq]


title: H3.3K27M iMEFs H3K27Ac rep2 [D127C70]


title: Eed_KO iMEFs rep1 [A988T13 RNA-seq]


title: Eed_KO iMEFs H3K27me3 rep1 [D127C61]


title: Ezh2_KO iMEFs H3K27Ac rep2 [D127C66]


title: Ezh2_KO iMEFs rep1 [A988T03 RNA-seq]


title: Treg, SOC [Pool12_CKDL210006264-1a-AK1572-N502]


title: H3.3K27M iMEFs H3K27me3 rep1 [D127C59]


title: iPSC-derived preosteoblast, sample 47


title: H3.3K27M iMEFs H3K27me3 rep2 [D127C60]


title: iPSC-derived osteoblast, sample 48

value: osteoblast


title: Superinfection (Superinfected_7_3)

city: Tel Aviv

first: ofir

last: cohn

address: Tel Aviv University

country: Israel

institute: Tel Aviv University

data_processing:
We applied a joint alignment of sequencing reads for both the mouse genome and the influenza virus genome, and then applied a joint quantification of both the virus and mouse transcripts.
Raw counts were derived with featureCounts. Raw read counts were imported into R studio and were then normalized using DESeq2 package
Assembly: mm9
Supplementary files format and content: comma-delimited csv file including DESeq2 normalized reads

growth_protocol: Virus was grown in allantoic fluid of 10-day-old embryonated chicken eggs at 37°C for 72 h. Allantoic fluid was harvested and viral titres were determined by standard plaque assay in Madin–Darby canine kidney. S. pneumoniae (ATCC 6303, a type 3 encapsulated strain) was grown for 16 h at 370C in 5% CO2 on Columbia Agar plates supplemented with 5% (vol/vol) sheep blood.

extract_protocol:
Lung tissues were collected into RNAlater (Qiagen). Lysis was performed with QIAzol (Qiagen). RNA isolation was performed according to miRNeasy kit protocol (Qiagen).
mRNA quality was checked using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. All RNA Integrity Numbers (RINs) were higher than 8. cDNA libraries were prepared using 2µg of isolated RNA according to the manufacturer’s instructions of the SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen). DNA size and quality were checked using the Agilent 2100 Bioanalyzer, according to the manufacturer’s instructions. Libraries were quantified by using the Qubit DNA HS Assay kit (Invitrogen). The amplified libraries, each sample having its own index primer, were pooled at a total concentration of 2 nM and sequenced using the Illumina HiSeq platform (Technion Genome Center, Israel).

treatment_protocol: Mice were anesthetized intraperitoneally with ketamine and xylazine cocktail and subjected to four treatments: PBS control, IAV alone, S. pneumoniae alone, and IAV infection followed by S.pneumoniae infection.

tag: strain

value: Lungs

tag: time (days after first infection)

tag: infection

value: Superinfection


title: 22RV1_shC_rep3

city: Minneapolis

first: Stephen

last: Jameson

state: MN

address: Wallin Medical Biosciences Bldg, MMC 641

department: Lab Medicine and Pathology

institute: University of Minnesota

data_processing:
Fastq files containing 150 bp paired-end reads were aligned to the GRCh38 reference genome using HiSat2 (v. 2.1.0). Subread (v. 2.0.3) was used to quantify gene expression using the version 100 GRCh38 annotation from Ensembl. Count data were filtered to only keep genes that had a cpm (counts per million) value greater than 1 cpm in at least two samples across all experimental conditions.
Assembly: GRCh38
Supplementary files format and content: 2.27.23 Pitzen Raw Count Matrix.csv contains counts obtained from Subread prior to normalization as described above.

source_name: Cell Line

growth_protocol: CWR22Rv1 cells were maintained in RPMI 1640 + 10% FBS

extract_protocol:
Total RNA was extracted from cells using the ReliaPrep RNA miniprep system (Promega).
RNA was submitted to the University of Minnesota Genomics Center for RNA-seq library synthesis using a TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: CWR22Rv1 cells were transduced with lentivirus encoding shCtrl, shAR-1, or shAR-2, followed by two sequential rounds of selection with 2 μg/mL puromycin dihydrochloride (Gibco, A11138-03). Infected cells were expanded and seeded in 6-well plates at 500,000 cells per well and grown for 72 h in normal RPMI 1640 + 10% FBS media. The cells infected with shCtrl lentivirus were further expanded, seeded in 6-well plates, and treated 24 h post-seeding with DMSO (vehicle control) or 0.8 μM IST5-002. Media was refreshed every 24 h for a total treatment time of 72 h.

value: Cell Line

value: Prostate Cancer

value: Control shRNA


title: PRC2 WT iMEFs rep2 [A988T02 RNA-seq]

value: WT


title: 22RV1_shC_rep1


title: iPSC-derived osteoblast, sample 45

value: differentiation day21


title: iPSC-derived MSC, sample 46

value: mesenchymal stem cell


title: Ezh2_Y641F iMEFs H3K27me3 rep1 [D127C57]


title: 22RV1_shC_rep2


title: Eed_KO iMEFs H3K27me3 rep2 [D127C62]


title: Superinfection (Superinfected_7_2)


title: 22RV1_shC_IST5_rep3

value: Control shRNA + 72 hr 0.8 uM IST5-002 treatment


title: iPSC-derived preosteoblast, sample 44

value: preosteoblast

value: differentiation day 7


title: Ezh2_KO iMEFs H3K27me3 rep2 [D127C56]

value: iMEFs


title: 22RV1_shC_IST5_rep2


title: Superinfection (Superinfected_7_1)


title: Treg, noppx [Pool1_CKDL210006264-1a-N701-N502]

value: CD4+ Treg

value: No prophylaxis


title: Ezh2_KO iMEFs H3K27me3 rep1 [D127C55]


title: PRC2 WT iMEFs H3K27me3 rep2 [D127C54]


title: iPSC-derived osteoblast, sample 42


title: 22RV1_shC_IST5_rep1


title: Superinfection (Superinfected_6_2)


title: Ezh2_Y641F iMEFs H3K27me3 rep2 [D127C58]


title: Superinfection (Superinfected_6_1)


title: 22RV1_shC_DMSO_rep3

value: Control shRNA + 72 hr DMSO treatment


title: PRC2 WT iMEFs H3K27me3 rep1 [D127C53]


title: Superinfection (Superinfected_5.75_1)


title: 22RV1_shC_DMSO_rep2


title: 22RV1_shC_DMSO_rep1


title: iPSC-derived MSC, sample 40

value: differentiation day 0


title: iPSC-derived osteoblast, sample 39

value: osteoblast


title: PRC2 WT iMEFs rep1 [A988T01 RNA-seq]


title: Eed_KO iMEFs H3K27me2 rep1 [D127C81]


title: Superinfection (Superinfected_5.5_2)

value: Lungs


title: H3.3K27M iMEFs H3K27me2 rep2 [D127C80]


title: 22RV1_shAR847_rep3

value: shRNA targeting AR (2)


title: Superinfection (Superinfected_5.5_1)

value: Superinfection


title: iPSC-derived MSC, sample 43


title: iPSC-derived preosteoblast, sample 38


title: iPSC-derived MSC, sample 37


title: Eed_KO iMEFs H3K27me2 rep2 [D127C82]


title: H3.3K27M iMEFs H3K27me2 rep1 [D127C79]


title: iPSC-derived osteoblast, sample 36


title: 22RV1_shAR847_rep1

value: Cell Line

value: Prostate Cancer


title: Superinfection (Superinfected_5.291_3)


title: Ezh2_Y641F iMEFs H3K27me2 rep2 [D127C78]


title: 22RV1_shAR574_rep3

value: shRNA targeting AR (1)


title: Superinfection (Superinfected_5.75_2)


title: Superinfection (Superinfected_5.291_1)


title: iPSC-derived preosteoblast, sample 35


title: 22RV1_shAR574_rep2


title: Ezh2_Y641F iMEFs H3K27me2 rep1 [D127C77]


title: 22RV1_shAR574_rep1


title: iPSC-derived MSC, sample 34


title: iPSC-derived osteoblast, sample 33

value: differentiation day21


title: iPSC-derived preosteoblast, sample 41


title: Ezh2_KO iMEFs H3K27me2 rep2 [D127C76]


title: Ezh2_KO iMEFs H3K27me2 rep1 [D127C75]


title: P29T1-444287 H3K27Ac rep2 [D851-D842C24]

data_processing:
Adapters and low‐quality bases (<Q20) were removed from Cut&Run-Seq reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were mapped to the mouse reference genome mm10 with Bowtie2 (v2.2.5) using default parameters. PCR duplicates were with with Picard Tools MarkDuplicates (v1.97).
BigWig files were created using DeepTools bamCoverage (v3.0.2) with the following parameters: --normalizeUsingRPKM –ignoreForNormalization chrX chrY –samFlagInclude 64 –extendReads. Reads overlapping problematic, blacklisted regions (mm10-blacklist.v2.bed) were excluded from the computation of coverage with the option --blackListFileName.
In addition to scaling by library size, in order to remove any composition biases, we calculated a normalizing factor using the BioconductoR csaw::normFactors function. The normalization factor was passed onto DeepTools bamCoverage with the parameter --scaleFactor.
Processing of ChIP-Seq reads was done similarly to Cut&Run-Seq reads. Reads were however mapped to the human reference genome assembly hg19.
Assembly: mm10 for Cut&Run-Seq libraries; hg19 for ChIP-Seq libraries
Supplementary files format and content: BigWig files of genome-wide enrichment of the probed histone modification.

source_name: Follicular lymphoma

value: Follicular lymphoma

value: EZH2 mut.


title: iPSC-derived preosteoblast, sample 32

value: preosteoblast


title: 22RV1_shAR847_rep2


title: PRC2 WT iMEFs H3K27me2 rep2 [D127C74]

value: WT


title: Superinfection (Superinfected_5.125_2)


title: P29T1-444287 H3K27Ac rep1 [D851-D842C23]


title: iPSC-derived MSC, sample 31

value: mesenchymal stem cell


title: Superinfection (Superinfected_5.208_1)


title: PRC2 WT iMEFs H3K27me2 rep1 [D127C73]

value: iMEFs


title: Superinfection (Superinfected_5.208_2)


title: P23T1-436388 H3K27Ac rep2 [D851-D842C22]


title: Superinfection (Superinfected_5.125_1)


title: Eed_KO iMEFs H3K4me3 rep2 [D387C140]


title: iPSC-derived osteoblast, sample 30


title: Superinfection (Superinfected_5.291_2)


title: IAV infection (IAV_7_2)

value: IAV infection


title: Eed_KO iMEFs H3K4me3 rep1 [D387C139]


title: P23T1-436388 H3K27Ac rep1 [D851-D842C21]


title: iPSC-derived preosteoblast, sample 29

value: differentiation day 7


title: H3.3K27M iMEFs H3K4me3 rep2 [D387C138]


title: IAV infection (IAV_7_1)


title: IAV infection (IAV_6)


title: iPSC-derived MSC, sample 28

value: differentiation day 0


title: P70T2-374143 H3K27Ac rep2 [D851-D842C18]


title: P25T1-438117 H3K27Ac rep1 [D851-D842C19]


title: IAV infection (IAV_5.75_2)


title: IAV infection (IAV_5.75_1)


title: Ezh2_Y641F iMEFs H3K4me3 rep2 [D387C136]


title: P70T2-374143 H3K27Ac rep1 [D851-D842C17]


title: iPSC-derived MSC, sample 25


title: Ezh2_Y641F iMEFs H3K4me3 rep1 [D387C135]


title: IAV infection (IAV_5.291_2)


title: P28T1-468558 H3K27Ac rep2 [D851-D842C16]

value: EZH2 WT


title: iPSC-derived osteoblast, sample 24

value: osteoblast


title: Ezh2_KO iMEFs H3K4me3 rep2 [D387C134]


title: IAV infection (IAV_5.291_1)

value: Lungs


title: Ezh2_KO iMEFs H3K4me3 rep1 [D387C133]


title: P28T1-468558 H3K27Ac rep1 [D851-D842C15]


title: P13T1-422898 H3K27Ac rep2 [D851-D842C14]


title: iPSC-derived MSC, sample 22


title: iPSC-derived preosteoblast, sample 23


title: PRC2 WT iMEFs H3K4me3 rep2 [D387C132]


title: IAV infection (IAV_5_2)


title: IAV infection (IAV_5_1)


title: H3.3K27M iMEFs H3K4me3 rep1 [D387C137]


title: P13T1-422898 H3K27Ac rep1 [D851-D842C13]


title: iPSC-derived osteoblast, sample 27


title: IAV infection (IAV_4_3)


title: PRC2 WT iMEFs H3K4me3 rep1 [D387C131]


title: P20T1-432387 H3K27Ac rep2 [D851-D842C12]


title: iPSC-derived osteoblast, sample 21


title: iPSC-derived preosteoblast, sample 26


title: IAV infection (IAV_4_2)


title: Eed_KO iMEFs H2AUb rep2 [D387C110]


title: P20T1-432387 H3K27Ac rep1 [D851-D842C11]


title: iPSC-derived MSC, sample 19


title: IAV infection (IAV_4_1)


title: Eed_KO iMEFs H2AUb rep1 [D387C109]


title: P121T1-565213 H3K27Ac rep2 [D851-D842C10]


title: iPSC-derived osteoblast, sample 18


title: H3.3K27M iMEFs H2AUb rep2 [D387C108]


title: IAV infection (IAV_3_2)


title: P121T1-565213 H3K27Ac rep1 [D851-D842C09]


title: iPSC-derived preosteoblast, sample 17


title: iPSC-derived MSC, sample 16


title: P122T2-565463 H3K27Ac rep2 [D851-D842C08]


title: Ezh2_Y641F iMEFs H2AUb rep2 [D387C106]


title: IAV infection (IAV_2_2)


title: iPSC-derived osteoblast, sample 15


title: Ezh2_Y641F iMEFs H2AUb rep1 [D387C105]


title: IAV infection (IAV_2_1)


title: IAV infection (IAV_1_2)


title: Ezh2_KO iMEFs H2AUb rep2 [D387C104]


title: P100T2-525120 H3K27Ac rep2 [D851-D842C02]


title: P123T3-574265 H3K27Ac rep1 [D851-D842C05]


title: iPSC-derived preosteoblast, sample 14


title: iPSC-derived MSC, sample 13


title: P123T3-574265 H3K27Ac rep2 [D851-D842C06]


title: iPSC-derived preosteoblast, sample 20


title: Ezh2_KO iMEFs H2AUb rep1 [D387C103]


title: IAV infection (IAV_1_1)


title: iPSC-derived osteoblast, sample 12


title: P100T2-525120 H3K27Ac rep1 [D851-D842C01]


title: SP infection (SP_7)

value: SP infection


title: iPSC-derived preosteoblast, sample 11


title: PRC2 WT iMEFs H2AUb rep1 [D387C101]


title: H3.3K27M iMEFs H2AUb rep1 [D387C107]


title: P14T2-531043 H3K27me3 rep1 [D347-D340C24]

description: Longitudinal; time point: 1


title: SP infection (SP_6_2)


title: PRC2 WT iMEFs H2AUb rep2 [D387C102]


title: IAV infection (IAV_3_1)


title: P42T2-522492 H3K27me3 rep2 [D347-D340C22]

description: Longitudinal; time point: 2


title: Ezh2_Y641F iMEFs PRC2i 2µM rep2 [D448-D447T111 RNA-seq]

value: UNC1999 2µM


title: SP infection (SP_6_1)


title: iPSC-derived osteoblast, sample 9


title: iPSC-derived MSC, sample 10


title: SP infection (SP_5.75)


title: PRC2 WT iMEFs PRC2i 2µM rep2 [D448-D447T108 RNA-seq]


title: iPSC-derived preosteoblast, sample 8


title: P42T2-522492 H3K27me3 rep1 [D347-D340C21]

description: Longitudinal; time point: 2


title: Ezh2_Y641F iMEFs PRC2i 0.25µM rep2 [D448-D447T110 RNA-seq]


title: SP infection (SP_5.291)


title: P42T1-496439 H3K27me3 rep2 [D347-D340C19]

description: Longitudinal; time point: 1


title: PRC2 WT iMEFs PRC2i 0.25µM rep2 [D448-D447T107 RNA-seq]


title: iPSC-derived MSC, sample 7


title: SP infection (SP_5.208)


title: iPSC-derived osteoblast, sample 6


title: P42T1-496439 H3K27me3 rep1 [D347-D340C18]

description: Longitudinal; time point: 1


title: SP infection (SP_5.125)


title: P14T3-543842 H3K27me3 rep1 [D347-D340C26]

description: Longitudinal; time point: 2


title: Ezh2_Y641F iMEFs PRC2i 2µM rep1 [D448-D447T105 RNA-seq]


title: P119T2-669855 H3K27me3 rep1 [D347-D340C16]

description: Longitudinal; time point: 2


title: iPSC-derived preosteoblast, sample 5


title: Ezh2_Y641F iMEFs PRC2i 0.25µM rep1 [D448-D447T104 RNA-seq]


title: P119T1-561105 H3K27me3 rep2 [D347-D340C14]

description: Longitudinal; time point: 1


title: Mock infection (Mock_6_2)

value: Mock infection


title: iPSC-derived MSC, sample 4


title: Mock infection (Mock_7)


title: PRC2 WT iMEFs PRC2i 0.25µM rep1 [D448-D447T101 RNA-seq]


title: iPSC-derived osteoblast, sample 3


title: Mock infection (Mock_6_1)


title: P119T1-561105 H3K27me3 rep1 [D347-D340C13]

description: Longitudinal; time point: 1


title: PRC2 WT iMEFs PRC2i 2µM rep1 [D448-D447T102 RNA-seq]


title: iPSC-derived preosteoblast, sample 2


title: P124T2-628394 H3K27me3 rep2 [D347-D340C11]

description: Longitudinal; time point: 2


title: Ezh2_Y641F iMEFs rep6 [D729T18 RNA-seq]


title: Mock infection (Mock_5.75)


title: Mock infection (Mock_5.291)


title: P124T2-628394 H3K27me3 rep1 [D347-D340C10]

description: Longitudinal; time point: 2


title: iPSC-derived MSC, sample 1


title: P124T1-577820 H3K27me3 rep2 [D347-D340C08]

description: Longitudinal; time point: 1


title: AMO1 cells, Naringenin 48h - 2

city: Catanzaro

first: Claudia

last: Veneziano

address: Viale Europa, Località Germaneto

department: Department of Experimental and Clinical Medicine

country: Italy

institute: "Magna Graecia" University of Catanzaro

data_processing:
Torrent Suite software v5.14.0 was used to align and process the raw sequences. Output normalized counts (in read per milion) were generated as .chp files.
Assembly: hg19
Supplementary files format and content: .chp file for each Sample

growth_protocol: AMO1 MM cells were treated with Hesperetin (250uM) and Naringenin (250uM) for 48h, then cells were collected and immediately resuspended in Trizol Reagent. Thus, RNA was extracted for RNA sequencing analysis.

extract_protocol:
RNA was extracted with the fenol/chloroform method, quality and quantity controlled with the NanoDrop system (Invitrogen).
Libraries preparation was manually performed using the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel, according to the Ion AmpliSeq Library Kit Plus.

treatment_protocol: AMO1 MM cells were plated in 6 well plate at a density of 500000 cells/mL in a final volume of 2mL per well, and treated with Hesperetin and Naringenin for 48h.

value: Multiple Myeloma plasma cells

value: Naringenin 250uM


title: Ezh2_Y641F iMEFs rep4 [D557C06 RNA-seq]


title: Ezh2_Y641F iMEFs rep5 [D729T17 RNA-seq]


title: Mock infection (Mock_5)


title: P124T1-577820 H3K27me3 rep1 [D347-D340C07]

description: Longitudinal; time point: 1

value: Follicular lymphoma


title: AMO1 cells, Hsperetin 48h - 2

value: Hesperetin 250uM


title: Mock infection (Mock_4)


title: Ezh2_Y641F iMEFs PRC2i ctrl rep2 [D448-D447T109 RNA-seq]

value: UNC2400 (ctrl for UNC1999)


title: AMO1 cells, Vehicle 48h - 2

value: Vehicle


title: Mock infection (Mock_3)


title: P93T2-418953 H3K27me3 rep2 [D347-D340C03]

description: Longitudinal; time point: 1

value: EZH2 mut.


title: Ezh2_Y641F iMEFs PRC2i ctrl rep1 [D448-D447T103 RNA-seq]

value: iMEFs


title: Mock infection (Mock_2)


title: P93T2-418953 H3K27me3 rep1 [D347-D340C02]

description: Longitudinal; time point: 1


title: AMO1 cells, Hsperetin 48h -1


title: Mock infection (Mock_1)


title: PRC2 WT iMEFs PRC2i ctrl rep2 [D448-D447T106 RNA-seq]

value: WT


title: P28T5-AH2667 H3K27me3 rep1 [D330C21]

description: Longitudinal; time point: 3


title: AMO1 cells, Vehicle 48h - 1


title: PRC2 WT iMEFs PRC2i ctrl rep1 [D448-D447T100 RNA-seq]


title: P28T4-593746 H3K27me3 rep2 [D330C20]

description: Longitudinal; time point: 2


title: 19 months SYN Rep 4

city: Lausanne

first: Martino

last: Ugolini

state: Vaud

address: Genopode

department: CIG

country: Switzerland

institute: UNIL

description: rRNA depleted RNA

data_processing:
Basecalling: FASTQ files obtained from Illumina’s bcl2FastQ 2.20.0.422
Adapter sequence clipping: Cutadapt 1.18 (-b AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -B AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 18) (Martin, 2011)
Quality-based trimming: Trimmomatic 0.38 (PE -phred33 SLIDINGWINDOW:5:22 MINLEN:18 TOPHRED33) (Bolger, Lohse, & Usadel, 2014).
Reads corrected with Rcorrector 1.0.3.1 (Song & Florea, 2015)
Reads derived from rRNA filtered out with SortMeRNA 2.1 (Kopylova, Noé, & Touzet, 2012), using rRNA sequences retrieved from the Rfam database and the Silva database.
Mapping: Segemehl 0.3.4 in split-read mode (Hoffmann et al., 2009)
Raw counts: featureCounts function 1.6.0 of the Subread package (Liao, Smyth, & Shi, 2014) (-p and --minOverlap 10 –s 1 -t exon -g gene_id).
Differentially expressed junctions (DEJs) identified using the software DIEGO (Doose et al., 2018) and LeafCutter (Y. I. Li et al., 2018).
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: Tab-delimited files of raw counts and differentially expressed junctions (DEJs)

source_name: Cortex-derived Synaptosomes (SYN)

extract_protocol:
Synaptosomes were extracted from cerebral cortices of different ages as previously described (Gray & Whittaker, 1962; Moczulska et al., 2014). Total homogenate samples were kept before proceding with synaptosome enrichment. Synaptosome samples were processed for RNA extraction according to (Smalheiser et al., 2014), and RNA was then extracted from the appositely prepared synaptosome samples and from TH samples through acidic phenol-chloroform extraction according to (Chomczynski, 1993).
10ng of RNA was used for library preparation, which was done using the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (TaKaRa, #635006) according to the manufacturer’s instructions. The obtained libraries are depleted for 18S and 28S rRNAs

tag: age

value: 19 months

value: cerebral cortex


title: Eed_KO iMEFs rep6 [D729T20 RNA-seq]


title: 19 months SYN Rep 3

description: rRNA depleted RNA


title: P93T3-442281 H3K27me3 rep1 [D347-D340C05]

description: Longitudinal; time point: 2


title: defp replicate 3

city: Ithaca

first: Heather

last: Feaga

address: 123 Wing Dr

institute: Cornell University

data_processing:
Reads were processed with Geneious. 27 bp from the 5' end  and 108 base pairs from the 3' end were trimmed to leave only the 16 base pair Tn-insertion site.
Reads were mapped with Geneious
Assembly: NC_000964
Supplementary files format and content: Excel file with tallied reads (RPKMs) of transposon insertions

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: bacterial cell

growth_protocol: LB 37C

extract_protocol:
Cell lysis, ammonium acetate precipitation of proteins, followed by isopropanol precipitation of gDNA
6 µg gDNA was digested with 3 units of MmeI for 2.5 hours at 37 °C, then treated with 6 units of antarctic phosphatase for 1 hour at 37 °C. DNA was then extracted with 300 µl  phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated with 50 µL 3M sodium acetate and 500 µL isopropyl alcohol. Dried pellets were dissolved in 27.5 µL 2 mM Tris-HCl pH 8.5. The DNA was ligated with one volume of 200-µM annealed adapters HRH-Tn1 and HRH-Tn2 in 1 mM tris-Cl pH 8.5. The ligated DNA was purified with the Qiagen PCR purification kit and amplified with the primers HRH-Tn3 and HRH-Tn4.

treatment_protocol: Transformed with transposon library

value: bacterial cell

value: defp


title: Eed_KO iMEFs rep5 [D729T19 RNA-seq]


title: P28T4-593746 H3K27me3 rep1 [D330C19]

description: Longitudinal; time point: 2


title: Ezh2_Y641F iMEFs rep3 [D557C05 RNA-seq]


title: defp replicate 1


title: defp replicate 2


title: PRC2 WT iMEFs rep6 [D729T14 RNA-seq]


title: 19 months SYN Rep 1

description: rRNA depleted RNA


title: P28T1-468558 H3K27me3 rep1 [D256-D251C02]

description: Longitudinal; time point: 1

value: EZH2 WT


title: AMO1 cells, Naringenin 48h - 1


title: PRC2 WT iMEFs rep5 [D729T13 RNA-seq]


title: 5 months TH Rep 4

description: rRNA depleted RNA

source_name: Cortex-derived Total Homogenate (TH)

value: 5 months


title: P162T2-AA6534 H3K27me3 rep2 [D164C19]

description: Longitudinal; time point: 3


title: WT replicate 3


title: H3.3K27M iMEFs rep4 [D557C12 RNA-seq]


title: WT replicate 2


title: H3.3K27M iMEFs rep3 [D557C11 RNA-seq]


title: 5 months TH Rep 3

description: rRNA depleted RNA


title: WT replicate 1


title: P162T3-593921 H3K27me3 rep2 [D330C18]

description: Longitudinal; time point: 2


title: P162T2-AA6534 H3K27me3 rep1 [D164C17]

description: Longitudinal; time point: 3


title: 19 months SYN Rep 2

description: rRNA depleted RNA


title: Drought treated 'Tarocco' Blood orange juice sac, 50 days after storage, Biol rep 3

city: Changsha

first: Ling

last: Sheng

address: Donghu

institute: Hunan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: http://citrus.hzau.edu.cn/orange/（Citrus sinensis v3.0)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Citrus sinensis

source_name: fruit juice sac

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruit juice sac

tag: developmental stage

value: postharvest stage

tag: line

value: ‘Tarocco’ Blood orange

value: Drought


title: P28T1-468558 H3K27me3 rep2 [D256-D251C03]

description: Longitudinal; time point: 1

value: Follicular lymphoma


title: Eed_KO iMEFs rep4 [D557C10 RNA-seq]


title: Eed_KO iMEFs rep3 [D557C09 RNA-seq]


title: Drought treated 'Tarocco' Blood orange juice sac, 50 days after storage, Biol rep 2


title: P162T2-440167 H3K27me3 rep2 [D330C16]

description: Longitudinal; time point: 1


title: P162T3-593921 H3K27me3 rep1 [D330C17]

description: Longitudinal; time point: 2


title: 5 months SYN Rep 4

description: rRNA depleted RNA


title: Drought treated 'Tarocco' Blood orange juice sac, 50 days after storage, Biol rep 1


title: 5 months SYN Rep 3

description: rRNA depleted RNA


title: Ezh2_KO iMEFs rep4 [D557C04 RNA-seq]


title: 5 months TH Rep 1

description: rRNA depleted RNA


title: Drought treated 'Tarocco' Blood orange juice sac, 30 days after storage, Biol rep 3


title: P162T2-440167 H3K27me3 rep1 [D330C15]

description: Longitudinal; time point: 1


title: Ezh2_KO iMEFs rep3 [D557C03 RNA-seq]


title: P16T3-609478 H3K27me3 rep2 [D330C13]

description: Longitudinal; time point: 2


title: 5 months SYN Rep 2

description: rRNA depleted RNA


title: PRC2 WT iMEFs rep4 [D557C02 RNA-seq]


title: Drought treated 'Tarocco' Blood orange juice sac, 30 days after storage, Biol rep 2


title: 5 months SYN Rep 1

description: rRNA depleted RNA


title: Drought treated 'Tarocco' Blood orange juice sac, 30 days after storage, Biol rep 1


title: P16T3-609478 H3K27me3 rep1 [D330C12]

description: Longitudinal; time point: 2


title: PRC2 WT iMEFs rep3 [D557C01 RNA-seq]


title: 5 months TH Rep 2

description: rRNA depleted RNA


title: P16T1-477055 H3K27me3 rep2 [D233C09]

description: Longitudinal; time point: 1


title: Drought treated 'Tarocco' Blood orange juice sac, 0 days after storage, Biol rep 3


title: 3 weeks SYN Rep 3

description: rRNA depleted RNA

value: 3 weeks


title: Drought treated 'Tarocco' Blood orange juice sac, 0 days after storage, Biol rep 2


title: 3 weeks SYN Rep 2

description: rRNA depleted RNA


title: P54T2-650598 H3K27me3 rep1 [D330C07]

description: Longitudinal; time point: 2


title: P16T1-477055 H3K27me3 rep1 [D233C08]

description: Longitudinal; time point: 1


title: 3 weeks SYN Rep 1

description: rRNA depleted RNA


title: Drought treated 'Tarocco' Blood orange juice sac, 0 days after storage, Biol rep 1


title: P54T1-519949 H3K27me3 rep1 [D233C23]

description: Longitudinal; time point: 1


title: Control 'Tarocco' Blood orange juice sac, 50 days after storage, Biol rep 3

value: Control


title: P89T2-409205 H3K27me3 rep1 [D330C05]

description: Longitudinal; time point: 2


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 8

city: Gimcheon

first: Yeongdon

last: Ju

state: Gyeongsangbuk-do

address: 214, Daehak-ro, Gimcheon-si

department: Department of Biomedical Laboratory Science

institute: Gimcheon University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
TMM+CPM normalization was performed by EdgeR.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Plasma

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

value: Plasma

tag: cycle

value: FOLFOX 7 cycles

tag: grade

value: grade 2


title: WGBS_ExE_E5.5_rep1

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

data_processing:
10X Genomic single-cell 3' RNA-seq
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", default parameters).
Assembly: mm10
Supplementary files format and content: For all samples there is one tar gz archive containing the gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix.
PolyA RNA-seq
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the human reference genome mm10 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
Assembly: mm10
Supplementary files format and content: tsv of TPM values
Total RNA-seq
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
To remove rRNA all reads were first aligned against the rDNA databank (rfam-5s-database-id98) using STAR and unmapped reads were kept for the next step.
Reads were subsequently aligned against the human reference genome mm10 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
Assembly: mm10
Supplementary files format and content: tsv of TPM values
Bisulfite-Seq
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads, max 150 reads).
Assembly: mm10
Supplementary files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

source_name: Embryo

extract_protocol:
Purelink Genomic DNA mini kit (Invitrogen)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: Embryo

value: Strain:CD-1; embryo sex:male/female

value: wild-type

value: no treatment


title: Control 'Tarocco' Blood orange juice sac, 50 days after storage, Biol rep 2


title: Control 'Tarocco' Blood orange juice sac, 50 days after storage, Biol rep 1


title: P89T2-409205 H3K27me3 rep2 [D330C06]

description: Longitudinal; time point: 2

value: EZH2 mut.


title: Control 'Tarocco' Blood orange juice sac, 30 days after storage, Biol rep 3


title: 3 weeks SYN Rep 4

description: rRNA depleted RNA

value: cerebral cortex


title: P89T1-374818 H3K27me3 rep2 [D164C09]

description: Longitudinal; time point: 1


title: WGBS_Epi_E5.5_rep1


title: WGBS_ESC3D_rep2

value: 3D epiblast stem cells

value: Mouse pluripotent stem cells

value: Cultured in 3D Matrigel with FGF2-ActivinA-XAV-Noggin


title: P89T1-374818 H3K27me3 rep1 [D164C07]

description: Longitudinal; time point: 1


title: WGBS_ESC3D_rep1


title: Control 'Tarocco' Blood orange juice sac, 30 days after storage, Biol rep 2

value: fruit juice sac

value: postharvest stage

value: ‘Tarocco’ Blood orange


title: P121T1-565213 H3K27me3 rep2 [D256-D251C24]

value: Follicular lymphoma


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 4


title: WGBS_Embryo3D_rep2


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 7


title: P121T1-565213 H3K27me3 rep1 [D256-D251C23]


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 3


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 2


title: WGBS_Embryo3D_rep1


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 6


title: P100T2-525120 H3K27me3 rep1 [D256-D251C20]


title: Control 'Tarocco' Blood orange juice sac, 0 days after storage, Biol rep 2

value: Control


title: Control 'Tarocco' Blood orange juice sac, 0 days after storage, Biol rep 3


title: Plasma, FOLFOX 3 cycles & grade 1, Day0, sample 8

value: Plasma

value: FOLFOX 3 cycles

value: grade 1


title: E7.5_rep2

description:
E7.5_Epi_rep2
RNA_TPM.tsv

extract_protocol:
RNA was extracted from the epiblast of E3.5, E4.5, E5.5, E6.5, and E7.5 following the manufacturer's protocol (PicoPure RNA isolation kit; KIT0204; ThermoFisher Scientific) and eluted in 7 L elution buffer. The full eluate was utilized to prepare the library. Prior to the construction of the library, the integrity and quality of the RNA were evaluated using a 4200 Agilent TapeStation device and RNA ScreenTape reagents (Agilent). Samples having a RIN > 7.0 for RNA integrity were used.
The library was generated with the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input kit (634485, Takara Bio) following the manufacturer's instructions, with the exceptions listed below. To account for the input differences, fragmentation of RNA was done for 6 minutes at 85 °C on E3.5 and E4.5 epiblast samples, and for 4 minutes at 94 °C on E5.5, E6.5, and E7.5 epiblast samples. Adapters and indices from Illumina were added to distinguish the libraries (SMARTer RNA Unique Dual Index kit, 634451, Takara Bio). Instead of NucleoMag beads, the libraries were purified with AMPure XP beads (A63880, Beckman Coulter). ZapR v3 and R-probes v3 were used to deplete ribosomal cDNA (supplied with the kit). Libraries were amplified for thirteen cycles, purified, and analyzed for quality and concentration using a 4200 Agilent TapeStation instrument and D5000 ScreenTape reagents (Agilent).
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: Embryo


title: P123T3-574265 H3K27me3 rep2 [D256-D251C18]


title: Plasma, FOLFOX 7 cycles & grade 3, Day0, sample 1

value: FOLFOX 7 cycles

value: grade 3


title: E7.5_rep1

description:
E7.5_Epi_rep1
RNA_TPM.tsv

value: Strain:CD-1; embryo sex:male/female

value: wild-type

value: no treatment


title: Plasma, FOLFOX 2 cycles & grade 1, Day0, sample 7

value: FOLFOX 2 cycles


title: Plasma, FOLFOX 7 cycles & grade 2, Day0, sample 5

value: grade 2


title: P123T3-574265 H3K27me3 rep1 [D256-D251C17]

value: EZH2 mut.


title: Control 'Tarocco' Blood orange juice sac, 30 days after storage, Biol rep 1

value: fruit juice sac


title: E6.5_rep3

description:
E6.5_Epi_rep3
RNA_TPM.tsv


title: E6.5_rep2

description:
E6.5_Epi_rep2
RNA_TPM.tsv


title: Plasma, FOLFOX 3 cycles & grade 2, Day0, sample 6


title: P100T2-525120 H3K27me3 rep2 [D256-D251C21]


title: Plasma, FOLFOX 3 cycles & grade 2, Day0, sample 5


title: P122T2-565463 H3K27me3 rep1 [D256-D251C11]


title: E7.5_rep3

description:
E7.5_Epi_rep3
RNA_TPM.tsv


title: Control 'Tarocco' Blood orange juice sac, 0 days after storage, Biol rep 1

value: postharvest stage


title: E6.5_rep1

description:
E6.5_Epi_rep1
RNA_TPM.tsv


title: Plasma, FOLFOX 2 cycles & grade 1, Day0, sample 4


title: P70T2-374143 H3K27me3 rep2 [D233C27]


title: Plasma, FOLFOX 3 cycles & grade 1, Day0, sample 3


title: P70T2-374143 H3K27me3 rep1 [D233C26]


title: NHA_PEF-5_2

type: RNA

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

description: Gene expression data from PEF-5 treated NHA cells after 24 hours from exposure

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 ug were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using TAC software using RMA.

label: biotin

source_name: Normal Human Astrocytes (primary)

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: Cells were cultured in ABM Basal Medium supplemented with AGM SingleQuots Supplements (Lonza).

extract_protocol: RNA was extracted after 24 hours from treatment using QIAzol and miRNeasy Micro Kit from Qiagen.

treatment_protocol: Cells were exposed to electric fields via electroporation cuvettes (0.1-cm gap) connected to a pulse generator (Schaffner NSG504). Electric pulses of exponential shape were used in our experiments. Their amplitude and duration were maintained at 300 V (for an electric field of 0.3 MV/m) and 40 μs at full width at half maximum, respectively. Cells were exposed to 5 electric pulses with an interpulse interval of 1 Hz.

value: treatment (PEF-5)

tag: sample

value: NHA


title: Plasma, FOLFOX 3 cycles & grade 1, Day0, sample 2


title: E5.5_rep1

description:
E5.5_Epi_rep1
RNA_TPM.tsv


title: Plasma, FOLFOX 2 cycles & grade 1, Day0, sample 1


title: E5.5_rep2

description:
E5.5_Epi_rep2
RNA_TPM.tsv


title: P29T1-444287 H3K27me3 rep1 [D233C20]

value: Follicular lymphoma


title: P29T1-444287 H3K27me3 rep2 [D233C21]


title: P122T2-565463 H3K27me3 rep2 [D256-D251C12]


title: GIST-T1, InsH, rep2

city: Boston

first: Kyung Lock

last: Kim

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-seq reads were aligned using STAR 2.5.3 to the hg38 human reference
RSEM (v1.3.2) was used for obtaining read counts and transcripts per million.
DESeq2 (v1.38.3) was used for differential expression genes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and TPM values for each Sample

growth_protocol: GIST-T1 cell line was obtained from Cosmo Biosciences. Cells were passaged in DMEM with 10% serum, 1X antibiotics and 1X Glutamax (Life Technologies).

extract_protocol:
RNA was isolated using an RNeasy Plus Kit (Qiagen). RNA concentration was measured by NanoDrop (Thermo Scientific) and quality was determined by TapeStation (Agilent).
For each sample, 1 μg of the total RNA was used for RNA-seq library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB).

value: cell line established from a metastatic GIST

value: InsH


title: NHA_PEF-5_1


title: NHA_PEF-5_3


title: P25T1-438117 H3K27Ac rep2 [D851-D842C20]

extract_protocol:
Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018).
In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes.
In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes.
Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction.
Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100).


title: NHA_sham_4

description: Gene expression data from untreated (sham) NHA cells

value: control (sham)


title: NHA_PEF-5_4


title: NHA_sham_2


title: E4.5_rep2

description:
E4.5_Epi_rep2
RNA_TPM.tsv

value: Embryo


title: NHA_sham_3


title: P25T1-438117 H3K27me3 rep1 [D233C17]


title: E5.5_rep3

description:
E5.5_Epi_rep3
RNA_TPM.tsv


title: NHA_sham_1


title: GIST-T1, InsF, rep2

value: InsF


title: P23T1-436388 H3K27me3 rep2 [D233C15]


title: E3.5_rep3

description:
E3.5_ICM_rep3
RNA_TPM.tsv


title: GIST-T1, InsE, rep2

value: InsE


title: P23T1-436388 H3K27me3 rep1 [D233C14]


title: D283_PEF-5_4

description: Gene expression data from PEF-5 treated D283_Med cells after 24 hours from exposure

source_name: Medulloblastoma cell line

growth_protocol: D283_Med cells were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% FBS, 2mM glutamine and 100 U penicillin-0.1mg streptomycin/ml.


title: E4.5_rep3

description:
E4.5_Epi_rep3
RNA_TPM.tsv

value: Strain:CD-1; embryo sex:male/female


title: E3.5_rep1

description:
E3.5_ICM_rep1
RNA_TPM.tsv

value: wild-type


title: GIST-T1, control, rep2

value: WT


title: D283_sham_4

description: Gene expression data from untreated D283_Med cells


title: D283_PEF-5_3


title: D283_sham_3


title: P20T1-432387 H3K27me3 rep1 [D256-D251C29]

value: EZH2 WT


title: GIST-T1, InsH, rep1


title: P141T1-606917 H3K27me3 rep2 [D256-D251C27]


title: D283_PEF-5_2


title: GIST-T1, InsG, rep1

value: InsG


title: EpiLC_rep3

description:
EpiLC_rep3
RNA_TPM.tsv

source_name: cell line

extract_protocol:
RNA was isolated from the samples according to the manufacturer's instructions using the RNeasy kit (74004, Qiagen).
1 µg RNA was used as input for the library preparation. Prior to the construction of the library, the integrity and quality of the RNA were evaluated using a 4200 Agilent TapeStation device and RNA ScreenTape reagents (Agilent). Samples having a RIN > 7.0 for RNA integrity were used. The library was generated with the TruSeq Stranded mRNA capture kit (20020594, KAP Biosystems) following the manufacturer's instructions, with the exceptions listed below. Unique Dual-Indexed (UDI, KAPA biosystems) adapters were ligated and the libraries were amplified for 8 cycles. Quality and concentration were measured using a 4200 Agilent TapeStation instrument and D5000 ScreenTape reagents (Agilent).
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: cell line

value: 2D epiblast-like stem cells

value: Mouse pluripotent stem cells

value: ESCs cultured for 48h in FGF2-ActivinA


title: GIST-T1, InsF, rep1


title: E4.5_rep1

description:
E4.5_Epi_rep1
RNA_TPM.tsv

value: no treatment


title: P141T1-606917 H3K27me3 rep1 [D256-D251C26]

value: Follicular lymphoma


title: EpiLC_rep1

description:
EpiLC_rep1
RNA_TPM.tsv


title: P20T1-432387 H3K27me3 rep2 [D256-D251C30]


title: P13T1-422898 H3K27me3 rep2 [D233C06]


title: Hi-C, N.furzeri rep2

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

institute: The Hebrew University of Jerusalem

data_processing:
As an initial step, Hi-C sequencing reads were processed against the previously published Nothobranchius furzeri genome assembly (GCA_001465895.2_Nfu_20140520) using the Juicer pipeline for analyzing Hi-C datasets (version 1.8.9 of Juicer Tools). The resulting Hi-C matrices were then used as input to the 3D DNA pipeline (Dudchenko et al. 2017)  for automated scaffolding. Manual correction of obvious assembly and scaffolding errors was carried out using Juicebox. After finalizing the scaffolding, Hi-C reads were reprocessed against the new assembly using the Juicer pipeline. The Hi-C assembly was aligned to the published genome (GCA_001465895.2_Nfu_20140520) by using LAST (https://gitlab.com/mcfrith/last/-/blob/main/doc/last-papers.rst).
Assembly: Nfu_20140520
Supplementary files format and content: hic file

organism: Nothobranchius furzeri

source_name: Tail

growth_protocol: Fibroblast cells were prepared and cultured as described previously. Briefly, following sedation, a 2–3 mm section of tissue was trimmed from the tail fin using a sterile razor blade, and disinfected for 10 min with a 25 ppm iodine solution (PVP-I, Holland Moran 229471000) in DPBS (Biological Industries). After rinsing with DPBS, tissue samples were incubated for 2 h with 1 ml of an antibiotic solution containing Gentamicin (50 µg/ml Gibco) and PrimocinTM (50 µg/ml, InvivoGen) in DPBS at room temperature. The samples were then transferred to an enzymatic digestion buffer (200 µl, in a 24-well plate) containing Dispase II (2 mg/mL, Sigma Aldrich) and Collagenase Type P (0.4 mg/mL, Merck Millipore) in Leibovitz's L-15 Medium (Gibco), and were dissociated mechanically with a sterile pair of scissors. The digested tissue was mixed with 400 µl of complete Leibovitz's L-15 growth medium (Gibco), supplemented with Fetal Bovine Serum (15% FBS, Gibco), penicillin/streptomycin (50 U/ml, Gibco), Gentamicin (Gibco, 50 µg/ml) and PrimocinTM (50 µg/ml, InvivoGen). For the first 7 days, cells were washed daily with fresh media before adding new media. The cells were incubated at 28°C in a humidified incubator (Binder, Thermo Scientific) with normal air composition until a stable cell-line was generated.

extract_protocol:
The Hi-C procedure used to map 3D genomic interactions in killifish was adapted from previous studies as follows. Trypsinized killifish fibroblasts (2.5 X 10^6) were crosslinked using 37% formaldehyde (Sigma) at a final concentration of 1% for 15  min at room temperature. The formaldehyde was then quenched with 2.5 M glycine (at a final concentration of 0.25 M), and the cells were centrifuged at 2,000g for 5 min, washed once with 1× PBS, and stored at −80 °C. For use, the cells were lysed in 250 µl of cold Hi-C Lysis Buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl,0.2% Igepal CA630) and incubated on ice for 15 minutes, followed by centrifugation at 2,500 g for 5 minutes, a wash with 500 µL cold Hi-C Lysis Buffer, and centrifugation at 2,500 g for 5 minutes. The pellet was resuspended in 50 µl 0.5% SDS, and incubated at 62◦C for 10 minutes. The SDS was quenched by adding 145 µl H2O and 25 µl 10% Triton X-100, followed by a 15-minute incubation at 37◦C.
Restriction digestion was carried out by adding 25 µl of 10× NEBuffer 2 and 100 U of the MboI restriction enzyme (NEB, R0147), followed by a 2 h incubation at 37◦C in a Thermomixer at 900 rpm. The reaction was then incubated at 62 °C for 20 min to inactivate the restriction enzyme. Fragment ends were filled in by adding: 37.5 µl 0.4 mM biotin-14-dATP (ThermoFisher Scientific, # 19524-016); 1.5 µl each of 10 mM dCTP, dGTP, and dTTP; and 8 µl of 5 U µl−1 DNA Polymerase I Large (Klenow) Fragment (NEB M0210). The reaction was incubated at 37 °C in a Thermomixer at 900 rpm. for 45 min. Fragment end ligation was carried out by adding 663  µl H2O, 120  µl 10× NEB T4 DNA ligase buffer (NEB B0202), 100  µl 10% Triton X-100, 12  µl BSA (10  mg/ml, NEB) and 5  µl 400  U/µl T4 DNA ligase (NEB M0202), and incubating at room temperature for 4  h with rotation. Nuclei were then pelleted by centrifugation at 3,500 g for 5 minutes, resuspended in 130 µl ChIP Elution Buffer (1% SDS, 0.1 M NaHCO3), supplemented with Proteinase K, and incubated at 65◦C overnight to reverse crosslinking. Samples were then sonicated using a Covaris E220, and the DNA was purified using the MinElute PCR Purification Kit (Qiagen #28006), with elution in a total volume of 300 µ1× EB buffer.
Biotin-labeled DNA was purified on 20 µl of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602), which were separated on a magnetic stand, washed with 400 µl of 1× TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20), and resuspended in 300 µl of 2× Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl). The sonicated DNA was added to the beads and the mixture was incubated for 15 minutes at room temperature on a rotator. After separation on a magnetic stand, the beads were washed with 600 µl 1× TWB, and were heated at 55◦C in a Thermomixer with shaking for 2 minutes. After removal of the supernatant on a magnetic stand, the TWB wash and 55◦C incubation were repeated. Final libraries were prepared on beads using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645) as follows: End repair was carried out by resuspending the beads in 50 µl 1× EB buffer, and adding 3 µl NEB Ultra End Repair Enzyme and 7 µl NEB Ultra End Repair Enzyme, followed by incubation at 20◦C for 30 minutes, and then at 65◦C for 30 minutes.
Adapters were ligated to DNA fragments by adding 30 µl Blunt Ligation mix, 1 µl Ligation Enhancer, and 2.5 µl NEB Adapter, incubating at 20◦C for 20 minutes, and then adding 3 µl USER enzyme, and incubating at 37◦C for 15 minutes. Beads were then separated on a magnetic stand and washed with 600 µl TWB for 2 minutes at 55◦C, 1000 rpm in a Thermomixer. After separation on a magnetic stand, the beads were washed in 100 µl 0.1 × TE buffer, then were resuspended in 16 µL 0.1 × TE buffer, and heated at 98◦C for 10 minutes. For PCR, 5 µl of each of the i5 and i7 NEB Next sequencing adapters were added together with 25 µl 2× NEB Ultra PCR Master Mix. The reaction was incubated at 98◦C for 30 s followed by 12 cycles of 98◦C for 10 s, 65◦C for 30 s, and 72◦C for 1 minute, followed by incubation at 72◦C for 5 minutes. The beads were separated on a magnetic stand, and the supernatant was cleaned with 1× AMPure XP beads. Libraries were sequenced in a paired-end format on an Illumina NextSeq instrument using NextSeq 500/550 high output kits.

value: Tail

value: Fibroblast


title: EpiLC_rep2

description:
EpiLC_rep2
RNA_TPM.tsv


title: D283_sham_2

value: control (sham)


title: P13T1-422898 H3K27me3 rep1 [D233C05]


title: GIST-T1, control, rep1

value: cell line established from a metastatic GIST


title: Hi-C, N.furzeri rep1


title: GIST-T1, InsE, rep1


title: GIST-T1, InsG, rep2


title: GIST-T1, WT, WCE, rep1

data_processing:
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10
PCR duplicates were removed by Picard toolkit 2.9.2.
ChIP-Seq density tracks were generated by bedgraph to BigWig format after RPM normalization.
Peaks were called with MACS3, correcting against input controls.
Assembly: hg38
Supplementary files format and content: ChIP-seq density tracks in BigWig format

extract_protocol:
For ChIP-seq, cultured cells were fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418). H3K27ac was immunoprecipitated with a polyclonal rabbit H3K27ac antibody from Active Motif (cat 39133).  H3K27me3 was immunoprecipitated with a polyclonal rabbit H3K27me3 antibody, clone C36B11 (Cell Signaling 9733).
ChIP DNA was used to generate sequencing libraries by NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).


title: EpiSC_rep2

description:
EpiSC_rep2
RNA_TPM.tsv

value: 2D epiblast stem cells

value: Conversion of ESCs via FGF2-ActivinA treatment


title: P42T1-492439 [D334T44 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 mut.


title: D283_sham_1


title: D283_PEF-5_1

value: treatment (PEF-5)