title: Input

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: Fragmented genomic DNA

data_processing:
Illumina Casava (v. 1.8.2) software used for basecalling.
Sequenced reads were mapped to hg18 genome using CASAVA (v.1.8.2)
The sequence reads were normalized as reads per million per nucleotide (RPM).
Genome_build: hg18
Supplementary_files_format_and_content: Bedgraph

source_name: HeLa cell line

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagles Medium (DMEM, WelGENE Inc., Daegu, Korea) supplemented with 10% FBS (Fetal bovine serum; WelGENE Inc.) and 100 µg/ml penicillin-streptomycin (WelGENE Inc.), at 37°C, 5% CO2.

extract_protocol:
HeLa cells transiently expressing Flag-Za or Flag-Zaa were cross-linked with 1% formaldehyde for 10 minutes at room temperature and cross-linking was quenched with 137 mM glycine. After nucleus extraction, isolated nucleus pellets were resuspended in Sonication buffer (50mM HEPES [pH7.9], 140mM NaCl, 1mM EDTA, 1% triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 1X protease inhibitor). The chromatin was sonicated to the range of 100-300 bp, and then immunoprecipitated overnight using an anti-Flag antibody (Sigma, USA).
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by  Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

tag: cell line

value: HeLa


title: rat hypothalamus Fru_rep1

status: Public on Jul 13 2016

type: SRA

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

country: USA

institute: UCLA

description: replicate 1

library_source: transcriptomic

data_processing:
We tested data qualities by using Principal Component Analysis, hierarchical cluster analysis and variances test, and excluded one of the samples (Hypo_Fru_rep4) as an outlier.
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: rat hypothalamus

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2000 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).

tag: strain

value: Sprague Dawley

tag: tissue

value: hypothalamus

tag: treatment

value: fructose


title: rat hypothalamus Ctrl_rep3

description: replicate 3


title: rat hypothalamus Fru_rep2

description: replicate 2


title: rat hypothalamus Fru_rep3

description: replicate 3


title: rat hypothalamus Ctrl_rep4

description: replicate 4


title: Flag-Zaa

description: ChIP with Flag antibody

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: expression

value: transiently expressing Flag-Zaa

tag: chip antibody

value: anti-Flag (Sigma, catalog# F1804, lot# SLBF6631)


title: MNase-Seq

city: Ithaca

first: Wojciech

last: Pawlowski

state: NY

address: Bradfield Hall, Room 403

department: Plant Breeding and Genetics

institute: Cornell University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the B73 reference genome sequence (release AGPv2) using the Burrows-Wheeler Aligner (BWA)
Data were filtered base on unique mapping
peak calling using MACS with parameter bandwidth 800
bed file were used to calculated ratio of nucleasome occupancy
Ratio calculated by treatment divided by control from peak regions
Genome_build: B73 (release AGPv2)
Supplementary_files_format_and_content: [.bed] reports peaks, counts, ratios of nucleasome occupancy

organism: Zea mays

source_name: Flower

extract_protocol: Nuclei were prepared as described in the ChIP protocol except that EDTA was omitted from buffers.  Nuclei pellet was resuspended in 500 μl Digestion Buffer (50 mM Tris-HCl pH8.0, 5 mM CaCl2, 0.1 mM PMSF, 1 µg/ml cOmplete Protease Inhibitor Cocktail (Roche, Penzberg, Germany)). Samples were sonicated for 5 second and treated with 0.02 U /µl of micrococcal nuclease (NEB, Ipswich, MA, USA) for 10 min at room temperature.  The reaction was stopped with 10 mM EDTA and DNA was prepared as in the ChIP protocol.  The purified DNA was separated in a 2% agarose gel and fragments ~150 bp in size were recovered.  Approximately 100 ng of mononucleosome DNA was used for Illumina library construction.  As a control, randomly fragmented chromatin was prepared by sonication to produce 200 - 500 bp fragments.

tag: inbred line


title: yolk_E11.5 (Sample 26)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
processed data file: Timeline.xlsx
ys_11.5_dispo_2.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: bowtie2 with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

organism: Mus musculus

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
Cells were FACS sorted into lysis buffer and RNA was processed from the lysates
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: 5 mg/kg poly I:C to pregnant females at embryonic day 12.5 or 14.5

value: CX3CR1-GFP+ C57BL/6J

value: Yolk sac

tag: selection marker

tag: developmental stage


title: yolk_E11.5 (Sample 25)

description:
processed data file: Timeline.xlsx
ys_11.5_dispo_1.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: yolk_E10.5 (Sample 23)

description:
processed data file: Timeline.xlsx
ys_10.5_dispo_1.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Flag-Za

description: ChIP with Flag antibody

value: transiently expressing Flag-Za


title: rat hypothalamus Ctrl_rep1

description: replicate 1


title: rat hypothalamus Ctrl_rep2

description: replicate 2


title: rat hippocampus Fru_rep4

description: replicate 4

source_name: rat hippocampus

value: hippocampus


title: yolk_E10.5 (Sample 24)

description:
processed data file: Timeline.xlsx
ys_10.5_dispo_2.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: brain_day9 (Sample 21)

description:
processed data file: Timeline.xlsx
mic_day9_b.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: Brain


title: rat hippocampus Fru_rep3

description: replicate 3


title: rat hippocampus Fru_rep2

description: replicate 2


title: E.14.5_PBS_injected_newborn (Sample 29)

description:
processed data file: PolyIC.xlsx
NB_PBS_inj_e14_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: PBS injection E14.5

value: newborn


title: brain_day6 (Sample 19)

description:
processed data file: Timeline.xlsx
mic_day6_a.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: brain_day9 (Sample 22)

description:
processed data file: Timeline.xlsx
mic_day9_c.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: brain_day3 (Sample 18)

description:
processed data file: Timeline.xlsx
mic_day3_b.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: rat hippocampus Fru_rep1

description: replicate 1


title: rat hippocampus Ctrl_rep4

description: replicate 4


title: brain_day3 (Sample 17)

description:
processed data file: Timeline.xlsx
mic_day3_a.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: rat hippocampus Ctrl_rep3

description: replicate 3


title: brain_E16.5 (Sample 16)

description:
processed data file: Timeline.xlsx
mic_E16_5_b.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: rat hippocampus Ctrl_rep2

description: replicate 2


title: H9 2n_mRNA

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

country: China

institute: institute of biochemistry and cell biology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and raw read count for each sample

source_name: G0/G1 normal ESCs

growth_protocol: human ESCs were cultured on feeder in human ES medium supplemented with 10μM Y-27635

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA) RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany) total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ESCs were washed with DPBS and trypsinizd with Accutase and collected by centrifugation. After Hoechst33342 staining,G0/G1 cells (1C DNA content) were harvested by FACS.

tag: passage

tag: gender

value: female

tag: cell type

value: embryonic stem cells


title: hPGES2 2n_mRNA

source_name: G0/G1 diploid ESCs from parthenogenetic blastocysts


title: brain_E14.5 (Sample 14)

description:
processed data file: Timeline.xlsx
mic_E14_5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: hPGES2 1n_mRNA

source_name: G0/G1 haploid ESCs from parthenogenetic blastocysts


title: Hippocampus_adult_8wk (Sample 12)

description:
processed data file: Timeline.xlsx
hipo_b
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: human fibroblast_mRNA

source_name: human forskin fibroblast

value: male

value: somatic cells


title: hPGES1 2n_mRNA


title: Hippocampus_adult_8wk (Sample 11)

description:
processed data file: Timeline.xlsx
hipo_a
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: hPGES1 1n_mRNA

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA), RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany) total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: cortex_adult_8wk (Sample 9)

description:
processed data file: Timeline.xlsx
cortex_a
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: brain_E16.5 (Sample 15)

description:
processed data file: Timeline.xlsx
mic_E16_5_a.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: DC_ATAC_HP109_Replicate2

city: Montreal

first: Genevieve

last: Deblois

state: Quebec

address: 2950, chemin de Polytechnique

country: Canada

institute: Université de Montréal

description:
GD_ATAC_22
Replicate of GD_ATAC_16
processed data file:
HP109_1_16-22_vs_input_mi8_25_downsample_peaks.narrowPeak

data_processing:
Library strategy: ATAC-seq
Reads were filtered for quality and trimming using FASTX Toolkit 0.0.13.1
Filtered reads were aligned to the Mouse genome (mm10) using BWA(Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-1760). Duplicate reads were marked and removed using Picard (https://github.com/broadinstitute/picard). For comparisons the larger dataset was downsampled to match the size of smaller dataset using Picard (https://github.com/broadinstitute/picard).
Peaks were called using MACS2.0 (https://github.com/taoliu/MACS/)(Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome biology 2008;9:R137)
Genome_build: mm10
Supplementary_files_format_and_content: [.narrowPeak] Bed files were generated using MACS2.0 with default parameters. Bed files contain peak calls on merged reads using corresponding inputs as control.

source_name: DC_ATAC_HP109, DCs

growth_protocol: Primary bone marrow derived dendritic cells (DCs) were grown from the bone marrow of C57Bl/6 using GM-CSF. Total bone marrow cells were seeded in 6-well plates and grown for 9 days with 20ng/mL GM-CSF. Media containing GM-CSF was replenished on day 3, 6 and 8.

extract_protocol:
Lysates were extracted from sorted nuclei using a nuclei lysis buffer (according to ATAC-seq protocol from Buenrostro et al 2013). Transposase reaction was carried out following the protocol of the Nextera DNA library preparation kit (illumina).
Libraries were prepared using the NeBNext buffer and appropriate ATAC-seq libraries adaptors (Illumina, Buenrostro et al, 2013). The llibrary was size-selected using the DNA on a ChIP technology.
ATAC-seq library and ATAC-seq adaptors (Buenrostro et al, 2013)

treatment_protocol:
DCs were stably transduced on day 2 of culture with retrovirus expressing either a control vector or a vector to overexpress/knockdown PCGF6
DCs were flow-sorted based on co-expression of the reporter human CD8 and the lineage marker CD11c

tag: transduced vector

value: PCGF6-knock-down vector (HP109)

tag: growth conditions

value: Grown in media containing 20ng/mL GM-CSF


title: cortex_adult_8wk (Sample 10)

description:
processed data file: Timeline.xlsx
cortex_b
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: IgG

description: ChIP with non-specific IgG antibody

data_processing:
RTA (Real Time Analysis. v1.18) used for basecalling.
Sequenced reads were mapped to hg18 genome using Bowtie2 (v.2.2.5)
The sequence reads were normalized as reads per million per nucleotide (RPM).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files with BigWig format

extract_protocol:
HeLa cells transiently expressing Flag-Zaa were cross-linked with 1% formaldehyde for 10 minutes at room temperature and cross-linking was quenched with 137 mM glycine. After nucleus extraction, isolated nucleus pellets were resuspended in Sonication buffer (50mM HEPES [pH7.9], 140mM NaCl, 1mM EDTA, 1% triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 1X protease inhibitor). The chromatin was sonicated to the range of 100-300 bp, and then immunoprecipitated overnight using an anti-Flag antibody (F1804, Sigma, USA) or anti-mouse IgG antibody (sc-2025. Santa cruz, USA). Input was taken from starting material before immunoprecipitation.
ChIP DNA for Zaa biological replicates and control DNA (IgG ChIP and input) were used for sequencing library construction. Sequencing libraries were prepared using Aceel-NGS DNA library kits according to the manufacturer's instructions.  PCR products were purified with HiAccuBead (AccuGene, Korea). Purified PCR products are eluted in low-EDTA TE buffer.

value: HeLa

value: non-specific IgG antibody


title: Input 2

description: Fragmented genomic DNA

value: Fragmented genomic DNA


title: yolk_E12.5 (Sample 7)

description:
processed data file: Timeline.xlsx
YS_12.5_new_dispomix_2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: yolk_E12.5 (Sample 8)

description:
processed data file: Timeline.xlsx
YS_12.5_new_dispomix_3
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: brain_day6 (Sample 20)

description:
processed data file: Timeline.xlsx
mic_day6_c.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: yolk_E13.5 (Sample 28)

description:
processed data file: Timeline.xlsx
ys_13.5_dispo_2.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Spinal_cord_adult_8wk (Sample 6)

description:
processed data file: Timeline.xlsx
SC_b
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Zaa_2

description: ChIP with Flag antibody

value: Flag antibody


title: Spinal_cord_adult_8wk (Sample 5)

description:
processed data file: Timeline.xlsx
SC_a
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: CX3CR1-GFP+ C57BL/6J


title: Zaa_1

description: ChIP with Flag antibody


title: brain_E13.5 (Sample 13)

description:
processed data file: Timeline.xlsx
mic_E13_5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: DC_ATAC_mi8_Replicate2

description:
GD_ATAC_19
Replicate of GD_ATAC_13
processed data file:
mi8_1_13-19_vs_input_mi8_25_downsample_peaks.narrowPeak

source_name: DC_ATAC_mi8, DCs

value: Primary bone marrow derived dendritic cells (DCs)

value: control vector for OE (mi8)


title: rat hippocampus Ctrl_rep1

description: replicate 1

value: Sprague Dawley

value: hippocampus


title: Fru_DHA_hypothalamus_rep3

description: processed data file: Hypothalamus_fpkm_processed.txt

data_processing:
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

tag: fed with

value: fructose and DHA for 6 wks

value: hypothalamus


title: brain_E10.5 (Sample 4)

description:
processed data file: Timeline.xlsx
Brain_10.5_2.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: Brain


title: mild DCM hiPSC-CMs at 2 weeks #2

city: stanford

first: Kazuki

last: Kodo

address: campus street

institute: Stanford

data_processing:
Paired-end fastq sequence reads from each sample were assembled against hg19 using the Tophat v2.0.6  with the Illumina-supplied hg19 gene-model annotation file ( gtf annotation).
The expression level (FPKM) was estimated by Cufflinks.
Cuffdiff was used to call differentially expressed genes with false discovery rate less than 0.05. Cuffdiff was run against the UCSC iGenomes GTF file from Illumina.
Subsequent to determining which genes were differentially expressed, FPKM was used for ﬁltering, and visualization purposes.
Genome_build: hg19

molecule: polyA RNA

source_name: cardiomyocytes

growth_protocol: hiPSCs were grown to 90% confluence and differentiated subsequently into beating cardiomyocytes using a small molecule-based monolayer method adapted after4 and described in detail previously.3 10 days after cardiac differentiation, hiPSC-CM monolayers were purified using non-glucose culture medium containing RPMI-1640 without glucose (Life technologies) and B27 supplement (Life technologies). Non-glucose culture medium was changed every two days and after 5 days, hiPSC-CMs were dissociated using TripleE (10 min), washed and plated onto matrigel-coated plates in culture medium with glucose.

extract_protocol:
Total RNA was extracted and quantified using miRNeasy Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol. An additional DNAseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. Following the Qiagen RNA sample preparation protocol, 10 ug of total RNA was used to generate index-tagged paired-end cDNA libraries.5 Briefly, mRNAs were purified by polyA enrichment procedure using Dynal Oligo(dT) beads (Life technologies).
mRNA fragmentation was performed using RNA Fragmentation Reagents (Life technologies) with incubation at 70oC for 1 min to obtain 200-300b fragments. cDNA was generated using SuperScript Double-Stranded cDNA Synthesis Kit (Life technologies). Illumina sequencing adapters were ligated to cDNA using LigaFast (Promega) and PE Adapter Oligo Mix (Illumina, San Diego, CA). PCR was performed on the adapter-ligated cDNA with 2X Phusion DNA polymerase Master Mix (New England Biolabs, Ipswich, MA) using the following conditions: denaturation 98°C for 30 seconds, followed by 15 cycles of denaturation 98°C for 10 seconds, annealing 65°C for 30 seconds, and extension 72°C for 30 seconds, ending with an extension at 72°C for 5 min. After cDNA libraries were generated using the sample preparation kit, quality of the libraries was checked using Bioanalyzer (Agilent Technologies).

treatment_protocol: hiPSC-CMs were cultured in RPMI with B27 supplement and 2% FBS 2 days before experiment to accelerate the proliferation.

value: induced pluripotent stem cell derived cardiomyocytes

tag: passages

tag: genotype

tag: cardiac phenotype

value: asymptomatic DCM


title: brain_E12.5 (Sample 2)

description:
processed data file: Timeline.xlsx
BRAIN_12_5_b
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

tag: strain


title: LVNC sibling2 hiPSC-CMs at 2 weeks #1

value: asymptomatic LVNC


title: input for DCs

description:
GD_ATAC_25
input

source_name: input for DCs

value: input for all the DCs


title: brain_E10.5 (Sample 3)

description:
processed data file: Timeline.xlsx
Brain_10.5_1.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

tag: tissue


title: control hiPSC-CMs at 2 weeks #2

value: TBX20 wt/wt

value: no cardaic disease


title: DC_ATAC_LMP8_Replicate2

description:
GD_ATAC_21
Replicate of GD_ATAC_15
processed data file:
LMP8_1_15-21_vs_input_mi8_25_downsample_peaks.narrowPeak

source_name: DC_ATAC_LMP8, DCs

value: control vector for KD (LMP8)

value: Grown in media containing 20ng/mL GM-CSF


title: DC_ATAC_mi8_Replicate1

description:
GD_ATAC_13
Replicate of GD_ATAC_19
processed data file:
mi8_1_13-19_vs_input_mi8_25_downsample_peaks.narrowPeak


title: DC_ATAC_HP109_Replicate1

description:
GD_ATAC_16
Replicate of GD_ATAC_22
processed data file:
HP109_1_16-22_vs_input_mi8_25_downsample_peaks.narrowPeak

value: PCGF6-knock-down vector (HP109)


title: DC_ATAC_LMP8_Replicate1

description:
GD_ATAC_15
Replicate of GD_ATAC_21
processed data file:
LMP8_1_15-21_vs_input_mi8_25_downsample_peaks.narrowPeak


title: brain_E12.5 (Sample 1)

description:
processed data file: Timeline.xlsx
BRAIN_12_5_a
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: CX3CR1-GFP+ C57BL/6J

tag: treatment


title: control hiPSC-CMs at 2 weeks #1


title: DC_ATAC_OE_Replicate1

description:
GD_ATAC_14
Replicate of GD_ATAC_20
processed data file:
OE2_1_14-20_vs_input_mi8_25_downsample_peaks.narrowPeak

source_name: DC_ATAC_OE, DCs

value: Primary bone marrow derived dendritic cells (DCs)

value: PCGF6-overexpressing (OE)


title: DC_ATAC_OE_Replicate2

description:
GD_ATAC_20
Replicate of GD_ATAC_14
processed data file:
OE2_1_14-20_vs_input_mi8_25_downsample_peaks.narrowPeak


title: Control_rep3

city: University Park

first: John

middle: H

last: Golbeck

state: Pennsylvania

address: 328 South Frear Laboratory

department: Department of Biochemistry and Molecular Biology

institute: The Pennsylvania State University

data_processing:
Basecalls performed using CASAVA version 1.5
Raw Illumina reads were trimmed and filtered with Trimmomatic to remove adapters and low quality bases.
Alignment to the S. oneidensis MR-1 chromosome (NCBI RefSeq: NC_004347) and megaplasmid (NCBI RefSeq: NC_004349) was performed using Bowtie (maximum seed mismatch of 2 and seed length of 28)
The number of trimmed reads assigned to genes were estimated with the Python script HTseq-count
Differentially expressed genes were determined with DESeq2  using the likelihood ratio test (LRT)
Genome_build: ASM14616v2
Supplementary_files_format_and_content: Tab-delimited text files include gene count values for each sample

organism: Shewanella oneidensis

source_name: Cell culture_Control

growth_protocol: Shewanella oneidensis MR-1 were grown in continuous flow reactors. Throughout the experiment, agitation was maintained at 200 rpm and culture maintained at pH 7.0 at 30 °C.

extract_protocol:
10 mL of cells were mixed with ice-cold 5% citrate-saturated phenol in ethanol. Total RNA was prepared using a hot phenol extraction.  Samples were treated with DNase I for an hour at 37 °C.  RNA samples were treated with Ribo-Zero™ (Epicentre) to remove rRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: A 20% dissolved oxygen tension (DOT) was maintained until the culture reached stationary phase. The bioreactor was then switched to continuous mode with a dilution rate of 0.05 h−1 while DOT was still maintained at 20%. After 48 hours in continuous mode, a reference sample of cells was harvested for RNA isolation (control). The automatic DOT control was then turned off and DOT was reduced from 20% to 0% (within 3-5 minutes). Once the DOT was no longer measurable by a polarographic O2 electrode, the first sample was taken (t=0). However, note that this was not an anaerobic state; air was still being provided to the reactor, but with DOT just below detection of the polarographic O2 electrode. Samples were subsequently taken at 15 min intervals for an hour.

tag: time (after dot was no longer measurable by a polarographic o2 electrode)

tag: sample type

value: Cell culture

tag: shortname


title: Control_rep2


title: S-H4K8ac_ChIPSeq

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Base calling was performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2.2.5 with default arguments
Read counts were computed using Deeptools bamCoverage version 1.5.11 binSize=50 fragmentLength=200 missingDataAsZero=yes
Peaks were called using SICER with the following parameters : W200, G600, FDR 0.01
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated with Deeptools bamCoverage. Scores represent the number of reads extended to 200 bp that fall into a 50 bp sliding window.
Supplementary_files_format_and_content: .interval bed (SICER peaks)

source_name: Spermatogenic cells (spermatocytes)

extract_protocol:
About 100 μg of mononucleosomes were used for each ChIP. ChIP experiments were carried out overnight at 4 °C, in LSDB 350 buffer (glycerol 20%, Hepes 50 mM, MgCl2 3 mM, KCl 350 mM, Na Butyrate 10 mM, Complete Protease Inhibitor Cocktail Tablets (Roche)), with 5 μg of antibodies (rabbit H4K8ac, rabbit antiH4K5ac, rabbit anti H4K8bu, rabbit anti H4K5bu) previously coupled to magnetic beads (Dynabeads protein G (Invitrogen)) for 4 h in 1X PBS, BSA 5 μg/μl. The beads were then washed five times in LSDB 350 buffer, and nucleosomes were eluted with the elution buffer (SDS 1%, 1X TE). DNA was purified from the nucleosomes, and the immunoprecipitated DNA was sequenced. The DNA corresponding to an aliquot of nucleosomes before immunoprecipitation (input) was also sequenced.
ChIP-seq libraries were prepared following the Ovation Ultralow DR Multiplex System protocols (NuGEN Technologies INC, San Carlos, CA), followed by a size selection (200-700bp) step using SPRIselect beads (Beckman Coulter, Brea, CA).

treatment_protocol: Mononucleosomes were prepared from fractionated spermatocytes and round spermatids and used for ChIP-seq analyses following the protocols described in Gaucher et al. 2012 (EMBO J. 31(19):3809-20. PMID: 22922464)

value: Oncins France 1

tag: chip antibody

value: H4K8ac (gift from Dr H. Kimura)

value: spermatocytes

value: testis


title: 60mins_rep3

source_name: Cell culture_60mins


title: S-H4K5ac_ChIPSeq

value: H4K5ac (gift from Dr H. Kimura)

tag: developmental stage


title: S-Input_ChIPSeq


title: TFH cells [CC6]

city: La Jolla

first: Changchun

last: Xiao

state: California

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

data_processing:
Reads pre-processedusing FastX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit) for conversion to FASTA format, removing the adaptors, collapsing the identical sequences into uniquely tagged reads with number of counts for each tag, and discarding reads shorter than 18 nucleotide in length.
Sequence reads for each sample were examined for quality control using FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) monitoring sequence quality scores, GC content, sequence duplication levels, and overrepresented sequences for adaptor contamination
Reads were aligned to Pre-built Bowtie indexed Mouse genome, M. musculus UCSC mm9, using Bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml).
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
Candidates for novel miRNAs were typically in very low abundance and constituted less than 1% of the mapped reads in each sample and therefor were excluded from the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: read counts

source_name: spleen

extract_protocol:
RNA was harvested using Trizol reagent.
Approximately 1 µg of total RNA was used for Next Generation Sequencing following the standard Illumina protocol, TruSeq_SmallRNA_SamplePrep_Guide_15004197_C.pdf, using 12 cycles of PCR.
3’ Adapter Ligation. 10 pmol of 3’-adenylated DNA adapter (5’-AppTGGAATTCTCGGGTGCCAAGGddC) is combined with 1 ug total RNA in a 4 ul volume, heated to 70 degrees C for 2 minutes and then placed on ice.  In a separate tube, 2 uL 10X T4 RNA Ligase 2 Truncated reaction buffer(NEB), 2 uL 50% PEG8000 (NEB), 1 uL RNase OUT (Lifetech) and 1 uL T4 RNA Ligase 2 Truncated enzyme (NEB) were combined and added to the RNA/3’adapter mix and incubated at 28 degrees C for one hour. This mixture was then heated to 70 degrees C for 2 minutes.  5’ Adapter Ligation. Next, 1 uL water, 1 uL 10 mM ATP, 1 uL T4 RNA Ligase and 1 uL 5’ RNA adapter (25 pmol, 5’-GUUCAGAGUUCUACAGUCCGACGAUC) were added and incubated at 28°C for 1 hour.  Reverse Transcription. Next, 1 uL of a 10 uM solution of RT primer (5’-GCCTTGGCACCCGAGAATTCCA) was added to 6 uL of the 5’adapter ligation mix above heated to 70 degrees C for 2 minutes and then transferred to ice. This was then combined with a solution containing: 2 uL of 5X First Strand Buffer (Superscript II buffer, Lifetech), 0.5 uL of 12.5 mM dNTPs, 1 uL 0.1 M DTT, 1 uL RNaseOUT (Lifetech), and 1 uL Superscript II (200 U/uL). The reaction was incubated at 50 degrees C for 1 hour and then placed on ice.
PCR. The 12.5 uL reverse transcription reaction above was then added to a tube containing: 30 pmol of Illumina Truseq Universal PCR primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA); 30 pmol of Illumina Truseq Barcoded PCR primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA, where XXXXXX, correspond to standard Illumina Truseq barcodes); and 25 uL of 2X KAPA HiFi HotStart ReadyMix PCR Kit in a 50 uL total volume. The reaction was heated to 98 degrees C for 1 minute, and then cycled 12 times with 98 degrees C for 10 seconds, 60 degrees C for 30 seconds, and 72 degrees C for 15 seconds, followed by a single incubation at 72 degrees C for 5 minutes. The resulting PCR products were isolated using AmpureXp magnetic bead purification (Agencourt, Beckman-Coulter) and then purified on 4% Agarose gel.

treatment_protocol: Two to three month old C57BL/6 mice were immunized with OVA/alum/LPS intraperitoneally. On day 7 after immunization, naïve (CD4+CD44-CXCR5-PD1-), pre-TFH (CD4+CXCR5intPD1lo), and TFH (CD4+CXCR5hiPD1hi) cells were FACS-sorted from splenocytes.

value: spleen

value: wild type

value: TFH (CD4+CXCR5hiPD1hi)


title: TFH cells [CC5]


title: Pre-TFH cells [CC3]

value: pre-TFH (CD4+CXCR5intPD1lo)


title: Naïve CD4 T cells [CC2]

value: naive (CD4+CD44-CXCR5-PD1-)


title: R-H4K8bu_ChIPSeq

source_name: Spermatogenic cells (round spermatids)

value: H4K8bu (PTM biolabs)

value: round spermatids


title: 45mins_rep3

source_name: Cell culture_45mins


title: 60mins_rep1


title: R-H4K8ac_ChIPSeq


title: S-H4K8bu_ChIPSeq


title: Naïve CD4 T cells [CC1]


title: dKO3

city: Hong Kong

first: Han

last: ZHU

address: Room 6312, Academic Building, HKUST

department: Department of Life Science

institute: HKUST

data_processing:
Illumina Casava1.8 software used for basecalling.
Data quality was examined using FastQC software
Pair end Raw reads were mapped to the reference genome (mm10) using TopHat with the -G parameter
Cufflinks was used to assemble and calculate FPKM value for each transcript. And Cuffdiff was used to call significantly differential expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. BigWig files are created initially from wiggle (wig) type files, using the program wigToBigWig. The resulting bigWig files are in an indexed binary format. gene_exp.diff file [sample_1=mdx and sample_2=dKO].

source_name: Muscle Satellite cells

extract_protocol:
RNA were extracted with the NucleoSpin® RNA XS kit from Macherey-Nagel. For each sample, 1 ng total RNA were used for sequencing
cDNA reverse transcripition was performed with the SMART-Seq™ Ultra™ Low Input RNA Kit for Sequencing form Clontech. Adaptor ligation and barcoding was carried out with the Ovation® Ultralow Library Systems from Nugen.

value: C57BL/10ScSn backcrossed with C57BL/6 for at least 7 generations

value: Muscle Satellite cells

tag: genotype/variation

tag: age


title: dKO2

tag: cell type


title: R-H4K5bu_ChIPSeq

value: H4K5bu (PTM biolabs)


title: R-H4K5ac_ChIPSeq


title: 45mins_rep2


title: 45mins_rep1


title: Pre-TFH cells [CC4]


title: 30mins_rep3

source_name: Cell culture_30mins


title: Control_rep1


title: R-Input_ChIPSeq


title: dKO1


title: mdx3

value: Dystrophin-/-


title: 30mins_rep2

value: Cell culture


title: mdx2


title: Layer C3

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

description: layerC replica 3

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.2.2. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using the Bowtie mapper (version 0.12.9, parameters -n 2 -l 34 -e 70 -k 2 –best). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from UCSC (mm10) was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: Brain-Piriform Cortex

extract_protocol:
RNA was extracted from the collected tissue using the RNeasy Micro Kit (Qiagen)
Ovation RNA-Seq system NuGEN

treatment_protocol: Fresh-frozen brain section were used to collect the piriform layers by laser capture.

value: 8 weeks

value: piriform cortex


title: Layer C1

description: layerC replica 1


title: 30mins_rep1


title: Layer B2

description: layerB replica 2


title: Layer B3

description: layerB replica 3


title: 15mins_rep3

source_name: Cell culture_15mins


title: Layer B1

description: layerB replica 1


title: 15mins_rep2


title: 15mins_rep1


title: Layer A3

description: layerA replica 3


title: mdx1


title: Layer C2

description: layerC replica 2


title: Layer A1

description: layerA replica 1


title: KO mac rep1

status: Public on Jul 12 2016

first: Wenyuan

last: Wang

state: cA

address: 651 Charles E Young Drive

data_processing:
Library strategy: ATAC-seq
Demultiplexing was carried out using in house Unix shell script followed by mapping to mouse genome (mm9) using Bowtie.
Peaks were identified with MACS and Manorm analysis was used to identify differentially accessible regions
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

source_name: BM Mac1+ myeloid cells

extract_protocol:
After nuclear extraction, transposition reaction (Nextera DNA Library Prep Kit, Illumina) was carried out at 37oC for 30 minutes.
12 cycles of PCR amplification was carried out using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs).

value: Mac1+ myeloid cells

value: bone marrow (BM)


title: WT mac rep2


title: 0mins_rep1

source_name: Cell culture_0mins


title: 0mins_rep2


title: KO mac rep2


title: KO preB rep3

source_name: BM pre-B cells

value: pre-B cells


title: Layer A2

description: layerA replica 2


title: KO preB rep2


title: WT mac rep1


title: KO preB rep1


title: H3K27Ac_ChIP

data_processing:
Demultiplexing of pooled samples was performed with in house shell scripts.
Reads were then mapped to the mouse mm9 reference genome using bowtie retaining only uniquely mapping reads with two mismatches.
Peaks were identified with MACS1467.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
FACS sorted BM pre-B cells (7-10 moths old) were washed and crosslinked 10 minutes at room temperature with 1% formaldehyde in PBS plus protease inhibitor (PI). Glycine was added at a final concentration of 125 mM and tubes were further mixed for 5 min at room temperature.
ChIP reactions were performed with the Diagenode True MicroChIP X 16 kit as the manufactur's instruction.
ChIP-Seq library preparation was carried out with the NuGen Ovation Ultralow System V2 1-16. Library amplification was performed for 15 cycles. All library preparation steps were carried out as stated in the user manual.

value: BM pre-B cells


title: WT preB rep3

value: wild type


title: H3K4Me3_ChIP


title: WT preB rep2


title: S-H4K5bu_ChIPSeq

value: Oncins France 1

value: spermatocytes

value: testis


title: WT preB rep1


title: Stage-40_rep2

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
The assemblying was performed by using Trinity (Grabherr et al., 2011) (v2014-04-13p1, with parameters "--glue_factor 0.01 --min_iso_ratio 0.1”).
A single combined non-redundant transcriptome assembly was created by clustering all contigs from all stage assemblies using USEARCH (Edgar, 2010) (v7.0.1090, with parameters “-cluster_smallmem -id 0.95 -strand both”) and only selecting the “centroid” contig from each cluster.
The contigs of the combined assembly were first mapped to transcripts from another species by running BLAST (NCBI BLAST v2.2.18) with either the RefSeq RNA (via BLASTN), or protein (via BLASTX) sequences for that species as the database and each contig as a query. Contigs were assigned to transcripts by taking the best BLAST hit with E-value < 10-5. For each sample, the expected fragment counts for each contig (as computed by RSEM), were then converted to comparative transcript counts by summing the counts of contigs mapped to the same transcript. Similarly, gene-level counts were obtained by summing the counts of transcripts that were annotated with the same gene symbol.
Quantification of each RNA-seq sample was then performed using RSEM v1.1.6 (Li and Dewey, 2011) using the combined transcriptome assembly as the reference database. RSEM was run with the default options for paired-end data except for the “--no-polyA” option, which was used because the assembled contigs were not guaranteed to include polyA+ tails. By default, RSEM uses the Bowtie aligner (Langmead et al., 2009) to map the reads against the contigs and we had Bowtie v0.12.1 installed for this purpose.
Genome_build: NCBI RefSeq (12/7/2009 ), Human used for BLAST analysis
Supplementary_files_format_and_content: text  file with gene expression values

organism: Ambystoma mexicanum

source_name: Developmental Stages

growth_protocol: We de-jellied and collected embryos at 20°C over the course of development

extract_protocol:
We then extracted total RNA from homogenized samples using the RNeasy Mini Kit (Qiagen).
Samples for Paired-end sequencing  were prepared via the Illumina TruSeq RNA protocol (PolyA selection). Samples for single-end sequencing were prepared via the Illumina ScriptSeq protocol (Ribo-zero).  Paired-end samples are pooled (six per lane) and sequenced 2 x 101bp paired end reads on the Illumina HiSeq 2000 with TruSeq v3 chemistry and Single-end samples are pooled and sequenced at the length of 65bp.

treatment_protocol: Each embryo was placed into RNA Later (Qiagen), preserving them until all could be processed in parallel. Each sample was comprised of a single embryo. Samples were homogenized with a Fisher Power Gen 125 tissue homogenizer.

value: embryo


title: EAChm KD-2

city: Nagasaki

first: TAKEYA

last: NAKAGAWA

address: 1-12-4 sakamoto

department: Biochemistry

country: Japan

institute: Nagasaki unversity

description: Sample 6

data_processing:
Basecalls performed using Illumina MiSeq
RNA-seq reads were aligned to the Release 5 (dm3) genome assembly using Illumina MiSeq
Partek genomic suite was used to generate RPKMs.  Quantification was performed using transcript-level and a significant signal was filtered by including at least one of the signal having more than one RPKM.
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: RPKM

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: S2 cells were grown in Schneider’s Drosophila media (Gibco) with 10% FBS.

extract_protocol:
S2 cells were collected.Total RNA was isolated using ISOGEN II reagent (NIPPON GENE), according to the manufacturer’s protocol.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina)

tag: cell line

value: EAChm KD


title: Input_DNA_UTX_KO_NKT

city: boston

first: Luca

last: Pinello

state: MA

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

data_processing:
Chip-seq were aligned with Bowtie 1 with the following parameters -n 1 -m 1 -S --best --strata -p 6
Atac-seq reads were aligned with Bowtie2 with the following parameters --local -X 2000
Aligned files were sorted, merged and duplicates were removed with Picard (1.81) with default parameters
Bedgraph were obtained with bedtools and converted to bigwig using the UCSC utility bedgraphtobigwig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files with read per millions

source_name: NKT cells

growth_protocol: Sex- and age-matched animals between 8 and 12 weeks of age were used for experiments

extract_protocol:
Thymi were removed from mice and NKT cells were sorted from thymocytes by flow cytometry. For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For ATAC-seq, DNA was isolated following transopsition reaction.
Libraries were prepared according to instructions for ChIP-seq using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit  and for ATAC-seq using Illumina Nextera DNA preparation kit

value: thymus

value: UTX KO


title: control-1

description: Sample 1

value: control


title: Stage-40_rep3


title: ATAC_SEQ_KO_NKT

data_processing:
Library strategy: ATAC-Seq
Chip-seq were aligned with Bowtie 1 with the following parameters -n 1 -m 1 -S --best --strata -p 6
Atac-seq reads were aligned with Bowtie2 with the following parameters --local -X 2000
Aligned files were sorted, merged and duplicates were removed with Picard (1.81) with default parameters
Bedgraph were obtained with bedtools and converted to bigwig using the UCSC utility bedgraphtobigwig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files with read per millions


title: EAChm KD-1

description: Sample 5


title: chameau KD-2

description: Sample 4

value: chameau KD


title: Stage-40_rep1


title: H3K27ac_WT_NKT


title: H3K4me3_UTX_KO_NKT


title: Stage-24_rep2


title: ATAC_SEQ_WT_NKT


title: H3K27me3_WT_NKT


title: control-2

description: Sample 2


title: Input_DNA_WT_NKT


title: Stage-24_rep3


title: Stage-19_rep3


title: Stage-24_rep1


title: Stage-4_rep1


title: H3K4me3_WT_NKT


title: Stage-3_rep3


title: Stage-3_rep1


title: Stage-2_rep3


title: H3K27me3_UTX_KO_NKT


title: Stage-19_rep2


title: Stage-19_rep1


title: Stage-16_rep3


title: Stage-16_rep1


title: Stage-2_rep1


title: chameau KD-1

description: Sample 3


title: Stage-14_rep3


title: Stage-14_rep2


title: Stage-3_rep2


title: Stage-16_rep2


title: Stage-2_rep2


title: Stage-9_rep2


title: Stage-12_rep2


title: Stage-10_rep1


title: Stage-12_rep3


title: Stage-11_rep2


title: Stage-1_rep2


title: Stage-9_rep1


title: Stage-11_rep3


title: Stage-10_rep2


title: Stage-8_rep3


title: Stage-9_rep3


title: Stage-10_rep3


title: Stage-12_rep1


title: Stage-8_rep1


title: Stage-8_rep2


title: Sample_AN16_1_mM_Choline_12_9

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

description:
Double deletion with choline replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

data_processing:
Read quality was checked with FastQC.
Samples were aligned to the NC_007650 and NC_007651 chromosomes using BWA.
Duplicate reads were marked using Picard (version 1.110; Broad Institute of MIT and Harvard, [http://broadinstitute.github.io/picard/])
Gene counts were calculated using summarizeOverlaps from the GenomicRanges package.
Differential expression was called using the DESeq package [34] in R (version 3.0.1; R Development Core Team, [https://www.r-project.org/]).
Genome_build: NC_007650, NC_007651
Supplementary_files_format_and_content: Excel spread sheet of normalized reads and comparisons in log2(x) (".lfc"). Includes P value (".p") and false discovery rate (".fdr").

organism: Burkholderia thailandensis E264

source_name: bacterial cells

growth_protocol: Wild type, ΔgbdR1, ΔgbdR2, and ΔgbdR1Δgbdr2 strains were streaked from frozen stocks onto LB agar plates and incubated overnight at 37 oC. These plates were used to inoculate 3 mL MOPS with 20 mM pyruvate and 5 mM glucose cultures which were incubated for 18 hours at 37 oC on a rotary wheel.

extract_protocol:
Cells from 1.5 mL of culture were collected by centrifugation and the resultant pellets were resuspended in RNA Protect Bacteria Reagent (Qiagen) and incubated at room temperature for 10 minutes. Cells were collected by centrifugation and resuspended in 50 µL 10 mM Tris, 1 mM EDTA (TE) buffer with 3 mg/mL lysozyme and incubated at room temperature for 5 minutes. To each of these resuspensions, 1 µL 20 mg/mL proteinase K, 0.5 µL of 10% SDS, 1 µL of DNase I (RNase-free, Ambion), and 2 µL of 50 mM MgCl2 were added and samples were incubated for 5 minutes at room temperature.  RNA was then prepared using the Qiagen RNeasy kit according to the manufacturer’s instructions. Eluate from this purification was further treated with 11 µL 10x DNase I buffer and 2 µL DNase I (RNase-free, Ambion) and incubated at 37 oC for 20 minutes to remove contaminating DNA and re-purified using the Qiagen RNeasy protocol with the optional on-column DNase I step. The resulting purified RNA was assessed for purity by PCR and quantified by bioanalyzer chip, depleted of 16S and 23S rRNA by using MICROBExpress™ Bacterial mRNA Enrichment (Ambion), and subsequently reassessed by Bioanalyzer (Agilent Technologies).
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: To initiate the experiment, 1 mL of these cultures was added to 2 mL of pre-warmed MOPS with 30 mM pyruvate or 2 mL MOPS with 30 mM pyruvate and 1.5 mM choline; resulting in final concentrations of 20 mM pyruvate and 1 mM choline. These cultures were incubated for four hours at 37 oC.

value: 1 mM choline

tag: barcode index

value: GTTTCG


title: Sample_AN19_1_mM_Choline_12_6

description:
ΔgbdR2 with choline, replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: deltagbdR2 (deltaBTH_II0968)

value: GGCTAC


title: Sample_AN3_1_mM_Choline_12_6

description:
ΔgbdR1 with choline, replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: deltagbdR1 (deltaBTH_II1869)

value: TAGCTT


title: Sample_AN19_No_Choline_12_9

description:
ΔgbdR2 without choline, replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

value: No choline

value: ATGTCA


title: Sample_AN3_1_mM_Choline_12_9

description:
ΔgbdR1 with choline, replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

value: GTGAAA


title: Sample_AN16_No_Choline_12_6

description:
Double deletion without choline replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: ACTTGA


title: Sample_AN16_1_mM_Choline_12_6

description:
Double deletion with choline replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: CTTGTA


title: Stage-14_rep1

value: embryo


title: Sample_AN16_No_Choline_12_9

description:
Double deletion without choline replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

value: CCGTCC


title: Sample_AN19_No_Choline_12_6

description:
ΔgbdR2 without choline, replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: CAGATC


title: Sample_AN3_No_Choline_12_9

description:
ΔgbdR1 without choline, replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

value: AGTTCC


title: Sample_AN19_1_mM_Choline_12_9

description:
ΔgbdR2 with choline, replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

value: GTGGCC


title: Stage-7_rep3


title: CDKAL1-/- -HES3 -HF

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq 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"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Transcript 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: hESCs derieved beta cells

growth_protocol: hESC stepwise differnetiation protocol, The full protocol has been submitted as a manuscript for peer review.

extract_protocol:
Qiagen RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GFP+ cells sorted by FACS

value: human beta cells

tag: tag

value: GFP+


title: CDKAL1-/- -HES3


title: WT-HES3


title: Sample_AN3_No_Choline_12_6

description:
ΔgbdR1 without choline, replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: GCCAAT


title: Stage-7_rep1


title: Stage-7_rep2


title: WT-HES3-HF


title: HCC827_ZEB_b

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

data_processing:
MAPRSeq version 1.2.1.3 (http://bioinformaticstools.mayo.edu/research/maprseq/)
Genome_build: hg19
Supplementary_files_format_and_content: text

source_name: human lung adenocarcinoma cell

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum in the absence of antibiotics.

extract_protocol:
Total RNA are extracted from 80-90% confluent cultured cells by using Qiagen RNeasy total RNA preparation mini kit (#217004) exactly as instructed by the manufacturer's product manual. 100-200 ng total RNA is used for the subsequent library construction and sequencing.
RNA sample quality is assessed, followed by poly-A selection and fragmentation of 100 nanograms to 1 microgram of starting total RNA. Subsequently, the fragments undergo reverse transcription with random primers and second-strand synthesis to generate double-stranded cDNA. Ends are repaired and adenylated, followed by adaptor and index ligation. Finally, the products are denatured and PCR-enriched to generate the final genomic library. The libraries undergo quality control for quantitative and qualitative thresholds.

tag: transfection

value: in vitro cultured lung cancer cell line

tag: passage


title: Stage-1_rep1


title: HCC827_ZEB_c


title: Stage-6_rep3


title: Bacterioides TEX treated

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
Anaerobic (mid-log), Library with TEX treatment
total RNA after TEX (terminator exonuclease) treatment

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (READemption version 0.3.5)
Coverage calculation and normalisation (READemption version 0.3.5)
Genome_build: NC_016776.1
Supplementary_files_format_and_content: Read coverages normalized by total number of aligned reads in wiggle format

organism: Bacteroides fragilis 638R

source_name: in vitro culture in complex medium

growth_protocol: Overnight cultures of Bacteroides fragilis 638R wild type strain or mutant strains were diluted into Brain Heart Infusion Broth suppplemented with hemin, cysteine, and sodium bicarbonate. The culture was grown to mid-logarithmic phase at A550 of 0.5 ( Rocha et al. 1996, J. Bacteriol. 178:6895)

extract_protocol:
Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.

tag: growth stage

value: in virtro culture, mid-logarithmic phase


title: Sample_MJ358_No_Choline_12_6

description:
wt without choline, replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

tag: strain

tag: genotype

value: wild type

value: ACAGTG


title: HCC827_3-1_c

value: empty pcDNA3.1 vector plasmid

tag: tissue


title: Stage-6_rep1


title: HCC827_ZEB_a


title: HCC827_3-1_b


title: Sample_MJ358_1_mM_Choline_12_9

description:
wt with choline, replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

tag: treatment

value: 1 mM choline

value: GTCCGC


title: Bacterioides TEX untreated

description: Anaerobic (mid-log), Library without TEX treatment


title: HCC827_3-1_a


title: Stage-5_rep1


title: Sample_MJ358_No_Choline_12_9

description:
wt without choline, replicate 2.
Regulation of Choline Catabolism in Bt.xlsx

value: No choline

value: AGTCAA


title: Stage-5_rep2

value: embryo


title: Sample_MJ358_1_mM_Choline_12_6

description:
wt with choline, replicate 1.
Regulation of Choline Catabolism in Bt.xlsx

value: GATCAG


title: Stage-4_rep3


title: Stage-4_rep2


title: E_salsugineum_shandong_H3K56ac_chip

status: Public on Jul 11 2016

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: ChIP seq data for E. salsugineum H3K56ac

data_processing:
For CHIP-seq data: Raw ChIP reads were trimmed for adapters and low-quality bases using Trimmomatic version 0.32 (Bolger et al. 2014). Reads were trimmed for TruSeq version 3 single-end adapters with maximum of two seed mismatches, palindrome clip threshold of 30 and simple clip threshold of 10. Additionally, leading and trailing bases with quality less than 10 were removed; reads shorter than 50 bp were discarded. Trimmed reads were mapped to the TAIR10 genome using bowtie2 version 2.2.3 (Langmead et al. 2012) with default options. Mapped reads were sorted using samtools verison 1.2 (Li et al. 2009) then clonal duplicates were removed using samtools version 0.1.9 (Li et al. 2009). BAM files were then converted to BED files using bedtools v2.21.1 (Quinlan and Hall 2010).
Genome_build: A. thaliana = TAIR10; A. lyrata = v1.0; B. rapa = FPsc v1.3; B. oleracea = TO1000 v1.0; C. rubella = v1.0; E. salsugineum = v1.0
Supplementary_files_format_and_content: BED file of CHIP-Seq data

organism: Eutrema salsugineum

source_name: E. salsugineum Shandong H3K56ac

growth_protocol: All plants with the exception of met1/sdg7/sdg8 mutants and their controls were sown onto soil and grown in growth chamber under 18 hr light, 6 hr dark at 23-25C. met1/sdg7/sdg8 mutants and their wild-type controls were sown and germinated on MS media.

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).
CHIP-seq: Immunoprecipitated DNA was end repaired using the End-It DNA Repair Kit (Epicentre, Madison, WI) according to the manufacturer’s instructions. DNA was purified using Sera-Mag (Thermo Scientific, Waltham, MA) at a 1:1 DNA to beads ratio. The reaction was then incubated for 10 minutes at room temperature, placed on a magnet to immobilize the beads, and the supernatant was removed. The samples were washed two times with 500µL of 80% ethanol, air dried at 37C and then resuspended in 50ul of 10 mM Tris-Cl pH8.0. Finally, the samples were incubated at room temperature for 10 minutes, placed on the magnet, and the supernatant was transferred to a new tube, which contained reagents for “A-tailing.” A-tailing reactions were performed at 37C according to the manufacturers instructions (New England Biolabs, Ipswich, MA). The samples were cleaned using Sera-Mag beads as previously described. Next, adapter ligation was performed using Illumina Truseq Universal Y-adapters and T4 DNA ligase (New England Biolabs, Ipswich, MA) overnight at 16C. A double clean-up using the Sera-Mag beads was performed to remove any adapter-adapter dimers and the elution was used for 15 rounds of PCR. Lastly, samples were cleaned up one final time using the procedures described above.

tag: accession

value: Shandong

value: leaf

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: E_salsugineum_shandong_H3K36me3_chip

description: ChIP seq data for E. salsugineum H3K36me3

source_name: E. salsugineum Shandong H3K36me3

tag: chip antibody

value: Abcam

tag: chip antibody lot #


title: Stage-6_rep2

tag: developmental stage


title: Stage-5_rep3


title: E_salsugineum_shandong_H3K9me2_chip

description: ChIP seq data for E. salsugineum H3K9me2

source_name: E. salsugineum Shandong H3K9me2

value: Cell signalling


title: A_thaliana_H3K56ac_chip

description: ChIP seq data for A. thaliana H3K56ac

organism: Arabidopsis thaliana

source_name: A. thaliana H3K56ac Chip


title: E_salsugineum_shandong_H2A.Z_chip

description: ChIP seq data for E. salsugineum H2A.Z

data_processing:
For MethylC-seq data: Reads were trimmed, aligned, and methylation called using the methylpy pipeline (Schultz et al. 2015). The genome is converted into a forward strand reference (all Cs to Ts) and a reverse strand reference (all Gs to As). Cutadapt (Martin et al. 2011) is used to trim adaptor sequences and then bowtie (Langmead et al. 2009) aligns reads to the two converted reference genomes. Only uniquely aligned reads are retained and the non-conversion rate calculated from unmethylated reads aligned to the chloroplast genome or spiked in unmethylated lambda DNA.
For RNA-seq data: Raw FASTQ reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32 (Bolger et al. 2014). Reads were aligned using Tophat v2.0.13 (Trapnell et al. 2010) supplied with a reference GFF file and the following arguments: -I 50000 --b2-very-sensitive --b2-D 50. Transcripts were then quantified using Cufflinks v2.2.1 (Trapnell et al. 2012) supplied with a reference GFF file.
For CHIP-seq data: Raw ChIP reads were trimmed for adapters and low-quality bases using Trimmomatic version 0.32 (Bolger et al. 2014). Reads were trimmed for TruSeq version 3 single-end adapters with maximum of two seed mismatches, palindrome clip threshold of 30 and simple clip threshold of 10. Additionally, leading and trailing bases with quality less than 10 were removed; reads shorter than 50 bp were discarded. Trimmed reads were mapped to the TAIR10 genome using bowtie2 version 2.2.3 (Langmead et al. 2012) with default options. Mapped reads were sorted using samtools verison 1.2 (Li et al. 2009) then clonal duplicates were removed using samtools version 0.1.9 (Li et al. 2009). BAM files were then converted to BED files using bedtools v2.21.1 (Quinlan and Hall 2010).
Genome_build: A. thaliana = TAIR10; A. lyrata = v1.0; B. rapa = FPsc v1.3 (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_BrapaFPsc);  B. oleracea = TO1000 v1.0 (GCF_000695525.1); C. rubella = v1.0 (GCF_000375325.1);  E. salsugineum = v1.0 (GCF_000478725.1)
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_total.tsv”) column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0
Supplementary_files_format_and_content: RNAseq data column 1 = gene_ID = gene identifier; column 2 = FPKM = gene expression in fragments per kilobase per million (FPKM)
Supplementary_files_format_and_content: BED file of H2A.Z CHIP-Seq data

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).
RNA-seq: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
CHIP-seq: Immunoprecipitated DNA was end repaired using the End-It DNA Repair Kit (Epicentre, Madison, WI) according to the manufacturer’s instructions. DNA was purified using Sera-Mag (Thermo Scientific, Waltham, MA) at a 1:1 DNA to beads ratio. The reaction was then incubated for 10 minutes at room temperature, placed on a magnet to immobilize the beads, and the supernatant was removed. The samples were washed two times with 500µL of 80% ethanol, air dried at 37C and then resuspended in 50ul of 10 mM Tris-Cl pH8.0. Finally, the samples were incubated at room temperature for 10 minutes, placed on the magnet, and the supernatant was transferred to a new tube, which contained reagents for “A-tailing.” A-tailing reactions were performed at 37C according to the manufacturers instructions (New England Biolabs, Ipswich, MA). The samples were cleaned using Sera-Mag beads as previously described. Next, adapter ligation was performed using Illumina Truseq Universal Y-adapters and T4 DNA ligase (New England Biolabs, Ipswich, MA) overnight at 16C. A double clean-up using the Sera-Mag beads was performed to remove any adapter-adapter dimers and the elution was used for 15 rounds of PCR. Lastly, samples were cleaned up one final time using the procedures described above.


title: E_salsugineum_shandong_RNAseq

description: RNA-seq data for E. salsugineum Shandong


title: A_thaliana_H3K9me2_chip

description: ChIP seq data for A. thaliana H3K9me2

source_name: A. thaliana H3K9me2 Chip


title: Col-0_RNAseq_2

description: RNA-seq for A. thaliana Col-0 WT replicate 2


title: met1_epiRIL_01_RNAseq_1

description: RNA-seq for A. thaliana epiRIL 01 replicate 1

value: met1 epiRIL 01


title: E_salsugineum_yukon_RNAseq

description: RNA-seq data for E. salsugineum Yukon

value: Yukon


title: ibm1_MethylC-seq

description: Whole Genome Bisulphite Sequencing of A. thaliana ibm1 mutants


title: met1_epiRIL_01_RNAseq_3

description: RNA-seq for A. thaliana epiRIL 01 replicate 3


title: met1_epiRIL_28_MethylC-seq

description: Whole Genome Bisulphite Sequencing of A. thaliana met1 epiRIL line 28

value: met1 epiRIL 28


title: A_thaliana_H3K27me3_chip

description: ChIP seq data for A. thaliana H3K27me3

source_name: A. thaliana H3K27me3 Chip


title: met1_epiRIL_01_MethylC-seq

description: Whole Genome Bisulphite Sequencing of A. thaliana met1 epiRIL line 1


title: E_salsugineum_shandong_H3K27me3_chip

description: ChIP seq data for E. salsugineum H3K27me3

source_name: E. salsugineum Shandong H3K27me3


title: met1_epiRIL_12_MethylC-seq

description: Whole Genome Bisulphite Sequencing of A. thaliana met1 epiRIL line 12

value: met1 epiRIL 12


title: A_thaliana_H2A.Z_chip

description: ChIP seq data for A. thaliana H2A.Z


title: Col-0_RNAseq_1

description: RNA-seq for A. thaliana Col-0 WT replicate 1


title: A_thaliana_H3K4me3_chip

description: ChIP seq data for A. thaliana H3K4me3

source_name: A. thaliana H3K4me3 Chip


title: E_salsugineum_yukon_MethylC-seq

description: Whole Genome Bisulphite Sequencing of E. salsugineum (Yukon)


title: met1_epiRIL_01_RNAseq_2

description: RNA-seq for A. thaliana epiRIL 01 replicate 2


title: RNAseq_titration_Dox0.0_rep2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
RNA-seq:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned o the human genome using Bowtie v0.12.8. with default parameters.
Bam files were generated using Samtools v0.1.18.
Raw count tables for each ensembl gene were generated using the summarizeOverlaps {GenomicAlignments} function in R.
Differentially expressed genes were called using the edgeR package in R.
hg19
txt file containing log2FC, p-value and adjusted p-value. For detailed description see additional README.txt. Raw count matrices are provided as txt file.
Supplementary_files_format_and_content: fixedStep wiggle files

source_name: U2OS cells

growth_protocol:
U2OS cells were grown in DMEM (Sigma) suppelmented with 10% FCS (Biochrom) and penicillin/streptomycin (Sigma).
U2OS cells were grown in DMEM (Sigma) suppelmented with 10% FCS (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol:
For RNA-seq, total RNA was extracted using the RNeasy mini columns (Qiagen) including on-column DNase I digestion.
PolyA+-RNA was isolated from total with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used for library preparation following the manufacturer’s instruction. Size selection of the libraries was performed with the AMPure XP Beads (Beckman Coulter), followed by 12 PCR cycle for amplification. Library quantification and quality was assessed using the Experion Automated Electrophoresis System (Bio-Rad).

treatment_protocol:
Cells were grown with the indicated doxycycline concentration for 30h.
Cells were grown with the indicated doxycycline concentration for 30h.

tag: antibody

value: non


title: Col-0_MethylC-seq

description: Whole Genome Bisulphite Sequencing of A. thaliana Col-0: resequencing of new sample for comparison to ibm1 mutants


title: E_salsugineum_shandong_H3K4me3_chip

description: ChIP seq data for E. salsugineum H3K4me3

source_name: E. salsugineum Shandong H3K4me3


title: A_thaliana_H3K36me3_chip

description: ChIP seq data for A. thaliana H3K36me3

source_name: A. thaliana H3K36me3 Chip


title: ChIPseq_MYC_Dox0.0

data_processing:
ChIPseq:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned o the human genome usingBowtie v0.12.8. with default settings.
Samples were normalized to the same number of aligned reads.
Bam files were generated using Samtools v0.1.18.
For the generation of wiggle files MACS v1.4.2 was used with a fixed step of 10bp.
hg19
fixedStep wiggle files
Supplementary_files_format_and_content: fixedStep wiggle files

extract_protocol: For ChIP-seq, libraries from GEO record GSE44672 were used and sequenced deeper.

value: c-MYC N262 (Santa Cruz, sc764)

tag: cell line


title: ChIPseq_MYC_Dox1.0


title: RNAseq_titration_Dox1.0_rep2


title: Col-0_RNAseq_3

description: RNA-seq for A. thaliana Col-0 WT replicate 3


title: ChIPseq_input


title: RNAseq_titration_Dox0.05_rep2


title: RNAseq_titration_Dox0.0_rep1


title: RNAseq_titration_Dox0.05_rep1


title: RNAseq_titration_Dox1.0_rep1


title: RNAseq_titration_Dox0.01_rep1


title: RNAseq_titration_Dox0.1_rep2


title: RNAseq_depletion_siMYC_rep1


title: RNAseq_titration_Dox0.1_rep1


title: RNAseq_depletion_siCTR_rep1


title: RNAseq_titration_Dox0.01_rep2


title: RNAseq_depletion_siCTR_rep2


title: RNAseq_depletion_siCTR_rep3


title: STHSC L-GMP Tumor rep 2

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Short Term Hematopoietic Stem Cell-Derived LGMP Tumor Cell

data_processing:
Library strategy: ATAC-seq
Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample.
Reads were aligned to the mouse mm9 assembly using bowtie2. Only reads that uniquely mapped to the genome were used in subsequent analysis. Duplicate reads were eliminated to avoid potential PCR amplification artifacts and to eliminate mtDNA duplicates. Samples with <10 million uniquely aligned reads were considered noisy and were excluded from the analysis.
ATAC-seq peaks in each sample were identified using MACS2 with the following settings: MACS2-2.1.0.20140616/bin/macs2 callpeak -t <input tag file> -f BED -n <output peak file> -g 'mm' --nomodel --shift -100 --extsize 200 -B –broad.
Genome_build: mm9
Supplementary_files_format_and_content: .txt files include macs2 peak data for each Sample

source_name: Short Term Hematopoietic Stem Cell-Derived L-GMP Tumor Cell

extract_protocol:
Cryopreserved leukemic bone marrow samples were thawed, and 50,000 LSCs (L-GMP; GFP+ Lin- Sca-1- c-Kit+ CD34+ FcγR+) were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688)
ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688

value: Bone Marrow

tag: age

value: 6-12 weeks

value: WT


title: Tet2_3aDKO H3K27me3 ChIP-Seq

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

description: technical replicate of biological replicate 1

data_processing:
use bowtie2/2.2.7 to align chip sequencing reads to the mouse genome mm9
use MACS2 to identify the peaks of CMS
Genome_build: mm9
Supplementary_files_format_and_content: BED files include chromosome, start, end, peak name, peak enrichment -log(q-value)

source_name: Hematopoietic stem cells (HSC)

growth_protocol: bone marrow was isolated from Tet2 KO and Dnmt3a-Tet2 DKO mice and transplanted into CD45.1 receipient mice for 2 serial transplantation. Donor derved HSC (CD45.2+ CD150+ CD48- Sca1+ ckit+ Lin-) are isolated by FACS after the sacrifice of mice.

extract_protocol: HSCs purified as indicated above were sorted and crosslinked with 1% formaldehyde at room temperature (RT) for 10 min, and the reaction was stopped by 0.125M glycine at RT for 5 min. Cross-linked cells were lysed and sonicated to 200-500 bp fragments (Bioruptor, Diagenode). ChIP-qualified antibodies (H3K27me3 Millipore 07-449) were added to the sonicated chromatin and incubated at 4°C overnight. Following this, 10 μl of protein A magnetic beads (Dynal, Invitrogen) previously washed in RIPA buffer were  added  and incubated for an additional 2 hours at 4°C. The bead: protein complexes were washed three times with RIPA buffer and twice with TE buffer. Following transfer into new 1.5 ml collection tube, genomic DNA was eluted for 2 hours at 68°C in 100 µl Complete Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K), and combined with a second elution of 100 µl Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl) for 10 min at 68°C. ChIPed DNA was purified by MinElute Purification Kit (Qiagen) and eluted in 12 µl elution buffer.  ChIP-seq library is constructed using Rubicon Genomics ThruPLEX DNA-seq Kit following the manufacture's protocol.

treatment_protocol: The HSCs used in this study is from genetic engineering mouse model which Tet2 is knocked-out or both Tet2 and Dnmt3a is knocked-out.

tag: cell type

value: Hematopoietic stem cell

tag: genotype/variation

value: Tet2 and Dnmt3a double knockout

value: H3K27me3 (Millipore, catalog# 07-449)


title: RNAseq_depletion_siMYC_rep2


title: MPP L-GMP Tumor rep 2

description: Multipotent Progenitor Cell-Derived LGMP Tumor Cell

source_name: Multipotent Progenitor Cell-Derived L-GMP Tumor Cell


title: STHSC L-GMP Tumor rep 1


title: Sample49.ReverbDKO.BMDM.RNA-seq.Pam3CSK4.6h

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description: N\A

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 (NCBI 37) genome using default parameter for bowtie (RNA-Star, respectively). Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and other analyses in the study.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), text files (RNA-Seq data).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow was extracted and differentiated for 5 - 7 days in 30% L929 cells, 20% fetal bovine serum (FBS)/RPMI-1640 containing 100U/ml penicillin/streptomycin in petri dishes supplemented with MCSF 1 after 4 days and replated after this time in 10% fetal bovine serum (FBS)/RPMI-1640 with 100U/ml penicillin/streptomycin supplemented with MCSF

extract_protocol:
RNA-Seq: Total RNA was isolated using TRIzol LS (ThermoFisher Scientific) and resuspended
with UltraPure water (ThermoFisher Scientific) supplemented with 1U/μL SUPERase-In
 (Ambion) then treated with TURBO DNA-free kit (Ambion). Poly(A) selection was performed
using the MicroPoly(A)Purist kit (Invitrogen) according to the manufacturer’s instructions.
Poly(A) RNA was fragmented using RNA Fragmentation Reagents (Ambion) for 10 min at 70°C
and purified by running through a Micro Bio-Spin P-30 column (Bio-Rad) according to the
manufacturer’s instructions. 30ng RNA was utilized for subsequent library preparation.
ChIP-Seq:Briefly, for cFos, p65, Nrf2, and Smad3 ChIPs, macrophages were first cross-linked in 2mM dissuccinimidyl glutarate (Pierce 20593) in PBS for 30 minutes, followed by subsequent 1% formaldehyde (Sigma) cross-linking in PBS for 10 minutes at room temperature. For H3K27ac ChIPs, cells were cross-linked using 1% formaldehyde in PBS for 10 minutes at room temperature. After cross-linking, glycine (Sigma) was added to a final concentration of 0.2625 M to quench the reaction. Subsequently, cross-linked macrophages were centrifuged (5 minutes, 1200 rpm, 4°C), washed twice with PBS, and pellets snap frozen and stored at -80°C. For ChIP of H3K27Ac, p65, and Smad3, frozen cell pellets were resuspended in cell lysis buffer (10 mM HEPES/KOH pH 7.9, 85 mM KCl, 1 mM EDTA, 1.0% IGEPAL CA-630 (Sigma), 1x protease inhibitor cocktail (Roche), 1 mM PMSF). After five minutes lysis on ice, cells were centrifuged (5 minutes, 4000 rpm, 4°C), and the supernatant was removed. The pellet was then resuspended in nuclear lysis buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF) and the chromatin was sheared by sonication on wet ice with a Bioruptor Standard Sonicator (Diagenode) for three 15 min cycles each alternating 30 sec on and 30 sec off on the high setting. Additional Triton X-100 was added to the sonicated chromatin to 10% of the final volume and the lysate was cleared by centrifugation (5 minutes, 14000 rpm, 4˚C). Input was then saved for subsequent analysis. For cFos ChIP, pellets were suspended in 50 mM Tris pH 8.0, 60 mM KCl, 0.5% IGEPAL, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF, followed by 10 minutes of incubation on ice and centrifugation at 2,000 x g for 3 minutes at 4°C. The pellet was then suspended in 0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris pH 8.0, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF. The chromatin suspension was sheared by sonication on wet ice with a Bioruptor Standard Sonicator (Diagenode) for three 15 min cycles each alternating 30 sec on and 30 sec off on the high setting, followed by centrifugation for 10 minutes at maximum speed at 4°C. The chromatin was diluted 5x with 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris pH 8.0, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF. An input sample was saved for subsequent analysis.
ChIP-Seq: Antibodies against p65 (sc-372), cFos (sc-7202) and Nrf2 (sc-13032) were purchased from Santa Cruz Biotechnology, against Smad3 (ab28379) from Abcam, and against H3K27ac (39135) from Activ Motif. Protein A or G dynabeads (Invitrogen) pre-bound with antibody was added to the diluted cell lysate overnight at 4˚C. Immunoprecipitated complexes were washed three times with 20 mM Tris/HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, three times with 10 mM Tris/HCl pH 7.4 at 20°C, 250 mM LiCl, 1% Triton X-100, 1% sodium deoxycholate, 1 mM EDTA, and two times with Tris-EDTA plus 0.1% Tween-20 before eluting two times with 50 µL elution buffer (TE, 1% SDS, 30 and 10 minutes, room temperature). Elution buffer was also added to the input. After pooling the eluted samples, the sodium concentration was adjusted to 300 mM and cross-links were reversed overnight at 65°C. Samples were treated with 0.5 mg/ml proteinase K for 1 hour at 55˚C and 0.25 mg/ml RNase A for 1 hour at 37˚C before DNA was isolated using the ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. For library preparation, NEXTflex DNA barcode adaptors (BioO Scientific) were ligated to the genomic DNA. Polymerase chain reaction mediated library amplification was performed and final libraries were size selected on 10% TBE gels (Invitrogen). Libraries were PCR-amplified for 12-14 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.

treatment_protocol: For ChIP-seq experiments, cells were left untreated or treated by adding 100ng/ml KDO2-lipid A ("KLA"), or 1ng/ml tumor growth factor β  ("TGFγ"), or replacing the seeding media with fresh, warm media ("vehicle") or warm tissue homogenate. For RNA-seq experiments, cell media was replaced with fresh, warm media (no treatment) or that containing 300ng/ml Pam3CSK4 ("Pam3"), 50ng/ml polyinosinic:polycytidylic acid ("PolyIC"), 100ng/ml KDO2-Lipid A ("KLA"), 100ng/ml KDO2-Lipid A plus 10 U/ml recombinant interferon γ ("KLA-IFNγ"), 20ng/ml interleukin 4 ("IL4"), or 1ng/ml tumor growth factor β ("TGFβ") for the indicated treatment times.

value: ReverbDKO

value: Pam3CSK4 6h

tag: chip (antibody)


title: MPP L-GMP Tumor rep 1


title: Tet2KO H3K27me3 ChIP-Seq

value: Tet2 knockout


title: GMP L-GMP Tumor rep 1

description: Granulocyte-Macrophage Progenitor Cell-Derived LGMP Tumor Cell

source_name: Granulocyte-Macrophage Progenitor Cell-Derived L-GMP Tumor Cell


title: CMP L-GMP Tumor rep 2

description: Common Myeloid Progenitor Cell-Derived LGMP Tumor Cell

source_name: Common Myeloid Progenitor Cell-Derived L-GMP Tumor Cell


title: GMP L-GMP Tumor rep 2


title: MSCF7_125_rep3

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
TopHat with default settings and sample type "fr-secondstrand" for directional libraries
ArrayStar (DNASTAR) with default RNA sequencing settings.  Imported BAM files from TopHat output.
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated text files include RPKM values for each sample

source_name: marrow derived MSC

growth_protocol: Marrow derived MSC (mdMSC) were obtained from Dr. Janet Rubin, cryopreserved and expanded no more than 10 passages.  The MSCs were cultured in minimum Eagle’s medium alpha (MEMα) modification supplemented with 10% fetal bovine serum from Hyclone (Logan, UT), and 1% penicillin-streptomycin from Invitrogen.  For differentiation, cells were grown to confluency and then transferred to either osteogenic differentiation media (10 mM β–glycerophosphate and 50 µg/mL ascorbic acid) or adipogenic differentiation media (5 µg/mL insulin, 50 µM indomethacin, 0.1 µM dexamethasone) for the indicated lengths, replenishing the media every 2-3 days until assay.

extract_protocol:
RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH) with an additional LiCl extraction. Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions
Directional RNA-seq libraries were prepared with the Epicentre (Madison, WI) ScriptSeq v2 RNA-seq Library Preparation Kit per manufacturer’s instructions.  Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: MSC cells were differentiated to days 0, 7, and 15 were treated with 100nM of 1,25(OH)2D3 (or ethanol vehicle) for 24 hours prior to RNA harvesting.

value: marrow-derived mesenchymal stem cells

tag: differentiation time point (day)

tag: differentiation media

value: adipogenic


title: MSCF7_125_rep2


title: Sample40.WT.BMDM.RNA-seq.Pam3CSK4.6h

description: N\A

tag: strain


title: CMP L-GMP Tumor rep 1

tag: tissue

tag: genotype


title: RNAseq_depletion_siMYC_rep3


title: MSCF7_125_rep1

tag: treatment


title: MSCF7_Veh_rep3

value: vehicle


title: MSCF7_Veh_rep2


title: MSCB7_125_rep3

value: osteogenic


title: MSCB15_125_rep1


title: MSCF7_Veh_rep1


title: MSCB7_125_rep1


title: MSCB15_125_rep2


title: MSCB7_Veh_rep2


title: MSCB15_Veh_rep3


title: MSCB7_Veh_rep3


title: MSCB7_Veh_rep1


title: MSCB7_125_rep2


title: MSCD0_Veh_rep2


title: MSCB15_Veh_rep1


title: MSCD0_125_rep3


title: MSCD0_Veh_rep1


title: MSCF7_Input

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and MACS.
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: *.bed files contain the ChIP-seq peak locations, *.bedgraph files are for display in the UCSC genome browser

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB, Mol Endo. 2012). Briefly, samples were subjected to immuno-precipitation using either a control IgG antibody or the indicated experimental antibody (VDR, RXR, H3K4me1, H3K4me2, H3K4me3, H3K27Ac, H3K5Ac, H3K9Ac, H4K20me1, H3K36me3, or H3K9me3).  To remove the calcified matrix from the differentiated cells, the cells were subjected to three 15 minute 300mM EDTA washes following fixation. Subsequently, matrix mix was subjected to 2x10 pulses with a Polytron Homogenizer (Power Gen 125, Fisher Scientific) while in NCP 1 buffer (Hepes 10mM pH 6.5, EDTA 10mM, EGTA 0.5mM, Triton X-100 0.25%).  Resulting cell pellet was resuspended in NCP 2 buffer (Hepes 10mM pH 6.5, EDTA 1mM, EGTA 0.5mM, NaCl 200mM) and remainder of protocol was followed.  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The ChIP samples were repeated in biological replicate in the same manner (minimum of 2 replicates). Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Where indicated, MSC cells were treated with 100nM of 1,25(OH)2D3 for 3 hours prior to ChIP assay.


title: MSCD0_125_rep2


title: MSCB15_Input


title: MSCB7_Input


title: MSCF7_H3K36me3125_rep1


title: MSCF7_H3K36me3125_rep2


title: MSCF7_H3K36me3Veh_rep1


title: MSCD0_125_rep1


title: MSC_Input


title: MSCB15_125_rep3


title: MSCF7_H3K4me3125_rep2


title: MSCB15_Veh_rep2


title: MSCF7_H3K4me1125_rep2


title: MSCF7_H3K4me1Veh_rep2


title: MSCD0_Veh_rep3


title: MSCF7_H3K4me1Veh_rep1


title: MSCF7_H3K9Ac125_rep2


title: MSCF7_H3K9Ac125_rep1


title: MSCF7_H3K4me3Veh_rep1


title: MSCF7_H3K4me3Veh_rep2


title: MSCF7_H3K9AcVeh_rep1


title: MSCF7_H3K4me3125_rep1


title: MSCF7_H3K9AcVeh_rep2


title: MSCF7_H4K5Ac125_rep2


title: MSCF7_H3K36me3Veh_rep2


title: MSCF7_H4K5AcVeh_rep2


title: MSCF7_PPARgVeh_rep2


title: MSCF7_H4K5Ac125_rep1


title: MSCF7_H4K5AcVeh_rep1


title: MSCF7_PPARgVeh_rep1


title: MSCF7_RXR125_rep2

value: RXR (Santa Cruz, ΔN-197, sc-774, lot# G2310)


title: MSCF7_RXRVeh_rep2


title: MSCF7_Runx2Veh_rep2

value: RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411)


title: MSCF7_RXR125_rep1


title: MSCF7_CEBPaVeh_rep1


title: MSCF7_CEBPbVeh_rep2

value: C/EBPβ (Santa Cruz, C-19, sc-150, lot# F3011)


title: MSCF7_CEBPbVeh_rep1


title: MSCF7_RXRVeh_rep1


title: MSCF7_Runx2Veh_rep1


title: MSCF7_VDR125_rep2

value: VDR (Santa Cruz, C-20, sc-1008, lot# A0912)


title: MSCF7_H3K4me1125_rep1


title: MSCF7_VDRVeh_rep2


title: MSCB15_H3K36me3125_rep2


title: MSCF7_VDRVeh_rep1


title: MSCB15_H3K36me3Veh_rep2


title: MSCB15_H3K36me3125_rep1


title: MSCF7_VDR125_rep1


title: MSCB15_H3K4me3125_rep1


title: MSCB15_H3K4me3Veh_rep1


title: MSCB15_H3K4me3125_rep2


title: MSCB15_H3K4me3Veh_rep2


title: MSCF7_CEBPaVeh_rep2


title: MSCB15_H3K4me1125_rep1


title: MSCB15_H3K9Ac125_rep1


title: MSCB15_H3K9Ac125_rep2


title: MSCB15_H3K4me1Veh_rep2


title: MSCB15_H3K4me1Veh_rep1


title: MSCB15_H3K36me3Veh_rep1


title: MSCB15_Runx2Veh_rep2


title: MSCB15_Runx2Veh_rep1


title: MSCB15_H4K5AcVeh_rep1


title: MSCB15_H3K9AcVeh_rep2


title: MSCB15_H4K5AcVeh_rep2


title: MSCB15_H3K9AcVeh_rep1


title: MSCB15_H4K5Ac125_rep2


title: MSCB15_H4K5Ac125_rep1


title: MSCB15_CEBPbVeh_rep2


title: MSCB15_CEBPbVeh_rep1


title: MSCB15_VDR125_rep1


title: MSCB15_VDR125_rep2


title: MSCB15_RXR125_rep1


title: MSCB15_VDRVeh_rep2


title: MSCB15_VDRVeh_rep1


title: MSCB7_H3K36me3Veh_rep1


title: MSCB15_H3K4me1125_rep2


title: MSCB15_RXR125_rep2


title: MSCB7_H3K4me3125_rep1


title: MSCB7_H3K4me3125_rep2


title: MSCB15_RXRVeh_rep1


title: MSCB7_H3K36me3Veh_rep2


title: MSCB7_H3K36me3125_rep1


title: MSCB7_H3K4me3Veh_rep2


title: MSCB7_H3K4me1125_rep1


title: MSCB7_H3K4me3Veh_rep1


title: MSCB7_H3K36me3125_rep2


title: MSCB15_RXRVeh_rep2


title: MSCB7_H3K9AcVeh_rep1


title: MSCB7_H3K9Ac125_rep2


title: MSCB7_H4K5Ac125_rep1


title: MSCB7_H3K4me1Veh_rep1


title: MSCB7_H4K5AcVeh_rep1


title: MSCB7_H3K9AcVeh_rep2


title: MSCB7_PPARgVeh_rep2


title: MSCB7_H3K9Ac125_rep1


title: MSCB7_H4K5AcVeh_rep2


title: MSCB7_H3K4me1125_rep2


title: MSCB7_Runx2Veh_rep2


title: MSCB7_Runx2Veh_rep1


title: MSCB7_CEBPbVeh_rep1


title: MSCB7_CEBPbVeh_rep2


title: MSCB7_RXR125_rep1


title: MSCB7_VDRVeh_rep2


title: MSC_H3K36me3125_rep1


title: MSCB7_RXR125_rep2


title: MSC_H3K36me3125_rep2


title: MSCB7_CEBPaVeh_rep2


title: MSCB7_RXRVeh_rep2


title: MSC_H3K36me3Veh_rep2


title: MSCB7_PPARgVeh_rep1


title: MSCB7_H3K4me1Veh_rep2


title: MSCB7_H4K5Ac125_rep2


title: MSC_H3K36me3Veh_rep1


title: MSC_H3K4me3Veh_rep2


title: MSC_H3K4me3125_rep2


title: MSC_H3K4me3125_rep1


title: MSCB7_CEBPaVeh_rep1


title: MSC_H3K4me3Veh_rep1


title: MSCB7_VDRVeh_rep1


title: MSCB7_VDR125_rep1


title: MSCB7_VDR125_rep2


title: MSCB7_RXRVeh_rep1


title: MSC_H3K4me1Veh_rep1


title: MSC_H3K4me1Veh_rep2


title: MSC_H3K4me1125_rep2