title: nm2

city: Zhenjiang

first: Pingyang

last: Wang

state: Jiangsu province

address: Nanxu street

department: School of Biotechnology

institute: Jiangsu University of Science and Technology

description: non-molting in 2nd instar

data_processing:
Quality analysis was conducted for the original data obtained using the Illumina HiSeqTM2000 platform
Clean reads were screened by filtering out low-quality reads
The sequences were aligned to the silkworm genome database SilkDB.
QC of the alignment was performed to determine whether resequencing was needed.
Downstream analyses, including gene expression and deep analyses, proceeded based on the observed gene expression (e.g., principal component analysis/correlation/screening of differentially expressed genes). Deep analyses based on DGE were also performed, including Gene Ontology (GO) enrichment analysis and KEGG pathway enrichment analysis.
Genome_build: SilkDB (http://silkworm.swu.edu.cn/silkdb/)
Supplementary_files_format_and_content: All files are named with sample name followed by content name using files format of excel. The processed data include the FPKM of two samples wildtype C603 and nm2 mutant, the differentially expressed genes between C603 and nm2 with FDR≤0.001, BlastGo and KEGG results of C603 and nm2 respectively.

organism: Bombyx mori

source_name: head

growth_protocol: The silkworm strains C603 and nm2 were provided by The Sericulture Research Institute, Chinese Academy of Agricultural Sciences (Zhenjiang, China). The silkworms were fed fresh mulberry leaves under standard conditions with alternating 12 hours of illumination and 12 hours of darkness at 25±2 °C. The heads of C603 stain and nm2 mutant were collected from every six silkworms in the pre-molting stage of 2nd instar. All samples were frozen and stored at -80 °C.

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa, China) and dissolved in RNase-free water. The concentration of total RNA was determined using a NANODROP1000 microspectrophotometer (Thermo, USA) after treatment with DNase.
The treated mRNA was enriched using oligo (dT) magnetic beads. By mixing with fragmentation buffer, the mRNA was fragmented into short fragments. Then, the first strand of cDNA was synthesized using random hexamer primers. Buffer, dNTPs, RNase H and DNA polymerase I were subsequently added to synthesize the second strand. Next, the double-stranded cDNA was purified with magnetic beads. End repair and 3’-end single A (adenine) nucleotide addition were then performed. Finally, sequencing adaptors were ligated to the fragments, and the fragments were enriched via PCR amplification. During the quality control (QC) step, an Agilent 2100 Bioanaylzer and an ABI StepOnePlus Real-Time PCR System were used to qualify and quantify the sample library. The library products were then ready for sequencing via the Illumina HiSeqTM 2000 platform at the Beijing Genomics Institute (BGI).

treatment_protocol: The nm2 mutant appears normal in the first instar, but at the beginning of the pre-molting stage of the second instar, it is unable to molt and becomes lustrous, which lasts for 6 to 8 days, followed by death of the larva.

tag: developmental stage

value: 2th instar

tag: status

value: pre-molting

value: head


title: ACT88F-W1118 Thorax Skeletal muscle

status: Public on Jul 03 2017

type: SRA

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

country: USA

institute: Texas A&M University Health Sciences Center

library_source: transcriptomic

data_processing:
Sample libraries were sequenced using the Illumina HiSeq 2500.
Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings.
Between 7 and 12 million (1X50) base pair reads were generated per library and mapped to the Drosophila genome (Release 6).
Expression was recorded as RPKM: reads per kbp per million reads.
Gene Ontology clustering analysis was performed using FlyMine
Genome_build: Drosophila genome (Release 6)
Supplementary_files_format_and_content: Expression was recorded as RPKM: reads per kbp per million reads.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Thorax Skeletal muscle

growth_protocol: All flies were reared on standard yeast and cornmeal based food at 25°C and 65% humidity on a 12 hr light/dark cycle, The standard yeast and cornmeal based food was made with the following protocol: 14g Agar/165.4g Malt Extract/ 41.4g Dry yeast/ 78.2g Cornmeal/ 4.7ml propionic acid/ 3g Methyl 4-Hydroxybenzoate/ 1.5L water.

extract_protocol:
Intact fly thorax, carcass (with all of the eggs and intact intestines removed) and intestines were dissected in PBS. Total RNA was extracted using Trizol reagent and used as template to generate sample libraries for RNA sequencing
sample libraries for RNA sequencing were generated using the TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: In order to standardize metabolic results, 2-3 days after eclosion, adult flies were placed on a simple sugar-yeast (SY) diet for 10 days. The standard SY diet was made with the following protocol (as previously described in (Skorupa et al., 2008)); 1.0g agar/10g sucrose/ 10g yeast/ 0.3 ml propionic acid/100 ml water. Ingredients were combined, heated to at least 102°C, and cooled before pouring.

tag: genotype/variation

tag: ages

value: 10 days

tag: tissue

value: Thorax Skeletal muscle


title: C603

country: China

description: developed normally


title: C57BL/6_WT

city: Durham

first: Mari

middle: L

last: Shinohara

state: NC

department: Immunology

institute: Duke University School of Medicine

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of C57BL/6_WT and C57BL/6 Spp1-/-, using 10X Cellranger v1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for FACS-sorted BM multi-potent progenitor (MPP) cells Mus musculus C57BL/6, and Mus musculus C57BL/6 Spp1-/-. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.
Supplementary_files_format_and_content: Barcodes ending in -1 correspond to WT , barcodes ending in -2 correspond to MUTANT.

organism: Mus musculus

extract_protocol:
FACS-sorting the Lin–Sca-1+c-kit+CD34+Flt3L+ (MPP) population from total bone marrow cells
10X Single Cell 3'

treatment_protocol: 20 hrs after intraperitoneal injection of thioglycollate

tag: genotype


title: C57BL/6 Spp1-/-

source_name: FACS-sorted BM multi-potent progenitor (MPP) cells


title: LPS_6h_rep2

city: Epalinges

first: Ping-Chih

last: Ho

state: Vaud

address: Ch. des Boveresses 155

department: Department of Fundamental Oncology

country: Switzerland

institute: University of Lausanne

description: Processed data in Series supplementary file MP_RAWCOUNT_MATRIX.txt

data_processing:
Reads shorter than 25 bp after the trimming were removed
The remaining reads were aligned to the mouse genome (mm10) with STAR. htseq-count was used to quantify the number of reads mapping to each gene, using the 'union' counting mode to handle reads overlapping several genes.
We kept only genes with reads in at least 3 samples, leaving in total 12,715 genes (11,042 unique gene ID) for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw count sample matrix file

source_name: stimulation: LPS 6h

growth_protocol: Bone marrow cells were culture in macrophage differentiation procedure in which 20% L929 conditional media puls 80% normal DMEM media with FBS for 7 days.

extract_protocol:
Trizol combined with Rnaeasy kit.
Trueseq straded RNA

treatment_protocol: Macrophages were stimulated in the indicated condition mentioned in the study associated with this database.

tag: cell type

value: Bone marrow-derived macrophages

tag: strain

value: C57BL6/J wild type


title: CTRL_rep1

source_name: stimulation: control


title: ET_AKG_w_o_Gln_rep3

description: Processed data in Series supplementary file ET_RAWCOUNT_MATRIX.txt

source_name: endotoxin-tolerant macrophages - alpha-ketoglutarate - without Gln


title: IL4_6h_rep1

source_name: stimulation: IL4 6h


title: CTRL_rep2


title: LPS_6h_rep1


title: ET_w_o_Gln_rep3

source_name: endotoxin-tolerant macrophages - without Gln


title: ET_AKG_w_o_Gln_rep4


title: Saline P10 male litter 1

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Sample reads were demultiplexed and processed in the Illumina BaseSpace Environment
Reads were mapped to the mm10 mouse genomic reference with ethe STAR aligner
Abundance estimate of raw read counts per transcript was done with the htseq-count algorithm
Library size normalization to produced normalized expression (normalized read counts) was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Rattus norvegicus

source_name: amygdala

extract_protocol:
Subjects were deeply anaesthetized with isofluorane, decapitated, and brains were frozen on dry ice and stored at -80˚C. On a microtome, punches (~1uM3) were be collected of the BLA, as well as the prefrontal cortex, nucleus accumbens, bed nucleus of the stria terminalis, and the hippocampus. Transcriptomics was assessed in male amygdala micropunches from P10 (n = 4 saline, 4 vpa) and P21 (n = 7 saline, 6 vpa). RNA sequencing libraries were prepared by the Yerkes Nonhuman Primate Genomics Core (NHPGC). Total RNA was prepared using the QIAGEN RNEasy Micro Kit. Libraries were generated from 5 ng of Total RNA using the CLONTECH SMARTer HV kit, and barcoding and sequencing primers were added using NexteraXT DNA kit. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell. The clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pregnant females were orally gavaged with either 500 mg/kg of VPA (Sigma-Aldrich, St. Louis, Missouri) diluted in 0.9% saline or saline alone once daily on embryonic days 11-13.

value: amygdala

value: Sprague-Dawley

tag: develpmental stage

tag: Sex

value: male


title: ET_w_o_Gln_rep4


title: ACT88F-Foxo RNAi Gut

source_name: Gut

value: ACT88F>Foxo RNAi

value: Gut


title: ET_AKG_w_o_Gln_rep2


title: IL4_6h_rep2


title: ET_w_Gln_rep4

source_name: endotoxin-tolerant macrophages - with Gln


title: ET_w_Gln_rep3


title: ET_w_o_Gln_rep2


title: ET_w_Gln_rep2


title: RNA restimulated cytotoxic T lymphocytes  (Nfatc2ko)

city: Würzburg

first: Stefan

last: Klein-Hessling

address: Josef-Schneider-Str. 2

department: Institute of Pathology

country: Germany

institute: University of Würzburg

description: Nfatc2-/- CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2. 5h restimulation by TPA (5 ng/ml) and ionomycin (0.5 microM).

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC genomics workbench (v7.5.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with read counts and RPKM

extract_protocol:
total RNA from each sample was isolated by using Trizol and quality of RNA was assessed on a RNA6000 Nano Chip and a Bioanalyzer2100 (Agilent)
Barcoded mRNA-seq cDNA libraries were prepared from 500ng of total RNA (RIN>8) using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay. Barcoded RNA-Seq libraries were onboard clustered usingHiSeq® Rapid SR Cluster Kit v2 using 8pM and 59bps were sequenced on the Illumina HiSeq2500 using HiSeq® Rapid SBS Kit v2 (50 Cycle). The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol.

value: spleen

value: cytotoxic T lymphocytes


title: RNA restimulated cytotoxic T lymphocytes (Nfatc1 fl/fl.CD4cre)

description: Nfatc1-/-CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2. 5h restimulation by TPA (5 ng/ml) and ionomycin (0.5 microM).

value: Nfatc1 fl/fl.CD4cre


title: RNA unstimulated cytotoxic T lymphocytes (Nfatc1 fl/fl.CD4cre)

description: Nfatc1-/- CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2.


title: RNA unstimulated cytotoxic T lymphocytes

description: WT CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2.

source_name: unstimulated cytotoxic T lymphocytes

value: wildtype


title: RNA unstimulated cytotoxic T lymphocytes  (Nfatc2ko)

description: Nfatc2-/- CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2.


title: ChIP restimulated cytotoxic T lymphocytes (Nfatc1/A-Bio.Rosa26BirA)

library_source: genomic

data_processing:
50 bp sequence reads that passed the Illumina quality filtering were aligned to the mouse genome assembly version of July 2007 (NCB I37/mm9), using the Map with Bowtie for Illumina (version 1.1.2) with the following parameters: Bowtie settings to use=full; Skip the first n reads (-s)=0; Only align the first n reads (-u)= -1; Trim n bases from high-quality (left) end of each read before alignment (-5)= 0; Trim n bases from low-quality (right) end of each read before alignment (-3)= 0; Maximum number of mismatches permitted in the seed (-n)= 2; Maximum permitted total of quality values at mismatched read positions (-e)= 70; Seed length (-l)= 35; Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)= Round to nearest 10; Number of mismatches for SOAP-like alignment policy (-v)= -1; Whether or not to try as hard as possible to find valid alignments when they exist (-y)= Do not try hard; Report up to n valid alignments per read (-k)= 1; Whether or not to report all valid alignments per read (-a)= Do not report all valid alignments; Suppress all alignments for a read if more than n reportable alignments exist (-m)= -1; Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)= False; Write all reads that could not be aligned to a file (--un)= False; Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)= doBest; Maximum number of backtracks permitted when aligning a read (--maxbts)= 800; Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)= do not use strata option; Override the offrate of the index to n (-o)= -1; Seed for pseudo-random number generator (--seed)= -1; Suppress the header in the output SAM file= False; Job Resource Parameters= no;
Peak calling was done using MACS (Galaxy Version 1.0.1) with default parameters, a genome size of 2,700,000,000 bp (mm9) and the reads from Rosa26BirA IP as control sample to identify peaks that were filtered for P values of <10-5
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: ChIP CTL+ Nc1A-Bio.BirA

growth_protocol: CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2.

extract_protocol:
Chromatin from 1x10^7 fixed CTLs was prepared using a lysis buffer containing 1% SDS and sonicated by a Vibra-Cell VCX 130 before precipitation of chromatin by streptavidin beads
Sequencing libraries were prepared using 7ng decrosslinked and purified DNA employing the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® according to the manual (incl. size selection and 15 cycles of final PCR). All quality controls were done using Invitrogen’s Qubit HS assay and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay. Barcoded libraries were onboard clustered usingHiSeq® Rapid SR Cluster Kit v2 using 8pM and 50bps were sequenced on the Illumina HiSeq2500 using HiSeq® Rapid SBS Kit v2 (50 Cycle). The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol

treatment_protocol: 5h restimulation by TPA (5 ng/ml) and ionomycin (0.5 microM)

value: CD8+ T cells

tag: chromatin precipitation

value: streptavidin beads


title: ET_AKG_w_o_Gln_rep1


title: Husk rep1 technical replicate 2

city: Cologne

first: Johan

last: Zicola

address: Carl-von-Linné

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

description:
processed data file:
DNase_husk.bw
DNase_husk.bed

data_processing:
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering of ChIP-seq reads were done using FastX Toolkit and PRINSEQ (Q20).
ChIP-seq reads were aligned to the AGPv3 genome assembly using BWA
Non-uniquely mapped reads were filtered out using samtools (MAPQ20)
Peaks were called using MACS2 (-q 0.001, -broad)
Genome_build: AGPv3
Supplementary_files_format_and_content: bed files were generated using MACS2; bigwig files were converted from wig output from MACS2 using wigToBigWig tool (SPMR)

organism: Zea mays

source_name: Husk

growth_protocol: Plants grown till stage V2 (Abendroth et al 2011) or till flowering (ears with emerging silks, before pollination) in greenhouse, 16h of light per day. Temperature above 22°C

extract_protocol:
DNase I digestion of the chromatin and DNase I digestion of gDNA (naked DNA)
Library constructed with the Ovation Ultralow DR Multiplex kit (NuGEN)

tag: line

value: stage silk emerging 2-5 cm

value: inner layer husk


title: ET_w_Gln_rep1


title: Husk rep2


title: Husk rep1


title: ChIP restimulated cytotoxic T lymphocytes (Rosa26BirA)

source_name: ChIP CTL+ BirA


title: RNA activated CD8+ T cells (Nfatc2ko)

description: Nfatc2-/- CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 72h.

source_name: activated CD8+ T cells (Nfatc2ko)

value: activated CD8+ T cells


title: RNA activated CD8+ T cells (Nfatc1 fl/fl.CD4cre)

description: Nfatc1-/- CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 72h.


title: Naked DNA


title: IST rep2

description:
processed data file:
DNase_ist.bw
DNase_ist.bed

source_name: Seedling

value: V2 seedling

value: inner stem tissue


title: RNA activated CD8+ T cells

description: WT CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 72h.

source_name: activated CD8+ T cells


title: CEBPBi_TAM

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
Raw reads were aligned to GENCODE (Harrow et al., 2012) defined transcripts and then human reference genome (hg19) using Tophat (Langmead et al., 2009) allowing up to 2 mismatches.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

organism: Homo sapiens

source_name: Breast epithelial cell

growth_protocol: All cultures were performed at 37°C under 5% CO2. The breast epithelial cell line (MCF-10A-ER-Src) was grown in DMEM/F12 with 5% charcoal-stripped fetal bovine serum (Invitrogen) and supplements(Iliopoulos et al., 2009). Cells were seeded at 1 × 106 cells per 10-cm culture dish and cultured overnight. MCF-10A-ER-Src cells were treated by 1 µM 4-hydroxy-tamoxifen for various time points to induce transformation.

extract_protocol: Briefly, RNA was extracted using mRNeasy Mini Kit following the manufacturer’s instruction.  RNA-seq libraries were prepared using TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126) as per manufacturer’s instruction. RNA-seq libraries were sequenced by Bauer Core Facility using Hiseq 2000.

value: CEBPBi

tag: agent

value: TAM


title: SOX15i_TAM


title: TCF7L2i_TAM


title: Ctrl_EtOH_b.RNA

value: Ctrl

value: EtOH


title: FOSL2i_TAM


title: H3K9me3_TAM36hr_rep1

data_processing:
Paired-end raw Fastq reads were aligned to human reference genome (hg19) using Bowtie (Langmead, Trapnell et al. 2009) allowing up to 2 mismatches. Only the uniquely mappable reads were used for subsequent analyses. For ChIP-seq data for H3K27ac, H3K4me3 and H3K4me1, we used MACS (Zhang, Liu et al. 2008) to call peaks. For ChIP-seq for H3K27me3, H3K9me3 and H3K36me3, we used SICER (Zang et al. 2009) to call peaks, which is better for identifying broad read peaks.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

extract_protocol: Cells were treated with ethanol or tamoxifen (1 µM) for 24 hours and then cross-linked using ethylene glycol bis (succinimidyl succinate) (EGS), disuccinimidyl glutarate (DSG) and disuccinimidyl suberate (DSS) mixture (2.5 µM each) for 45 minutes at room temperature. After this initial crosslinking, cells were further fixed using 1% formaldehyde for 20 minutes at room temperature and then quenched by glycine (0.125 M). Chromatin in sonication buffer (50 mM HEPES, pH7.5, 140 mM NaCl, 2mM EDTA, 2mM EGTA, 1% Triton-100 and 0.4% SDS) was sheared using Branson Microtip Sonifier 450 (12 cycles of 15 second at a sonication setting of output 4 and duty cycle 60%) to a size mostly between 100-150 bp.  The sonicated chromatin solution was diluted to 0.085% SDS and immunoprecipitated with antibodies against H3K4me3 (ab8580), H3K27ac (ab4729), H3K4me1 (ab8895), H3K36me3 (ab9050), H3K27me3 (ab6002) and H3K9me3 (ab8898).  Immunoprecipitated chromatin was decrosslinked using RNase Cocktail (Ambion, AM2286) and Pronase (Roche, 10165921001). ChIP DNA was end repaired, addition of “A” and adapters ligation and PCR amplification to produce ChIP-seq libraries. The DNA concentration was measured by Bioanalyzer before sequencing using Hiseq 2000 at the Bauer Core Facility, Harvard.

tag: antibody

tag: time point


title: Ctrl_TAM_b.RNA


title: NFE2L2i_TAM


title: FOSL1i_TAM


title: Ctrl_TAM.RNA


title: H3K9me3_TAM12hr_rep1


title: ET_w_o_Gln_rep1

value: Bone marrow-derived macrophages

value: C57BL6/J wild type


title: RNA_met-2_set-25_eemb_20°C_rep1

status: Public on Jul 04 2017

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce6 (WS190) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS190 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce6 (WS190)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (Sanger identifiers) and width of genes, following columns contain raw counts of reads overlapping each gene for each sample.

organism: Caenorhabditis elegans

source_name: early embryo

growth_protocol: RNA was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.
Libraries were prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

value: early embryo


title: Ctrl_EtOH.RNA


title: H3K9me3_TAM02hr_rep1


title: IST rep1


title: H3K9ac_ChIP_husk_rep1

city: Amsterdam

first: Maike

last: Stam

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description:
H3K9ac_husk.bed
H3K9ac_husk.bw

data_processing:
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering of ChIP-seq reads were done using FastX Toolkit and PRINSEQ (Q20).
ChIP-seq reads were aligned to the AGPv4 genome assembly using BWA
Non-uniquely mapped reads were filtered out using samtools (MAPQ20)
Peaks were called using MACS2 (-q 0.001, -broad)
Genome_build: AGPv4.32
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: bigwig files were converted from wig output from MACS2 using wigToBigWig tool (SPMR)

source_name: Husk tissue

growth_protocol: B73 maize plants were grown till stage V2 (Abendroth et al 2011) or till flowering (ears with emerging silks, before pollination) in greenhouse (16h of light per day, average temperature = 23°C)

extract_protocol:
Plant tissues were fixed with formaldehyde (3%) followed by nuclei extraction, sonication and Immunoprecipitation with H3K9ac antibody (ab10812). Immunoprecipitated DNA was recovered  by decrosslinking and purified on column.
Libraries were prepared according to KAPA Hyperprep kit (KK8500) instructions, using illumina Trueseq indexed adapters.

treatment_protocol: V2 Seedlings were dissected to extract the inner stem: the outer leaves, including sheath, and also exposed leaf blades were removed. Soft husk leaves were obtained after longitudinal section of the ear including husk, removal of the ear tissue as well as the lignified most external husk leaves layers.

value: inner layer husk, stage silk emerging 2-5 cm


title: input_DNA_husk

description:
H3K9ac_husk.bed
H3K9ac_husk_ip.bw


title: H3K9me3_TAM00hr_rep1


title: input_DNA_V2

description:
H3K9ac_ist.bed
H3K9ac_ist_ip.bw

source_name: V2 inner stem tissue

value: inner stem tissue V2 seedling


title: H3K9ac_ChIP_husk_rep2

description:
H3K9ac_husk.bed
H3K9ac_husk.bw


title: H3K4me3_TAM02hr_rep2


title: H3K9ac_ChIP_husk_rep3

description:
H3K9ac_husk.bed
H3K9ac_husk.bw


title: H3K4me3_TAM00hr_rep2


title: H3K4me3_TAM24hr_rep2


title: H3K9ac_ChIP_V2_rep1

description:
H3K9ac_ist.bed
H3K9ac_ist.bw


title: H3K4me1_TAM02hr_rep2


title: H3K4me1_TAM24hr_rep2


title: H3K9ac_ChIP_V2_rep2

description:
H3K9ac_ist.bed
H3K9ac_ist.bw


title: H3K4me1_TAM00hr_rep2


title: H3K4me1_TAM12hr_rep1


title: starvation_M

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Lactococcus lactis subsp. lactis NCDO712. The FASTA file, contig lengths and gff of gene annotations are available on the series record.
Supplementary_files_format_and_content: Tab delimited text file with read counts, RPKM and normalized RPKM

organism: Lactococcus lactis

source_name: Cell culture

growth_protocol: Cells were grown as standing cultures in GM17.

extract_protocol:
Cell were lysed using glassbead and total RNA was isolated using phenol/chloroform and ethanol precipitation
cDNA library was prepared by employing a ScriptSeqtm Complete Kit for Bacteria

treatment_protocol: Cells were re-suspended after growth to an OD600 of 0.9 in fresh GM17 containing 0.25% glucose (G*M17) and subjected to one of the following stress conditions: control (G*M17 at 30⁰C), cold (G*M17 at 10⁰C), heat (G*M17 at 42⁰C), acid (G*M17 set at pH 4.5 with lactic acid), osmotic stress (G*M17 containing 2.5% NaCl) and oxidative stress (G*M17, shaking at 250 rpm). For starvation stress, the cell pellets were re-suspended in filter-sterilized phosphate-buffered saline (PBS). 'Whey' refers to the whey-permeate medium for growing lactobacilli strains.

tag: stress

value: starvation


title: whey_wt_P


title: whey_wt_O


title: H3K4me1_TAM02hr_rep1


title: whey_glucose_R


title: H3K4me1_TAM36hr_rep1


title: H3K4me1_TAM00hr_rep1


title: H3K36me3_TAM36hr_rep1


title: whey_glucose_Q


title: DTP_TSA_ChIP_Input

city: South San Francisco

first: Suchit

last: Jhunjhunwala

state: CA

address: 1 DNA Way, MS-444A

institute: Genentech

data_processing:
Sequencing reads were aligned to human genome build hg19 with BWA using default parameters (Li 2013).
Alignments were filtered to extract only reads that belonged to matching pairs; pairs of reads that spanned on the average ~350-400 nt and were in the correct orientation. Read pairs with mapping quality 0 (high quality mappings to multiple locations) were not used for further analysis; in addition, presumptive PCR duplicates and reads that did not pass Illumina’s purity filter were removed.
Total number of reads was normalized according to the total number of reads that map to the Drosophila dm3 genome from each sample.
H3K9me3 ChIPseq peaks were called with SICER using input files as control (Zang et al., 2009).
Genome_build: hg19
Supplementary_files_format_and_content: Coverage files in bigWig format were generated by extending reads to 380 nt in silico and counting tags for 50-nt bins over the genome. Tab delimited text files report the genomic location along with the average number of tags for each H3K9me3-enriched regions (ChIPseq peaks).

source_name: NSCLC

growth_protocol: PC9 cells were cultured at 37 °C with 5% CO2 in RPMI-1640 (Invitrogen) supplemented with 10% FBS (HyClone).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
Illumina sequencing libraries were prepared from the ChIP and input DNAs following standard enzymatic steps consisting of end-polishing, dA-addition, and adaptor ligation. The resulting DNA libraries were quantified and sequenced as 150 bp paired-end reads using Illumina’s HiSeq 2500. The average size of the sequenced fragments were around 380 bp.

treatment_protocol: To generate DTPs, PC9 cells were treated with 1 μM erlotinib for 8 days. Media was replaced with fresh media supplemented with erlotinib every 3 days. Cells that survive the 8 day-treatment were considered DTPs. DTP_TSA samples were generated by treating DTPs on day 8 of erlotinib treatment with 50 nM TSA for 5 hours.

tag: cell line

tag: chip antibody

tag: treatment

value: 8 day 1 μM erlotinib + 5 hour 50 nM TSA


title: PC9_ChIP_Input


title: starvation_N


title: DTP_ChIP_Input

value: 8 day 1 μM erlotinib


title: H3K36me3_TAM12hr_rep1


title: oxygen_K

value: oxygen


title: H3K36me3_TAM02hr_rep1


title: salt_J

value: salt


title: DTP_TSA_H3K4me3_ChIPseq

value: H3K4me3 (Cell Signaling 9751)


title: DTP_H3K4me3_ChIPseq


title: H3K36me3_TAM00hr_rep1


title: DTP_H3K9me3_ChIPseq

value: H3K9me3 (abcam ab8898)


title: H3K27me3_TAM36hr_rep1


title: oxygen_L


title: salt_I


title: PC9_H3K9me3_ChIPseq


title: acid_H

value: acid


title: H3K27me3_TAM12hr_rep1


title: DTP_TSA_H3K9me3_ChIPseq


title: acid_G


title: H3K27me3_TAM02hr_rep1


title: heat_E

value: heat


title: ALDH_Low_Erl

data_processing:
Library strategy: ATAC-seq
Sequencing reads were aligned to human genome build hg19 using bowtie with essentially the same parameters as described previously (Buenrostro et al Nature Methods 2013). The reporting parameter was changed from -m1 to -M1 in order to include a randomly selected single alignment for reads mapping to multiple locations.
Genome-wide accessibility data was calculated using a 150 bp sliding window (step size = 20bp) to calculate the number of overlapping paired-end fragments. The paired-end fragments were represented as the coordinate for the first and last base of the fragment, which correspond to the accessible bases. All samples were normalized to the total number of reads per 10 million reads sequenced.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the software available from UCSC (Kent et al., 2010).

extract_protocol:
Nuclei were isolated before the transposition reactions were carried out as described in Buenrostro et al Nature Methods 2013.
Sequencing libraries were prepared using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: To generate DTPs, PC9 cells were treated with 1 μM erlotinib for 8 days. Media was replaced with fresh media supplemented with erlotinib every 3 days. Cells that survive the 8 day-treatment were considered DTPs. DTP_TSA samples were generated by treating DTPs on day 8 of erlotinib treatment with 50 nM TSA for 5 hours. ALDH_High and ALDH_Low samples were obtained from PC9 cells treated with DMSO or 1 μM erlotinib erlotinib for 12 hours as indicated prior to aldefluor sorting by FACS.

value: 12 hour 1 μM erlotinib


title: heat_F


title: ALDH_High_DMSO

value: 12 hour DMSO


title: ALDH_Low_DMSO


title: cold_D

value: cold


title: H3K27ac_TAM24hr_rep2


title: H3K27ac_TAM02hr_rep2


title: cold_C


title: ALDH_High_Erl


title: DTP_ATACseq


title: PC9_ATACseq


title: DTP_TSA_ATACseq


title: control_B

value: none (control)


title: H3K27ac_TAM00hr_rep2


title: H3K27ac_TAM12hr_rep1


title: H3K27ac_TAM02hr_rep1


title: control_A


title: WT

city: Shanghai

first: Tongtong

last: Guo

address: 300 Feng Lin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Chinese Academy of Sciences

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis:1.Remove reads with adaptors.2.Remove reads in which unknown bases are more than 10%.3.Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
Assessment of sequencing
Statistics of gene expression level: The gene expression is calculated by the numbers of reads mapped to the reference sequence and every gene.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 10-day seedling

extract_protocol:
Total RNA was harvested using Trizol reagent
After extracting the total RNA from the samples, mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads and mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeqTM 2000.

value: seedling

tag: age

value: 10 day

value: wild type


title: RNA restimulated cytotoxic T lymphocytes

description: WT CD8+T cells were stimulated with plate bound αCD3 (5ng/ml) and αCD28 (10ng/ml) for 48h, harvested and cultivated for additional 3d with medium containing 100ng/ml hIL-2. 5h restimulation by TPA (5 ng/ml) and ionomycin (0.5 microM).

source_name: restimulated cytotoxic T lymphocytes

value: wildtype

value: spleen

value: cytotoxic T lymphocytes


title: DNase-seq TAM24hr

data_processing:
Raw Fastq reads were aligned to human reference genome (hg19) using Bowtie (Langmead, Trapnell et al. 2009) allowing up to 2 mismatches. Only the uniquely mappable reads were used for subsequent analyses. The expression level in a sample was measured by the Reads per Million (RPM) value.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol: The procedures for DNase treatment of chromatin and library preparation was described in (Thurman et al., Nature, 2012).


title: DNase-seq TAM06hr


title: H3K27me3_TAM00hr_rep1


title: DNase-seq TAM00hr2


title: H3K27ac_TAM36hr_rep1


title: 7b: PC9+TSA (50nM ,5hours) RNA-seq

data_processing: The expression quantification was done using the Salmon method (Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Nat Meth (2017))

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from above samples using Qiagen RNAeasy extraction kit.  RNA was treated with DNAse.  ERCC spike-in control was added based on cell number according to manufacturers recommendations.
Libraries were generated from poly-A-selected RNA

treatment_protocol: PC9 cells were treated with 50nM TSA for five hours.  No media change.

value: PC9+TSA (50nM ,5hours)


title: H3K27ac_TAM00hr_rep1


title: 6b: PC9 +carboplatin (50uM,72h) RNA-seq

treatment_protocol: PC9 cells were treated with 50μM carboplatin for 72 hours.  Media with fresh drug replaced daily.

value: PC9 +carboplatin (50uM,72h)


title: SP-3 (IgG1 memory B cells CD73-CD80+ rep 3)

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
Paired end RNA-seq reads in fastq format were aligned to the mm9 genome assembly using STAR aligner [Dobin et al. 2013] version 2.3.
Gene annotations were derived from Mouse Gencode version M1.
Counts of reads mapping over Gencode version M1 gene features were obtained using the featureCounts method of the R/bioconductor subread package [Liao et al. 2014] version 1.5.0-p1.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files containing counts of reads over Mouse Gencode version M1 gene features

source_name: Pooled spleen and mesenteric lymph nodes

extract_protocol:
BALB/c mice were infected with N. brasiliensis.  B cell subsets were sorted ten weeks later from pooled spleen and mLN of three mice per replicate in quadruplicates.  RNA was isolated using Arcturus PicoPure® RNA Isolation Kit (Life Technologies). RNA quality was assessed by a Bioanalyzer (Agilent Technologies).
The RNA samples were subjected to cDNA synthesis using NuGEN® Ovation® RNA-Seq System V2 kit according to manufacturer's protocol. Libraries were made using NuGEN® Encore® Rapid Library Systems kit according to manufacturer's protocol with 500ng of cDNA. The libraries were subjected to an indexed paired-end sequencing run of 2 x 51bp on an Illumina HiSeq 2000.

value: BALB/c

value: IgG1 memory B cells CD73-CD80+

tag: sorting


title: gc-3 (IgG1 germinal center cells rep 3)

value: IgG1 germinal center cells


title: DN-4 (IgG1 memory B cells CD73-CD80- rep 4)

value: IgG1 memory B cells CD73-CD80-


title: 5b: PC9+erlotinib (1uM, 24 hours) RNA-seq

treatment_protocol: PC9 cells were treated with 1uM erlotinib for 24 hours.  No media change.

value: PC9+erlotinib (1uM, 24 hours)


title: gc-4 (IgG1 germinal center cells rep 4)


title: Naive-3 (naive B cell rep 3)

value: Naive B cells


title: 3c: PC9DTP+TSA (50nM, 5hours) RNA-seq

treatment_protocol: PC9 DTP cells were treated with 50nM TSA for 5 hours.  No media change.

value: PC9DTP+TSA (50nM, 5hours)


title: 5c: PC9+erlotinib (1uM, 24 hours) RNA-seq


title: 3a: PC9DTP+TSA (50nM, 5hours) RNA-seq


title: Naive-4 (naive B cell rep 4)


title: 3b: PC9DTP+TSA (50nM, 5hours) RNA-seq


title: DN-3 (IgG1 memory B cells CD73-CD80- rep 3)


title: DP-4 (IgG1 memory B cells CD73+CD80+ rep 4)

value: IgG1 memory B cells CD73+CD80+


title: DNase-seq TAM00hr1


title: crwn1 crwn2

tag: tissue

value: crwn1 crwn2


title: 2b: PC9DTP RNA-seq

treatment_protocol: To generate DTPs, PC9 cells were treated with 1 μM erlotinib for 8 days. Media was replaced with fresh media supplemented with erlotinib every 3 days. Cells that survive the 8 day-treatment were considered DTPs. ALDH_High and ALDH_Low samples were obtained from PC9 cells treated with DMSO or 1 μM erlotinib erlotinib for 12 hours as indicated prior to aldefluor sorting by FACS.


title: 5a: PC9+erlotinib (1uM, 24 hours) RNA-seq


title: 2c: PC9DTP RNA-seq


title: 6a: PC9 +carboplatin (50uM,72h) RNA-seq


title: 6c: PC9 +carboplatin (50uM,72h) RNA-seq


title: 7a: PC9+TSA (50nM ,5hours) RNA-seq


title: gc-2 (IgG1 germinal center cells rep 2)


title: SP-4 (IgG1 memory B cells CD73-CD80+ rep 4)


title: 2a: PC9DTP RNA-seq


title: 7c: PC9+TSA (50nM ,5hours) RNA-seq


title: DP-3 (IgG1 memory B cells CD73+CD80+ rep 3)


title: SP-2 (IgG1 memory B cells CD73-CD80+ rep 2)


title: 1c: PC9+DMSO RNA-seq

treatment_protocol: DMSO


title: Naive-2 (naive B cell rep 2)


title: 1b: PC9+DMSO RNA-seq


title: DN-2 (IgG1 memory B cells CD73-CD80- rep 2)


title: 1a: PC9+DMSO RNA-seq


title: DP-2 (IgG1 memory B cells CD73+CD80+ rep 2)


title: gc-1 (IgG1 germinal center cells rep 1)


title: 6c: ALDH_High_Erl_OCSA ATAC-seq

data_processing:
Sequencing reads were aligned to human genome build hg19 using BWA with the MEM mode. Aligned reads mapped to mitochondria genome, aligned reads with no proper pairs, low mapping quality and duplicates, supplementary alignments were further removed for downstream analysis.
For comparative analysis, the number of usable reads for each sample were normalized to the smallest number of usable reads among all samples under comparison.
Usable reads of all triplicates were combined for each experimental condition after normalization of read counts for downstream analysis.
All peaks were detected using MACS 1.4.2 with p-value 1e-7 and nomodel option. Peak filtering was performed by removing false peaks in the ENCODE blacklist.
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks

extract_protocol:
Prior to the assay, cells were cryopreserved in culture media containing 5% DMSO. The cells were then thawed in a 37C water bath, pelleted at 500g for 5 min at 4C, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013) with some modifications.
Cell pellets were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), pelleted at 500g for 10 min at 4C, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure XP beads (Beckman Coulter).

value: 12 hour 1 μM erlotinib


title: SP-1 (IgG1 memory B cells CD73-CD80+ rep 1)


title: 6b: ALDH_High_Erl_OCSA ATAC-seq


title: DN-1 (IgG1 memory B cells CD73-CD80- rep 1)


title: 6a: ALDH_High_Erl_OCSA ATAC-seq


title: DP-1 (IgG1 memory B cells CD73+CD80+ rep 1)


title: 5b: ALDH_Low_Erl_OCSA ATAC-seq


title: Tet2 -/- proliferating Neural Stem cells.Foxo3a-ChIPseq

first: Bing

last: Yao

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

description: ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Genome_build: mm9

source_name: Neural stem cells

growth_protocol: Briefly, forebrains without the olfactory bulb (4 mice/genotype, age- and sex-matched) were dissociated mechanically, followed by enzymatic digestion using PPD (2.5 units/ml papain, 1 unit/ml DNase I, 200 mg/100 ml Dispase II) in Dulbecco's modified Eagle's medium high glucose (Cellgro). After filtering through a 70-μm cell strainer (catalog number 252350; BD Falcon), the single cell suspension was loaded onto 50% Percoll (Sigma). The NSPCs were separated from other cells by ultracentrifugation at 12,700 rpm for 30 min at 20 °C using an SW41 Rotor (Beckman, CA). The fraction containing NSPCs (immediately above the red blood cell layer in the gradient) was collected, washed with phosphate-buffered saline, and cultured with Dulbecco's modified Eagle's medium/F-12 medium containing 20 ng/ml FGF-2 (catalog number K1606; Peprotech), 20 ng/ml epidermal growth factor (catalog number A2306; Peprotech), 1% N2 supplement (catalog number 17502-048; Gibco), 1% antibiotic-antimycotic (catalog number 15240-062; Gibco), and 2 mM L-glutamine (catalog number 25030-081; Gibco) in a 5% CO2 incubator at 37 °C. Half of the medium was replaced every 2–3 days.

extract_protocol:
Five to ten million NSCs were treated with 1% formaldehyde for 10 min at room temperature with gentle shaking. Fixation was terminated by adding 2M Glycine to reach 0.125M final concentration, and continue shaking for additional 5min. Cells were collected by cell scrapers and spin down at 1500 rpm for 10 min.  Cell pellet was resuspended in 1ml Nuclei Swelling Buffer (10 mM Hepes/pH7.9, 0.5% NP-40, 1.5 mM MgCl2, 10 mM KCl, 0.5 mM DTT and protease inhibitor cocktail), incubated on ice for 10 min and centrifuged at 5000 rpm for 5 min. Nuclear pellets were further lysed in 1ml SDS lysis buffer (20 mM Hepes/pH7.9, 25% glycerol, 0.5% NP-40, 0.5% Triton X-100, 0.42 M NaCl, 1.5 mM MgCl2, 0.2 mM EDTA and protease inhibitor cocktail). Cell lysate were sonicated 5 times with 6-9W output to obtain DNA fragments between 200-500bp. After sonication, nuclear lysate was cleared by centrifugation at 13000 rpm for 10 min to keep supernatant. The nuclear lysate was diluted with 3-4 volumes of dilution buffer (0.01% SDS, 1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, 16.7 mM Tris-HCl/pH8.0 and protease inhibitor cocktail). Immunoprecipitation was performed with antibodies specific to Foxo3a (1:1000, Bethyl) rotating overnight at 4ºC. 20 μl Protein-G Dynabeads (Life technologies) were added for additional 2 hours. TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl/pH 8.1), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-HCl/pH 8.1), TSE III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl/pH 8.1), and washed twice with TE buffer before eluted with 1% SDS and 0.1 M NaHCO3. The elution was incubated at 65 ºC for at least 6 hours to reverse the formaldehyde cross-linking, then DNA fragments were purified by using PCR Purification Kit (Qiagen). ChIPed DNA was subjected to library preparation. For genomic DNA extraction, Genomic DNA was first sonicated to 100-500bp, and mixed with 100 ml solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 250 mM UDP-6-N3-Glu and 2.25 mM wild-type b-glucosyltransferase. Reactions were incubated for 1 h at 37°C. DNA substrates were purified via Qiagen DNA purification kit. 150 mM dibenzocyclooctyne modified biotin was then added to the purified DNA, and the labeling re- action was performed for 2 h at 37°C. The biotin-labeled DNA was enriched by Streptavidin-coupled Dynabeads (Dynabeadsw MyOneTM Streptavidin T1, Life Technologies) and purified by Qiagen DNA purification kit for library preparation. RNA isolation was done by Trizol.
25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. The RNA-seq libraries were sequenced as 50-cycle pair-end runs using Illumina HiSeq 2000.

tag: genotype


title: 5c: ALDH_Low_Erl_OCSA ATAC-seq


title: 5a: ALDH_Low_Erl_OCSA ATAC-seq


title: Wildtype proliferating Neural Stem cells.Foxo3a-ChIPseq

description: ChIP-seq

value: Wildtype


title: 4a: ALDH_High_DMSO_OCSA ATAC-seq

value: 12 hour DMSO


title: Tet2 -/- proliferating Neural Stem Cell.5hmC-2


title: Wildtype proliferating Neural Stem Cell.5hmC-1


title: Tet2 -/- proliferating Neural Stem Cell.5hmC-1


title: Wildtype proliferating Neural Stem Cell.5hmC-2


title: 3b: ALDH_Low_DMSO_OCSA ATAC-seq


title: Tet2 -/- differentiating Neural Stem Cell RNAseq-2

description: RNA-seq


title: 2c: DTP_OCSA ATAC-seq

value: 8 day 1 μM erlotinib


title: 3a: ALDH_Low_DMSO_OCSA ATAC-seq


title: Naive-1 (naive B cell rep 1)

tag: cell type


title: Tet2 -/- differentiating Neural Stem Cell RNAseq-1

description: RNA-seq


title: 2b: DTP_OCSA ATAC-seq


title: Wildtype differentiating Neural Stem Cell RNAseq-2

description: RNA-seq


title: Wildtype differentiating Neural Stem Cell RNAseq-1

description: RNA-seq


title: 1b: PC9_OCSA ATAC-seq

value: DMSO


title: 1c: PC9_OCSA ATAC-seq


title: 4c: ALDH_High_DMSO_OCSA ATAC-seq


title: 4b: ALDH_High_DMSO_OCSA ATAC-seq


title: 1a: PC9_OCSA ATAC-seq


title: Tet2 -/- proliferating Neural Stem Cell RNAseq-1

description: RNA-seq


title: Tet2 -/- proliferating Neural Stem Cell RNAseq-2

description: RNA-seq


title: Wildtype proliferating Neural Stem Cell RNAseq-2

description: RNA-seq


title: Wildtype proliferating Neural Stem Cell RNAseq-1

description: RNA-seq


title: Segment_12_rep1and2_PCR2

status: Public on Jul 02 2017

city: Scarborough

first: Guillaume

middle: J

last: Filion

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: UTSC

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S12_fitness.txt.gz

data_processing:
Library strategy: Amplicon sequencing
Individual sequence variants were recovered from pair-end reads with the following steps: The constant region between the two variable regions was identified by inexact matching allowing up to 20% errors using the Seq library version 1.1.2 (https://github.com/ezorita/seeq). The reads are not oriented because the Illumina sequencing adapters were added by ligation, so the constant regions was searched on both reads. Forward and reverse reads were swapped when a match was found on the reverse read. This ensured that all the sequences are in the same orientation. For multiplexing purposes, the sample identity was encoded in the left and right primers used to PCR-amplify the variants. To demultiplex the reads, we used inexact matching with the candidate primers, allowing up to 20% errors. To merge the reads, the sequence of the reverse reads was reverse complemented and the constant region was searched by inexact matching allowing up to 20% errors. The position of the constant part in each read indicated how they must be stitched together. In the region of overlap, the consensus sequence was determined by picking the nucleotide with highest quality as indicated in the quality line of the fastq files. If 'N' persisted in the final sequence, the reads were discarded. The PCR primers were trimmed so that all the sequences of the same competition would start and end at the same location.
Reads that did not have the constant region, that could not be oriented or that could not be demultiplexed were discarded. The remaining errors in the reads were corrected by sequence clustering. We used starcode version 1.0 (https://github.com/gui11aume/starcode) with default parameters and allowing up to two errors. The corrected reads were translated using the genetic code. Variants encoding the same proteins were not merged; they were kept separate for downstream analyses.
The sequence variants were translated using the universal genetic code. Nonsense codons and final codons with less than three nucleotides (indicating a frameshift) were replaced by the underscore character. Finally, the absolute read counts for each variant at time 0 h, 12 h and 168 h of growth, were collected for each replicate.
For fitness estimation, variants with less than 10 reads in any of the biological or technical replicates were discarded. The mean relative frequency per million reads of each variant was computed over the replicates. To eliminate the influence of outliers, the mean was replaced by the median if the absolute difference between the mean and the median was greater than the median. The fitness of a variant was then estimated by minimizing the relative squared error of an exponential fit as detailed at https://github.com/Lcarey/HIS3InterspeciesEpistasis .
Supplementary_files_format_and_content: *PCR1.txt, *PCR2.txt: Tab-delimited text files include absolute read counts for each variant at time 0 h, 12 h and 168 h of growth.
Supplementary_files_format_and_content: *_fitness.txt.gz: Tab-delimited text files include fitness estimations.

organism: Saccharomyces cerevisiae

source_name: Whole cell

growth_protocol: Saccharomyces cerevisiae (strain LBCY47) libraries of mutants were grown in 500 ml of glucose synthetic complete dropout medium lacking uracil with 200 mg/L of G418 at 30°C at 220 RPM for 6-8 h with initial cell density of 1 million cells/ml. ~10 billion cells were inoculated into 1 l of synthetic complete dropout medium lacking histidine, and grown at 30°C at 220 RPM for 168 h with 12 h between bottlenecks of ~10 billion cells.

extract_protocol:
To extract plasmid DNA, 5 billion cells from each sample were incubated in 300 μL of zymolyase buffer (1 M sorbitol, 0.1 M sodium acetate, 60mM EDTA (pH 7.0), 2 mg/ml zymolyase, 1% 2-Mercaptoethanol) at 37°C for 3 h. The plasmid DNA was purified from the obtained spheroplasts using QIAprep Spin Miniprep Kit (QIAGEN, 27104) according to the manufacturer's protocol.
NGS libraries were prepared from 100 ng of the purified DNA amplicons using Ovation Rapid DR System (Nugen, 0319-32) according to manufacturer's instructions.

tag: strain


title: 3c: ALDH_Low_DMSO_OCSA ATAC-seq


title: Segment_10_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S10_fitness.txt.gz


title: Segment_12_rep1and2_PCR1


title: Segment_08_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S08_fitness.txt.gz


title: Segment_11_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S11_fitness.txt.gz


title: Segment_08_rep1and2_PCR1


title: Segment_11_rep1and2_PCR1


title: Segment_07_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S07_fitness.txt.gz


title: Segment_09_rep1and2_PCR1

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S09_fitness.txt.gz


title: Segment_06_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S06_fitness.txt.gz


title: Segment_06_rep1and2_PCR1


title: Segment_05_rep1and2_PCR1

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S05_fitness.txt.gz


title: Segment_10_rep1and2_PCR1


title: 2a: DTP_OCSA ATAC-seq


title: Segment_09_rep1and2_PCR2


title: Segment_05_rep1and2_PCR2


title: Segment_07_rep1and2_PCR1


title: Segment_04_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S04_fitness.txt.gz


title: Segment_03_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S03_fitness.txt.gz


title: Segment_02_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S02_fitness.txt.gz


title: Segment_03_rep1and2_PCR1


title: Segment_02_rep1and2_PCR1


title: Segment_01_rep1and2_PCR2

description:
Combination of yeast species.
This Sample represents 2 biological replicates.
Processed data file: S01_fitness.txt.gz


title: ID-seq PKIS screen

status: Public on Jul 01 2017

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

institute: Radboud University

description: Antibody specific DNA-tag.

data_processing:
Library strategy: ID-seq
bcl2fastq conversion v2.16.0.10.
Split reads from fastq files using R-package immunoSeq version 1.0.0.
Remove duplicate reads and count unique barcodes.
Match barcode sequences to antibody and sample.
Supplementary_files_format_and_content: The txt files are the index files used to match DNA-barcode sequences to antibody and samples for that specific experiment.
Supplementary_files_format_and_content: The .tsv files contain the barcode counts with matched antibody and sample specific information.

molecule: other

source_name: primary human keratinocytes

extract_protocol:
DNA-tags were released from immuno-stained cell populations using 1.5 hour DTT treatment.
Released DNA-tags were used in an overhang PCR reaction that adds sample-specific barcode sequence. Then a pool of these barcoded DNA-tags was used for a second PCR to add Illumina adaptor and index sequence to the DNA fragments.

tag: cell strain

value: Knp

value: primary human keratinocytes


title: ID-seq cell-dilution

description: Antibody specific DNA-tag.


title: ID-seq antibody-dilution sample-prep repl 1

description:
Antibody specific DNA-tag.
File 'JvBIV136_123_antibody_barcode_index.txt' is identical to file 'JvBIV123_antibody_barcode_index.txt'.
File 'JvBIV136_123_well_barcode_index.txt' is identical to file 'JvBIV123_well_barcode_index.txt'.


title: ID-seq EGF time-series

description: Antibody specific DNA-tag.


title: Segment_04_rep1and2_PCR1


title: RNAseq.S29

city: Ipswish

first: V K Chaithanya

last: Ponnaluri

state: Massachusetts

address: 240 County Road, 3W031

department: Genome Biology

institute: New England Biolabs

data_processing:
For WGBS, adaptor and low quality sequences (Phred score < 20) were trimmed from WGBS reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter of --paired. Reads were mapped to the human reference genome hg19 using Bismark with Bowtie2. CpG methylation was extracted from uniquely mapped reads using Bismark methylation extractor with the parameter of -p --no_overlap --merge_non_CpG. Differential methylation analysis was carried out using the bsseq package. Regions with 3 CpG sites and a mean methylation difference of 0.1 across both replicates were considered significantly differentially methylated.
For RNA-seq, sequencing reads were mapped to hg19 using TopHat2 (-r 60 --library-type fr-firststrand) with a known transcriptome file supplied (UCSC May 23, 2014). The number of reads mapped to each known gene were counted using htseq-count tools (-t exon -s reverse -i gene_id) and analyzed with DESeq2, where a negative binomial generalized linear model test is implemented on raw counts. The p-value of differential expression was corrected using Benjamini-Hochberg adjustment method and adjusted p-value was obtained. Genes with adj p-value < 0.1 were considered significantly differentially expressed. Sample distance was calculated using Euclidean distance on the rlog-transformed counts. Heatmap were generated using the Z-scored-transformed rlog values of significantly changed genes. Gene ontology analysis was carried out using the WebGestalt. Multiple comparisons were corrected using Bonferroni correction.
Genome_build: hg19

source_name: Human embryonic kidney

growth_protocol: HEK293 stable clones were cultured in DMEM media supplemented with 10% of Fetal Bovine Serum.

extract_protocol:
Genomic DNA were extracted using Easy-DNA™ gDNA Purification Kit (Life Technologies). Total RNA were extracted using TRIZol reagent.
For WGBS, 1 μg of genomic DNA from stable clones overexpressing GFP-SAHH or control vector fragmented by sonication, end-repaired and dA-tailed according to manufacturer’s conditions (New England Biolabs). Methylated NEB Illumina loop adaptor was ligated to DNA (E7370S, New England Biolabs). Ligated library was digested with USER and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research). Libraries were enriched by PCR using EpiMark Hot Start Taq DNA Polymerase (New England Biolabs). For RNA-seq, libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs) per the manufacturer’s instructions. Average insert size of libraries was 200 bp.

treatment_protocol: SAHH was cloned into pEGFP vector (Clonetech). HEK-293 stable cell line overexpressing GFP-SAHH was generated by selecting the cells transfected with SAHH constructs in 800 μg/mL of G418. After a week in culture single colonies were picked up and verified by western blotting using anti-GFP antibody.

tag: overexpression

value: GFP - SAHH


title: RNAseq.G17

value: GFP Control


title: ID-seq antibody-dilution sample-prep repl 2

description:
Antibody specific DNA-tag.
File 'JvBIV123_antibody_barcode_index.txt' is identical to file 'JvBIV136_123_antibody_barcode_index.txt'.
File 'JvBIV123_well_barcode_index.txt' is identical to file 'JvBIV136_123_well_barcode_index.txt'.


title: RNAseq.G13


title: WGBS.G17


title: RNAseq.S27


title: RNA_MRC5_exoRNA_1

city: Philadelphia

first: Yu

last: Qiu

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

description: exosome RNA

data_processing:
Basecalls performed using Illumina CASAVA software.
Raw reads were trimmed for adaptor sequence using cutadapt v1.9 (parameter -q 10 -m 30 -O 4)
Trimmed reads were mapped to consensus rRNA sequences and RN7SL1 using bowtie2 v2.2.4 to remove rRNA reads and get more accurate count of 7SL RNA (parameter --fr --no-mixed --no-discordant)
Reads were then aligned with STAR v2.4.0k to GRCm38/mm10 reference genome (parameter --outFilterMultimapNmax 100 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06)
Non primary alignment and QC failed reads were removed with samtools (parameter -F 772)
Aligned and filtered reads were counted against GENCODE annotation v21  and RepeatMasker features (UCSC genome browser) using Subread v1.4.6 (parameter -s 2 -minReadOverlap 10)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited txt file including raw read count for gene features and repeatmasker features.

source_name: MRC5 stroma cell mono-culture exosome

growth_protocol: All human breast cancer and/or stromal cell lines were cultured at 37oC in DMEM supplemented with 10% exosome depleted FBS, 100U/ml penicillin and 100µg/ml streptomycin.  For co-culutre experiment, stroma cells and breast cancer cells were mixed at 1:1.

extract_protocol:
Exosomes were isolated from conditioned media collected at 48-72 hours by serial high speed ultracentrifugation, or using 10% final concentration of polyethylene-glycol and low speed centrifugation. Exosome RNA was extracted with TRIzol.
Library was prepared by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) without the fragmentation step.

tag: culture

value: mono-culture


title: RNA_Cocx_exoRNA_2

description: exosome RNA

source_name: MRC5 and 1833 (breast cancer) co-culture exosome

value: MRC5 and 1833

value: co-culture


title: RNA_MRC5_exoRNA_2

description: exosome RNA


title: WGBS.S29


title: Segment_01_rep1and2_PCR1


title: WGBS.S27


title: P1_pre

description: exosome RNA

data_processing:
Basecalls performed using Illumina CASAVA software.
Raw reads were trimmed for adaptor sequence using cutadapt v1.9 (parameter -q 10 -m 30 -O 4)
Trimmed reads were mapped to consensus rRNA sequences and RN7SL1 using bowtie2 v2.2.4 to remove rRNA reads and get more accurate count of 7SL RNA (parameter --fr --no-mixed --no-discordant)
Reads were then aligned with STAR v2.4.0k to GRCm38/mm10 reference genome (parameter --outFilterMultimapNmax 100 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06)
Non primary alignment and QC failed reads were removed with samtools (parameter -F 772)
Aligned and filtered reads were counted against GENCODE annotation v21  and RepeatMasker features (UCSC genome browser) using Subread v1.4.6 (parameter -s 2 -minReadOverlap 10)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited txt file including raw read count for gene features and repeat masker features.

growth_protocol: Serum from patients with cancer were obtained through the UPENN RadOnc Biosample Repository. Blood was collected using yellow top Vacutainer (BD) and centrifuged at 3000rpm for 10 minutes. The samples were then frozen at -80oC until use.

extract_protocol:
500µl of serum was spun at 2000xg for 15 minutes, filtered through a 0.22µm filter, and then purified by serial high speed ultracentrifugation.
Library was prepared by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) without the fragmentation step.

tag: patient identity

tag: xrt stage

value: before


title: P1_post

description: exosome RNA

value: post


title: RNA_Cocx_exoRNA_1

description: exosome RNA


title: WGBS.G13


title: NAIVE

city: NEW YORK

first: Lukas

middle: Edward

last: Dow

state: New York

address: 413 East 69th Street, BB1318

department: Medicine

institute: Weill Cornell Medicine

data_processing:
The quality of the raw FASTQ files were checked with FastQC. Raw FASTQ reads were mapped to mouse reference GRCm38 using STAR two-pass alignment (v2.4.1d; --outFilterMismatchNmax 5), estimated gene expression using cufflinks (v2.2.1, default parameters), and quantified per-gene counts using HTseq (v0.6.0, default parameters).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file containing FPKM values for each sample. Comma-delimited file containing per-gene counts for each sample.

source_name: Intestinal organoid

extract_protocol:
RNA was extracted using TRIzol according to the manufacturers instructions and contaminating DNA was removed by DNase treatment for 10 mins and column purification (Qiagen RNAeasy). cDNA was prepared from 1 µg total RNA using qScript reverse transcription kit (Quantabio, #95047).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestinal organoid

tag: culture condition

value: ENR media

tag: genotype/variation

value: Dox naive (WT)


title: P1_xrt

description: exosome RNA

value: during


title: P2_xrt

description: exosome RNA


title: EN_F

value: EN media

value: Ptprk-Rspo3 (P-Rspo3)


title: ID-seq Signal-to-background and AG1478 treatment

description: Antibody specific DNA-tag.


title: EN4d


title: EN_M


title: P2_pre

description: exosome RNA


title: A5_plus

value: Apc delta/delta (Apc)


title: EN15d


title: A6_plus


title: NAIVE_F


title: A1_plus


title: A2_plus


title: A6

value: APC flox/flox (WT)


title: LIPO


title: A1


title: mut_vitc_rnaSeq

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Department of Microbiology & Immunology

institute: University of British Columbia

data_processing:
Base-calling was performed using RTA v2 on the NextSeq 500 platform
Reads aligned to a custom transcriptome reference (build from mm10 and Ensembl v71 annotations) were then ‘repositioned’ on to genomic coordinates, transforming reads that span exon–exon junctions into large-gapped alignments.
Using repositioned reads we generated genome-wide coverage profiles (wiggled files) using a custom BAM2WIG java program (http://www.epigenomes.ca/tools.html).
Differentially expressed genes were identified using a custom DEfine matlab tool (FDR cutoff=0.05) considering only those genes with an RPKM > 0.01
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file

source_name: HOXA9 IDH1 R132H

growth_protocol: Cells were plated at a density of 5x105 cells/ml in 4mL DMEM medium (Stem Cell Technologies, Vancouver, Canada) supplemented with 10% heat inactivated fetal bovine serum (Life Technologies) and 6 ng/ml murine IL-3, 10 ng/ml human IL-6, and 20 ng/ml murine SCF (Peprotech, Hamburg, Germany).

extract_protocol:
RNA-seq library construction according to standard operating procedures (http://www.epigenomes.ca/protocols-and- standards) under "Strand Specific 96-well Library Construction for Illumina Sequencing".
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

treatment_protocol: For vitamin C treated samples, daily addition (0h, 24h, 48h) of vitamin C to a final concentration of 0.345mM before harvesting at 72h after the first treatment

value: HOXA9 immortalized bone marrow

value: Vitamin C

tag: vector genotype

value: IDH1 R132H


title: mut_unt_tfchip_input

data_processing:
Base-calling was performed using RTA v2 on the NextSeq 500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a and 20 million reads were randomly subsampled from each library using   SAMtools (v0.1.2). Input libraries were used as controls
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
A custom java program (bamToWig) was used to generate wig files for downstream analysis and visualization. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Peaks were called using MACS2 (V2.1.0.2) on narrow mode with q<1e-5 using the input as a control
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file

extract_protocol:
Frozen cell pellets (10e7 cells) were cross-linked by formaldehyde (1% final concentration) and washed by PBS. Cells were lysed and chromatin was Covaris E-220 Sonicator (Covaris). Chromatin fragments were incubated with protein G and A Sepharose beads (GE Healthcare) for two hours at 4oC to eliminate non-specific binding. Unbound chromatin fragments were separated from the beads and incubated with no antibody at 4oC overnight in IP buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 90mM NaCl, 0.1% Triton X-100, 0.1% Deoxycholate, 0.1% SDS). After incubation, IPs were washed twice with ChIP wash buffer (20mM Tris-HCl pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and once with final ChIP wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). IPs were eluted in elution buffer (1% SDS, 100mM Sodium Bicarbonate) and incubated at 68oC for 2 hours to reverse crosslinks. DNA fragments were stripped from histones and purified using QIAquick PCR Purification Kit (Qiagen) and subjected to 8 cycles of paired-end indexing PCR. Illumina sequencing  libraries were generated as previously described. Libraries were PCR amplified and sequenced on the Illumina NextSeq 500 platform following the manufacturer’s protocols (Illumina, Hayward CA.)
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: Untreated


title: A5


title: A2


title: mut_unt_runx1

data_processing:
Base-calling was performed using RTA v2 on the NextSeq 500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a and 20 million reads were randomly subsampled from each library using   SAMtools (v0.1.2)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
A custom java program (bamToWig) was used to generate wig files for downstream analysis and visualization. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Peaks were called using MACS2 (V2.1.0.2) on narrow mode with q<1e-5
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file

extract_protocol:
Frozen cell pellets (10e7 cells) were cross-linked by formaldehyde (1% final concentration) and washed by PBS. Cells were lysed and chromatin was Covaris E-220 Sonicator (Covaris). Chromatin fragments were incubated with protein G and A Sepharose beads (GE Healthcare) for two hours at 4oC to eliminate non-specific binding. Unbound chromatin fragments were separated from the beads and incubated with RUNX1 (Abcam; ab23980) antibody at 4oC overnight in IP buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 90mM NaCl, 0.1% Triton X-100, 0.1% Deoxycholate, 0.1% SDS). After incubation, IPs were washed twice with ChIP wash buffer (20mM Tris-HCl pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and once with final ChIP wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). IPs were eluted in elution buffer (1% SDS, 100mM Sodium Bicarbonate) and incubated at 68oC for 2 hours to reverse crosslinks. DNA fragments were stripped from histones and purified using QIAquick PCR Purification Kit (Qiagen) and subjected to 8 cycles of paired-end indexing PCR. Illumina sequencing  libraries were generated as previously described. Libraries were PCR amplified and sequenced on the Illumina NextSeq 500 platform following the manufacturer’s protocols (Illumina, Hayward CA.)
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: Anti-Runx1; Abcam; ab23980


title: mut_unt_rnaSeq

data_processing:
Base-calling was performed using RTA v2 on the NextSeq 500 platform
SAMtools (v0.1.2). Input libraries were used as controls
Using repositioned reads we generated genome-wide coverage profiles (wiggled files) using a custom BAM2WIG java program (http://www.epigenomes.ca/tools.html).
Differentially expressed genes were identified using a custom DEfine matlab tool (FDR cutoff=0.05) considering only those genes with an RPKM > 0.01
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file


title: mut_vitc_runx1