title: mESC_KMT2C-D_dKO_WGBS

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Bisulphite reads were aligned to the reference mouse genome (mm10) using version 1.2 of an internally developed pipeline, publicly available for download from https://github.com/luuloi/Meth10X.
Adaptor sequences were removed using in-house bash script in paired end mode following library prep kit guide
Bwa-meth verion 0.20 (https://github.com/brentp/bwa-meth) was used to align reads to mm10 using bwa version 0.7.13 (https://github.com/lh3/bwa).
Generated bam files were merged and PCR duplicates were removed using Picard tools 2.3.0 (http://broadinstitute.github.io/picard).
Quality of the merged bam files was assessed using Qualimap 2.2.1 (Okonechnikov et al., 2016).
DNA methylation and SNP  calling was performed using MethylDackel (https://github.com/dpryan79/MethylDackel) and Biscuit (https://github.com/zwdzwd/biscuit).
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: mouse ESCs with a complete loss of KMT2C/D (dKO)

growth_protocol: Mouse ESCs were cultured as previously described (Dorighi et al., 2017)

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Mini kit (Qiagen, USA).
CEGX TrueMethyl Seq (Cambridge Epigenetix, UK)
post-bisulphite adapter tagging

treatment_protocol: no treatment

tag: tissue type

value: Embryonic stem cells

value: complete loss of KMT2C/D (dKO)


title: Bio49_50uM_PMB_187927

status: Public on Jan 23 2019

type: SRA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

description:
sample_counts.txt
sample name in processed data file:
3-E_PMB.187927.bam

library_source: transcriptomic

data_processing:
Reads were aligned to the hg38 genome using STAR v2.5.2b
Aligned data were read into R and summarized as counts per gene using the Bioconductor TxDb.Hsapiens.UCSC.hg38.knownGene package in concert with the GenomicAlignments package
Data were converted to counts/million counts, along with observation-level weights using the Bioconductor limma function voomWithQualityWeights
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tab-delimited matrix of gene counts, with Entrez Gene IDs in the first column, and the BAM file names in the header

molecule: total RNA

organism: Homo sapiens

source_name: Kidney cells

growth_protocol: In brief, tissue was finely minced under sterile conditions, subjected to collagenase digestion with shaking at 37°C for 30 minutes, mixed 1:1 with horse serum, vortexed, and allowed to briefly settle, and supernatant was harvested. The cell suspension was centrifuged, washed, and plated in T25 flasks containing DMEM/F12 media supplemented with insulin, transferrin, selenium, and hydrocortisone. The Nortis devices were constructed with an extracellular matrix of type I collagen, and the cell chamber was coated with type IV collagen to facilitate cell adhesion. Cultures of primary renal epithelial cells, upon reaching greater than 80% confluency, were subjected to trypsin digestion and manual cell scraping to obtain single-cell suspensions. The cells were counted, washed, and resuspended at a concentration of 20 × 106 cells/ml, and 1–2 μl were injected into the Nortis device. Cells were incubated to allow matrix adhering for 12 hours before initiating flow at a rate of 0.5 μl/min. The integrity of the tubule cell structure was assessed grossly by light microscopy weekly.

extract_protocol:
Cells cultured within the kidney MPS were isolated after 48 hours of treatment, and total RNA was isolated using the Quagen RNeasy Micro Kit
The RNA library was prepared using a SMARTer Stranded Total RNA Sample Prep Kit - Low Input Mammalian (Takara 634861)

treatment_protocol: Kidney MPS were exposed to 50 μM of PMB, or 50 μM of NAB739, or 50μM of NAB741, or 10uM PMO, or 10uM PSO,or control for 48 hours

tag: cell type

value: primary renal epithelial cells

tag: growth protocol

tag: treatment

value: 50 uM PMB

tag: donor


title: Bio49_50uM_PMB_187926

description:
sample_counts.txt
sample name in processed data file:
2-E_PMB.187926.bam


title: genomic DNA from tumor, ccRCC sample 10

type: genomic

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description: ccRCC Tumor Tissue Sample

hyb_protocol: bisulphite converted DNA (EZ DNA methylation gold) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing: Fluorescence intensities were extracted using the Methylation module (1.9.0) in the Genome Studio software (V2011.1). CpG-sites at chromosome X and Y, detection p-value>0.05, nbeads <=3 or located within 3 bp from known SNP in any the samples 1-127 were filtered (set to NA) in samples 1-127. CpG-sites meeting the criteria in any of Pat1-Pat6 and Tumor free samples (116-127) were filtered in samples Pat1-Pat6. Bead types were normalized using the BMIQ method.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: ccRCC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted accordint to standard protocols and DNA purity and concentration determined by spechtrophotometry.

treatment_protocol: Tumor samples were snap-frozen after extirpation and stored at -80 degrees celcius.

tag: age

tag: gender

value: Male

tag: tnm stage

value: TNM II

tag: progress status (m0-pf

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: genomic DNA from tumor, ccRCC sample 15

description: ccRCC Tumor Tissue Sample

value: Female


title: Bio50_2D_187924

description:
sample_counts.txt
sample name in processed data file:
BIO50-K_2D.187924.bam


title: F18 normal human diploid fibroblasts non-irradiated

type: RNA

city: Quebec city

first: Patrick

middle: J

last: Rochette

state: Quebec

address: 1050 chemin Ste-Foy - H2-10

department: Axe Médecine Régénératrice

country: Canada

institute: CHU de Québec – Université Laval

description: gene expression of non-irradiated cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The file log2_and_linear_values.txt includes the log2 and linear values used to create heat maps. Linear values were used to calculate the fold change between control and UVA-irradiated samples.

source_name: non-irradiated cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: All four fibroblasts cell strains were grown in the same culture medium : Dulbecco Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% antibiotics.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: Cells were chronically irradiated or not with 20 kJ/m^2 UVA, 2 times a day, 4 days a week for 5 weeks

tag: tissue

value: skin

value: Normal human diploid fibroblasts

tag: Sex

value: female


title: Trincr1-ko_2iL_rep2

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

country: China

institute: Peking University

description:
replicate2
WT_Trincr1-ko_2iL_PDL_FPKM.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR v2.5.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1
For RIP-seq,reads aligned to non-polyA transcripts were excluded. To calculate fold enrichment for RIP, we normalized the FPKM value of every transcript to the average of all transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample in txt file

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin-coated plates in 2i+LIF medium which is consist of N2B27 supplemented with MEK inhibitor PD0325901 (1.0 μM), GSK3 inhibitor CHIR99021 (3.0 μM) and leukemia inhibitory factor (1,000 unit /ml).

extract_protocol:
For RNA-seq,cells were treated with TRIzol and followed with phase seperation,  RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.For RIP-seq,The RNA in input lysis and  precipitated beads were extracted by TRIzol.
For RNA-seq,total RNA was subjected to two rounds of purification using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds cDNA was ligated to adaptors and sequenced with illumina Hiseq2000 platform.For RIP-seq,Input RNA were treated as the total RNA in RNA-seq,the IP RNA RNA from RIP experiment was directly used for the synthesis of ds-cDNA.

treatment_protocol: For PD+LIF experiments, ESCs were first plated in 2i+LIF for 24 hr, then washed once with 1xPBS and changed to N2B27 supplemented with PD+LIF, cultured for another 4 days before analysis with medium changed every other day.For RIP-seq, 3XFLag-Trim71 overexpressing and empty ESCs cultured in 2i+LIF medium were UV-crosslinked and lysed in lysis buffer. 1/40 lysis was taken as input. The remaining lysis was subjected to immunoprecipitation using FLAG antibody.

tag: strain

tag: developmental stage

value: 3.5 days

value: embryonic stem cells

tag: genotype/variation

tag: media


title: IP_empty_rep1

description:
replicate1
Trim71_RIP.txt

value: empty

tag: antibody

value: FLAG


title: Bio49_Control_187930

description:
sample_counts.txt
sample name in processed data file:
7-E_Ctrl.187930.bam


title: WT_PDL_rep2

value: wild type

value: PDL


title: mESC_KMT2C-D_dCD_WGBS

library_source: genomic

source_name: mouse ESCs with a point mutation in the catalytic SET domain (dCD) of KMT2C and KMT2D

value: Embryonic stem cells

tag: genotype


title: Bio49_50uM_PMB_187928

description:
sample_counts.txt
sample name in processed data file:
4-E_PMB.187928.bam


title: Trincr1-ko_2iL_rep1

description:
replicate1
WT_Trincr1-ko_2iL_PDL_FPKM.txt


title: WT_PDL_rep1


title: genomic DNA from tumor, ccRCC sample 9

description: ccRCC Tumor Tissue Sample

value: TNM I


title: mBlood_KMT2D_HOM_WGBS

source_name: blood (B cell-depleted) from mice with the homozygous chr15: 98,835,228 A>T  mutation in KMT2D (Ile5482Asn)

growth_protocol: A single cell suspension of the spleen was obtained by gently mashing the solid tissue through a 70 μm nylon mesh filter. Bulk B cell purification was performed by cell staining based on the Miltenyi Biotec Pan-B Cell Isolation Kit Mouse II protocol, followed by manual MACS cell separation by negative depletion

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen, USA)
Mouse B cell genomic DNA and B cell-depleted blood DNA was sheared to an average size of 800 bp. 200ng of sheared DNA was used for the bisulphite reaction, library preparation and indexing carried out according to the manufacturer’s instructions (CEGX TrueMethyl Seq, UK). Paired-end 150bp sequencing was performed for each library on the Illumina HiSeqX platform using the HiSeq X™ Ten Reagent Kit v2.

value: blood (B cell-depleted)

value: HOM


title: Bio50_10uM_PSO_187922

description:
sample_counts.txt
sample name in processed data file:
40-K_PSO.187922.bam

value: primary renal epithelial cells

value: 10uM PSO


title: Bio49_2D_187923

description:
sample_counts.txt
sample name in processed data file:
BIO49-K_2D.187923.bam


title: WT_2iL_rep2


title: mBlood_KMT2D_HET_WGBS

source_name: blood (B cell-depleted) from mice with the heterozygous chr15: 98,835,228 A>T  mutation in KMT2D (Ile5482Asn)

value: HET


title: Bio50_10uM_PSO_187921

description:
sample_counts.txt
sample name in processed data file:
33-K_PSO.187921.bam


title: mESC_KMT2C-D_WT_WGBS

source_name: mouse ESCs with the wild type KMT2C/D

tag: tissue type

value: wild type KMT2C/D


title: mBcells_KMT2D_HOM_WGBS_rep2

source_name: mouse spleen B cells with the homozygous chr15: 98,835,228 A>T  mutation in KMT2D (Ile5482Asn)

tag: cell type

value: Spleen bulk B cells


title: mBlood_KMT2D_WT_WGBS

source_name: blood (B cell-depleted) from the wild type KMT2D mice

value: WT


title: WT_2iL_rep1


title: Bio50_10uM_PMO_187919

description:
sample_counts.txt
sample name in processed data file:
31-_K_PMO.187919.bam

tag: growth protocol

value: 10uM PMO


title: Total CD4+ T cells_CsA_PI_2_RNA-seq

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

data_processing:
Adapters were removed using cutadapt.
Trimmed reads were pseudoaligned to the mm10 transcriptome using Kallisto.
Genome_build: mm10
Supplementary_files_format_and_content: Count table

source_name: Spleen

growth_protocol: Total splenic CD4+ T cells were isolated from C57BL/6 mice

extract_protocol:
Total RNA was extracted using Qiagen kits.
Clontech SMART-seq

treatment_protocol: CD4+ T cells were pre-treated for 1h ethanol or CsA (1uM) and then left unstimulated or stimulated with PMA (10nM) and Ionomycin (1uM) for 2h

value: CD4+ T cells

tag: isolation

value: Untouched CD4+ cell purification


title: Total CD4+ T cells_CsA_PI_3_RNA-seq


title: F18 normal human diploid fibroblasts UVA-irradiated

description: gene expression of chronically UVA-irradiated cells

source_name: chronically UVA-irradiated cells

value: skin

value: Normal human diploid fibroblasts

value: female


title: genomic DNA from tumor, ccRCC sample 6

description: ccRCC Tumor Tissue Sample

value: Male

value: TNM III

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: Bio50_10uM_PSO_187920

description:
sample_counts.txt
sample name in processed data file:
32-K_PSO.187920.bam

tag: treatment

tag: donor


title: mBcells_KMT2D_WT_WGBS_rep2

source_name: mouse spleen B cells with the wild type KMT2D


title: Total CD4+ T cells_ethanol_PI_3_RNA-seq


title: genomic DNA from tumor, ccRCC sample 5

description: ccRCC Tumor Tissue Sample

tag: age

tag: gender

value: Female

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: genomic DNA from tumor, ccRCC sample 12

description: ccRCC Tumor Tissue Sample

tag: tnm stage

tag: progress status (m0-pf

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: Total CD4+ T cells_CsA_PI_1_RNA-seq


title: Bio50_10uM_PMO_187918

description:
sample_counts.txt
sample name in processed data file:
28-K_PMO.187918.bam

value: primary renal epithelial cells


title: Bio50_10uM_PMO_187917

description:
sample_counts.txt
sample name in processed data file:
22-K_PMO.187917.bam


title: genomic DNA from tumor, ccRCC sample 7

description: ccRCC Tumor Tissue Sample


title: Total CD4+ T cells_ethanol_PI_2_RNA-seq


title: genomic DNA from tumor, ccRCC sample 3

description: ccRCC Tumor Tissue Sample


title: Bio50_Control_187915

description:
sample_counts.txt
sample name in processed data file:
34-K_Ctrl.187915.bam

value: Control


title: mBcells_KMT2D_WT_WGBS

data_processing:
Bisulphite reads were aligned to the reference mouse genome (mm10) using version 1.2 of an internally developed pipeline, publicly available for download from http://github.com/astatham/Bisulphite_tools.
Adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters.
Bismark v0.8.326 was used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”
PCR duplicates were removed using Picard v1.91 (http://broadinstitute.github.io/picard)
Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”
Genome_build: mm10
Supplementary_files_format_and_content: bw; mouse_KMT2Dmut_WGBS_bigTable.tsv.gz

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen, USA)
Mouse B cell genomic DNA was sheared to an average size of 800 bp. 200ng of sheared DNA was used for the bisulphite reaction, library preparation and indexing carried out according to the manufacturer’s instructions (CEGX TrueMethyl Seq, UK). Paired-end 150bp sequencing was performed for each library on the Illumina HiSeqX platform using the HiSeq X™ Ten Reagent Kit v2.

value: Spleen bulk B cells


title: mBcells_KMT2D_HOM_WGBS

value: HOM


title: genomic DNA from tumor, ccRCC sample 1

description: ccRCC Tumor Tissue Sample

value: TNM II


title: Total CD4+ T cells_ethanol_PI_1_RNA-seq

value: CD4+ T cells


title: Bio50_Control_187914

description:
sample_counts.txt
sample name in processed data file:
27-K_Ctrl.187914.bam


title: mBcells_KMT2D_HET_WGBS

source_name: mouse spleen B cells with the heterozygous chr15: 98,835,228 A>T  mutation in KMT2D (Ile5482Asn)

value: HET


title: genomic DNA from tumor, ccRCC sample 2

description: ccRCC Tumor Tissue Sample


title: Bio50_Control_187916

description:
sample_counts.txt
sample name in processed data file:
39-K_Ctrl.187916.bam


title: Total CD4+ T cells_CsA_US_3_RNA-seq

value: Untouched CD4+ cell purification


title: Bio50_Control_187913

description:
sample_counts.txt
sample name in processed data file:
21-K_Ctrl.187913.bam


title: ctrl10

city: Shanghai

first: Jia

middle: yi

last: Liu

address: Fengyang road 458，Huangpu District

institute: Changzheng Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each Sample

source_name: urinary exosomes

extract_protocol:
A MiRNeasy Serum/Plasma Kit (QIAGEN, Valencia, CA, USA) was used to extract RNA from urinary exosome samples in accordance with the manufacturer’s protocol.
Fragmented RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA). The libraries were paired-end sequenced (PE150, Sequencing reads were 150 bp) at Guangzhou RiboBio Co., Ltd. (Guangzhou, China)using IlluminaHiSeq 3000 platform.

tag: disease state

value: Normal control

tag: tumor stage

value: control

tag: sample type

value: urinary exosomes


title: Total CD4+ T cells_CsA_US_2_RNA-seq

tag: strain


title: ctrl9


title: genomic DNA from tumor, ccRCC sample 4

description: ccRCC Tumor Tissue Sample

value: Male

value: TNM I


title: ctrl8

value: Female


title: Total CD4+ T cells_CsA_US_1_RNA-seq


title: Total CD4+ T cells_ethanol_US_3_RNA-seq


title: insR_GSK-LSD1_rep2

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

description: SET- 2 LSD1 (Leu659_Asn660insArg, insR) were treated with GSK-LSD1 for 48 hours

data_processing:
bcl2fastq2 (version 2.2) was used for base-calling.
Adapter contamination, polyA read through, and low quality tails were removed usign bbduk (version 38.23) with the following parameters: ref=polyA.fa.gz,truseq_rna.fa.gz k=13 int=f ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
Read mapping was performed with STAR (version 2.6.0c)  with the following parameters: --genomeDir ENSEMBL.homo_sapiens.release-75 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
Reads aligned over annotated genes were quantified using HTSeq (version 0.9.1) with the following command: htseq = count -f bam -s yes
DESeq2 normalized counts are in the tab-delimited text file SET2_DMSOandGSK_DESeqNormalizedCounts.txt containing Transcript_ID in the first column and values for each sample in subsequent columns.
Genome_build: hg19
Supplementary_files_format_and_content: Both the processed count matrix and the HTSeq raw counts file for each individual sample are provided

molecule: polyA RNA

source_name: insR SET-2 cells, GSK-LSD1, 48 hours

growth_protocol: SET-2 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
RNA was harvested using the Rneasy Plus kit (Qiagen).
RNA libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

treatment_protocol: Cells were seeded at 500,000 cell/mL and then treated with DMSO (0.1% v/v) or 250 nM GSK-LSD1 (Sigma Aldrich) for 48 hours. Cells were then washed twice with cold PBS and snap frozen.

tag: cell line

tag: genotype/variation

value: drug-resistant SET-2 LSD1 (Leu659_Asn660insArg)

value: acute myeloid leukemia


title: Total CD4+ T cells_ethanol_US_2_RNA-seq


title: insR_GSK-LSD1_rep1


title: insR_DMSO_rep3

description: SET- 2 LSD1 (Leu659_Asn660insArg, insR) were treated with DMSO for 48 hours

source_name: insR SET-2 cells, DMSO, 48 hours

value: DMSO


title: ctrl7


title: insR_DMSO_rep2


title: ctrl5


title: Total CD4+ T cells_ethanol_US_1_RNA-seq


title: Total CD4+ T cells_Comp10_PI_3_RNA-seq

treatment_protocol: CD4+ T cells were pre-treated for 1h with DMSO or Compound 10 (12.5uM) and then left unstimulated or stimulated with PMA (10nM) and Ionomycin (1uM) for 2h


title: Total CD4+ T cells_Comp10_PI_2_RNA-seq


title: ctrl4


title: ctrl3


title: insR_GSK-LSD1_rep3


title: ctrl1


title: Total CD4+ T cells_Comp10_PI_1_RNA-seq


title: genomic DNA from tumor, ccRCC sample 8

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: Utest10

value: clear cell renal cell carcinoma

value: Furhmann Grade III


title: WT_GSK-LSD1_rep2

description: wt SET-2 cells were treated with GSK-LSD1 for 48 hours

source_name: WT SET-2 cells, GSK-LSD1, 48 hours

value: wild type


title: WT_GSK-LSD1_rep1


title: Total CD4+ T cells_DMSO_PI_2_RNA-seq

value: CD4+ T cells


title: ctrl2


title: mBcells_KMT2D_HET_WGBS_rep2

value: Spleen bulk B cells

tag: genotype

value: HET


title: ctrl6

value: Normal control


title: WT_DMSO_rep3

description: wt SET-2 cells were treated with DMSO for 48 hours

source_name: WT SET-2 cells, DMSO, 48 hours


title: Total CD4+ T cells_DMSO_PI_1_RNA-seq

value: Untouched CD4+ cell purification


title: Total CD4+ T cells_Comp10_US_1_RNA-seq


title: Utest8

value: Furhmann Grade II

value: urinary exosomes


title: Utest7

value: Male


title: WT_DMSO_rep2


title: Total CD4+ T cells_DMSO_US_2_RNA-seq


title: WT_DMSO_rep1

data_processing:
bcl2fastq2 (version 2.2) was used for base-calling.
Adapter contamination, polyA read through, and low quality tails were removed usign bbduk (version 38.23) with the following parameters: ref=polyA.fa.gz,truseq_rna.fa.gz k=13 int=f ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
Read mapping was performed with STAR (version 2.6.0c)  with the following parameters: --genomeDir ENSEMBL.homo_sapiens.release-75 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
Reads aligned over annotated genes were quantified using HTSeq (version 0.9.1) with the following command: htseq = count -f bam -s yes
DESeq2 normalized counts are in the tab-delimited text file SET2_DMSOandGSK_DESeqNormalizedCounts.txt containing Transcript_ID in the first column and values for each sample in subsequent columns.
Genome_build:GSM3436194 GSM3436195 GSM3436196 GSM3436197 GSM3436198 GSM3436199 GSM3436200 GSM3436201 GSM3436202 GSM3436203 GSM3436204 GSM3436205 GSM3436206 GSM3436207 GSM3436208 GSM3436209 GSM3436210 GSM3436211 GSM3436212 GSM3436213 GSM3436214 GSM3436215 GSM3436216 GSM3436217 GSM3436218 GSM3436219 GSM3436220 GSM3436221 GSM3436222 GSM3436223 GSM3436224 GSM3436225 hg19
Supplementary_files_format_and_content: Both the processed count matrix and the HTSeq raw counts file for each individual sample are provided


title: Utest9

value: Female


title: Total CD4+ T cells_Comp10_US_2_RNA-seq


title: insR_DMSO_rep1

value: drug-resistant SET-2 LSD1 (Leu659_Asn660insArg)


title: Utest6


title: WT_GSK-LSD1_rep3

value: acute myeloid leukemia


title: insR_GSK_H3K4ME2

data_processing:
bcl2fastq2 (version 2.2) was used for base-calling.
Reads were aligned to hg19 using BWA mem.
Resulting alignment bam files were converted to sam files using SAMtools (version 0.1.19).
Resulting alignment sam files were sorted using samtools (version 0.1.19).
Duplicates were removed with Picard tools (version 2.18.5) using the following command: MarkDuplicates VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true.
ChIP-Seq BigWig tracks were generated using the BEDTools2 (version 2.26.0) genomeCoverageBed command followed by the UCSC bedGraphToBigWig utility.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig density files were generated by BEDTools2 and UCSC tools.

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Sonication of crosslinked cells was calibrated such that DNA was sheared to between 300bp and 2000bp.
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

treatment_protocol: Cells were seeded at 500,000 cell/mL and then treated with DMSO (0.1% v/v) or 250 nM GSK-LSD1 (Sigma Aldrich) for 48 hours. Cells were then washed twice with cold PBS, and snap frozen on dry ice.

tag: chip antibody

value: AB_2614985 (H3K4me2-human antibody, Active Motif 39141, LOT# 01008001)


title: insR_GSK_GFI1B

tag: cell type

value: AB_449000 (GFI1B antibody, Abcam ab26132, LOT# GR318193-8)


title: Naïve CD4 T cells_Comp10_PI_3_RNA-seq

growth_protocol: Splenic CD4+ T cells were isolated from C57BL/6 mice, and naïve CD4+CD62L+CD69- T cells were sorted.

treatment_protocol: Sorted cells were pre-treated for 1h with DMSO or Compound 10 (12.5uM) and then left unstimulated or stimulated with PMA (10nM) and Ionomycin (1uM) for 2h

value: CD4+CD62L+CD69- sorted cells


title: insR_GSK_H3K27AC

value: AB_2561016 (H3K27ac-mouse antibody, Active Motif 39133, LOT# 31814008)


title: insR_GSK_LSD1

value: LSD1 (Bethyl Laboratories A300-215A, LOT# 2


title: insR_GSK_Input


title: Utest5

value: clear cell renal cell carcinoma


title: Naïve CD4 T cells_Comp10_PI_1_RNA-seq

value: CD4+ T cells


title: Utest4


title: Naïve CD4 T cells_DMSO_PI_2_RNA-seq


title: insR_DMSO_H3K27AC

value: DMSO


title: Utest1

value: Furhmann Grade I


title: Naïve CD4 T cells_DMSO_PI_1_RNA-seq


title: Naïve CD4 T cells_Comp10_US_2_RNA-seq


title: insR_DMSO_H3K4ME2


title: Naïve CD4 T cells_Comp10_US_1_RNA-seq


title: Naïve CD4 T cells_DMSO_US_3_RNA-seq


title: Total CD4+ T cells_DMSO_US_1_RNA-seq


title: WT_GSK_H3K27AC

value: wild type


title: insR_DMSO_Input


title: insR_DMSO_LSD1


title: WT_GSK_H3K4ME2


title: Naïve CD4 T cells_DMSO_US_1_RNA-seq


title: WT_GSK_LSD1


title: Utest3

value: Furhmann Grade I-II


title: Utest2


title: insR_DMSO_GFI1B


title: WT_GSK_Input


title: WT_DMSO_H3K4ME2


title: WT_DMSO_H3K27AC


title: Naïve CD4 T cells_Comp10_PI_2_RNA-seq


title: WT_DMSO_GFI1B


title: WT_DMSO_LSD1

value: LSD1 (Bethyl Laboratories A300-215A, LOT# 2)


title: WT_DMSO_Input


title: Naïve CD4 T cells_DMSO_US_2_RNA-seq


title: WT_GSK_GFI1B


title: OTUD1 Sev

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

institute: Institude of Systems Biomedicine

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

source_name: Bone marrow

growth_protocol: For bone marrow derived macrophages (BMDM), bone marrow cells were isolated from femurs and tibiae of 10 week old WT or Otud1 knock out C57BL/6 mice. Cells were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin and 20 ng/mL recombinant murine GM-CSF (Peprotech) in a 10 cm dish for 7 days before experiments. Mature macrophages were harvested by incubating with PBS-EDTA for 10 minutes and cultured on 6-well for further experiments.

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected by HSV-1(17 strain) or SeV (Cantell strain) for 0 or 6 hours

value: Bone marrow derived macrophages

value: 10 weeks

tag: infection

value: SeV for 6 hr


title: GIST_T1_ERCC_IMJQ1_24h_2

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

description:
RNA-seq in a human GIST cell line treated with imatinib, JQ1 or control.
GIST_T1_RNA_all_fpkm_exprs_norm.txt

data_processing:
Cell-count normalized RNA-seq data were aligned using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
FPKM values were normalized to ERCC spike-in.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files, with cell count and ERCC normalized FPKM, are in text format

source_name: KIT-dependent GIST cell line

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen). RNA was normalized to cell count, then ERCC RNA Spike-In Control (Ambion) was added to allow for cell count normalization of gene expression changes.
Libraries for Illumina NextSeq 500 sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced with single-end 75 bp reads.

treatment_protocol: Cells were treated with the indicated drug(s) at 500 nM.

value: Combination imatinib and JQ1 24 hours


title: GIST_T1_ERCC_IMJQ1_24h_1


title: OTUD1 Hsv

value: HSV-1 for 6 hr


title: GIST_T1_ERCC_JQ1_24h_2

value: JQ1 24 hours


title: GIST_T1_ERCC_JQ1_24h_3


title: WT Sev

value: wild-type


title: GIST_T1_ERCC_IMJQ1_24h_3


title: GIST_T1_ERCC_JQ1_24h_0


title: WT Hsv


title: GIST_T1_ERCC_IM_24h_3

value: Imatinib 24 hours


title: cerebral malaria E U133A array

city: Tübingen

first: Angelica

last: Boldt

address: Wilhelmnstr 27

country: Germany

institute: Institute for Tropical Medicine

description: Gene expression data from pooled RNA of whole blood from 4 children with cerebral malaria

hyb_protocol: After purification and precipitation at -20°C, we fragmented 20 µg of this cRNA by heat and ion-mediated hydrolysis at 94°C [200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc] and hybridized it to the microarray. We also added increasing concentrations of spiked controls expected to hybridize to the 5’ and 3’ transcript regions of the Escherichia coli genes bioB, bioC and bioD and of the cre gene of the P1 bacteriophage. We hybridized the arrays with the targets at 45°C for 16 h and then washed them at 25°C with 6 x saline sodium phosphate-EDTA (0.9 M NaCl, 60 mMNaH2PO4, 6 mM EDTA+0.01% Tween 20) for 10 min, followed by a stringent wash at 50°C with 100 mM MES, 0.1 M [Na+], 0.01% Tween 20 for 12 min. We then stained the arrays with 10 μg/ml phycoerythrin-conjugated streptavidin (Molecular Probes Europe BV, Leiden, Netherlands) during 10 min. We did the hybridization, washing and staining procedures using the GeneChip® Fluidics Station 400 (Affymetrix, Santa Clara, CA).

scan_protocol: We determined the fluorescence intensities using a laser confocal scanner (Agilent GeneArray ® Scanner), with excitation 488 nm, spot size 4 µm and pixel space 3µm and analyzed the scanned images using Affymetrix® Microarray Suite version 5.0 (Affymetrix, Santa Clara, CA).

data_processing: We standardized for sample loading and variations in staining by scaling the signals on all arrays to constant target intensity (TGT 150).All microarray results were homogeneous with respect to average background, noise (Raw Q) and percent of genes called present, had spiked control signals within the expected range and adequate 3’/5’ ratio values (under 3) of the signals of the housekeeping gene transcripts (GAPDH, 18SrRNA). The scaling factors of all arrays compared to each other did also not differ by a factor higher than 3.3. These facts allowed us to compare the signals between the microarrays of two groups, totalizing 25 AxCo, 25 UxA, 25 UxCo, 25 SxCo, 25 SxA, 25 SxU, 26 CexCo, 25 CexA, 25 CexU, and 25 SxU comparisons for U133A and U133B (but two U133B microarrays of asymptomatic infection and one of cerebral malaria could not be used due to low hybridization quality, in this case totalizing 15 AxCo and 20 CexCo, CexA, CexU and CexS U133B comparisons). We calculated the signals on the arrays, the signal ratios between them and the corresponding measure of likelihood of change and direction (called “change p-value”) with aid of the Affymetrix® Microarray Suite version 5.0 (Affymetrix, Santa Clara, CA). We excluded probe sets whose signal intensities reached values under 50 in all the investigated groups and considered the expression of a certain gene as increased or decreased if it varied positively by a factor ≥ 1.9 or negatively by a factor ≤ -1.9 and the corresponding change p-value resulted in decreases to lower than 0.15 or in increases to higher than 0.85, respectively, in at least 15 comparisons. We used the one class analysis of the Significance Analysis of Microarrays (SAM) program for the signal ratios (logged on base 2) to identify those genes having significant changes at a false discovery rate of 0.004%.

label: biotin

source_name: pooled whole blood RNA of 4 African children with cerebral malaria

label_protocol: We prepared cRNA and labeled it with biotinylated UTP and CTP by in vitro transcription using a T7 promoter-coupled double-stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc., Farmingdale, NY).

extract_protocol: We extracted whole blood RNA using the PAXgene Blood RNA System (Qiagen, Hilden), pooled it in equal amounts to a total of 5 µg from four individuals and synthesized the first- and second-strand cDNA by using the SuperScript Double-Stranded cDNA Synthesis Kit (Life Technologies Inc., Rockville, MD) and an oligo-dT24-T7 primer.

tag: tissue

value: pooled whole blood RNA of 4 samples

tag: developmental stage

value: children

tag: diesease status

value: with cerebral malaria


title: cerebral malaria C U133A array


title: cerebral malaria F U133A array


title: cerebral malaria D U133A array


title: GIST_T1_ERCC_IM_24h_2

tag: treatment


title: cerebral malaria G U133A array


title: severe malaria B U133A array

description: Gene expression data from pooled RNA of whole blood from 4 children with severe malaria

source_name: pooled whole blood RNA of 4 severely anemic African children with malaria

value: with malaria associated with severe anemia


title: severe malaria D U133A array


title: WT Mock

tag: age


title: GIST_T1_ERCC_JQ1_6h_3

value: JQ1 6 hours


title: GIST_T1_ERCC_IM_24h_1


title: H1975 cell lines

city: Hwasun-gun

first: Seung-won

last: Lee

state: Jeollanam-do

address: 264 Seoyang-ro, Hwasun-eup

country: South Korea

institute: Chonnam National University Medical School

description: microRNA form lung cancer cell lines

hyb_protocol: biotin-labeled sample were hybridized using GeneChip® Hybridization Oven to the Affymetrix miRNA microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the GeneChip® Scanne

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: H1975 cell lines

label_protocol: 1 ug total RNA using the FlashTag™ Biotin HSR RNA Labeling Kit

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Lung cancer cell line


title: OTUD1 Mock


title: H1650 cell lines

description: microRNA form lung cancer cell lines

source_name: H1650 cell lines


title: severe malaria C U133A array


title: A549 cell lines

description: microRNA form lung cancer cell lines

source_name: A549 cell lines


title: uncomplicated malaria H U133A array

source_name: pooled whole blood RNA of 4 African children with uncomplicated malaria

value: with uncomplicated malaria


title: severe malaria A U133A array


title: uncomplicated malaria F U133A array

description: Gene expression data from pooled RNA of whole blood from 4 children with uncomplicated malaria


title: Tum_1k_H3_TAF_R1

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

institute: University of Mainz

description:
Input control for H3 TAF ChIP-Seq from Drosophila
Used as control while processing

data_processing:
Library strategy: TAF-ChIP
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila sample and K562 samples against hg38 (ensemble release 84).
The mapped bam files were normalized to RPKM using deepTools, and bigwig coverage file was generated
Genome_build: dm6 (Drosophila melanogaster), hg38 (K562 Cells)
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks

organism: Drosophila melanogaster

source_name: Neural Stem Cells (Type II)

extract_protocol:
Conventional libraries: After precipitating and pelleting, DNA was dissolved in 30 μl of TE buffer pH 8.0. The recovered DNA was converted into libraries using NebNext Ultra II DNA library preparation kit, following manufacturer’s protocol.
TAF-ChIP: Fixed cells were directly sorted in 240 μl of 140mM RIPA (10mM Tris-Cl pH 8.0, 140mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS), and sonicated with 3 cycles at low power settings for breaking the nuclei. 15 μl of Protein A and G Dynabeads were coupled to 1 μg of specific antibody in the blocking buffer (RIPA 140mM supplemented with 0.2 mg/ml BSA, 0.05 mg/ml of glycogen and 0.2 mg/ml of yeast t-RNA) for 3 hrs at 4°C. The unfragmented chromatin were centrifuged at 14000 rpm for 10 minutes at 4°C, and the supernatant was transferred to the tube with blocked and antibody coupled beads. The samples were incubated at 4°C overnight with head over tail rotations. The samples were then washed twice briefly with 300 μl of home made tagmentation buffer (20 mM Tris(hydroxymethyl)aminomethane pH 7.6; 10 mM MgCl2; 20% (vol/vol) dimethylformamide) using magnetic rack for beads separation. The washed beads were resupended in 20 μl of 1X tagmentation DNA buffer (Nextera XT Kit) containing 1 μl of Nextera DNA tagmentation enzyme and incubated at 37 °C for 40 minutes with constant shaking in a thermoblock at 500 rpm. Following the tagmentation, the beads were washed as following; once with 140mM RIPA (10mM Tris-Cl pH 8.0, 140mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS), four times with 250mM RIPA (10mM Tris-Cl pH 8.0, 250mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS) and twice with TE buffer pH8.0 (10mM Tris-Cl pH 8.0 and 0.1mM EDTA pH8.0). The samples after proteinase K treatment for reverse-crosslinking were subjected to phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 μl of TE buffer pH 8.0. The DNA was amplified in a 100 μl reaction with 1X NEBNext High-Fidelity PCR Mix with primers containing molecular indices (listed in Table 1) with following program; 72 °C for 3min, {98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 30 seconds} for 12 cycles, 72 °C for 5 minutes, and hold at 4 °C. The PCR reaction was purified with beads based size selection to remove any fragment that might be of larger than 1000 bp size. Ampure Xp beads were added to the PCR reaction in a ratio of 0.2X ratio to bind larger fragments. The magnetic beads were separated with the help of magnetic rack and supernatant was transferred to a fresh tube. Ampure Xp beads were added to the PCR reaction in a ration of 0.8X to bind the target library. After PCR purification, libraries were analyzed on Agilent Bioanalyzer for size distribution and the concentration was measured using Qubit fluorometer. The finished libraries were pooled in equimolar amounts and sequenced on illumina NextSeq 500.

value: Neural Stem Cells (Type II)

tag: tissue type

value: Larval brain

tag: ip target


title: GIST_T1_ERCC_JQ1_6h_2


title: uncomplicated malaria E U133A array


title: uncomplicated malaria G U133A array


title: Tum_Conv_Input_H3K9Me3

description:
Input control for conventional H3K9Me3 ChIP-Seq from Drosophila
Used as control while processing

value: Fragmented Input Control

value: Input


title: GIST_T1_ERCC_JQ1_6h_1


title: Tum_Conv_Input_H3K4Me3

description:
Input control for conventional H3K4Me3 ChIP-Seq from Drosophila
Used as control while processing


title: GIST_T1_ERCC_IM_6h_3

value: Imatinib 6 hours


title: GIST_T1_ERCC_IM_6h_2


title: Asymptomatic F U133A array

description: Gene expression data from pooled RNA of whole blood from 4 children with asymptomatic infection

source_name: pooled whole blood RNA of 4 African children with asymptomatic infection

value: with asymptomatic Plasmodium falciparum infection


title: uncomplicated malaria D U133A array


title: Tum_1k_H3_TAF_R2


title: Asymptomatic G U133A array


title: Tum_Conv_H3K9Me3_R1

description: Conventional Tum NSCs H3K9Me3 ChIP Seq Replicate1

value: Active Motif (Cat No- 39161)


title: Tum_Conv_H3K9Me3_R2

description: Conventional Tum NSCs H3KMe3 ChIP Seq Replicate2


title: GIST_T1_ERCC_IM_6h_1


title: Tum_Conv_H3K4Me3_R2

description: Conventional Tum NSCs H3K4Me3 ChIP Seq Replicate2

value: ab8580 (Abcam)


title: GIST_T1_ERCC_DMSO_3

value: DMSO


title: GIST_T1_ERCC_DMSO_2


title: Tum_Conv_H3K4Me3_R1

description: Conventional Tum NSCs H3K4Me3 ChIP Seq Replicate1


title: Tum_1K_H3K9Me3_R2

description: 1000 Tum NSCs H3K9Me3 Profile Replicate2


title: Tum_1K_H3K9Me3_R1

description: 1000 Tum NSCs H3K9Me3 Profile Replicate1


title: GIST_T1_ERCC_DMSO_1


title: severe malaria E U133A array


title: GIST-T1_JQ1_BRD4_input

description: ChIP-seq or input control from human cell line

data_processing:
All Chip-Seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a ThruPLEX DNA-seq Kit (Rubicon).

value: 500 nM of JQ1


title: Asymptomatic C U133A array

value: pooled whole blood RNA of 4 samples


title: Tum_1K_H3K4Me3_R2

description: 1000 Tum NSCs H3K4Me3 Profile Replicate2


title: GIST-T1_JQ1_BRD4

value: BRD4, Bethyl Laboratories A301-985A100


title: Tum_1K_H3K4Me3_R1

description: 1000 Tum NSCs H3K4Me3 Profile Replicate1


title: Asymptomatic B U133A array

value: children


title: controls C U133A array

description: Gene expression data from pooled RNA of whole blood from 4 healthy children

source_name: pooled whole blood RNA of 4 healthy African children

value: healthy


title: controls NA06 U133A array


title: GIST-T1_Imatinib_BRD4_input

value: 500 nM of Imatinib


title: GIST-T1_Imatinib_BRD4


title: controls E U133A array


title: GIST-T1_DMSO_BRD4_input

value: DMSO for 24 hours.


title: controls NA01 U133A array


title: YJATAC0453: gDNA

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial biology

country: Taiwan

institute: Academia Sinica

data_processing:
ATAC-seq reads were aligned using bowtie2
The abundance was calculated by using bamCoverage
Genome_build: AGPv4
Supplementary_files_format_and_content: Coverage track is BigWig format

organism: Zea mays

source_name: Seedlings

growth_protocol: B73 maize seeds were sown in potting media and the growth condition is at 28 °C with light intensity of 200 μmol/m2/s on a 14/10-hr day/night cycle.

extract_protocol:
Seeding maize tissue were chopped by a double edge razor blade and the slurry was filtered through Miracloth, followed by filtration through a 20 µm nylon mesh twice to remove large debris. After centrifugation, the nuclei were pelleted together with chloroplasts and starch grains. The pellet was resuspended in the CRB buffer where chloroplasts burst. Filter this nuclei suspension through a 10-µm mesh twice. Load approximately 400 ul of this green-colored nucleus suspension on top of the Percoll-Sucrose gradient and centrifuge the tube. Nuclei fractionated at the interface between CRB and SCB layer are transferred and pelleted in NEB buffer.
Maize seedling genomic DNA was extract by MagMax Plant DNA Kit (Thermo Fisher Scientific).
Freshly isolated nuclei and extracted gDNA were sujected to fragmentation and tagging. After cleanup, first PCR was performed to amplify DNA fragments and add barcodes. Second, the secondary PCR cycle numbers were determined by qPCR. The quality of constructed library was checked by Qubit and Bioanalyzer. Sequencing was performed with Illumina HiSeq 4000.

tag: line

value: Seedlings

value: wild type

tag: molecule subtype

value: genomic DNA


title: Asymptomatic A U133A array


title: GIST-T1_DMSO_BRD4


title: YJATAC0432: 2500 nuclei

value: Extracted nuclei


title: Control 3

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3  NC_002947.4  L27758.1
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

organism:
Pseudomonas putida
Escherichia coli

source_name: E. coli bacteria + P. putida bacteria + IncPα plasmid

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid were cultured in triplicate in 10 mL 0, 0.05, 10.0, and 50.0 mg/L carbamazepine, at 25 °C, without shaking

tag: e. coli strain

tag: p. putida strain

tag: plasmid

value: IncPalpha RP4 plasmid

tag: protocol

value: control


title: GIST-48B_JQ1_input

source_name: KIT-Independent GIST cell line


title: GIST-48B_JQ1_H3K27Ac

value: H3K27ac, Abcam ab4729


title: Control 2


title: 5 CAB4 Pi+ JHL135

city: Saint-Hyacinthe

first: Philippe

last: Vogeleer

address: 3200 rue Sicotte

institute: Université de Montréal

description: Gene expression data from Δpst mutant OD0.6 rep2

hyb_protocol: Following fragmentation, 1 ug of cDNA were hybridized for 16 hr at 45C on E. coli Genome 2.0 Array . Hybridizations were performed at the Génome Québec Innovation Centre (McGill University, Montréal, Canada).  the Génome Québec Innovation Centre (McGill University, Montréal, Canada).

scan_protocol: Scans were performed at the Génome Québec Innovation Centre (McGill University, Montréal, Canada) according to http://www.affymetrix.com/estore/ guidelines

data_processing: Data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation, Expression levels obtained from 3 independent biological replicates were compared using Robustness of the data was further enhanced by the EB (Wright and Simon) algorithm and p-value calculation,   further enhanced by the EB (Wright and Simon) algorithm and p-value calculation. Since the RMA algorithm  diminished the false positive rate and compressed the fold  change, a 1.5-fold change cut-off value was used for determination of the differentially expressed genes  FlexArray 1.1 software  independent biological replicates were compared using  FlexArray 1.1 software  robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation.

organism: Escherichia coli O157:H7 str. EDL933

source_name: Δpst mutant OD0.6

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells from overnight LB cultures were inoculated into 25mL of Mops medium containing 1.32 mM KH2PO4 with a starting OD600 at 0.15 and grown to an OD600 0.6.

extract_protocol: RiboPure™-Bacteria Kit (Ambion, Austin, TX)

tag: genotype

value: {delta}pst mutant

tag: phenotype

value: PhoB activation

tag: bacterial density


title: 4 CAB3 Pi+ JHL134

description: Gene expression data from Δpst mutant OD0.6 rep1


title: 2 WT6 Pi+ JHL132

description: Gene expression data from EDL933 OD0.6 rep2

value: WT


title: 1 WT5 Pi+ JHL131

description: Gene expression data from EDL933 OD0.6 rep1


title: 6 CAB5 Pi+ JHL136

description: Gene expression data from Δpst mutant OD0.6 rep3


title: 3 WT7 Pi+ JHL149

description: Gene expression data from EDL933 OD0.6 rep3


title: controls B U133A array


title: GIST-48B_Imatinib_H3K27Ac

tag: chip antibody


title: YJATAC0433: 5000 nuclei

tag: tissue


title: GIST-48B_Imatinib_input


title: Control 1


title: 50-3

value: 50.0 mg/L carbamazepine


title: GIST-48B_DMSO_input


title: 50-1


title: 50-2


title: GIST-48B_DMSO_H3K27Ac


title: 10-3

value: 10 mg/L carbamazepine


title: GIST-T1_JQ1_input

value: 500 nM of JQ1


title: 10-2


title: 10-1


title: paired normal lung tissue of of patient No.6

city: Zhoushan

first: yun

middle: li

last: Xu

address: No. 739, Dingshen Road, Lincheng Street, Dinghai District  Zhoushan City, Zhejiang Province, China

institute: Zhoushan hospital

description: Gene expression data from normal lung tissue

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: normal lung tissue

label_protocol: Total RNA were amplified, labeled and purified by using Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: To accurately acquire tumor cells and normal cells from lung tissues, samples were microdissected using a laser capture microdissection system (Applied Biosystems® ArcturusXT™, ABI)

value: normal tissue


title: Invasive lung adenocarcinoma tissue of patient No.6

description: Gene expression data from invasive lung adenocarcinoma tissue

source_name: Invasive lung adenocarcinoma tissue

value: tumor tissue


title: GIST-T1_Imatinib_input

value: 500 nM of Imatinib


title: paired normal lung tissue of of patient No.4


title: 0_05-3

value: 0.05 mg/L carbamazepine


title: GIST-T1_Imatinib_H3K27Ac


title: LV E10_1

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

hyb_protocol: Labeled complementary RNA (cRNA) products were hybridized onto bead arrays, washed and stained with streptavidin-Cy3 according to standard Illumin protocol

scan_protocol: Gene chips were scanned using the Scanner 3000 7G

data_processing: cRNAs were profiled using Illumina Mouse WG-6 v2 BeadChips and analyzed in Genespring GX 11.0. Data were quality filtered to exclude signal intensities below background, and expression profile differences of 4 fold or greater at a significance threshold of 0.01 or less were compiled into upregulated and downregulated transcript lists.

source_name: embryo

label_protocol: Standard Illumina protocol

extract_protocol: AVC and the primary ventricle of E9.0 and E10.0 mouse embryos were dissected out and RNA was extracted with a Zymo research kit.

value: LV


title: LV E10_3


title: LV E9_3


title: LV E10_2


title: Invasive lung adenocarcinoma tissue of patient No.4

source_name: lung adenocarcinoma tissue


title: LV E9_2


title: 0_05-2


title: paired normal lung tissue of of patient No.3


title: LV E9_1


title: AVC E9_3

value: AVC


title: GIST-T1_DMSO_input

source_name: KIT-dependent GIST cell line

value: DMSO for 24 hours.


title: GIST-T1_JQ1_H3K27Ac


title: 0_05-1


title: Invasive lung adenocarcinoma tissue of patient No.3


title: paired normal lung tissue of of patient No.2


title: Invasive lung adenocarcinoma tissue of patient No.5


title: Invasive lung adenocarcinoma tissue of patient No.2


title: JJN3 DC-1-192 1

status: Public on Jan 22 2019

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

data_processing:
Reads were trimmed using trimmomatic before mapping hg19 human reference using bwa-mem
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using an in house tool.  In counting reads, at least 20 bases of a read had to map to the exon for that read to be counted and reads had to have the same orientation as the exon to be counted (i.e., taking into account strandedness information)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and transcript level count for each sample.

source_name: Plasma cell

growth_protocol: JJN3 cells were routinely cultured in DMEM media containing 20% foetal bovine serum (FBS), 1% sodium pyruvate and 1% penicillin and streptomycin. Cells were maintained at a density between 0.5-2x10^6 cells/ml at a temperature of 37 degrees celsius in 5% CO2 atmostpheric conditions.

extract_protocol:
Treated and untreated JJN3 samples were resuspended in Trizol reagent (Thermo Fisher) and RNA was extracted using an RNeasy mini-prep kit (Qiagen). Total RNA quality and quantity was assessed using an Agilent 2100 Bioanalyser and an RNA Nano 6000 kit (Agilent Technologies). Approximately 100-900ng of Total RNA with an RNA integrity number (RIN) >8 was depleted of ribosomal RNA and used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols
Following validation, the libraries were normalised to 4nM, pooled together and clustered on the cBot2 following the manufacturer's recommendations

treatment_protocol: JJN3 cells were treated with 30nM of either DC-1-170 or DC-1-192 for 4 hours at a density of 0.5x10^6 cells/ml in 24 well plates.

tag: disease stage

value: Plasma cell leukaemia

tag: passage


title: JJN3 DC-1-192 2


title: JJN3 DC-1-170 1


title: JJN3 DC-1-170 3


title: JJN3 DC-1-170 2


title: JJN3 DC-1-192 3


title: paired normal lung tissue of of patient No.1


title: AVC E10_3


title: Invasive lung adenocarcinoma tissue of patient No.1


title: AVC E9_2


title: JJN3 Untreated 3


title: JJN3 Untreated 2


title: AVC E9_1


title: JJN3 Untreated 1


title: HPVC (Ter010172)

hyb_protocol: Following fragmentation, cRNAs were hybridized on gene Chip HG-U133+2

data_processing:
Algorithm: ExpressionStat 5.0
Data analyzed using Gene spring were quality filtered to exclude signal intensities below background, and expression profile differences of 4 fold or greater at a significance threshold of 0.01 or less were compiled into upregulated and downregulated transcript lists

source_name: HUES cells derived endocardial cells

label_protocol: Biotinylated cRNA were synthetized from 1 ug RNA according to standart affymetryx protocol

growth_protocol: Human embryonic stem cells (HUES24) were cultured in K0-DMEM,15% serum replacement and 10 ng/ml FGF2 on MEF. Cells were splitted every 4 daysusing trypsin. The medium was changed every day

extract_protocol: RNA was extracted using Zymo reseach kit

treatment_protocol: Human embryonic stem cells were treated with 10 ng/ml BMP2 and 1 microM SU5402 for 4 days. Cells were sorted out using an anti CD15/SSEA1 antibody (Leschik et am 2008 nature protocol 3(9):1381-7 to generate CD15+ mesodermal cells . CD15+ cells were then rep^lated on MEF and treated with 30 ng/ml VEGF and 10 ng/ml FGF8 to generate human progenitor valvular cells ( HPVC)

tag: cell type

value: HUES-derived endocardial cells


title: HPVC (Ter010170)


title: HPVC (Ter010171)


title: HUES24 ES cell (Ter010173)

source_name: undifferentiated HUES cells

value: undifferentiated HUES cells


title: AVC E10_2

tag: age


title: PB3 D15

city: Cleveland Heights

first: Tolulope

last: Rosanwo

state: Ohio

address: 2741 Euclid Heights Blvd, Apartment 7

institute: Boston Children's Hospital

data_processing:
Analysis was performed using the Dana Farber Cancer Institute (DFCI) Center for Cancer Computational Biology (CCCB) custom pipeline. Raw sequencing reads were aligned to the hg19 reference genome using an RNA-specific Spliced Transcripts Alignment to a Reference (STAR) aligner. Quality control was done with FastQC. Read counts were calculated using the featureCounts in the Subread package.
Genome_build: hg19
Supplementary_files_format_and_content: excel files; We use the featureCounts tool to count sequencing reads mapping to the reference genome at the gene level. The counts are subsequently normalized between samples (using DESeq) to control for experimental sources of variation (e.g. library depth). These count-based files are the basis of many current RNA-Seq genomic analyses.

source_name: Human CD34+peripheral blood-derived hematopoietic progenitor cells

growth_protocol: erythroid differentiation was done with a human plasma-supplemented culture system. The basal erythroid differentiation media was composed of IMDM + 1% L-glutamine and 2% penicillin-streptomycin, 330 ug/mL holo-human transferrin, 10 ug/mL human insulin, 2 IU/mL heparin and 5-20% pool human plasma (Octoplasma). In phase 1 of differentiation (D0-D7), cells were suspended at a concentration of 1x105 – 3 x105 cells/mL in EDM with three supplements: 1 uM dexamethasone, 100 ng/mL SCF, 5 ng/mL IL-3, 3 IU/mL EPO for 7 days. Depending on expansion demand on media nutrition, a half media change occurred at day 3-4 of phase 1. During phase 2 (D8-D11), cells were maintained at the same concentration in the basal media supplemented with the same concentrations of EPO and SCF. In the final phase of differentiation (D11-D18), the cells were resuspended at a concentration of 1 x106 cells/mL or less in basal media and EPO (3 IU/mL) only.

extract_protocol: Total RNA was sent to the Center for Cancer Computational Biology at Dana Farber Cancer Institute (Boston, MA) for all library construction and sequencing. RNA was first put through quality control using Qubit (Life Tech) and the Bioanalyzer (Agilent).  RNA quantity was determined on the Qubit using the Qubit RNA Assay Kit (Life Tech) and RNA quality was determined on the Bioanalyzer using the RNA Pico Kit (Agilent).  Using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), 50-100ng of total RNA was converted into a DNA library following the manufacturer’s protocol, with no modifications. Following library construction, DNA libraries were then put through quality control. Library quantity was determined using the Qubit High Sensitivity DNA Kit (Life Tech) and library size was determined using the Bioanalyzer High Sensitivity Chip Kit (Agilent). Finally, libraries were put through qPCR using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) and run on the 7900HT Fast qPCR machine (ABI).  Libraries passing quality control were diluted to 2nM and sequenced on the NextSeq 500 (Illumina) at a final concentration of 2pM on a single read flowcell with 75 sequencing cycles, following all manufacturer protocols.

value: Erythroid progenitors

tag: genotype/variation

value: PB cRBCs


title: PB3 D11


title: WT1 D11

source_name: Human CD34+ iPS-derived hematopoietic progenitor cells

value: WT iRBCs


title: PB2 D11


title: SCA2 D11

value: SCA iRBCs


title: SCA3 D11


title: HUES24 ES cell (Ter010175)


title: WT3 D11


title: WT3 D15


title: PB1 D11


title: SCA3 D15


title: WT2 D15


title: SCA2 D15


title: HUES24 ES cell (Ter010174)


title: AVC E10_1


title: CD15+ mesodermal cells (Ter010163)

source_name: cells sorted using anti-CD15 antibody

value: CD15+ mesodermal cells


title: WT2 D11


title: CD15+ mesodermal cells (Ter010164)


title: CD15+ mesodermal cells (Ter010162)


title: PB1 D15


title: PB2 D15


title: SCA1 D11


title: ChIPseq_T2_SunTag_VP64_g4

first: Ashot

last: Papikian

address: 4045 Terasaki Life Sciences Building

institute: University of California, Los Angeles

data_processing:
For BS-seq samples, reads were uniquely aligned to the TAIR10 genome using BS-Seeker2 along with Bowtie.
For BS-seq samples, a filter was implemented to remove reads with three or more consecutively methylated cytosines in the CHH context, as previously described in Cokus et al., 2008 (Nature).
For BS-seq samples, after alignment, methylation was called using BS-Seeker2.
For RNA-seq samples, sequencing reads were first aligned to the TAIR10 gene annotation dataset using TopHat (2 mismatches allowed). If reads did not map to genes, they were aligned to the TAIR10 genome. Read counts were obtained by implementing HTSeq and subsequent differential expression analyses were done using DESeq (Bioconductor) and custom R scripts.
For ChIP-seq samples, analysis was done by uniquely aligning reads to the TAIR10 genome using Bowtie allowing two mismatches (-v 2). Subsequently, peaks were called using MACS2 with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq samples, processed data files are in the wig format.
Supplementary_files_format_and_content: For RNA-seq samples, processed data files are provided as text files.
Supplementary_files_format_and_content: For ChIP-seq samples, processed data files are in the bigWig format.

organism: Arabidopsis thaliana

source_name: whole plants

extract_protocol:
For ChIP-seq experiments, plants were first grown on MS plates for 2 weeks and 2 grams of tissue were then collected per sample. After grinding the tissue, samples were crosslinked in 1% formaldehyde, chromatin was extracted, and later sonicated using Bioruptor Plus (diagenode). Detailed experimental procedures for ChIP were performed as previously reported in Johnson et al., 2014 (Nature).
Libraries were prepared using the Ovation Ultralow Kit (NuGen).

tag: antibody

value: mouse monoclonal anti-HA.11 epitope tag antibodies (clone 16B12, Covance catalog# MMS-101R).

tag: ecotype

value: Col

value: whole plants


title: ChIPseq_Col0

value: wildtype


title: WGBS_T2_SunTag_VP64_g4_3

source_name: leaf tissue

extract_protocol:
For BS-seq experiments, genomic DNA was isolated using the DNeasy Plant Mini Kit (Qiagen).
For BS-seq experiments, 100ng of DNA was then used for subsequent shearing using a Covaris Ultrasonicator. Libraries were then prepared using either the Ovation Ultralow Methyl-Seq kit (NuGen) in conjuction with the EpiTect Bisulfite Kit (Qiagen), or the KAPA Hyper Prep Kit (KAPA Biosystems) in conjuction with either the EZ DNA Methylation-Lightning Kit (Zymo) or the EpiTect Bisulfite Kit (Qiagen).

value: leaf


title: HA_Ctrl_Rep2 [earlier passage]

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

data_processing:
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 68 bp single read (HiSeq Rapid SBS/Cluster Kit v2) . Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks

source_name: ChIP Seq of Ctrl HA

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol

treatment_protocol: S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.

tag: cell line

value: S2R+ Cells

value: Embryonic

value: HA-probe Antibody (F-7) (Santa Cruz, catalog# sc-7392, lot# I0916)


title: HA_Mago_RNAseT1_Rep2 [earlier passage]

description: Sample_imb_roignant_2016_11_12_Mago_HA_T1_2

source_name: ChIP Seq of Mago HA with RNAse treatment


title: HA_Mago_Rep1 [earlier passage]

description: Sample_imb_roignant_2016_11_09_Mago_HA_1

source_name: ChIP Seq of Mago HA


title: WGBS_T2_SunTag_VP64_g4_2


title: WGBS_Col0_forT2_SunTag_VP64_g4


title: WGBS_T2_5aa_SunTag_NtDRMcd_g4_2


title: HAMago_MagoKD_Rep1 [earlier passage]

description: Sample_imb_roignant_2016_11_13_Mago_KD_HA_1

source_name: ChIP Seq of Mago HA with Mago KD condition


title: HA_Ctrl_RNAseT1_Rep2 [earlier passage]

description: Sample_imb_roignant_2016_11_08_Wt_HA_T1_2

source_name: ChIP Seq of Ctrl HA with RNAse treatment


title: WGBS_T2_5aa_SunTag_NtDRMcd_g4_1


title: HA_Ctrl_Rep1 [earlier passage]


title: Input_HAMago_MagoKD [earlier passage]

description: Sample_imb_roignant_2016_11_04_Input_Mago_KD

source_name: Input sample for Mago HA in Mago KD condition


title: WGBS_fwa_forT1_5aa_SunTag_NtDRMcd_g4

value: fwa


title: Input_HA_Ctrl [earlier passage]

source_name: Input sample for Ctrl HA


title: HA_Mago_RNAseT1_Rep1 [earlier passage]

description: Sample_imb_roignant_2016_11_11_Mago_HA_T1_1


title: WGBS_T1_5aa_SunTag_NtDRMcd_g4_2


title: WGBS_T1_5aa_SunTag_NtDRMcd_g4_1


title: WGBS_T2_SunTag_VP64_nog_3


title: HA_Ctrl_RNAseT1_Rep1 [earlier passage]

description: Sample_imb_roignant_2016_11_07_Wt_HA_T1_1


title: HA_Mago_Rep2 [earlier passage]

description: Sample_imb_roignant_2016_11_10_Mago_HA_2


title: EL4_RNA_seq_rep1

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
The mouse GRCm38.91 reference genome was used for alignment. STAR v2.5 was used for aligning reads ATAC and ChIP-seq reads with parameters --alignIntronMax 1 --alignMatesGapMax 2000 --alignSJDBoverhangMin 9999 --alignSJoverhangMin 9999 --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 20. RNA-seq samples were analyzed with parameters --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignEndsType Local.  Reads aligned to the mitochondrial genome as well as reads mapping to multiple genomic loci were discarded. Picard minimized the PCR amplification bias in ATAC-, ChIP- and RNA-seq samples.
For calling peaks in ATAC-seq and H3K27Ac, H3K4me3, and H3K9Ac ChIP-seq, macs2 with parameters -p 1e-5 --nolambda --nomodel --keep-dup all with the corresponding input sample as control. For peak calling on broad ChIP-seq peaks K36me2 and K4me3 Epic v0.2.9 was used with the parameter –false-discovery-rate-cutoff 1e-7 and the corresponding input sample as control.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: Bed files of peaks called on ChIP-seq and ATAC-seq data are provided. RNA-seq .bw files.

growth_protocol: EL4 cells were obtained from ATCC TIB-39 (Batch 63681083). Cells were maintained in RPMI 1640 containing GlutaMAX (Gibco 72400-047) and supplemented with 10% serum and 1X Penicillin/Streptomycin (Gibco 15140-122) in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
RNA-seq libraries were prepared using the ? kit (Clontech) and were single-end sequenced for 75 bp.
Library were constructed using NEBNext Poly(A) mRNA Magentic Isolation module and NEB Ultra Directional RNA Library Prep Kit for Illumina (NEB). Libraries qualities were assed with Agilent BioAnalyzer 2100 (Agilent) and quantified using KAPA Library Quantification kit (KAPA Biosystems). Single end sequencing (75bp) was performed on a NextSeq 500.

value: T lymphocyte lymphoma

tag: strain


title: EL4_RNA_seq_rep2

extract_protocol:
RNA-seq libraries from 300,000 EL4 cells using RNAeasy Kit (Qiagen- 74014) according with manufacturer’s instructions and including DNAase digestion.
Library were constructed using NEBNext Poly(A) mRNA Magentic Isolation module and NEB Ultra Directional RNA Library Prep Kit for Illumina (NEB). Libraries qualities were assed with Agilent BioAnalyzer 2100 (Agilent) and quantified using KAPA Library Quantification kit (KAPA Biosystems). Single end sequencing (75bp) was performed on a NextSeq 500.


title: Input_HA_Mago [earlier passage]

description: Sample_imb_roignant_2016_11_02_Input_Mago

source_name: Input sample for Mago HA


title: WGBS_T1_22aa_SunTag_NtDRMcd_g4_2


title: WGBS_T1_22aa_SunTag_NtDRMcd_g4_1


title: HAMago_MagoKD_Rep2 [earlier passage]

description: Sample_imb_roignant_2016_11_14_Mago_KD_HA_2


title: EL4_ATAC_seq_rep1

extract_protocol:
ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., Nature Methods, 2013). Fifty thousand cells were pelleted at 550 x g and washed with 1 mL 1x PBS followed by lysis with 50ul lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Accessible chromatin was tagmented with Tn5 transposase (FC-121-1030; Illumina) for 30 minutes in a 37°C waterbath.
Tagmented DNA was amplified for 12 cycles of PCR, purified, paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.


title: EL4_ATAC_seq_rep2


title: input_DNA

extract_protocol:
Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the NEBNext Ultra II Library Prep Kit for Illuina (Part# E7645S). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.


title: H3K36me2_ChIPSeq_rep2

value: H3K36me2 (Millipore 07-274)


title: H3K27me3_ChIPSeq_rep1

value: H3K27me3 (Millipore 07-449)


title: H3K9Ac_ChIPSeq_rep1

value: H3K9Ac (Abcam ab4441)


title: H3K4me3_ChIPSeq_rep2

value: H3K4me3 (Millipore 04-745)


title: H3K27me3_ChIPSeq_rep2


title: H3K27Ac_ChIPSeq_rep2

value: H3K27Ac (Abcam ab4729)


title: H3K27Ac_ChIPSeq_rep1


title: H3K9Ac_ChIPSeq_rep2


title: H3K4me3_ChIPSeq_rep1


title: GMP2_WT_MO12 [RNA-Seq]

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

data_processing:
Differential gene expression analysis was performed with the RNA Express 1.0 workflow application (Illumina). Briefly, raw sequencing reads were adaptor trimmed and aligned to the mouse genome (mm10) with STAR aligner. Mapped reads were assigned to genes and differential gene expression was analysed using DESeq2. Four biological replicates were used for the DESeq2 analysis. Lowly expressed genes (mean count lower than 10) as well as outlier samples (based on DESeq2 variance model) were excluded and marked in the "status" column. Supplementary files: TAB-delimited files containing the final output tables of differentially expressed genes in MPP and GMP cells, respectively. The data is organised in columns with the titles: Gene, Status, baseMean, Log2FoldChange, lfcSE (log2 fold change standard error), p-value, p-adj (multiple correction adjusted p-value).
Genome_build: mm10

source_name: Hematopoietic cells sorted from bone marrow

extract_protocol:
Total RNA was extracted from FACS purified hematopoietic cell populations using RNeasy Micro Kit (Qiagen). Quality assessment of total RNA was performed using an RNA 6000 Pico Kit (Agilent) and only samples with a RNA integrity number above 8 were used for further analysis. RNA concentrations were determined using a Qubit RNA HS assay kit (ThermoFisher Scientific) and a Qubit 2.0 fluorometer.
A proportion of total RNA (2 ng) isolated from four biological replicates (individual mice with wildtype or Tet2-deficient hematopoiesis) was amplified and size-selected with the Ovation RNA amplification system v2 (NuGen, Cat: 7102) and sequencing adaptors were added to the resulting cDNA using the Ovation Ultra Low v2 system (NuGen) according to manufacturer´s instructions. RNA-seq libraries were quality checked using a DNA 1000 Kit (Agilent) and sequenced using an Illumina NextSeq 550 instrument (75bp single-end).

treatment_protocol: Single-cell suspensions of mouse bone marrow were erythrolysed, enriched for Kit expression (CD117 microbeads, Miltenyi Biotech) and stained with antibodies against surface markers: Lineage (B220-PECy5 (RA3-6B2, eBioscience), CD11b-PECy5 (M1/70, eBioscience), Ter119, PECy5 (TER-119, eBioscience), CD3e-PECy5 (145-2C11, eBioscience), Gr1-PECy5 (RB6-8C5, eBioscience)), Sca1-BV421 (D7, BD biosciences), cKit-AlexaFlour 780 (2B8, eBioscience), CD150-APC (TC15-12F12.2, Biolegend), CD48-PE (HM48-1, eBiocience), CD16/32-PECy7 (93, eBioscience). The following combination of surface markers was used to define hematopoietic progenitor populations: Multipotent Progenitors (MPPs), Lin-cKit+Sca1+CD48+CD150-; Granulocyte-Monocyte Progenitors (GMPs), Lin-cKit+Sca1-CD150-CD16/32+.

tag: age at isolation

value: 40 weeks (10mo)


title: GMP4_WT_MO16 [RNA-Seq]

value: Granulocyte-Monocyte Progenitors (GMPs), Lin-cKit+Sca1-CD150-CD16/32+


title: GMP5_Tet2KO_MO170 [RNA-Seq]


title: MPP7_Tet2KO_MO182 [RNA-Seq]

value: Multipotent Progenitors (MPPs), Lin-cKit+Sca1+CD48+CD150-


title: MPP8_Tet2KO_MO138 [RNA-Seq]


title: GMP1_WT_MO172 [RNA-Seq]


title: H3K36me2_ChIPSeq_rep1


title: MPP6_Tet2KO_MO180 [RNA-Seq]


title: MPP5_Tet2KO_MO170 [RNA-Seq]


title: MPP4_WT_MO164 [RNA-Seq]


title: MPP3_WT_MO14 [RNA-Seq]


title: paired normal lung tissue of of patient No.5

source_name: normal lung tissue

value: normal tissue


title: MPP2_WT_MO12 [RNA-Seq]


title: MPP1_WT_MO172 [RNA-Seq]


title: GMP8_Tet2KO_MO182 [RNA-Seq]


title: GMP6_Tet2KO_MO178 [RNA-Seq]


title: GMP3_WT_MO14 [RNA-Seq]


title: GMP7_Tet2KO_MO180 [RNA-Seq]


title: AML-IgG

description: Sonicated chromatin

data_processing:
Raw sequencing reads were trimmed to remove low quality nucleotides and adaptors with Trimmomatic using ILLUMINACLIP and mapped to the mouse genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) with (--very-sensitive) preset settings. Mapped reads were furthermore de-duplicated using PicardTools v2.7.1 markDuplicates function. Read trimming, mapping and de-duplication were performed using an in-house ChIP-seq processing pipeline (Snakemake) or the public server of the Galaxy Project (Afgan et al. 2016). Identification of sites with evidence of TET2 binding in hematopoietic cells was performed using MACS2 with default parameter settings and a q-value cutoff of 10-06. Peaks were called based on mapped reads from paired samples of wildtype and Tet2 knockout cells, and peak sets from biological duplicate experiments were concatenated and regions overlapping with at least 1 bp were merged. This resulted in identification of 19,706 TET2 binding sites in myeloid hematopoietic cells and 7,002 TET2 binding sites in bulk AML cells. Supplementary files: TAB-delimited files containing genomic coordinates (mm10) of TET2 binding sites in myeloid hematopoietic cells or AML cells. The data is organised in columns with the titles: chr (chromosome), start, end.
Genome_build: mm10

source_name: Acute Myeloid Leukemia cells grown in vitro

growth_protocol: Immortalized hematopoietic cells (AML1-ETO transduced) or Acute myeloid leukemia cells were cultured in suspension in non-tissue culture treated plasticware in StemPro-34 SFM media (ThermoFisher Scientific, Cat: 10639011) supplemented with 2mM GlutaMAX (GIBCO), 1X pen/strep (GIBCO), 0.1mM 2-mercaptoethanol (SIGMA), as well as the cytokines SCF (50ng/ml), IL-3 (10ng/ml), and IL-6 (10ng/ml) (PEPROTECH).

extract_protocol:
Cells were washed twice in ice-cold PBS and pelleted by centrifugation. The cells were resuspended in 10 ml ice-cold PBS and freshly prepared 0.25M disuccinimidyl glutarate (DSG) stock solution (dissolved in DMSO) to obtain a final concentration of 2mM DSG in PBS (ThermoFisher Scientific, Cat: 20593) and incubated at a rotating wheel for 30 min to allow equilibration to room temperature. Then, formaldehyde (Sigma, Cat: 252549) was added to obtain a final concentration of 1% and rotated for another 10 min at room temperature. Finally, the crosslinking reaction was stopped by addition of glycine to a final concentration of 125mM. The cells were spun down for 5 min at 350 x g rpm at room temperature and washed twice with ice-cold PBS. The cells were then resuspended in 5 mL SDS Buffer (50mM Tris-HCl pH 8.1, 100mM NaCl, 5mM EDTA, 0.5% SDS) containing 1 mM Phenylmethylsulfonyl fluoride (PMSF) and allowed to rotate for another 5 min. Finally, the cells were pelleted and resuspended in IP buffer (100mM Tris-HCl pH 8.6, 100mM NaCl, 5mM EDTA, 0.3% SDS, 1.7% TritonX-100) with proteinase inhibitors according to pellet size. Chromatin dissolved in IP buffer was sheared to an average size of 200-500 bp DNA fragments in a Bioruptor (Diagenode). The sonicated chromatin was diluted in SDS-free IP buffer to achieve a concentration of 0.1% SDS, spun down at 20,000 x g for 20 min to remove insoluble chromatin fraction and precleared with protein G Sepharose beads (GE healthcare) prior to immunoprecipitation. For immunoprecipitation of endogenous TET2, 1µg affinity-purified rabbit polyclonal antibody raised against N-terminal TET2 protein (TET2-N) (Helin lab) was incubated with 300µg chromatin overnight. The chromatin-antibody complexes were captured in a 3h incubation with protein-G Sepharose beads (GE healthcare). Washes of chromatin-antibody-bead complexes were performed as follows: Three washes with ice-cold 150mM wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), two washes with ice-cold 500mM wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), and one wash with ice-cold IP buffer with a final concentration of 0.1% SDS. After the last wash, DNA from TET2-N immunoprecipitations was decrosslinked by overnight incubation at 65oC in decrosslinking solution (1% SDS, 0.1M NaHCO3). IP’ed DNA was purified using the QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions.
ChIP-seq libraries for Illumina sequencing was prepared using the NEBNext Ultra II DNA library preparation kit (New England Biolabs) using an input of 1-3ng of IP’ed DNA (quantified using DNA HS assay kit (Qubit)) following the manufacturer’s instructions. Adaptor-ligated fragments were size-selected using AMPure XP beads (Beckman Coulter) to retain inserts of approximately 200bp prior to PCR amplification. Equimolar amounts of sample, with compatible indexes, were pooled and sequenced on Illumina NextSeq 550 (75bp single-end).

value: Npm1+/cA; Fl3+/ITD

tag: transgene

value: No transgene

value: IgG control

tag: antibody origin


title: AML-Input

description: Sonicated chromatin

value: Acute Myeloid Leukemia cells grown in vitro

tag: genotype


title: AML-Tet2KO, rep1

description: Sonicated chromatin

value: Npm1+/cA; Fl3+/ITD; Tet2-/-

value: anti-TET2 antibody

value: rabbit polyclonal antibody raised against N-terminal TET2 protein (TET2-N) (Helin lab)


title: AML-Tet2KO, rep2

description: Sonicated chromatin


title: AML-WT, rep1

description: Sonicated chromatin


title: AML-WT, rep2

description: Sonicated chromatin


title: Myeloid cells-IgG

description: Sonicated chromatin

source_name: Immortalized hematopoietic cells grown in vitro

value: Tet2fl/fl; AML1-ETO

value: MigR1-AML1-ETO (Addgene #12431)


title: Myeloid cells-WT, rep2

description: Sonicated chromatin

value: Immortalized hematopoietic cells grown in vitro


title: Myeloid cells-input

description: Sonicated chromatin


title: ES-Tet2FLAG_rep2

description: Sonicated chromatin

data_processing:
Raw sequencing reads were trimmed to remove low quality nucleotides and adaptors with Trimmomatic using ILLUMINACLIP and mapped to the mouse genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) with (--very-sensitive) preset settings.
Mapped reads were furthermore de-duplicated using PicardTools v2.7.1 markDuplicates function. Read trimming, mapping and de-duplication were performed using an in-house ChIP-seq processing pipeline (Snakemake) or the public server of the Galaxy Project (Afgan et al. 2016).
TET2 binding sites were defined by differential binding affinity analysis between biological replicate ChIP-seq samples. Briefly, peaks in ChIP experiments using either TET2-N or FLAG M2 antibodies were called over IgG background using MACS2 (Zhang et al. 2008) with 0.05 q-value cutoff. These sets of peaks were merged to derive a consensus peak set using "Diffbind" package from Bioconductor with following parameters: minOverlap = 1, filter = 5. Statistically significant differentially bound regions (FDR < 0.1 and log2 fold change > 0.5) between wildtype and Tet2 knockout (or FLAG-tagged and empty) were identified by DESeq2 corresponding to 19,480 and 15,322 TET2 binding sites in TET2-N and FLAG M2 ChIP experiments, respectively.
Bam files are transfromed to bigwig files using Biconductor package GenomicAlignments coverage() function.
Genome_build: mm10
Supplementary_files_format_and_content: Binary bigwig files containing trimmed, mapped and de-duplicated reads (mm10)

source_name: Embryonic Stem cells

growth_protocol: Embryonic stem cells were grown in gelation-coated plates in Dulbecco's Modified Eagle Medium (DMEM, Invitrogen Cat. No. 41966) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM Glutamax (GIBCO), 0.1 mM 2-Mercaptoethanol (GIBCO), 1x non-essential amino acids (GIBCO), 1x Pen-Strep (GIBCO), 3μM GSK-3 inhihibtor (CHIR99021), 1 μM MEK1 inhibitor (PD0325901) and leukemia inhibitory factor (LIF, lab made).

extract_protocol:
ES cells were washed twice in ice-cold PBS and pelleted by centrifugation. The cells were resuspended in 10 ml ice-cold PBS and freshly prepared 0.25M disuccinimidyl glutarate (DSG) stock solution (dissolved in DMSO) to obtain a final concentration of 2mM DSG in PBS (ThermoFisher Scientific, Cat: 20593) and incubated at a rotating wheel for 30 min to allow equilibration to room temperature. Then, formaldehyde (Sigma, Cat: 252549) was added to obtain a final concentration of 1% and rotated for another 10 min at room temperature. Finally, the crosslinking reaction was stopped by addition of glycine to a final concentration of 125mM. The cells were spun down for 5 min at 350 x g rpm at room temperature and washed twice with ice-cold PBS. The cells were then resuspended in 5 mL SDS Buffer (50mM Tris-HCl pH 8.1, 100mM NaCl, 5mM EDTA, 0.5% SDS) containing 1 mM Phenylmethylsulfonyl fluoride (PMSF) and allowed to rotate for another 5 min. Finally, the cells were pelleted and resuspended in IP buffer (100mM Tris-HCl pH 8.6, 100mM NaCl, 5mM EDTA, 0.3% SDS, 1.7% TritonX-100) with proteinase inhibitors according to pellet size. Chromatin dissolved in IP buffer was sheared to an average size of 200-500 bp DNA fragments in a Bioruptor (Diagenode). The sonicated chromatin was diluted in SDS-free IP buffer to achieve a concentration of 0.1% SDS, spun down at 20,000 x g for 20 min to remove insoluble chromatin fraction and precleared with protein G Sepharose beads (GE healthcare) prior to immunoprecipitation. For immunoprecipitation of endogenous TET2, 1µg affinity-purified rabbit polyclonal antibody raised against N-terminal TET2 protein (TET2-N) (Helin lab) was incubated with 300µg chromatin overnight. The chromatin-antibody complexes were captured in a 3h incubation with protein-G Sepharose beads (GE healthcare). For immunoprecipitation of 2xFL-TET2, 20µl of anti-FLAG M2 affinity gel (Sigma, A2220) was incubated with 300ug chromatin for 3h. Washes of chromatin-antibody-bead complexes were performed as follows: Three washes with ice-cold 150mM wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), two washes with ice-cold 500mM wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), and one wash with ice-cold IP buffer with a final concentration of 0.1% SDS. After the last wash, DNA from TET2-N immunoprecipitations was decrosslinked by overnight incubation at 65oC in decrosslinking solution (1% SDS, 0.1M NaHCO3). In FLAG M2 immunoprecipitations, IP’ed chromatin was initially eluted by three consecutive incubations (each 20 min on ice) in elution buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA) with 0.5mg/ml FLAG peptide (Peptide 2.0). The eluted fractions were pooled and decrosslinked by overnight incubation at 65oC in decrosslinking buffer. IP’ed DNA was purified using the QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions.
ChIP-seq libraries for Illumina sequencing was prepared using the NEBNext Ultra II DNA library preparation kit (New England Biolabs) using an input of 1-3ng of IP’ed DNA (quantified using DNA HS assay kit (Qubit)) following the manufacturer’s instructions. Adaptor-ligated fragments were size-selected using AMPure XP beads (Beckman Coulter) to retain inserts of approximately 200bp prior to PCR amplification. Equimolar amounts of sample, with compatible indexes, were pooled and sequenced on Illumina NextSeq 550 (75bp single-end).

value: Embryonic Stem cells

tag: endogenous epitope tag

value: 2x-Flag tagged TET2

value: FLAG M2 affinity gel

value: Sigma, Cat:A2220


title: Myeloid cells-Tet2KO, rep2

description: Sonicated chromatin

value: Tet2-/-; AML1-ETO


title: ES-Tet2KO_rep2

description: Sonicated chromatin

value: Empty


title: ES-Tet2KO_rep1

description: Sonicated chromatin


title: Myeloid cells-WT, rep1

description: Sonicated chromatin


title: ES-parental_rep2

description: Sonicated chromatin


title: ES-WT_rep1

description: Sonicated chromatin


title: ES-input

description: Sonicated chromatin


title: ES-WT_rep2

description: Sonicated chromatin


title: ES-IgG

description: Sonicated chromatin

value: IgG


title: ESC_KO1

description: DNA, fragmented and adaptor ligated by Tn5 transposase

data_processing:
Trimming of the adapters with Trimmomatic v0.33 with ILLUMINACLIP:NexteraPE-PE.fa:1:10:4:1:true TRAILING:3 MINLEN:20 parameters.
Aligned to mm10 genome using Bowtie2 v2.2.9 with -X 2000 -t –very-sensetive parameters.
Removed reads with MAPQ quality < 10 using samtools and awk scripts.
Removed mitochondrial reads using samtools and awk scripts.
Read start sites are adjusted +4/-5 using samtools and awk scripts.
Using PicardTools v2.9.0 sorted by coordinate and removed duplicated reads.
Removed indels with CIGAR “ID” using samtools and awk scripts.
Bam files are transfromed to bigwig files using Biconductor package GenomicAlignments coverage() function.
Genome_build: mm10
Supplementary_files_format_and_content: Binary bigwig files containing trimmed, mapped and de-duplicated reads (mm10)

source_name: Embryonic stem cells

growth_protocol: Embryonic stem cells were grown in gelation-coated plates in Dulbecco's Modified Eagle Medium (DMEM, Invitrogen Cat. No. 41966) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM Glutamax (GIBCO), 0.1 mM 2-Mercaptoethanol (GIBCO), 1x non-essential amino acids (GIBCO), 1x Pen-Strep (GIBCO), 3μM GSK-3 inhihibtor (CHIR99021), 1 μM MEK1 inhibitor (PD0325901) and leukemia inhibitory factor (LIF, lab made). Acute myeloid leukemia cells were cultured in suspension in non-tissue culture treated plasticware in StemPro-34 SFM media (ThermoFisher Scientific, Cat: 10639011) supplemented with 2mM GlutaMAX (GIBCO), 1X pen/strep (GIBCO), 0.1mM 2-mercaptoethanol (SIGMA), as well as the cytokines SCF (50ng/ml), IL-3 (10ng/ml), and IL-6 (10ng/ml) (PEPROTECH).

extract_protocol:
ATAC-seq libraries were generated as described previously (Buenrostro et al. 2013; Lara-Astiaso et al. 2014). Briefly, 10,000 freshly isolated cells (MPP, GMP, AML, and ES) were sorted by FACS into ice-cold FACS buffer (PBS + 2%FBS). The cells were pelleted using a swinging bucket centrifuge (500 x g, 10min, 4oC) with settings for low acceleration/deceleration and washed once in ice-cold PBS. The cell pellets were resuspended in 50μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) by gentle pipetting and immediately centrifuged one additional time (500 x g, 10min, 4oC). The supernatant was discarded and the pellet containing released nuclei were resuspended gently in 25μl 1xTD buffer containing 1.25μl Tn5 transposase (Nextera sample preparation kit, Illumina). The transposition reaction was allowed to proceed for 45min at 37oC whereafter DNA fragments were isolated using MinElute PCR purification columns (Qiagen) according to manufacturer’s instruction.
To generate multiplex libraries, the transposed DNA was initially amplified for 5x PCR cycles using 2.5μl each of dual-index primers (Nextera index kit, Illumina) and 2.5μl PCR primer cocktail (PPC, Illumina) in a 25μl reaction volume of 1x KAPA HiFi hot-start ready-mix (Kapa BioSystems). The hot-start polymerase was activated prior to adding to the reaction mix by performing a brief pre-incubation step of 3min at 95oC. The amplified fragments were size-selected with AMPure XP beads (0.5X) to remove fragments larger than 600bp and an aliquot was quantified to determine the optimal PCR cycle number to obtain 1/3 of maximum fluorescence intensity (Library quantification kit, Kapa Biosystems). Finally, PCR amplification was performed using the optimal number of cycles determined for each library (max. 18 cycles in total), size-selected with AMPure XP beads (0.5X) and eluted in resuspension buffer (Illumina). The size distribution of the libraries was evaluated on Bioanalyzer (Agilent) and sequenced on NextSeq 550 (Illumina) using 150bp or 75bp paired-end sequencing.

value: Bulk culture, non-sorted


title: ESC_KO2

value: No transgene


title: ESC_WT3


title: ESC_WT2


title: AML_Tet2KO3

source_name: Leukemic cells sorted from in vitro culture

value: Acute Myeloid Leukemia (AML) progenitor cells, CD11b-Gr1-CD16/32intCD34+


title: ESC_WT1


title: ESC_KO3


title: Myeloid cells-Tet2KO, rep1

description: Sonicated chromatin


title: AML_WT3

value: Npm1+/cA; Fl3+/ITD


title: AML_WT2


title: ES-parental_rep1

description: Sonicated chromatin


title: GMP8_Tet2KO

value: Granulocyte-Monocyte Progenitors (GMPs), Lin-cKit+Sca1-CD150-CD16/32+


title: AML_WT1


title: ES-Tet2FLAG_rep1

description: Sonicated chromatin


title: AML_Tet2KO1

value: Npm1+/cA; Fl3+/ITD; Tet2-/-


title: GMP7_Tet2KO


title: GMP6_Tet2KO


title: GMP5_Tet2KO


title: GMP4_WT


title: GMP2_WT


title: GMP3_WT


title: MPP8_Tet2KO_MO182

value: Multipotent Progenitors (MPPs), Lin-cKit+Sca1+CD48+CD150-


title: GMP1_WT