title: mut_vitc_wgbs

city: Vancouver

first: Martin

last: Hirst

address: 2125 East Mall

department: Department of Microbiology & Immunology

institute: University of British Columbia

description: WGBS treated DNA

data_processing:
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Bisulfite converted reads were aligned to mm10 using NovoAlign version 3.02.08 (Novocraft Technologies)
Fractional methylation calls were generated using a custom script that uses samtools (v0.1.8) mpileup to count the number of Cs (methylated) and T's (unmethylated) at each CpG in the genome.
DMRs were identified from WGBS sequence reads by scanning the genome for adjacent, differentially methylated CpGs (Δ0.25; p < 0.05) within 300bp windows.
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

extract_protocol:
Bisulfite conversion was performed on genomic DNA using the MethylEdge Kit (Promega) according to manufacturer recommendations. To monitor under and over conversion rates 1ng of fully methylated T7 phage and unmethylated lambda DNA were spiked into 100ng of sample gDNA prior to bisulfite conversion. The resulting pool was suspended in 5ul of EB buffer, added to 32.5 μl of MethylEdge Bisulfite Conversion Reagent and incubated at 98°C for 6 min followed by 54°C for 60 min. Bisulfite converted DNA was isolated with MagSi-DNA all-around beads (MagNa Medics) and desulfonation was performed on the beads for 15 min before 2 washes 80% ethanol and elution for 15 min @ 56C. cDNA was generated from the resulting single stranded template by adding 2.5 μl of 10 mM dNTP mix (NEB) and 2 μl of 500 μM random primer to the DNA and denaturing at 98°C for 1 min before quickly moving to ice and adding 5 μl of 10X NEB2 buffer (NEB) and 1 μl of 50 U/μl Klenow fragment (3′→5′ exo−) (NEB). The mixture was then incubated as follows: 4°C for 30 min; 4°C-37°C (1°C/min); 37°C for 30 min; 70°C for 10 min. After cDNA synthesis the DNA was purified using SeraMag magnetic beads (20% PEG; 1M NaOH) a 75ul:50ul bead:DNA ratio, and in 35 μl before standard Illumina library preparation beginning at the adapter ligation stage.
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: HOXA9 immortalized bone marrow

value: Vitamin C

tag: vector genotype

value: IDH1 R132H


title: GCLiPP resting Th2 experiment 2

status: Public on Jul 01 2017

type: SRA

city: San Francisco

first: Adam

middle: Jacob

last: Litterman

state: CA

address: 513 Parnassus Avenue, UCSF Box 0414, HSE-201

department: Microbiology and Immunology

country: USA

institute: UCSF

description:
RBP crosslinked RNA
biotinylated lystae, oligo-dT selection, streptavidin bead capture, Rnase T1 digestion, linker ligation, reverse transcription, cDNA amplification
Mouse_T_cells_combined_GCLiPP_positive_strand.bw
Mouse_T_cells_combined_GCLiPP_negative_strand.bw
Mouse_Th2_T_cells_GCLiPP_positive_strand.bw
Mouse_Th2_T_cells_GCLiPP_negative_strand.bw
Mouse_GCLiPP_peaks.bed

library_source: transcriptomic

data_processing:
For GCLiPP raw reads were demultiplexed by a custom script and linker trimmed with fastx_trimmer
Linker dimer reads were discarded and one uniquely aligning read with a given di-nucleotide randomer in the 3' RNA linker was kept for further analysis to remove PCR duplicates
GCliPP reads were aligned to mm10 using bowtie2
Peaks were called with in house perl scripts that convolved a normal distribution against observed read distribution at each nucleotide and looked of local maxima of correlation
RNAseq was aligned to mm10 with STAR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, reads per million at each location in the genome; bed, location of called peaks and voids of GCLiPP read density; csv, per gene expression data from RNAseq

molecule: total RNA

organism: Mus musculus

source_name: CD4 T cells

growth_protocol: Mouse T cells were grown on plates coated with anti-CD3 and anti-CD28 antibodies and the indicated cytokines for 5 days

extract_protocol:
Cells were lysed by re-suspension in PXL buffer without SDS. Cell debris were pelleted and supernatants were biotinylated with EZ-Link-NHS-SS-Biotin. Poly-A RNA was enriched by pulldown with oligo-dT beads. RNPs were captured with M-280 Streptavidin dynabeads and RNAs were digested with RNAse T1
Linkers were ligated on while RNPs were immobilized on M-280 beads and released by proteinase K digestion, size selected by TBE-Urea PAGE gel, gel extracted, reverse transcribed and used for cDNA amplification

treatment_protocol: Four hours before harvest cells were re-plated in fresh medium (resting) or re-stimulated with PMA/Ionomycin (stimulated). Cells were crosslinked with 8000 mJ high energy (254 nM) UV light

tag: strain

tag: culture conditions

value: IL-4, anti-Ifn-gamma, IL-2

tag: restimulation


title: cocx_cell_ctrl_2

city: Philadelphia

first: Yu

last: Qiu

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

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.

organism: Homo sapiens

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

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 or cellular RNA was extracted with TRIzol.
Library was prepared by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).  Fragmentation step was skipped for exosome RNA.

treatment_protocol: Either whole cells or whole exosomes were incubated at 37oC for 30 minutes in MNase Buffer (25mM Tris-HCl, 2.5mM CaCl2, 50mM NaCl, 1X PBS), with or without MNase and with or without 0.1% Triton X-100.

tag: cell line

value: MRC5 and 1833

tag: culture

value: co-culture

tag: fraction

value: cellular RNA

tag: treatment

value: no treatment


title: mut_unt_hchip_input

state: British Columbia

country: Canada

library_source: genomic

data_processing:
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a
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

molecule: genomic DNA

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:
Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
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

tag: cell type

value: Untreated

tag: chip antibody


title: cocx_cell_triton_2

value: 0.1% Triton X-100 and micrococcal nuclease


title: GCLiPP resting Th2 experiment 1


title: mut_unt_wgbs

description: WGBS treated DNA


title: cocx_cell_triton_1


title: mut_vitc_hchip_input


title: CLB-BER-Lud H3K27ac, ChIP-seq

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

data_processing:
ChIP-seq: Alignment with Bowtie2, default options
ChIP-seq: Quality filtering: Q > 20; duplicates kept
ChIP-seq: Peak calling with HMCan v1.30
ChIP-seq: Renormalization of wig profiles among all H3K27ac samples with an in-house R script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to renormalized signal; score in .bed files correspond to the likelihood of a region to be enriched in H3K27ac or to be a binding site of a TF
RNA-seq:TopHat2 v2.0.643 with the following parameters: global alignment, no mismatch in the 22 bp seed, up to three mismatches in the read, library type fr-firststrand
Genome_build: hg19/GRCh37

source_name: CLB-BER-Lud

growth_protocol:
ChIP-seq: Neuroblastoma cell lines were cultured at 37°C with 5% CO2 in a humidified atmosphere in RPMI (GE Healthcare, for CLB cell lines, SH-EP, GICAN and NB69), in IMDM (Gibco) for NB-EBc1 (according to the provided conditions) or DMEM (GE Healthcare, for other cell lines), with 10%, 15% or 20% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin (Gibco). Primary hNCC lines were grown as previously described under bioethical approval PFS14-011 from the French Biomedical Agency for the use of human embryonic material to S. Zaffran. Briefly, cells were grown in Glutamax DMEM:F12 [Gibco] supplemented with 12% FCS (Eurobio), 100 μg/ml penicillin/streptomycin, 10 mM HEPES, 100 ng/ml hydrocortisone, 10 μg/ml transferrin, 400 pg/ml 3,3,5-thio-iodo-thyronine, 10 pg/ml glucagon, 100 pg/ml epidermal growth factor, 1 ng/ml insulin and 200 pg/ml fibroblast growth factor 2 (all products supplied by Sigma-Aldrich except EGF and FGF2 from Gibco).
RNA-seq: Neuroblastoma cell lines were cultured at 37°C with 5% CO2 in a humidified atmosphere in RPMI (GE Healthcare, for CLB cell lines, SH-EP, GICAN and NB69), in IMDM (Gibco) for NB-EBc1 (according to the provided conditions) or DMEM (GE Healthcare, for other cell lines), with 10%, 15% or 20% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin (Gibco). Primary hNCC lines were grown as previously described under bioethical approval PFS14-011 from the French Biomedical Agency for the use of human embryonic material to S. Zaffran. Briefly, cells were grown in Glutamax DMEM:F12 [Gibco] supplemented with 12% FCS (Eurobio), 100 μg/ml penicillin/streptomycin, 10 mM HEPES, 100 ng/ml hydrocortisone, 10 μg/ml transferrin, 400 pg/ml 3,3,5-thio-iodo-thyronine, 10 pg/ml glucagon, 100 pg/ml epidermal growth factor, 1 ng/ml insulin and 200 pg/ml fibroblast growth factor 2 (all products supplied by Sigma-Aldrich except EGF and FGF2 from Gibco).

extract_protocol:
ChIP-seq: Chromatin preparation and ChIP were performed with Ideal ChIP-seq kit for histones or transcription factors according to the supplier's protocol (Diagenode )
ChIP-seq: llumina sequencing libraries were prepared from ChIP and input DNAs using the TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, DNA were subjected to consecutive steps of end-repair, dA-tailing and ligation to TruSeq indexed Illumina adapters. Size-selection was performed only for the H3K27ac ChIP (100 – 600 bp). After a final amplification step, the resulting DNA libraries were quantified using a qPCR method (KAPA library quantification kit) and sequenced on the Illumina HiSeq2500 instrument (rapid run mode; single reads 100 nts).
RNA-seq: Total RNA was extracted from fresh cells or frozen tumors using TRIzol® Reagent (Invitrogen), or AllPrep DNA/RNA Mini Kit (Qiagen) or NucleoSpin RNA kit (Macherey-Nagel; for the SK-N-SH cell line treated with chemotherapy). All samples were subjected to quality control on a Bioanalyzer instrument and only RNA with RIN (RNA Integrity Number) > 6 were used for sequencing.
RNA-seq: RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows performing a strand-specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library. After qPCR quantification, sequencing was carried out using 2 x 50 cycles (paired-end reads 50 nts) for all samples (except SH-EP, 2 x 100; Pair1-Relapse and Pair3-Relapse, 2 x 75; Pair2-Relapse, 2 x 150). Sequencing was performed with the Illumina HiSeq2500 instrument (high output mode).

treatment_protocol:
RNA-seq: Cells were not treated unless it is specified
RNA-seq: Treatment of cell lines with chemotherapy: SK-N-SH cells were plated in 6-well plates and then treated with cisplatin (7.5 µM) or doxorubicin (100 nM) for 7 days, medium and drugs were changed every 2 days. RNAs were extracted using NucleoSpin RNA kit (Macherey-Nagel).
RNA-seq: Doxycycline-inducible shRNA systems: PHOX2B-specific short hairpin RNAs sh1783 (5’-CCGGTGGAAGGCAGAAACCATTAAA- CTCGAGTTTAATGGTTTCTGCCTTCCATTTTTG-3’) and sh1437 (5’-CCGGAGTAATCG- CGCTAAGAATAAACTCGAGTTTATTCTTAGCGCGATTACTTTTTTG-3’) were selected from Sigma Mission shRNA library and cloned into the pLKO-Tet-On all-in-one system46 (Addgene). Lentiviral particles were produced in HEK293T cells and CLB-GA cells were infected as previously described4. SH-SY5Y cells were incubated with viral particules for 48 hours without polybrene. Selection with puromycin (Invitrogen) at 400 ng/ml or 1 µg/ml, respectively, was performed 24 h after infection and maintained during all culture experiments, for CLB-GA and SH-SY5Y cells, respectively. PHOX2B knockdown efficacy was assessed by Western blot 24 h/48 h/96 h after the addition of doxycycline (100 ng/ml or 1 μg/ml). For colony formation assays, 6x104 transduced cells were plated at day 0 in 6-well dishes and stained with crystal violet at day 11.

value: Neuroblastoma cell line

value: ab4729 (rabbit polyclonal, Abcam)


title: cocx_cell_ctrl_1


title: mut_vitc_H3K27ac

data_processing:
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a
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

value: Anti-H3K27ac; Hiroshi Kimura, Cell Biology Unit, Tokyo Institute of Technology


title: E8 rep2

city: Suita

first: Kouichi

last: Hasegawa

state: Osaka

address: 6F Techno Alliance Bldg. 2-8 Yamadaoka

department: StemRIM Institute of Regeneration-Inducing Medicine

country: Japan

institute: Osaka University

data_processing:
HCS version 2.0.12.0 and RTA version 1.17.21.3 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and  mapped to hg19/GRCh37 whole genome using QuasR  with parameters -m 1 --best --strata -v 2
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: embryonic stem cells

growth_protocol: KhES-1human ES cells in AKIT or Essential 8 culture media on 0.5µg/cm2 Laminin-E8 fragment-coated dishes.

extract_protocol:
Total RNAs were purified with RNAeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cells

tag: medium


title: mut_unt_H3K27ac


title: GCLiPP resting CD8 experiment 1

description:
RBP crosslinked RNA
biotinylated lystae, oligo-dT selection, streptavidin bead capture, Rnase T1 digestion, linker ligation, reverse transcription, cDNA amplification
Mouse_T_cells_combined_GCLiPP_positive_strand.bw
Mouse_T_cells_combined_GCLiPP_negative_strand.bw
Mouse_CD8_T_cells_GCLiPP_positive_strand.bw
Mouse_CD8_T_cells_GCLiPP_negative_strand.bw
Mouse_GCLiPP_peaks.bed

source_name: CD8 T cells


title: E8 rep1


title: AKIT rep3

value: AKIT


title: mut_vitc_H3K4me3

value: Anti-H3K4me3; Cell Signaling Technology:Catalogue# 9751S, lot #8


title: AKIT rep2


title: mut_unt_H3K4me3


title: AKIT rep1


title: mut_vitc_H3K4me1

data_processing:
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a
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 broad 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

value: Anti-H3K4me1; Diagenode:Catalogue #C15410037, lot A1657D


title: Fibroblasts uninfected Human BR2

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

description:
3D skin models were mock treated for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_8_br2

data_processing:
Basecalls were performed using standard software supplied by Illumina for HiSeq2500 sequencing.
Reads generated with HiSeq2000 were mapped with NextGenMap (version 0.4.12) using default settings and producing bam-files.
Genome_build: GRCh38.p2 and SC5314 assembly 21 where applicable
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. RPKM was calculated according to Mortazavi et al.

source_name: uninfected human skin model

growth_protocol: 3D skin models were grown in KGM-2 medium in 24 well plate transwell inserts with a pore size of 8 µm.

extract_protocol:
Tissue cell layers were separated, quickly washed in PBS and immediately frozen down in liquid nitrogen. Disruption was carried out using a Mixer Mill MM 200 (RETSCH) with a shaking frequency of 30/s. The resulting powder was resuspended in lysis buffer RLT (QIAGEN, Hilden, Germany) supplemented with 0.01% v/v of ß-mercaptoethanol. The extraction of total RNA was performed according to QIAGEN’s Protocol for the isolation of total RNA using the RNeasy Plus Mini Kit. Concentration and integrity of total RNA was analyzed using the Agilent 2100 Bioanalyzer using the RNA Nano kit.
TruSeq RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: Skin models were infection with 100 colony forming units of an overnight culture of C. albicans strain SC5314 in 5 µl PBS. Uninfected models were treated with mock PBS. Infected skin models were kept at 37°C in a humidified 5 % CO2-containing atmosphere for 24h

tag: tissue

value: S1F fibroblasts

tag: model type

value: Fibroblasts + Keratinocytes


title: mut_vitc_meDIPSeq

data_processing:
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Alignment to mm10 was performed by bwa (bwa-aln) version 0.5.7
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.
Pairwise, differential peaks between wild-type, mutant, untreated and vitamin C treated samples (DMRs) were called using MACS (macs14 1.4.2) with a threshold pe-5 and the MEDIPS R package (p<0.05)
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:
Genomic DNA was sonicated to approximately 200–400 bp with a Covaris E-220 Sonicator (Covaris) and end-repaired using standard Illumina library preparation protocol. DNA was immunoprecipitated with anti-5-methylcytidine antibody. Immunoabsorbed DNA fragments were recovered by adding a rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson ImmunoResearch) and incubating for 2h. To complete library preparation, the immuno-precipitated DNA was purified and subjected to two 10-cycle PCR reactions using 16 μl of DNA for each sample with paired-end Illumina PCR primers. A final size selection was performed to select all fragments <700 bp in size by electrophoresis in 8% polyacrylamide gel.
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: HOXA9 immortalized bone marrow

value: Vitamin C

value: IDH1 R132H


title: wt_vitc_meDIPSeq

source_name: HOXA9 IDH1 WT

value: IDH1 wt


title: Keratinocytes uninfected Human BR3

description:
3D skin models were mock treated for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_12_br3

value: Ker-CT keratinocytes


title: mut_unt_H3K4me1


title: mut_unt_meDIPSeq


title: Keratinocytes uninfected Human BR1

description:
3D skin models were mock treated for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_12_br1


title: Keratinocytes uninfected Human BR2

description:
3D skin models were mock treated for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_12_br2


title: mut_vitc_hmeDIPSeq

data_processing:
Library strategy: hMeDIP-Seq
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Alignment to mm10 was performed by bwa (bwa-aln) version 0.5.7
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.
Pairwise, differential peaks between wild-type, mutant, untreated and vitamin C treated samples (DMRs) were called using MACS (macs14 1.4.2) with a threshold pe-5 and the MEDIPS R package (p<0.05)
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:
Genomic DNA was sonicated to approximately 200–400 bp with a Covaris E-220 Sonicator (Covaris) and end-repaired using standard Illumina library preparation protocol. DNA was immunoprecipitated with anti-5-hydroxymethylcytidine antibody. Immunoabsorbed DNA fragments were recovered by adding a rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson ImmunoResearch) and incubating for 2h. To complete library preparation, the immuno-precipitated DNA was purified and subjected to two 10-cycle PCR reactions using 16 μl of DNA for each sample with paired-end Illumina PCR primers. A final size selection was performed to select all fragments <700 bp in size by electrophoresis in 8% polyacrylamide gel.
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: Anti-5-hydroxy-methylcytidine (Active Motif; Catalogue #39769)


title: Fibroblasts uninfected Human BR3

description:
3D skin models were mock treated for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_8_br3


title: 4H

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina CASAVA v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45" and were trimmed for adapter sequences using cutadapt with parameters "-O 5 -m 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11.
Gene abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: HES3 hESC derived INS-GFP+ cells-H1152 treated

growth_protocol: hESCs were cultured on feeders to 80-90% confluency, then treated with 3 μM CHIR99021 and 100 ng/ml activin A in RPMI supplemented with 2 mM GlutaMAX and 100 U/ml Pen/Strep for one day, and then 100 ng/ml activin A in RPMI supplemented with 0.2% fetal bovine serum (FBS), 2 mM GlutaMAX and 100 U/ml Pen/Strep. The medium was changed 2 days later to 50 ng/ml FGF7 in RPMI supplemented with 2 mM GlutaMAX, 100 U/ml Pen/Strep and 2% FBS, and maintained for an additional 2 days. Cells were transferred to 300 nM LDN193189, 2 μM retinoic acid, and 0.25 μM SANT-1 for the first 4 days and then to 300 nM LDN193189, 20 nM Phorbol 12,13- dibutyrate (PuBu), and 1 μM ALK5i in DMEM supplemented with 2 mM GlutaMAX, 100 U/ml Pen/Strep, and 1x B27 for an additional 4 days. The cells were treated with either DMSO or H1152 afterwards for additional 8 days.

extract_protocol:
total RNA was extracteed with the Absolutely RNA nanoprep Agilent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: at day 13 the cells were either treated with DMSO or H1152

value: HES3 hESC derived INS-GFP+ cells

tag: time in culture

value: 21 days


title: HET_HFD_L8

city: Portland

first: Jae

middle: W

last: Lee

state: OR

address: 3181 SW Sam jackson Rd

department: Pediatrics

institute: Oregon Health & Science University

data_processing:
Basecalls was performed using CASAVA software of Illumina
RNA-seq reads were aligned to the mm9 genome assembly using tophat2
The mapped reads were counted using HTSeq
Differential gene expression analysis was performed by Deseq
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited txt file were produced by Deseq

source_name: RNAseq-MLL4 het-HFD

growth_protocol: C57 black mice were grown to 8 weeks and then subjected to diet.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) and reverse transcription was performed using SuperScript III (Invitrogen).
Libraries were prepared according to the Illumina TruSeq protocol, validated using the bioanalyzer and real-time PCR, and then sequenced on the Illumina HiSeq 2000

treatment_protocol: High fat diet (HFD) or normal chow diet (ND) was fed to either control wild type or MLL4 het mice for 8 weeks.

value: C57 Black

value: liver

tag: genotype

value: MLL4 het

value: high fat diet


title: 1H


title: Fibroblasts uninfected Human BR1

description:
3D skin models were mock treated for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_8_br1


title: mut_unt_hmeDIPSeq

value: Untreated


title: wt_unt_meDIPSeq


title: 1D

source_name: HES3 hESC derived INS-GFP+ cells-DMSO treated

value: DMSO


title: 4D


title: GIMEN H3K27ac, ChIP-seq

source_name: GIMEN

value: Neuroblastoma cell line

value: ab4729 (rabbit polyclonal, Abcam)


title: HET_HFD_L7


title: HET_ND_L3

source_name: RNAseq-MLL4 het-ND

value: chow diet


title: HET_ND_L4


title: WT_HFD_L5

source_name: RNAseq-WT-HFD

value: wild-type


title: WT_HFD_L6


title: WT_ND_L2

source_name: RNAseq-WT-ND


title: WT_ND_L1


title: RNA Kc SXL #2 RNAi 3 days [Sample 114]

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description: PolyA RNA

data_processing:
RNA-seq alignment was performed using Tophat2 (2.0.5) against the reference genome (BDGP 5.74). Bedgraph files were generated using genomeCoverageBed (Bedtools) with –split parameter.
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.

organism: Drosophila melanogaster

source_name: Kc cells

extract_protocol: Total RNA was prepared from 4 million cells using RNeasy mini columns (Qiagen) and 2.5 μg of RNA was used for polyA selection. Libraries were prepared using New England Biolabs reagents according to protocols (E7490, E6150, E7525, E6111, E7442, E7335 and (Peleg et al., 2016)).

value: Kc

tag: gender

value: female

value: SXL #2 RNAi 3 days


title: RNA Kc SXL #1 RNAi 9 days [Sample 113]

description: PolyA RNA

value: SXL #1 RNAi 9 days


title: RNA Kc SXL #2 RNAi 6 days [Sample 115]

description: PolyA RNA

value: SXL #2 RNAi 6 days


title: RNA Kc SXL #2 RNAi 9 days [Sample 116]

description: PolyA RNA

value: SXL #2 RNAi 9 days


title: RNA Kc SXL #1 RNAi 3 days [Sample 111]

description: PolyA RNA

value: SXL #1 RNAi 3 days


title: RNA Kc SXL #1 RNAi 6 days [Sample 112]

description: PolyA RNA

value: SXL #1 RNAi 6 days


title: ChIP H3K36me3 Kc rep1 [Sample 103]

data_processing:
ChIP-seq reads were mapped to the reference genome (BDGP 5.74) using bowtie2 (2.0.2) with default settings. Tag directories were generated by the Homer software package (Heinz et al., 2010). Coverage and Input normalized Bedgraph files were obtained using the "makeUCSCfile" tool with default settings.
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.

extract_protocol: H3K36me3 ChIP-seq was performed on MNase digested chromatin as described previously (Straub et al., 2008 and Kasinathan et al., 2013) with some modifications. Cells were fixed in 1% formaldehyde for 1 min at 26°C, followed by quenching with 125 mM glycine and washing with PBS. Nuclei were released by resuspending in TM2+ with NP-40. MNase digestion was performed in TM2+IC using 4U MNase (Sigma Aldrich, resuspended in EX50 (Bonte & Becker, 1999)) in the presence of CaCl2 for 13 min at 37 °C. Reaction was stopped with EGTA and Triton-X-100, SDS, NaDOC and NaCl was added to final concentration as in RIPA Buffer. MNase digested chromatin was incubated for 1 h at 4°C while slight agitation and chromatin was solubilized by passing ten times through 27 G needle and centrifuged for 30 min at 15,000 g at 4°C. ChIP was performed from soluble chromatin using H3K36me3 antibody (ab9050, Abcam).

value: anti-H3K36me3 Abcam (ab9050)


title: RNA Kc GFP RNAi 9 days [Sample 110]

description: PolyA RNA

value: GFP RNAi 9 days


title: RNA S2 rep1 [Sample 106]

description: PolyA RNA

source_name: S2 cells

value: male

value: GFP RNAi


title: ChIP Input for H3K36me3 Kc rep1 [Sample 102]


title: ChIP Input for H3K36me3 S2 rep1 [Sample 98]


title: ChIP H3K36me3 S2 rep2 [Sample 101]


title: ChIP H3K36me3 Kc rep2 [Sample 105]


title: RNA Kc GFP RNAi 3 days [Sample 108]

description: PolyA RNA

value: GFP RNAi 3 days


title: ChIP Input for H3K36me3 S2 rep2 [Sample 100]


title: ChIP H3K36me3 S2 rep1 [Sample 99]


title: ChIP H4K16ac Kc rep2 [Sample 97]

extract_protocol: ChIP experiments (Covaris) were performed according to (Schauer et al., 2013) adapted to cell lines (Villa et al., 2016). Briefly, cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine, the cells were collected, washed and sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 min. MSL2 antibody was previously described in (Villa et al., 2012) and H4K16ac was acquired from Active Motif (#39167).

value: anti-H4K16ac Active Motif (#39167)


title: Family1420Set_GM12006

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

institute: HHMI/University of Michigan

data_processing:
Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.
Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 – 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.
Variants were called with Samtools (v0.1.16)
Genome_build: hg18

source_name: cultured B-cells

growth_protocol: Cultured B-cell lines were obtained from Coriell (Camden, NJ, USA). The B-cells were grown to a density of 5x105 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine.

extract_protocol: RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.

tag: sample

tag: family

tag: relation

value: maternal grandmother

tag: protocol

value: non-directional


title: ChIP Input Kc rep1 [Sample 94]


title: ChIP MSL2 S2 rep4 [Sample 93]

value: anti-MSL2 (Becker lab)


title: ChIP Input Kc rep2 [Sample 96]

value: Kc


title: UnrelatedSet2_GM12891

value: maternal grandfather


title: Family1420Set_GM12003

value: paternal grandfather


title: ChIP H4K16ac Kc rep1 [Sample 95]

value: female


title: RNA Kc GFP RNAi 6 days [Sample 109]

description: PolyA RNA

value: GFP RNAi 6 days


title: RNA S2 rep2 [Sample 107]

description: PolyA RNA


title: ChIP Input S2 rep3 [Sample 90]


title: ChIP MSL2 S2 rep3 [Sample 91]


title: UnrelatedSet2_GM12872


title: ChIP Input for H3K36me3 Kc rep2 [Sample 104]


title: UnrelatedSet2_GM12874


title: ChIP MSL2 S2 rep2 [Sample 89]


title: ChIP Input S2 rep2 [Sample 88]


title: ChIP H4K16ac S2 rep1 [Sample 87]


title: UnrelatedSet2_GM12814


title: ChIP MSL2 S2 rep1 [Sample 86]


title: Family1420Set_GM12004

value: paternal grandmother


title: Family1420Set_GM12005


title: ChIP Input S2 rep1 [Sample 85]


title: UnrelatedSet2_GM12762


title: 4C Kc SXL 2 [Sample 84]

data_processing:
Library strategy: 4C-Seq
4C-seq data processing was based on the FourCSeq Bioconductor package (Klein et al., 2015). Fastq files were de-multiplexed using a python script available in the package and aligned to the reference genome (BDGP 5.74) using bowtie2 (2.0.2) with "-local" settings. Reads were filtered for mapping quality (mapq > 1) and non-digested, self-ligated fragments were removed. Reads were counted for each valid DpnII fragment and obtained read counts per fragment. Bedgraphs were generated using the "writeTrackFiles" function.
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.

extract_protocol:
4C-seq was carried out on S2-DRSC cells (DGRC stock: 181) and Kc167 (DGRC stock: 1) in biological duplicates. RNAi was performed as described previously (Straub et al., 2005 and Alekseyenko et al., 2012)). After 7 days of RNA interference, cells were re-suspended in fresh medium and fixed with 1% formaldehyde for 10 min at room temperature. Fixing was quenched by adding glycine (final concentration 125 mM) and by cooling on ice. Cells were collected in a cooled centrifuge, snap frozen in liquid nitrogen and stored at -80°C.
4C-seq templates were generated on ~60 million fixed cells per replicate using 4-cutter restriction enzymes DpnII and NlaI, as described previously (Ghavi-Helm et al., 2014). Libraries were amplified using 100 ng 4C-seq templates and Pfu Turbo DNA polymerase in 8 PCR replicates, which were pooled for later analysis. Primers were designed to allow a multiplexing of 48 samples (for 12 viewpoints and 4 conditions) on a sequencing lane. Biological replicates were sequenced on two separate lanes of an Illumina NextSeq 500 sequencer.

value: SXL RNAi

tag: 4c viewpoint (chrx)


title: UnrelatedSet2_GM12716


title: ChIP Input S2 rep4 [Sample 92]

tag: cell line


title: 4C Kc SXL 2 [Sample 83]


title: UnrelatedSet2_GM12264


title: UnrelatedSet2_GM12717


title: 4C Kc SXL 2 [Sample 82]


title: 4C Kc SXL 2 [Sample 81]


title: 4C Kc SXL 2 [Sample 80]


title: UnrelatedSet2_GM12145


title: 4C Kc SXL 2 [Sample 79]


title: 4C Kc SXL 2 [Sample 78]


title: UnrelatedSet2_GM12813


title: UnrelatedSet2_GM12057


title: 4C Kc SXL 2 [Sample 77]


title: UnrelatedSet2_GM12044


title: UnrelatedSet2_GM12750


title: 4C Kc SXL 1 [Sample 76]


title: UnrelatedSet2_GM12815


title: UnrelatedSet2_GM12043


title: 4C Kc SXL 1 [Sample 75]


title: UnrelatedSet2_GM12005


title: 4C Kc SXL 1 [Sample 72]


title: 4C Kc SXL 1 [Sample 74]


title: UnrelatedSet2_GM12144


title: UnrelatedSet2_GM12003


title: 4C Kc SXL 1 [Sample 71]


title: UnrelatedSet2_GM12155


title: UnrelatedSet2_GM11994


title: UnrelatedSet2_GM11993


title: 4C Kc SXL 1 [Sample 73]


title: 4C Kc GFP 2 [Sample 68]


title: 4C Kc SXL 1 [Sample 70]


title: UnrelatedSet2_GM12056


title: UnrelatedSet2_GM11992


title: 4C Kc SXL 1 [Sample 69]


title: 4C Kc GFP 2 [Sample 67]


title: UnrelatedSet2_GM11882


title: 4C Kc GFP 2 [Sample 66]


title: UnrelatedSet2_GM11881


title: UnrelatedSet2_GM12006


title: UnrelatedSet2_GM11839


title: UnrelatedSet2_GM11832


title: UnrelatedSet2_GM12004


title: 4C Kc GFP 2 [Sample 65]


title: UnrelatedSet2_GM11831


title: 4C Kc GFP 2 [Sample 64]


title: 4C Kc GFP 2 [Sample 62]


title: 4C Kc GFP 2 [Sample 63]


title: UnrelatedSet2_GM11829


title: UnrelatedSet2_GM11830


title: CDKAL1-/-+MT1E

description: mRNA

data_processing:
Illumina bcl2fastq v2.17 was used for base calling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt with parameters "-O 5 -m 45 -q 10"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11.
Gene abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: hESC-derived insulin-GFP+ cells

growth_protocol: CDKAL1-/- hESCs were differentiated to pancreatic beta-like cells and then purified using cell sorting.

extract_protocol:
RNA was harvested using RNAase isolation kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESC-derived pancreatic beta-like cells

tag: genotype/vairation

value: CDKAL1-/-hESCs overexpressing MT1E


title: 4C Kc GFP 2 [Sample 60]


title: CDKAL1-/-

description: mRNA

value: CDKAL1-/- hESCs


title: UnrelatedSet2_GM07345


title: 4C Kc GFP 2 [Sample 59]


title: UnrelatedSet2_GM07056


title: UnrelatedSet2_GM07055


title: 4C Kc GFP 2 [Sample 58]


title: 4C Kc GFP 1 [Sample 57]


title: UnrelatedSet2_GM07034


title: MCF7 YBX1 Rep1

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Alignment: tophat v 2.1.0 'tophat --GTF Homo_sapiens.GRCh37.75.gtf --bowtie1 --no-novel-juncs --min-anchor 3 --num-threads 4  --output <outputFile> <Homo_sapiens.GRCh37.75.dna_sm.primary_assembly.fa> <inputFastq>'
Counts: Subread v1.5.1. 'featureCounts -t "exon" -g "gene_id -s 2  -p --primary -C  -T 4 -a Homo_sapiens.GRCh37.75.gtf -o <outputFile> <inputBam>'
Filtering: Exclude features with no hits in any sample
Differential expression analysis: DESeq2 v 1.14.0, R v3.3.2 - default DESeq2 analysis as recommended in manual 'estimate--> normalised counts
Genome_build: Homo sapiens GRCh37
Supplementary_files_format_and_content: Matrix table of nomalised counts

source_name: MCF-7 cell line stably overexpressing FLAG-tagged YBX1

growth_protocol: MCF-7 human breast cancer cells were cultured in DMEM (Invitrogen) supplemented with 10% FBS and antibiotics. Cells stably overexpressing NFIB/YBX1 were grown in the presence of geneticin (G418; Invitrogen). All cells were maintained at 37°C, 5% CO2.

extract_protocol:
RNA was extracted using the miRNeasy spin column kit (QIAGEN) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent).
mRNA-seq libraries were prepared from three biological replicates of each stable overexpression system using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: genotype/variation

value: MCF-7 stably overexpressing FLAG-tagged YBX1


title: UnrelatedSet2_GM07022


title: 4C Kc GFP 1 [Sample 56]

tag: treatment

value: GFP RNAi


title: MCF7 NFIB Rep3

source_name: MCF-7 cell line stably overexpressing FLAG-tagged NFIB

value: MCF-7 stably overexpressing FLAG-tagged NFIB


title: UnrelatedSet2_GM07000


title: 4C Kc GFP 1 [Sample 55]


title: MCF7 NFIB Rep2


title: 4C Kc GFP 2 [Sample 61]


title: 4C Kc GFP 1 [Sample 53]


title: MCF7 NFIB Rep1


title: 4C Kc GFP 1 [Sample 52]


title: MCF7 Parental Rep2

source_name: MCF-7 cell line

value: Parental MCF7


title: UnrelatedSet2_GM06993


title: MCF7 YBX1 Rep3


title: UnrelatedSet2_GM06985

value: maternal grandmother


title: 4C Kc GFP 1 [Sample 50]


title: SW1990 positive rep3

data_processing:
Base-calling was done using bcl2fastq2 Conversion Software v2.17.
Sequenced reads were trimmed for adaptor sequence, and  mapped to hg19/GRCh37 whole genome using QuasR  with parameters -m 1 --best --strata -v 2
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: pancreatic adenocarcinoma cells

growth_protocol: CFPAC-1 and SW-1990 cells were grown as monolayer cultures in Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum and 2 mM L-glutamine. Cells were passaged every 3-4 days upon reaching 70-80% confluence, using TrypLE (Gibco) for dissociation, and were subcultured in a split ratio of 1:5.

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit (Qiagen, 74104), and purified with DNase I (Qiagen, 79254). RNA was then quantified using the NanoDrop2000 spectrophotometer (Thermo Scientific). 1μg quantified total RNA was taken and enriched for PolyA using Oligo(dT) Microparticles.
Transcriptome library for sequencing was constructed according to SureSelect Strand-Specific RNA Library Prep Kit protocol outlined in “SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing” (Cat #5500-0135). Briefly, the mRNA was fragmented for 2 minutes at elevated temperature (94oC) in the presence of divalent cations and first strand cDNA was synthesized. The single stranded cDNA was cleaned up using HighPrep (Magbio, Cat #AC-60050). Strand Specificity is maintained by the addition of Actinomycin D at this step. Second strand cDNA was synthesized and end repaired using Second Strand Synthesis + End Repair mix. The cDNA was cleaned up using HighPrep (Magbio, Cat #AC-60050). Adapters were ligated to the cDNA molecules after addition of “A”- base. HighPrep cleanup was performed post ligation. The library was indexed and enriched for adapter ligated fragments using 10 cycles of PCR. The prepared library was quantified using Qubit and validated for quality by running an aliquot on D1000 Tapes. Finally, the adapter positive fragments were quantified using KAPA qPCR quantification kit (KAPA Biosystems; Cat #KK4824).

treatment_protocol: All cells were trypsinized and resuspended in GCTM-5 IgG1 antibody supernatant (primary antibody). The cells were incubated for 1 hour at 4°C, then washed thrice with FACS buffer (0.1% BSA, 2 mM EDTA in PBS) and subsequently incubated with the secondary antibody (goat anti-mouse HRP) for 30 minutes. Cells were washed thrice and resuspended at 2.E6 cells/ml for sorting. Flow cytometry was performed using BD FACSAria™ Fusion flow cytometer (BD Biosciences) and data was analysed by BD FACSDiva software provided with the system. The gates were chosen to include only highly positive and negative cell populations and the sorted cells were then used for RNA extraction.

tag: cell type

value: pancreatic adenocarcinoma

value: positive


title: 4C Kc GFP 1 [Sample 49]

value: Kc


title: MCF7 Parental Rep1


title: SW1990 positive rep1


title: MCF7 YBX1 Rep2


title: 4C Kc GFP 1 [Sample 48]


title: SW1990 positive rep2


title: 4C Kc GFP 1 [Sample 47]


title: SW1990 negative rep2

value: negative


title: 4C S2 MSL2 2 [Sample 46]

value: male

value: MSL2 RNAi


title: SW1990 negative rep3


title: 4C Kc GFP 1 [Sample 54]

value: female


title: SW1990 negative rep1


title: UnrelatedSet2_GM06994

value: paternal grandfather

value: non-directional


title: 4C S2 MSL2 2 [Sample 43]


title: CFPAC-1 positive rep2


title: 4C S2 MSL2 2 [Sample 45]


title: CFPAC-1 positive rep3


title: MCF7 Parental Rep3


title: 4C S2 MSL2 2 [Sample 42]


title: 4C Kc GFP 1 [Sample 51]


title: 4C S2 MSL2 2 [Sample 41]


title: CFPAC-1 positive rep1


title: CFPAC-1 negative rep3


title: CFPAC-1 negative rep2


title: CFPAC-1 negative rep1


title: 4C S2 MSL2 2 [Sample 39]


title: 4C S2 MSL2 2 [Sample 38]


title: 4C S2 MSL2 2 [Sample 40]


title: RNAseq stimulated CD8

description:
protocol was as described until elution from oligo-dT beads, then poly-A RNA was prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturers instructions
All_genes_RNAseq.csv

data_processing:
For GCLiPP raw reads were demultiplexed by a custom script and linker trimmed with fastx_trimmer
Linker dimer reads were discarded and one uniquely aligning read with a given di-nucleotide randomer in the 3' RNA linker was kept for further analysis to remove PCR duplicates
GCliPP reads were aligned to mm10 using bowtie2
Peaks were called with in house perl scripts that convolved a normal distribution against observed read distribution at each nucleotide and looked of local maxima of correlation
RNAseq was aligned to mm10 with STAR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, reads per million at each location in the genome; bed, location of called peaks and voids of GCLiPP read density; csv, per gene expression data from RNAseq

source_name: CD8 T cells

extract_protocol:
Cells were lysed by re-suspension in PXL buffer without SDS. Cell debris were pelleted and supernatants were biotinylated with EZ-Link-NHS-SS-Biotin. Poly-A RNA was enriched by pulldown with oligo-dT beads. RNPs were captured with M-280 Streptavidin dynabeads and RNAs were digested with RNAse T1
Linkers were ligated on while RNPs were immobilized on M-280 beads and released by proteinase K digestion, size selected by TBE-Urea PAGE gel, gel extracted, reverse transcribed and used for cDNA amplification

tag: strain

tag: culture conditions

tag: restimulation

value: PMA/Ionomycin


title: 4C S2 MSL2 1 [Sample 37]


title: RNAseq stimulated Th2

source_name: CD4 T cells

value: IL-4, anti-Ifn-gamma, IL-2


title: RNAseq resting CD8


title: 4C S2 MSL2 1 [Sample 35]


title: 4C S2 MSL2 1 [Sample 36]


title: 4C S2 MSL2 2 [Sample 44]


title: 4C S2 MSL2 1 [Sample 33]


title: 4C S2 MSL2 1 [Sample 32]


title: 4C S2 MSL2 1 [Sample 31]


title: 4C S2 MSL2 1 [Sample 30]


title: S. viridis A10.1 LLHC-F ZT46 REP1

city: St. Louis

first: Malia

last: Gehan

state: Missouri

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
BBTools (v36.20)   using parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo ktrim=l k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=20 minlen=20 (Bushnell, 2016). Any parameters not specified were run as default.
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to index the transcripts with the default parameters and the Setaria viridis transcripts fasta file (Sviridis_311_v1.1) from Phytozome (Goodstein et al., 2012).
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to quantify reads with parameters:-t 40 -b 100. Any parameters not specified were run as default.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Setaria viridis

source_name: Leaf Tissue

growth_protocol: Plants were grown under either 12 hour photocycles (12h light/12h dark) or 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C) then sampled every 2 hours for 48 hours under constant light and constant temperature conditions (32 deg C). Photocycle entrained samples are labeled LDHH-F, and thermocycle entrained samples are entrained LLHC-F.

extract_protocol: Wang et al. 2012; http://dx.doi.org/10.1371/journal.pone.0026426

tag: tissue

value: Leaf

tag: accession

tag: sample age

value: 10  Days  After Planting


title: S. viridis A10.1 LLHC-F ZT46 REP2

value: 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C)


title: S. viridis A10.1 LLHC-F ZT42 REP1


title: S. viridis A10.1 LLHC-F ZT48 REP1


title: S. viridis A10.1 LLHC-F ZT44 REP2


title: 4C S2 GFP 2 [Sample 28]

tag: gender

value: GFP RNAi


title: S. viridis A10.1 LLHC-F ZT42 REP2


title: 4C S2 GFP 2 [Sample 26]


title: S. viridis A10.1 LLHC-F ZT40 REP1


title: 4C S2 GFP 2 [Sample 25]


title: S. viridis A10.1 LLHC-F ZT38 REP1


title: 4C S2 GFP 2 [Sample 27]


title: 4C S2 MSL2 1 [Sample 34]


title: 4C S2 GFP 2 [Sample 23]


title: S. viridis A10.1 LLHC-F ZT44 REP1


title: 4C S2 GFP 2 [Sample 24]


title: S. viridis A10.1 LLHC-F ZT38 REP2


title: S. viridis A10.1 LLHC-F ZT48 REP2


title: 4C S2 GFP 2 [Sample 22]


title: 4C S2 MSL2 1 [Sample 29]


title: RNAseq resting Th2


title: S. viridis A10.1 LLHC-F ZT36 REP1


title: S. viridis A10.1 LLHC-F ZT40 REP2


title: 4C S2 GFP 2 [Sample 21]


title: S. viridis A10.1 LLHC-F ZT36 REP2


title: 4C S2 GFP 2 [Sample 20]


title: 4C S2 GFP 2 [Sample 19]


title: S. viridis A10.1 LLHC-F ZT34 REP1


title: S. viridis A10.1 LLHC-F ZT34 REP2


title: 4C S2 GFP 2 [Sample 18]


title: S. viridis A10.1 LLHC-F ZT32 REP1


title: 4C S2 GFP 2 [Sample 17]


title: S. viridis A10.1 LLHC-F ZT32 REP2


title: 4C S2 GFP 1 [Sample 16]


title: S. viridis A10.1 LLHC-F ZT30 REP1


title: S. viridis A10.1 LLHC-F ZT30 REP2


title: 4C S2 GFP 1 [Sample 14]


title: 4C S2 GFP 1 [Sample 11]


title: 4C S2 GFP 1 [Sample 13]


title: 4C S2 GFP 1 [Sample 12]


title: S. viridis A10.1 LLHC-F ZT24 REP2


title: S. viridis A10.1 LLHC-F ZT24 REP1


title: S. viridis A10.1 LLHC-F ZT22 REP1


title: S. viridis A10.1 LLHC-F ZT26 REP2


title: S. viridis A10.1 LLHC-F ZT28 REP2


title: S. viridis A10.1 LLHC-F ZT26 REP1


title: 4C S2 GFP 1 [Sample 7]


title: 4C S2 GFP 1 [Sample 9]


title: S. viridis A10.1 LLHC-F ZT22 REP2


title: 4C S2 GFP 1 [Sample 6]


title: S. viridis A10.1 LLHC-F ZT20 REP1


title: 4C S2 GFP 1 [Sample 5]


title: S. viridis A10.1 LLHC-F ZT20 REP2


title: S. viridis A10.1 LLHC-F ZT18 REP1


title: cont_24hours_rep3

city: Palmerston North

first: David

last: Wheeler

state: No State/International

address: Tennent Drive, Massey University (Turitea)

department: Institute of Fundamental Sciences

country: New Zealand

institute: Massey University

description: no nitrite provided

data_processing:
Adapters were removed using FastqMCF, quality trimming was performed using the SolexaQA++ dynamictrim utility, with minimum quality threshold of 20 (p=0.01); if after quality trimming the length of the reads became less than 65 bp we removed
Reads were aligned to the reference genome using Tophat V2.0.13 with the default paramaters except --library-type fr-firststrand
Raw read counts were generated from the resulting BAM files using HTSeq-count in Union mode and --stranded=reverse
Genome_build: Version 5 downloaded from JGI
Supplementary_files_format_and_content: Raw read counts per annotated gene

molecule: polyA RNA

organism: Chlamydomonas reinhardtii

source_name: cell pellet

growth_protocol: Cells were grown in darkness at 25 degrees C

extract_protocol:
mRNA was extracted using plant NucleoSpin RNA kit (Macherey-Nagel, Germany).
Illumina Tru-Seq stranded mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and treatment cultures of  Chlamydomonas reinhardtii (three of each) were incubated in darkness before the addition of 10 mM nitrite to the treatment flasks. Samples were collected from both groups at 15 min, 3 hours, and 24 hours post addition of nitrite to the treatment group.

tag: group

value: CONTROL

tag: timepoint

value: 24 hours


title: S. viridis A10.1 LLHC-F ZT16 REP1


title: cont_24hours_rep2

description: no nitrite provided


title: cont_3hours_rep3

description: no nitrite provided

value: 3 hours


title: cont_15min_rep3

description: no nitrite provided

value: 15 minutes


title: S. viridis A10.1 LLHC-F ZT28 REP1


title: cont_3hours_rep2

description: no nitrite provided


title: 4C S2 GFP 1 [Sample 10]


title: Embryos stage X replicate c

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description: 20-30 pulled embryos

data_processing:
Full genomic sequence for chicken (galGal3) was downloaded from Ensembl database. Full transcriptomic sequences were downloaded from Ensembl version 65. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
We assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: galGal3
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Gallus gallus

source_name: Eyal-Giladi stage X chick embryos

extract_protocol:
RNeasy Mini Kit - QIAGEN
TruSeq RNA library prep kit V2

tag: developmental stage

value: Eyal-Giladi stage X

value: embryo


title: 4C S2 GFP 1 [Sample 8]

value: male


title: S. viridis A10.1 LLHC-F ZT16 REP2


title: cont_15min_rep2

description: no nitrite provided


title: Embryos stage X replicate a

description: 20-30 pulled embryos


title: S. viridis A10.1 LLHC-F ZT14 REP1


title: cont_24hours_rep1

description: no nitrite provided


title: wt_fed_C

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
mRNA-seq reads were aligned to the ce6 genome by STAR (Dobin et al., 2013) and differentially expressed genes were identified by HOMER (Heinz et al., 2010) and EdgeR (Robinson et al., 2010)
Genome_build: ce6
Supplementary_files_format_and_content: bedGraph

organism: Caenorhabditis elegans

source_name: wild type

growth_protocol: Nematodes were grown at 20C on NGM plates seeded with OP50 bacteria when not starved.

extract_protocol:
Nematodes were harvested, flash frozen with liquid nitrogen, and RNA was harvested using Isol-RNA Lysis Reagent (Ref #2302700 5 PRIME), RNA was further cleaned using Qiagen RNeasy Protect Mini kit (Qiagen). Illumina TruSeq RNA Sample Prep kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA-seq: Libraries were prepared from purified RNA (TruSeq Illumina mRNA prep kit) and sequenced according to the manufacturer’s instructions (HiSeq v4 Illumina SR sequencing kit).

treatment_protocol: Nematodes were starved for 0, 1, 2, 3, 4, 6, or 16 hours by transfering them to empty NMG plates.

value: wild type

tag: starvation timepoint


title: Embryos stage X replicate b

description: 20-30 pulled embryos


title: S. viridis A10.1 LLHC-F ZT12 REP2


title: S. viridis A10.1 LLHC-F ZT14 REP2


title: S. viridis A10.1 LLHC-F ZT10 REP2


title: wt_fed_B


title: wt_fed_A


title: treat_24hours_rep3

description: 10mM nitrite

value: TREATMENT


title: S. viridis A10.1 LLHC-F ZT18 REP2


title: treat_3hours_rep3

description: 10mM nitrite


title: S. viridis A10.1 LLHC-F ZT10 REP1


title: wt_6H_C


title: S. viridis A10.1 LLHC-F ZT8 REP2


title: S. viridis A10.1 LLHC-F ZT8 REP1


title: S. viridis A10.1 LLHC-F ZT6 REP2


title: wt_6H_A


title: treat_24hours_rep2

description: 10mM nitrite


title: treat_15min_rep3

description: 10mM nitrite


title: wt_6H_B


title: 4C S2 GFP 1 [Sample 15]

tag: 4c viewpoint (chrx)


title: S. viridis A10.1 LLHC-F ZT12 REP1


title: treat_3hours_rep2

description: 10mM nitrite


title: wt_4H_C


title: S. viridis A10.1 LLHC-F ZT4 REP2


title: cont_3hours_rep1

description: no nitrite provided


title: treat_24hours_rep1

description: 10mM nitrite


title: cont_15min_rep1

description: no nitrite provided


title: treat_15min_rep2

description: 10mM nitrite


title: S. viridis A10.1 LLHC-F ZT4 REP1


title: treat_3hours_rep1

description: 10mM nitrite


title: S. viridis A10.1 LLHC-F ZT6 REP1


title: wt_4H_B


title: S. viridis A10.1 LLHC-F ZT2 REP2


title: wt_3H_A


title: wt_3H_B


title: S. viridis A10.1 LLHC-F ZT2 REP1


title: wt_4H_A


title: wt_2H_C


title: S. viridis A10.1 LDHH-F ZT48 REP2

value: 12 hour photocycles (12h light/12h dark)


title: wt_2H_B


title: M25 rep3

city: Pirassununga

first: Yonara

middle: de Gouveia

last: Cordeiro

state: São Paulo

address: Duque de Caxias Norte, 255

department: Veterinary Medicine

country: Brazil

institute: University of São Paulo

data_processing:
Sequencing quality was evaluated by FastQC software
Each sample was aligned against the reference genome (CanFam3.1) using TopHat 2.0.9 and Bowtie 2.1.0
PCR duplicates, not primary alignments and low quality reads were removed with Samtools
Final reads were counted using HTSeq
Genome_build: CanFam3.1
Supplementary_files_format_and_content: table files with reads counts for each gene

organism: Canis lupus familiaris

source_name: Primary cell culture

growth_protocol: Cells were cultured in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics, in 25cm³ flasks kept under controlled CO2 and temperature.

extract_protocol:
Total RNA of triplicate biological samples from each cell line was extracted with TRIZOLTM according to manufacturer’s recommendation. RNA quality and quantity were assessed using automated capillary gel electrophoresis on a Bioanalyzer 2100 with RNA 6000 Nano Labchips (Agilent Technologies Ireland, Dublin, Ireland), and only samples which presented an RNA integrity number (RIN) above 8.0 were used for further analysis.
Preparation of mRNA libraries was carried out using a TruSeq™ RNA Sample Prep Kit in accordance with TruSeq® RNA Sample Preparation v2 Guide (Illumina, USA).

value: Mammary Gland Tumor

tag: passage

tag: cell line


title: M25 rep2


title: S. viridis A10.1 LDHH-F ZT48 REP3


title: wt_2H_A

tag: genotype/variation


title: M25 rep1


title: M5 rep3


title: treat_15min_rep1

description: 10mM nitrite


title: S. viridis A10.1 LDHH-F ZT46 REP2

tag: treatment


title: S. viridis A10.1 LDHH-F ZT46 REP1


title: wt_3H_C


title: M5 rep2


title: wt_1H_B


title: S. viridis A10.1 LDHH-F ZT44 REP2


title: wt_1H_A


title: Spom.hsr1.KCl.T20_B

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

institute: Wisconsin Institute for Discovery

data_processing:
Reads were aligned to the reference genomes using TopHat with default setttings.
Gene expression levels were quantified using Cuffquant (Cufflinks 2.2.1 suite) with default settings.
Gene expression levels were normalized across all samples using Cuffnorm (Cufflinks2.2.1 suite) with default settings.
Genome_build: C. albicans was downloaded from the Candida Genome Database (accession number AACQ00000000); S. pombe was downloaded from PombeDB (accession numbers CU329670–CU329672); S. cerevisiae was downloaded July 2005 from the Saccharomyces Genome Database
Supplementary_files_format_and_content: Tab-delimited text files with normalized gene expression levels

organism: Schizosaccharomyces pombe

source_name: S. pombe hsr1 knockout with KCl stress at T=20, replicate B

growth_protocol: For each strain, cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and re-suspended into 3.5 mL BMW culture (with or without drug depending if WT or hog1Δ) and placed in a New Brunswick Scientific Edison model TC-7 roller drum on the fastest rotation until saturated (1-2 days). For each species, saturated cultures were diluted to OD600 ~ 0.001 – 0.008, where for each species care was taken to ensure that the OD600 of the WT and hog1Δ strains were the same. These starting cultures were further diluted serially at 1:4 in at least 6 rows of a 96 well plate with 2 biological replicates per strain. Growth curves were measured using the Biotek Synergy H1 Hybrid Reader with OD600 measurements every 15 minutes, operating at continuous low shaking at 30°C for each species.

extract_protocol:
Qiagen Yeast RNA extraction
Refer to Trombetta et al, 2014

treatment_protocol: Osmotic Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with BMW (Ctrl) or KCl to a final concentration of 0.4M. Samples were harvested at 0, 10, or 20 minutes following treatment.  After growth, 150ml of each culture was transferred to each of 100ml BMW (CTRL - defined in the Growth protocol) and 100ml BMW+KCl (EXP).  Both CTRL and EXP media were pre-warmed for 40-60 minutes in the shaker prior to the experiment. EXP media was either BMW + 0.5M KCl or 1M KCl yielding a final concentration of 0.2M KCl or 0.4M KCl, respectively, upon addition of the culture. In each case, CTRL media was added first, followed by the EXP media, whereupon the shaker was immediately activated to 180 rpm and the timer started simultaneously. Samples (20ml) were collected from the CTRL media + culture immediately upon activation of the shaker (T=0), then at T=10, 20, 40, and 80 minutes from the EXP media + culture.

tag: genotype

value: hsr1 knockout