title: SHBTU000016CAC

description:
Processed_Data
478


title: SHBTI000029CAC

status: Public on Sep 05 2017

type: SRA

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

country: USA

institute: University of Illinois at Chicago

description:
Processed_Data
475

library_source: genomic

data_processing:
Read-through sequences within raw sequencing reads were trimmed using Trimmomatic version 0.35. Low quality bases at the 5' (Phred quality score <5) and 3' (5bp-sliding window Phred score< 15) were also trimmed. Reads with a minimum length of 50bp were aligned to the human genome assembly GRCh37 using Bowtie2 version 2.2.6 with end-to-end alignment mode. For paired-end sequencing data, read pairs were concordantly aligned with fragment length <500bp and with up to 1 ambiguous base and four mismatched bases per 100bp length.
Raw sequencing reads profiled for 5mC were trimmed and aligned to GRCh37 using Bismark version 0.15.0 according to previously published data processing procedures.
Alignments with Mapping Quality Score (MAPQ) ≥10 were counted for overlap with genomic features using featureCounts of subread version 1.5.0-p1, without strand information.
Gene regions were defined as the regions between gene start sites and gene end sites annotated by GENCODE release 19.
CpG islands were annotated CpG islands by UCSC Table Browser plus +/- 1kb regions.
Genome_build: GRCh37
Supplementary_files_format_and_content: Plain text format. Processed_Data is a data frame with fields: 1) gene (official gene symbol; for 23 pairs of genes sharing the same official gene symbol, one from each pair assigned a new gene symbol as original_gene_symbol.dup); 2) pos (chr_start_stop) of genes; 3) raw counts of samples at genes. Reports hydroxy-methylation levels.
Supplementary_files_format_and_content: Plain text format. Processed_5mc_Data is a data frame with fields: 1) pos (chr_start_stop) of CpG islands; 2) raw counts of samples at CpG islands. Reports methylation levels.

molecule: genomic DNA

organism: Homo sapiens

source_name: tissue

growth_protocol: A total of 4ml of peripheral blood was collected from subject individuals using EDTA anticoagulant tubes. Tissue samples, including tumor and adjacent tissue samples, from patients were stocked at -80°C after surgical operation.

extract_protocol:
The plasma cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s protocol. Genomic DNA from tissues was isolated using the ZR Genomic DNA-Tissue Kits (Zymo Research) according to the manufacturer’s protocol.
First, the genomic DNA is fragmented using an enzymatic reaction. Next, the fragmented genomic DNA or the cfDNA were repaired and installed with the Illumina compatible adaptors. The glucosylation reactions were performed in a 25 μL solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 μM N3-UDP-Glc, and 1 μM βGT, at 37°C for 1 hr. The reaction was purified by Micro Bio-Spin 30 Column (Bio–Rad) into ddH2O. After that, 1 μL DBCO-PEG4-DBCO (Click Chemistry Tools, 4.5 mM stock in DMSO) was added to the reaction mixture. The reactions were incubated at 37°C for 2 hr. Next, the DNA was purified by Micro Bio-Spin 30 Column (Bio-–Rad). The purified DNA was incubated with 5 µL C1 Streptavidin beads (Life Technologies) in 2X buffer (1X buffer: 5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl) for 15 min according to the manufacturer’s instruction. The beads were subsequently washed eight times for 5 -min with 1X buffer. All binding and washing was done at room temperature with gentle rotation. The captured DNA fragments were amplified with 14-16 cycles of PCR amplification. The PCR products were purified using AMPure XP beads according to the manufacturer’s instructions. DNA concentration of each library was measured with a Qubit fluorometer (Life Technologies) and sequencing was performed on the Illumina Hi-Seq platform or NextSeq 500 platform.

treatment_protocol: Plasma sample was prepared within 6h by centrifuging twice at 1,350g for 12min, and then centrifuging at 13,500g for 12min. The prepared plasma samples (about 2ml/subject) were immediately stored at -80°C. About 10-25 mg tissue was collected using a scalpel after sample unfreezing.

tag: age

tag: gender (1=male, 2=female)

tag: disease site

value: stomach

tag: disease state

value: cancer

tag: tissue

value: adjacent tissue


title: SHBTU000018CAC

description:
Processed_Data
480

value: tumor


title: SHBTU000019CAC

description:
Processed_Data
481


title: SHBTI000023CAC

description:
Processed_Data
469


title: SHBTU000017CAC

description:
Processed_Data
479


title: SHBTI000021CAC

description:
Processed_Data
467


title: SHBTI000032CAC

description:
Processed_Data
476


title: SHBTI000024CAC

description:
Processed_Data
470


title: SHBTI000028CAC

description:
Processed_Data
474


title: SHBTI000017CAC

description:
Processed_Data
463


title: SHBTI000016CAC

description:
Processed_Data
462


title: SHBTI000027CAC

description:
Processed_Data
473


title: SHBTI000022CAC

description:
Processed_Data
468


title: SHBTI000025CAC

description:
Processed_Data
471


title: SHBTI000020CAC

description:
Processed_Data
466


title: SHBTU000011CAC

description:
Processed_Data
377


title: SHBTI000012CAC

description:
Processed_Data
373


title: SHBTI000011CAC

description:
Processed_Data
372


title: SHBTI000018CAC

description:
Processed_Data
464


title: SHBTU000009CAC

description:
Processed_Data
313


title: SHBTU000007CAC

description:
Processed_Data
309


title: SHBTI000019CAC

description:
Processed_Data
465


title: SHBTU000014CAC

description:
Processed_Data
380


title: SHBTU000013CAC

description:
Processed_Data
379


title: SHBTU000012CAC

description:
Processed_Data
378


title: SHBTI000004CAC

description:
Processed_Data
282


title: SHBTI000006CAC

description:
Processed_Data
285


title: SHBTI000005CAC

description:
Processed_Data
283


title: SHBTI000009CAC

description:
Processed_Data
291


title: SHBTU000010CAC

description:
Processed_Data
376


title: SHBTI000014CAC

description:
Processed_Data
375


title: SHBPL000009CAC

description:
cell free DNA
Processed_Data
237

source_name: blood

value: plasma


title: SHBPL000006CAC

description:
cell free DNA
Processed_Data
234


title: SHBPL000005CAC

description:
cell free DNA
Processed_Data
233


title: SHBTI000013CAC

description:
Processed_Data
374


title: SHBTU000005CAC

description:
Processed_Data
304


title: SHBTU000004CAC

description:
Processed_Data
303


title: SHBPL000002CAC

description:
cell free DNA
Processed_Data
230


title: SHBTU000003CAC

description:
Processed_Data
302


title: SHBTI000007CAC

description:
Processed_Data
287


title: SHBTI000010CAC

description:
Processed_Data
371


title: SHBTI000003CAC

description:
Processed_Data
281


title: ECFC_Drug_Treatment_Rep3

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

library_source: transcriptomic

data_processing:
Reads from the same condition and replicate number run on 2 different lanes were combined and mapped to the known hg19 transcripts (GTF file from the UCSC with the ENSEMBL assembly) using Bowtie version 2.2.4 using default values. Unmapped reads were then mapped to the hg19 genome.
Splice junctions were determined with TopHat version 2.0.12 using default values.
Transcript quantification was performed with CuffLinks version 2.2.1.
Identification of differentially expressed genes was performed with the CuffDiff from the Cufflinks package.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files represent the read per million mapped reads coverage of the RNA-Seq across the genome. The files were generated using the BEDTools suite (version 2.16.2) and UCSC genome browser standalone tools for Unix from the aligned reads output of TopHat version 2.0.12 using default values.
Supplementary_files_format_and_content: Text file contains quantification of Fragments Per Kilobase of transcript per Million mapped reads for each gene.

molecule: total RNA

growth_protocol: ECFCs were maintained in 10 cm diameter culture dish containing EGM-2 medium (Lonza) untill reaching subconfluency

extract_protocol:
Total RNA were extracted using RNeasy Mini Kit (Qiagen, Cat#74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ECFCs were treated for 72h with 5 µM GSK-343 and 2h with panobinostat 10 nM or same volume of DMSO

tag: clone id

value: ECFC clone2 cord6 p4

tag: cell type

value: Human umbilical cord blood MNCs-derived ECFCs

tag: passages

tag: treated with

value: 5 µM GSK-343 for 72hrs and 10nM panobinostat for 2hrs


title: ECFC_Control_Rep2

value: ECFC clone28 cord5 p4

value: DMSO (control)


title: SHBTU000006CAC

description:
Processed_Data
306


title: ECFC_Drug_Treatment_Rep2


title: H3K4Me1_ChIPseq_PrEC_rep2

city: Darlinghurst

first: Fatima

last: Valdes Mora

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: processed data file: PrEC_ChromHMM.bed.gz

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie (version 1.0.1), allowing up to three mismatches. Non-uniquely alignable reads were excluded.
Peaks were called using PeakRanger (version 1.16) with peak size set to broad and with input control set to a pooled control LNCaP or VCaP input.
Bigwig files were generated using a scaling factor of 1,000,000 reads/library size, average fragment length of 300 and duplicates removed.
ChromHMM v.1.10 was used to simultaneously partition the genome of PrEC and LNCaP cell lines into states. The same approach was employed for the VCaP cell line. Redundant states were then collapsed into seven distinct states and manually annotated by comparison to the published ChromHMM model for HMEC cells.
genome_build = hg19
processed data files format and content: bed file format

source_name: Human cell line

growth_protocol: PrEC cells were growth and maintained in  PrEGM media (Cambrex) at 37ºC with 5% CO2; LNCaP cells were growth and maintained in T-medium (Gibco) and 10% fetal bovine serum (FBS)  at 37ºC with 5% CO2. When reached 70-80% confluence cell were fixed with 1% formaldehyde for 10 min at room temperature.

extract_protocol: ChIP assays were carried out according to the manufacturer's protocol (Upstate Biotechnology). Briefly, ~ 2 x 10^6 cells were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C. The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibodies specific for Histone H2AZ (Active motif # 39113), acetylated Histone H2AZ (Abcam #ab18262), H3K4Me1 (Active Motif #39297), H3K27ac (Active Motif #39133), H3K9K14ac (Millipore #06-599.) and H3K36Me3 (Abcam ab9050-100). Ten ul of antibody was used for each immunoprecipitation. No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 ul H2O.

treatment_protocol: Human LNCaP or VCaP prostate cancer cells and were maintained in RPMI Medium 1640 (Gibco), or DMEM media 11995 (Gibco), respectively, and supplemented with 10% fetal bovine serum (FBS) for at least 72 hrs to 70-80% confluence. LNCaP cell were then seeded to 2.5x106 cell per 15cm dish and starved for 3 days in RPMI Medium 1640-no-phenol red (Gibco)  and 5% chracoal stripped FBS (CSFBS). Then LNCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 2h, 4h and 16h.  VCaP cell were then seeded to 2.5x106 cell per 15cm dish and starved for 3 days in DMEM media 11995 (Gibco)  and 2.5% chracoal stripped FBS (CSFBS). Then VCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 16h. Cells were then fixed with 1% formaldehyde for 10 min at room temperature.

value: Primary prostate epithelial cells. Cambrex Bio Science Cat. No. CC-2556

tag: passage number

tag: chip antibody

value: Active Motif Cat #39297


title: SHBPL000004CAC

description:
cell free DNA
Processed_Data
232


title: SHBPL000003CAC

description:
cell free DNA
Processed_Data
231


title: H3K9K14ac_ChIPseq_LNCaP

description: processed data file: LNCaP_ChromHMM.bed.gz

value: LNCaP clone FGC (ATCC CRL-1740). Androgen-sensitive human prostate adenocarcinoma cells

value: Millipore #06-599.


title: GM06990 ChIP-Seq Input

city: Thousand Oaks

first: Xianglong

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

data_processing:
ChIP-seq data: Reads were aligned to hg19 with BWA-MEM (version 0.7.5a-r405) using default parameters. Reads with low mapping quality (< 30) were removed. PCR duplicate reads were removed using Picard (version 1.100). For CTCF and H3K27ac, we used MACS2 (version 2.1.0.20150420) to call narrow peaks with default parameters. For H3K27me3, we used the broad peak calling in MACS2. For all peak calling, we used the corresponding whole-cell extract input library as background. For differential bound analysis, we used the R package diffBind (version 1.16.1) with the effective library size for read counts normalization. Then DBA_DESEQ2 method was employed to conduct the differential bound analysis.
genome build: hg19
processed data files format and content: ChIP-Seq data — chromosome name, start position of peak, end position of peak, length of peak region, absolute peak summit position, pileup height at peak summit, fold enrichment for this peak summit against random Poisson distribution with local lambda, integer score for display, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start

source_name: lymphoblastoid cell_wild type

extract_protocol:
Per chromatin immunoprecipitation (ChIP) 2 x 107 LCLs were crosslinked in 1% formaldehyde for 10 min at room temperature. The reaction was stopped by adding glycine to a final concentration of 0.125M and stirring for 5 min at room temperature. The cells were pelleted and washed with 1xPBS plus protease inhibitors to remove the crosslinking reagent. The cells were pelleted again and stored at minus 80 degrees until further use. On the day of the immunoprecipiation, the pellets were thawed and washed with 1xPBS plus Protease Inhibitors. The cells were pelleted and exposed to hypotonic buffer and broken with a Dounce homogenizer. The cell nuclei were pelleted and lysed in RIPA buffer. Chromatin was prepared using a Branson 250 Sonifier (7x 30 sec, 100% duty cycle). During the procedure the lysate was kept cold at all times.
A sample of the chromatin lysate was set aside as Input control. The rest of the chromatin lysate was used in the ChIP experiment using the following antibodies against H3K27Ac (Abcam ab4729), H2K27me3 (Cell Signaling 9733), and CTCF (Millipore 07-729). Control IgG from the corresponding species was used as negative control. The Chromatin-antibody complexes were pulled down using Protein G Dynabeads (Life Technologies). The isolated DNA was purified and tested for successful enrichment using quantitative PCR against known loci. Illumina sequencing libraries were prepared using Illumina TruSeq adapters and the enzymes specified in 2. Libraries of the size range of 350 to 650 bp were excised from an agarose gel and cleaned up using the Qiagen gel extraction kit. Libraries were PCR amplified for 14 cycles. Four to fives libraries were pooled on one HiSeq2000 lane and sequenced using 2x100 bp.

tag: cell line

value: lymphoblastoid cell

tag: genotype

value: wild type


title: GM17942 ChIP-Seq Input

source_name: lymphoblastoid cell_22q11del


title: ID00016 ChIP-Seq CTCF


title: ID00016 ChIP-Seq Input


title: H3K9K14ac_ChIPseq_PrEC


title: SHBPL000007CAC

description:
cell free DNA
Processed_Data
235


title: ID00014 ChIP-Seq CTCF


title: ECFC_Drug_Treatment_Rep1

value: ECFC clone28 cord5 p3


title: ID00015 ChIP-Seq Input rep1


title: ECFC_Control_Rep3


title: ID00014 ChIP-Seq Input


title: H3K27ac_ChIPseq_PrEC

value: Active Motif Cat #39133


title: GM12878 ChIP-Seq Input


title: ECFC_Control_Rep1


title: ID00015 ChIP-Seq CTCF


title: GM12878 ChIP-Seq CTCF rep2


title: ID00015 ChIP-Seq H3K27ac


title: GM17942 ChIP-Seq CTCF rep1


title: ID00014 ChIP-Seq H3K27ac


title: GM12878 ChIP-Seq CTCF rep1


title: GM06990 ChIP-Seq H3K27ac


title: ID00016 ChIP-Seq H3K27ac rep2


title: ID00016 ChIP-Seq H3K27ac rep1


title: GM17942 ChIP-Seq H3K27ac rep1


title: ID00015 ChIP-Seq Input rep2


title: ID00016 ChIP-Seq H3K27me3 rep2


title: GM12878 ChIP-Seq H3K27ac rep2


title: GM06990 ChIP-Seq H3K27me3


title: GM17942 ChIP-Seq H3K27ac rep2


title: GM12878 ChIP-Seq H3K27ac rep1


title: ID00016 ChIP-Seq H3K27me3 rep1


title: ID00016 RNA-Seq

data_processing:
RNA-Seq data: Reads were mapped to hg19 and transcriptome reference with TopHat 2 (version 2.0.9). TopHat 2 was run using default parameters but with the coverage search being turned off. The mapped reads were analyzed by Cufflinks (version 2.1.1). Differential expression was estimated with Cuffdiff (version 2.1.1).
genome build: hg19
processed data files format and content: RNA-Seq data — gene tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: GM17942 ChIP-Seq CTCF rep2


title: ID00014 ChIP-Seq H3K27me3


title: ID00014 RNA-Seq


title: GM12878 RNA-Seq


title: ID00015 ChIP-Seq H3K27me3


title: GM17938 RNA-Seq


title: GM12892 RNA-Seq


title: GM07939 RNA-Seq


title: GM17942 ChIP-Seq H3K27me3 rep2


title: GM12878 ChIP-Seq H3K27me3 rep1


title: GM19239 RNA-Seq


title: GM17942 ChIP-Seq H3K27me3 rep1


title: GM10847 RNA-Seq


title: ID00015 RNA-Seq


title: 82699 Hi-C

description: The file "500000.cbins.txt" is the bin index for all Hi-C samples. This file is available on the series record.

data_processing:
Library strategy: Hi-C
Hi-C data: As there might be ligation junctions in the reads, iterative mapping was performed using bowtie2 (version 2.1.0). Briefly, we cut all the reads to 25 bp first and mapped them to human genome. Then we extended the non-uniquely mapped reads by 5 bp to 30 bp and mapped them again. This process was repeated until the read length was extended to 101 bp. Each read end was mapped separately using single ends mode. Only uniquely mapping reads were used and PCR duplicate read pairs were removed. Hicpipe (version 0.9) was used to do the normalization.
genome build: hg19
processed data files format and content: Hi-C data — *contact.txt columns: bin1, bin2, expected count, observed count; 500000.cbins.txt column: bin number, chromosome, bin start, bin end, count.

source_name: lymphoblastoid cell_1q21del

extract_protocol:
Five million cells were spun down and resuspended in 9 ml fresh medium. Cells were fixed by adding 0.25 ml 37% formaldehyde and incubating for 10 minutes at room temperature. Phenol-chloroform was used to extract DNA
Cells were crosslinked by adding 0.25 ml 37% formaldehyde followed by cell lysis and chromatin digestion. DNA ends were filled in and ligated. After purifying the ligated DNA fragments, DNA was sheared to a size of 300-800 base pairs. Then biotin pulled-down DNA was submitted to paired end sequencing.


title: GM19238 RNA-Seq


title: GM18505 RNA-Seq


title: GM17938 Hi-C


title: GM12878 ChIP-Seq H3K27me3 rep2


title: GM18505 Hi-C


title: GM17942 RNA-Seq


title: GM10847 Hi-C


title: GM06990 RNA-Seq


title: GM07939 Hi-C


title: ID00016 Hi-C


title: 52425 Hi-C


title: GM12892 Hi-C


title: H2AZac_ChIPseq_LNCaP_16H_DHT

value: Abcam Cat #ab18262


title: H2AZac_ChIPseq_LNCaP_2H_DHT


title: GM06990 Hi-C


title: ID00015 Hi-C


title: H2AZac_ChIPseq_LNCaP_ETOH


title: GM19240 RNA-Seq


title: H2AZac_ChIPseq_LNCaP_rep1


title: Input DNA_LNCaP_rep1

value: none (input)


title: Input DNA_PrEC_rep2


title: H3K27me3_UT

city: Berlin

first: Tommaso

last: Mari

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück-Centrum für Molekulare Medizin

description:
RAW264.7_UT_27_segments.bed
RAW264.7_1h_27_segments.bed
RAW264.7_4h_27_segments.bed

data_processing:
Reads were mapped to the mm9 mouse reference genome using Bowtie 1.0.1 (PMID: 19261174). Reads from Pu.1 ChIP were aligned with paramenters -v3 -m10 -a --best --strata; reads from histone PTMs ChIP were aligned with parameters -v3 -m1 -a --best --strata
Peak calling was performed using MACS2 (PMID: 18798982): Pu.1 peaks were called with standard paramenters with the addition of --call-summits, histone PTMs peaks were called with standard paramenters with the addition of the --broad option
Aligned reads from histone PTMs ChIPs were used to generate a cromatin state model using ChromHMM (PMID: 22373907). First, aligned reads were binarized using the BinarizeBam function with standard paramenters; then binarized files were used to generate the chromatin state model using standard parameters. In each analysis models up to 30 states were evaluated and we chose the model with the maximum number of non-redundant states.
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.narrowPeak: list of Pu.1 peaks called by MACS2; *_peaks.broadPeak:list of hPTM peaks called by MACS; *.bw: bigwig files; *_segments.bed: segmentation file of the Chromatin state models generated by ChromHMM.

organism: Mus musculus

extract_protocol:
Approximately 10x106 of untreated or stimulated (1h and 4h with LPS, with or without 1h pre-treatment with flavopiridol) RAW cells were used for each experiment. Cells were crosslinked with 0.75% formaldehyde for 10 min at RT and chromatin was sonicated as described previously (Soldi et. Al, 2013). Each chromatin input was immunoprecipitated with 10 g of antibody. beads were washed in Buffer A (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 0.1% SDS, 1% Triton-100, 150 mM NaCl), Buffer B (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 0.1% SDS, 1% Triton-100, 300 mM NaCl) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and de-crosslinked overnight at 65°C. DNA was then purified by Qiaquick columns (QIAGEN) and quantified with Picogreen.
Library preparation for Illumina sequencing (HiSeq 2000) was carried out using a described protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013). The purified DNA libraries were quantified both with a 2100 Bioanalyzer (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 10 nM.

treatment_protocol: Cells were either untreated, or treated for 1 hr or 4 hrs with LPS (100 ng/ml), with or without a 1h pre-treatment with flavopiridol

value: macrophage; Abelson murine leukemia virus transformed

tag: treatment

value: untreated

tag: antibody

value: H3K27me3 (Cell Signaling 9733)


title: H3K27me3_LPS_1h

value: 1 hour LPS


title: ID00014 Hi-C


title: H3K4me1_LPS_4h_FL

value: pretreatment 1h flavopiridol + 4 hour LPS

value: H3K4me1 (Abcam 8895)


title: Input DNA_PrEC_rep1


title: H2AZac_ChIPseq_LNCaP_4H_DHT


title: H2AZac_ChIPseq_PrEC_rep1


title: Kidney_KD_Ketogenic5

city: San Francisco

first: John

middle: C

last: Newman

address: 1650 Owens Street

department: Geriatrics

institute: UCSF

description:
Kidney_RNAseq_summary.xlsx
KD.14_mm9.chr_q30.bam   Kidney_KD_Ketogenic5

data_processing:
The resulting single-end 50 base pair reads were trimmed of adaptors and low-quality reads using Fastq-mcf, then aligned to mouse reference sequences using TopHat 2.0.11 software. This resulted in approximately 40 million aligned reads per sample. For the liver data set, we excluded genes with <500 reads in total, and the software USeq DefinedRegionDifferentialSeq was used both to tally up per-gene counts, normalize these counts, and compute differential expression based using a negative binomial distribution for gene expression performed by DEseq version 1. For the kidney data set, per-gene counts were arrived at using Subread FeatureCounts, and then edgeR was used to both normalize the counts as CPM (counts per million) and to compute differential expression between samples. In this dataset, we excluding genes that did not have at least two samples (of 18) with initial CPM between 0.5 and 5. For both data sets, false discovery rate was calculated using the Benjamini-Hochberg method. The criteria for selection of a list of differentially expressed genes for use in subsequent pathway analysis included P=0.02 and Log2FC>0.379 (fold change>30%), which generated lists of several hundred genes per comparison. These criteria were chosen based on 1) the biological plausibility of the genes that met these criteria, including those previously confirmed as regulated by KD via Q-PCR; 2) the expectation from prior published work that KD or HF diet should alter the expression of hundreds or thousands of genes in the liver; and 3) to provide adequate power for pathway analysis while accepting caution in interpreting any individual gene. Our biological interpretation of the RNAseq data is based solely on list/pathway analysis, which is robust to uncertainties in individual genes.
Genome_build: mm9
Supplementary_files_format_and_content: These Excel files contain gene annotations, raw and processed transcript counts, and differential expression calculations for all samples of a given tissue.

source_name: Kidney

extract_protocol:
Tissues were homogenized in RNeasy buffer RLT using a using a handheld rotary homogenizer. RNA isolation proceeded using the RNeasy Mini kit (Qiagen) per the manufacturer’s protocol. The Gladstone Institutes Genomics Core carried out the downstream processing of the RNA samples. RNA integrity and concentrations were confirmed with an Agilent Bioanalyzer.
Libraries were constructed beginning with cDNA synthesis and amplification using Ovation RNAseq System V2 (NuGesn). This system features chimeric primers for first-strand synthesis with a unique 5’ RNA sequence and 3’ random hexamer or poly-T DNA, and single primer isothermal amplification of the resulting cDNA. A library is created from the amplified cDNA using the Ovation Ultralow DR Multiplex System (NuGen), then analyzed for quality via Bioanalyzer, and quantified by quantitative PCR (KAPA). Next-generation sequencing is done with a HiSeq 2000 (Illumina), with the 18 barcoded samples run in pools over 4 lanes in total. The total yield per sample varied from approximately 1500 to 3000 megabases.

treatment_protocol: Tissues were collected immediately upon euthanasia and snap-frozen in liquid nitrogen, then transferred to -80 degC for storage. Frozen tissue samples were stabilized in RNAlater-ICE (Qiagen) prior to homogenization.

tag: strain

value: C57BL/6 NIA

value: 12 months

tag: Sex

value: male

tag: diet

value: Ketogenic (10% protein, 90% fat by kcal)

value: Night (midnight-3am)


title: Kidney_KD_Ketogenic3

description:
Kidney_RNAseq_summary.xlsx
KD.10_mm9.chr_q30.bam   Kidney_KD_Ketogenic3

tag: age


title: GM12878 Hi-C

value: lymphoblastoid cell


title: Kidney_KD_Ketogenic0

description:
Kidney_RNAseq_summary.xlsx
KD.02_mm9.chr_q30.bam   Kidney_KD_Ketogenic0


title: Kidney_KD_Ketogenic1

description:
Kidney_RNAseq_summary.xlsx
KD.05_mm9.chr_q30.bam   Kidney_KD_Ketogenic1


title: Kidney_HF_High_Fat5

description:
Kidney_RNAseq_summary.xlsx
HF.18_mm9.chr_q30.bam   Kidney_HF_High_Fat5

value: High fat (10% protein, 75% fat, 10% carbohydrate by kcal)


title: JSL

city: Guanzhou

first: Jianrong

last: Lin

state: Guandong

address: WuShan

country: China

institute: South China Agricultural University

description: Small RNA-Seq

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, with ployA/T/G/C and masked for low-complexity or low-quality sequence, then mapped to Bombyx mori whole genome using bowtie v1.0.0.
Transcripts per million (TPM) were calculated using a protocol from Friedländer MR et al., Nucleic Acids Research. 2012.
Genome_build: ASM15162v1
Supplementary_files_format_and_content: *readcount.txt: Tab-delimited text files include read counts and TPM values for each Sample.

organism: Bombyx mori

source_name: HCl treatment eggs

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (cat#RS200-0036) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: egg

value: post-spawned day 4

tag: condition

value: HCl treatment


title: GM17942 Hi-C


title: Input DNA_LNCaP_rep2

value: LNCaP clone FGC (ATCC CRL-1740). Androgen-sensitive human prostate adenocarcinoma cells

value: none (input)


title: Kidney_HF_High_Fat2

description:
Kidney_RNAseq_summary.xlsx
HF.09_mm9.chr_q30.bam   Kidney_HF_High_Fat2


title: Kidney_KD_Ketogenic6

description:
Kidney_RNAseq_summary.xlsx
KD.17_mm9.chr_q30.bam   Kidney_KD_Ketogenic6


title: H3K27me3_LPS_4h

value: macrophage; Abelson murine leukemia virus transformed

value: 4 hour LPS


title: Kidney_KD_Ketogenic4

description:
Kidney_RNAseq_summary.xlsx
KD.11_mm9.chr_q30.bam   Kidney_KD_Ketogenic4


title: Kidney_KD_Ketogenic2

description:
Kidney_RNAseq_summary.xlsx
KD.08_mm9.chr_q30.bam   Kidney_KD_Ketogenic2


title: H3K4me1_UT_FL

value: pretreatment 1h flavopiridol


title: Kidney_Control_Diet4

description:
Kidney_RNAseq_summary.xlsx
Con.16_mm9.chr_q30.bam  Kidney_Control_Diet4

value: Control (10% protein, 12% fat, 78% carbohydrate by kcal)


title: PrEC_NOMe

data_processing:
Raw read pairs were aligned to the human genome (hg19) using bwa-meth, a bisulfite aware wrapper for the bwa-mem aligner.
Read pairs with identical strand, start and end positions were considered PCR duplicates and removed from downstream analysis using MarkDuplicates from the Picard toolset.
BisSNP v0.82.2 was then used to extract the methylation status of each WCG and GCH  site in each sample which was then transformed into a "bigTable" of counts of methylation and coverage.
Nucleosome deplete regions (NDRs) were detected using the findNDRs function of the aaRon R package https://github.com/astatham/aaRon
NDRs were detected by a 100bp sliding window in 20bp increments chi-squared test of GCH methylation versus the genome background with a p-value cutoff of -log10(p)>15,
significant windows overlapped and retained if a minimum 140bp in size.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: NDR bed files contain the -log10 pvalue in the name field (4th column)

growth_protocol: PrEC cells were growth and maintained in  PrEGM media (Cambrex) at 37ºC with 5% CO2; LNCaP cells were growth and maintained in T-medium (Gibco) and 10% fetal bovine serum (FBS)  at 37ºC with 5% CO2. When reached 70-80% confluence cell were harvested for nuclei extraction.

extract_protocol:
Cells were trypsinized and centrifuged for 7 mins at 1000rpm, then washed in ice-cold PBS and resuspended in 1mL ice-cold Nuclei Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA and 1% IGEPAL, plus protease inhibitors) per 5x106 cells and incubated on ice for 10 min. To obtain the nuclei, cells were dounce-homogenized for 15 times and incubated on ice for about 45 min, until single nuclei were visualized under the microscope. Nuclei were recovered by centrifugation at 3000 rpm for 5 min and washed in Nuclei Wash Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1mM EDTA containing protease inhibitors). Freshly prepared nuclei (2x105 cells) were resuspended in 1X M.CviPI reaction buffer (NEB), then treated with 150U of M.CviPI (NEB; 50,000U/mL) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20mM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
50ng of genomic DNA was bisulfite converted using the EZ DNA Methylation Gold kit (Zymo Research, Cat: D5005) following the manufacturer’s protocol. The bisulfite converted DNA was then subjected to library preparation using the EpiCenter kit (now known as the EpiGnome library preparation kit or TruSeq DNA Methylation kit, Illumina, Cat: EGMK81312). In this “post bisulfite conversion” library preparation method, single stranded bisulfite converted DNA was randomly primed to synthesize DNA strands with a specific sequence tag followed by 3’ tagging and PCR amplification using the FailSafe PCR enzyme (Gene Target Solutions,Cat: FSE51100). The PCR was performed for 10 cycles followed by purification using Agencourt AMPure XP beads (Beckman Coulter, Cat: A63881). The purified library was eluted in a final volume of 20ul pure water. Quality of the library obtained was checked using the DNA High sensitivity chip on the Agilent Bioanalyzer. The library was quantified using Qubit and KAPA Biosystems Library quantification kit according to manufacturer’s instructions.

treatment_protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS),  for at least 72 hrs to 70-80% confluence. LNCaP cell were then seeded to 2.5x106 cell per 15cm dish and starved for 3 days in RPMI Medium 1640-no-phenol red (Gibco)  and 5% chracoal stripped FBS (CSFBS). Then LNCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 2h, 4h and 16h. Cells were harvested for nuclei extraction.

value: Primary prostate epithelial cells. Cambrex Bio Science Cat. No. CC-2555


title: LNCaP_NOMe


title: Kidney_Control_Diet0

description:
Kidney_RNAseq_summary.xlsx
Con.01_mm9.chr_q30.bam  Kidney_Control_Diet0

value: C57BL/6 NIA


title: Kidney_Control_Diet1

description:
Kidney_RNAseq_summary.xlsx
Con.04_mm9.chr_q30.bam  Kidney_Control_Diet1

value: 12 months


title: Kidney_HF_High_Fat4

description:
Kidney_RNAseq_summary.xlsx
HF.15_mm9.chr_q30.bam   Kidney_HF_High_Fat4

value: male


title: ZYL

description: Small RNA-Seq

source_name: diapause eggs

tag: tissue

value: diapause


title: Kidney_HF_High_Fat1

description:
Kidney_RNAseq_summary.xlsx
HF.06_mm9.chr_q30.bam   Kidney_HF_High_Fat1

value: Night (midnight-3am)


title: Liver_KD_Ketogenic3

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic3

source_name: Liver

value: Ketogenic (10% protein, 90% fat by kcal)


title: Kidney_HF_High_Fat0

description:
Kidney_RNAseq_summary.xlsx
HF.03_mm9.chr_q30.bam   Kidney_HF_High_Fat0

value: High fat (10% protein, 75% fat, 10% carbohydrate by kcal)


title: Kidney_HF_High_Fat3

description:
Kidney_RNAseq_summary.xlsx
HF.12_mm9.chr_q30.bam   Kidney_HF_High_Fat3


title: Kidney_Control_Diet2

description:
Kidney_RNAseq_summary.xlsx
Con.07_mm9.chr_q30.bam  Kidney_Control_Diet2


title: Liver_KD_Ketogenic4

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic4


title: H3K36me2_UT_FL


title: Kidney_Control_Diet3

description:
Kidney_RNAseq_summary.xlsx
Con.13_mm9.chr_q30.bam  Kidney_Control_Diet3


title: Liver_HF_High_Fat5

description:
Liver_RNAseq_summary.xlsx
Liver_HF_High_Fat5


title: Liver_KD_Ketogenic6

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic6


title: Liver_HF_High_Fat0

description:
Liver_RNAseq_summary.xlsx
Liver_HF_High_Fat0


title: Liver_HF_High_Fat1

description:
Liver_RNAseq_summary.xlsx
Liver_HF_High_Fat1


title: Liver_Control_Diet4

description:
Liver_RNAseq_summary.xlsx
Liver_Control_Diet4


title: Liver_HF_High_Fat2

description:
Liver_RNAseq_summary.xlsx
Liver_HF_High_Fat2


title: Liver_HF_High_Fat4

description:
Liver_RNAseq_summary.xlsx
Liver_HF_High_Fat4


title: H3K36me2_LPS_4h_FL

value: pretreatment 1h flavopiridol + 4 hour LPS


title: Liver_KD_Ketogenic2

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic2


title: Liver_KD_Ketogenic1

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic1


title: Liver_HF_High_Fat3

description:
Liver_RNAseq_summary.xlsx
Liver_HF_High_Fat3


title: Liver_Control_Diet1

description:
Liver_RNAseq_summary.xlsx
Liver_Control_Diet1


title: Liver_Control_Diet2

description:
Liver_RNAseq_summary.xlsx
Liver_Control_Diet2


title: Liver_Control_Diet3

description:
Liver_RNAseq_summary.xlsx
Liver_Control_Diet3


title: C127 Input rep2

city: Oxford

first: Vincenzo

last: Di Cerbo

address: South Parks Road

country: United Kingdom

institute: University of Oxford

data_processing:
Single-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Peakcalling was performed with MACS2 using  samples in biological triplicate and input control as background.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files representing genome coverage of input and ChIP samples. Interval file with peak set for H3K4me3 in C127 cells.

source_name: Mouse mammary epithelial cell line

growth_protocol: Mouse C127 cells were grown at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Biosera) and 1x penicillin-streptomycin solution (Gibco).

extract_protocol:
H3K4me3 ChIP was performed by crosslinking cells in PBS with 1% formaldehyde for 15 min at 25˚C and was quenched with 150 mM glycine. For CFP1, KDM2B and RNAPII ChIP-seq, cells were fixed with 2 µM EGS for 1 h prior to the formaldehyde crosslinking. All ChIP-sequencing experiments were carried out as at least biological duplicate. Crosslinked cells were incubated in lysis buffer (50 mM HEPES KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA,10% Glycerol, 0.5% NP40, 0.25% TritonX-100) for 10 minutes at 4˚C. The released nuclei were then washed (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 minutes at 4˚C. Chromatin was resuspended (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), and sonicated for 50 min using a BioRuptor sonicator (Diagenode), shearing genomic DNA into 0.5–1 kb fragments. After sonication, TritonX-100 was added to a final concentration of 1.5%. Following centrifugation at 19000 g for 10 min at 4˚C, the supernatant containing soluble chromatin was isolated from the insoluble fraction. The relevant  antibodies were incubated with 750 µl of ProteinA Dynabeads (Novex) in PBS/BSA 0.5% rotating at 4˚C for 4 h. The beads were then washed three times in PBS/BSA 0.5%, to remove unbound antibody. Prior to immunoprecipitation, chromatin was diluted (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% TritonX-100) 10-fold (or 50-fold for H3K4me3). Immunoprecipitations were performed using 1 ml of diluted chromatin per 25 µl of antibody coated beads, and rotated overnight at 4˚C. This is equivalent to 5x10^6 cells (or 1x10^6 for H3K4me3 ChIP).  The IP was then washed one time with each of the following buffers: low salt buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 1% Triton X-100, 2 mM EDTA, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8, 500 mM NaCl, 1% Triton X-100, 2 mM EDTA, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8, 0.25 M LiCl, 1% NP-40, 1 mM EDTA, 1% Na-deoxycholate), followed by two washes with TE buffer. Elution was performed in 100 µl of elution buffer (100 mM NaCO3, 0.1% SDS) by vigorous shaking for 30 min at 30°C. Crosslinks were reversed by the addition of 4 µl of 5M NaCl and 2 µl of 500 µg/ml RNaseA (Roche) at 65˚C followed by incubation at 42˚C for 1.5 h with 1 µl of 20 mg/ml proteinaseK. ChIP DNA was purified ChIP DNA Clean & Concentrator kit (Zymo Research).
ChIP-seq libraries were generated as described previously (Blackledge et al., 2010) by the High-Throughput Sequencing centre at the Wellcome Trust Centre for Human Genetics (Oxford, United Kingdom) according to standard Illumina library generation protocol.

tag: replicate


title: Liver_Control_Diet0

description:
Liver_RNAseq_summary.xlsx
Liver_Control_Diet0


title: P0_NPD28

city: Philadelphia

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

institute: University of Pennsylvania

data_processing:
Illumina Casava-1.8.2 software was used for basecalling. Fastq files were generated from base calls using Illumina software bcl2fastq.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software (version 2.0.4) was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Sequences were mapped to GRCm38.p3 using STAR v2.4.0j with default parameters.
Reads mapping uniquely to genomic features as annotated in gencode version M4 were counted using htseq-count.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: text files for raw counts per sample

source_name: nucleus pulposus

extract_protocol:
Euthanasia of embryos and pups at each age was achieved via cervical dislocation followed by tracheotomy. Following euthanasia, for E12.5 embryos, whole, intact notochords were harvested under a dissecting microscope, any extraneous adjoining tissue carefully removed, immediately placed into TRIzol (Ambion; Austin, TX) and frozen. For P0 pups, anterior vertebral columns were harvested, and each disc space in the lumbar and thoracic regions was carefully bisected axially under a dissecting microscope on ice to expose the NPs. Gentle mechanical agitation in PBS buffer with 25 mM HEPES and 0.1% BSA to minimize cell stickiness was then used to dissociate NP cells from the surrounding tissue, and the resulting cell mixture was strained through a 50 µm mesh filter. The collected cells underwent fluorescence assisted cell sorting (FACS) in the PBS buffer described above and YFP-positive NDCs (~10,000-30,000 cells per litter) were collected directly into TRIzol LS (Ambion; Austin, TX) and frozen. RNA was extracted using serial TRIzol-chloroform extractions, then in-column treated with RNase-free DNase (Qiagen; Valencia, CA) on Direct-zol RNA MiniPrep columns (Zymo Research; Irvine, CA) and eluted following the manufacturer’s protocols.
Separate aliquots of extracted RNA samples were stored at -80 °C for either RNA quality analysis or RNA-Seq library preparation in order to reduce the number of freeze-thaw cycles. The quality of each RNA sample was verified using an Agilent BioAnalyzer and RNA 6000 Pico Kit (Santa Clara, CA). Only high quality total RNA (RNA integrity number >7) was used to prepare RNA-Seq libraries. Libraries were prepared using the TotalScript Kit (Illumina; San Diego, CA), which has been optimized for use in synthesizing RNA-Seq libraries from low amounts of total starting RNA (<5 ng).

tag: cell type

value: notochord-derived nucleus pulposus cells

tag: passage

value: primary

value: postnatal day 0


title: Liver_KD_Ketogenic5

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic5


title: P0_NPD30


title: P0_NPD27


title: C127 Input rep1


title: P0_NPD26


title: Liver_KD_Ketogenic0

description:
Liver_RNAseq_summary.xlsx
Liver_KD_Ketogenic0


title: E12.5_NPD4

source_name: notochord

value: notochordal cells

value: embryonic day 12.5


title: C127 GFP-CFP1 SID mut rep2

value: mouse monoclonal antiGFP 3E6, Invitrogen (#A11120)


title: C127 GFP-CFP1 CXXC and PHD mut rep2


title: E12.5_NPD3


title: C127 GFP-CFP1 SID mut rep1


title: C127 RNA PolII CTD rep2

value: 8WG16 Covance


title: E12.5_NDP10.2


title: E12.5_NPD9.2


title: C127 KDM2B rep2

value: In-house


title: C127 GFP-CFP1 PHD mut rep2


title: C127 RNA PolII CTD rep1


title: C127 Endogenous CFP1 rep2


title: C127 GFP-CFP1 CXXC and PHD mut rep1


title: C127 Endogenous CFP1 rep1

description:
C127_CFP1f_MERGED.bw
none


title: H3.3-HA ChIP-seq ES cells 4dRA 8hr DOX

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
ChIP-seq: Mapping using Bowtie to the mouse genome (mm9). Mapping only unique hits with up to 3 mismatches.
RNA-seq: Reads were mapped using TopHat to the mouse genome (mm9), and expression levels were calculated using cufflinks (with default parameters).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Following mapping, reads were extended to length of 500bp and genome-wide read coverage was calculated, normalized to 10M mapped reads per experiment, and saved as bigWig files.
Supplementary_files_format_and_content: RNA-seq:fpkm_tracking

source_name: H3.3-HA ChIP-seq ES cells 4dRA 8hr DOX

growth_protocol: Cells were cultured on gelatinized tissue culture plates in ESC media supplemented with LIF and the 2i inhibitors cocktail (mitogen activated protein kinase (MAPK)/extracellular-signal-regulated kinase (ERK) kinase (MEK) inhibitor PD0325901 and the glycogen synthase kinase 3 (GSK3) inhibitor CHIR99021). This media was shown to maintain mES cell self-renewal without the addition of exogenous factors. hygromycin b was also added as selection against loss of the HA-H3.3 construct for several passages.

extract_protocol:
ChIP-seq: was performed as described in Schlesinger and Goff, 2013. In short, cells from different time points after dox addition, with and without 4 days retinoic acid (4dRA) treatment, were collected and fixed. IP was done using Magna ChIP kit (Millipore) and DNA was purified using QIAquick PCR purification kit (Qiagen). ChIP Grade HA tag antibody was used (ab9110 from Abcam).
3'-end RNA-seq: Extraction, library preparation and sequencing was done using the RNesay kit (Qiagen) according to the manufacturer’s instructions, library preparation was done with QuantSeq 3′ mRNA-Seq Library Prep Kit by Lexogen.  Four RNA libraries were prepared: from ESCs and 4dRA cells without or with 4h Dox addition. Libraries were subjected to single-end sequencing using Illumina Next-Seq 500 platform.
ChIP-seq: Libraries were prepared as previously described (Blecher-Gonen et al., 2013).

treatment_protocol: For retinoic acid (RA) induced differentiation, cells were grown on gelatin-coated dishes for 4 days in ESC media with 1µM RA.

value: mESC 4dRA

value: HA antibody (ab9110 from Abcam)


title: C127 GFP-CFP1 PHD mut rep1


title: C127 GFP-CFP1 CXXC mut rep2


title: H3.3-HA ChIP-seq ES cells 8hr DOX

source_name: H3.3-HA ChIP-seq ES cells 8hr DOX

value: mESC


title: C127 GFP-CFP1 CXXC mut rep1


title: H3.3-HA ChIP-seq ES cells 4hr DOX

source_name: H3.3-HA ChIP-seq ES cells 4hr DOX


title: C127 GFP-CFP1 wt rep1


title: Batch8 (BC-PCR)

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
The read reading out the internal barcode was trimmed after 32nt. The internal barcode was assigned to a defined well via the experimental indices. A valid assignment required a minimal count of 3 per coordinate and a minimal fraction of 0.75 over alternative coordinates.  The internal barcodes were merged with the corresponding iPCR data if its count was higher than 20. This strategy was also used to verify the existing coordinates and uncover missing coordinates and/or additional integrations.
library strategy: BC-PCR
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is available in a database accessible through www.haplobank.at

source_name: embryonic stem cells

growth_protocol: see www.haplobank.at

extract_protocol:
see www.haplobank.at
see www.haplobank.at

treatment_protocol: see www.haplobank.at

value: embryonic stem cells

tag: tag

value: 4D pooling

tag: mutagen

value: Retro-EGT

tag: sequencing strategy

tag: library strategy

value: BC-PCR


title: C127 GFP-CFP1 wt rep2

tag: cell line

tag: chip antibody


title: C127 GFP rep1


title: C127 GFP rep2


title: Batch5 (BC-PCR)


title: Batch4 (BC-PCR)


title: Batch7 (BC-PCR)

value: Lenti-EGT


title: Batch6 (BC-PCR)


title: Batch9 (iPCR)

data_processing:
Based on the restriction enzyme used for genome digestion, the 1st read was cut at the first restriction site. A minimal length of 15nt was required. The sequence was aligned with bowtie against the mm10 genome. A maximum of 1 mismatch (-v 1) was allowed. Only unique alignments (-m 1) in the best strata are reported. The insert site is the 5'-end of the read. For samples of the 5' sequencing strategies, the strand gets changed to its opposite. The 2nd read reading out the internal barcode was trimmed after 32nt. The alignment/internal barcode pairs were assigned to a defined well via the experimental indices. A valid assignment required a minimal count of 3 per coordinate and a minimal fraction of 0.75 over alternative coordinates.  The internal barcodes were merged with the corresponding BC-BCR data if its count was higher than 20. This strategy was also used to verify the existing coordinates and uncover missing coordinates and/or additional integrations. Mapped insertions were intersected with the annotation (Ensemble 76) of all gene features including the intergenic region using BEDtools.
library strategy: inverse PCR
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is available in a database accessible through www.haplobank.at

value: inverse PCR


title: H3.3-HA ChIP-seq ES cells 4dRA 4hr DOX

source_name: H3.3-HA ChIP-seq ES cells 4dRA 4hr DOX


title: Batch3 (BC-PCR)


title: Batch2 (BC-PCR)


title: Batch1 (BC-PCR)


title: P0186_failed

city: Aurora

first: Philip

middle: David

last: Tatman

state: Colorado

department: Department of Pharmacology

institute: University of Colorado

data_processing:
Alignment with Tophat2
Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: fastq

source_name: heart left ventricle

extract_protocol:
mirVana kit
illumina TrueSeq

value: heart left ventricle

tag: diagnosis

value: idiopathic dilated cardiomyopathy


title: C127_BioCAP

description:
C127_BioCAP.bw
C127_NMI_Peaks.bed

data_processing:
For BioCAP and ATAC-seq, paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options and non-uniquely mapping reads were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.  Nascent RNA-seq (4sU-Seq) paired-end reads were initially aligned against rRNA genomic sequence (GenBank: BK000964.3) using bowtie2 to filter out rRNA fragments, prior to alignment against mm10  genome using the STAR RNA-seq aligner (Dobin et al., 2013). To improve mapping of nascent, intronic sequences, reads which failed to map using STAR were aligned against the genome using bowtie2 and reads which mapped more than once were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009).Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Peakcalling of non-methylated islands from BioCAP data was performed using MACS2.  ATAC-seq merged BAM files were used to make a genome tracks using DANPOS2, with the Tn5 control provided as background.  Merged nascent RNA-seq bam files were used to generate genome coverage tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome tracks for data visualisation. Peak file generated from BioCAP data to identify non-methylated island (NMI) intervals.

extract_protocol:
For each individual Bio-CAP experiment, 25 μl of NeutrAvidin Agarose Resin (Thermo Scientific, 29200) was washed with BC100 buffer and then incubated with 50 μl of 0.5 μg/μl biotinylated hKDM2b-CxxC protein diluted in BC100 buffer for 1 h at 4°C. The conjugated resin/CxxC protein was then washed with CAP100 buffer (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 100 mM NaCl). Genomic DNA was sonicated to an average size of 150-250 bp using a Diagenode Bioruptor. Sonicated DNA was then diluted in CAP100 buffer to a concentration of 16 μg/ml and a 100 μl Input sample was retained. For each Bio-CAP experiment, 500 μl of diluted sonicated DNA, corresponding to approximately 8 μg of DNA, was added to the conjugated CxxC resin. The DNA and resin were incubated at 4°C for 1 h with gentle mixing. The resin was then collected by centrifugation at 1500 g for 3 min at 4°C and the unbound flowthrough (FT) material was removed. The resin and any associated DNA was washed twice with 1 ml of CAP100 buffer, before the first elution was performed by adding 50 μl of CAP300 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 300 mM NaCl) to the resin and incubating at room temperature for 10 min. Following centrifugation a 50 μl elution fraction was carefully collected. The elution process was repeated using another 50 μl of CAP300 and the 300 mM elution fractions were pooled (giving a total volume of 100 μl). Subsequent elutions were performed in the same way using buffers with 500 mM, 700 mM and 1 M NaCl sequentially. Each 100 μl elution fraction, together with 100 μl of both the Input and FT samples, was purified using a PCR purification column (Qiagen) and DNA was eluted in a volume of 50 μl. The 700 mM and 1 M fractions were pooled for sequencing. Bio-CAP material was quantified using the High Sensitivity Qubit system (Invitrogen) and the fragmentation profile was assessed using a DNA HS Agilent 2200 TapeStation chip.   Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al., 2013). Briefly, 5 × 10^6 cells were harvested, washed with PBS and nuclei were isolated using 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10mM NaCl, 10mM Tris (pH 7.4), 3mM MgCl2), to remove as much of contaminating cytoplasmic and mitochondrial material as possible. Nuclei were then counted, and 5×10^4 nuclei were resuspended in Tn5 reaction buffer (10mM TAPS, 5mM MgCl2, 10% dimethylformamide) and 2 µl of Tn5 transposase (25 µM) made in house according to the previously described protocol (Picelli et al., 2014). Nuclei were then incubated for 30 min at 37°C, before isolation and purification of tagmented DNA using QiaQuick MinElute columns (Qiagen). To control for sequence bias of the Tn5 transposase, an ATAC “input” sample was generated, by tagmenting genomic DNA from ESCs with Tn5 for 30 min at 55°C.  Nascent RNA sequencing was performed by pulse labelling with 4-thiouridine (4sU) as previously described (Rädle B. et al., 2013). Confluent 15 cm plates were treated with 500 µM 4sU in 10 ml culture medium for 20 min. The 4sU-containing media was then aspirated and immediately replaced with 5 ml TRIZOL (Thermo Fisher Scientific). RNA was isolated by phenol-chloroform extraction using phase lock tubes (Eppendorf) and resuspend in nuclease-free water. Total RNA aliquots were treated with 6U Turbo DNase (Ambion) and incubated at 37°C for 30 min, followed by inactivation of the DNase according to the manufacturer’s instructions. 300 μg of the resulting total RNA were incubated with 2 μg Biotin-HPDP/μg RNA in biotinylation buffer (10 mM Tris-HCl pH 7.4 and 1 mM EDTA) under rotation for 1.5 h at RT. Unincorporated biotin-HPDP was removed by chloroform/isoamylalcohol extraction. To capture biotinylated RNA, μMACS streptavidin beads (Miltenyi) were added to the RNA suspension (1 μl of beads/ μg RNA) and rotated for 15 min at room temperature prior to loading onto μMACS minicolumns. Unlabelled RNA was removed by washing three times with 900 µl of wash buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween20) pre-heated at 65°C, then three more times with wash buffer at room temperature. Biotinylated RNA was then eluted in two rounds with 100 mM DTT and purified using an RNeasy miniElute kit (Qiagen).
BioCAP libraries were generated by the High-Throughput Sequencing centre at the Wellcome Trust Centre for Human Genetics (Oxford, United Kingdom) according to standard Illumina library generation protocol and sequenced on the Illumina HiSeq2000 platform with 51 bp reads.   ATAC-seq libraries were prepared by PCR amplification using custom made Illumina barcodes previously described (Buenrostro et al., 2013) and the NEBNext® High-Fidelity 2X PCR Master Mix. ATAC-seq libraries were sequenced on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.  For RNA-seq library generation, nascent RNA samples were initially depleted of ribosomal RNAs using the Low Input RiboMinus Eukaryote System v2 kit (Thermo Fisher). The recovered rRNA-depleted nascent RNA was used to prepare the cDNA libraries with NEBNext Ultra Directional RNA Library Prep Kit for Illumina and subject to sequencing on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.


title: P0172_control


title: Batch7 (iPCR)


title: H3.3-HA ChIP-seq ES cells 1hr DOX

source_name: H3.3-HA ChIP-seq ES cells 1hr DOX

tag: strain


title: C127_cap.input


title: Batch8 (iPCR)


title: P0168_failed


title: C127 KDM2B rep1


title: Batch5 (iPCR)


title: P0148_failed


title: Batch6 (iPCR)


title: H3K79me2_LPS_4h

description: Segmentation files: RAW264.7_UT_27_segments.bed, RAW264.7_1h_27_segments.bed, RAW264.7_4h_27_segments.bed

data_processing:
Reads were mapped to the mm9 mouse reference genome using Bowtie 1.0.1 (PMID: 19261174). Reads from Pu.1 ChIP were aligned with paramenters -v3 -m10 -a --best --strata; reads from histone PTMs ChIP were aligned with parameters -v3 -m1 -a --best --strata
Peak calling was performed using MACS2 (PMID: 18798982): Pu.1 peaks were called with standard paramenters with the addition of --call-summits, histone PTMs peaks were called with standard paramenters with the addition of the --broad option
Aligned reads from histone PTMs ChIPs were used to generate a cromatin state model using ChromHMM (PMID: 22373907). First, aligned reads were binarized using the BinarizeBam function with standard paramenters; then binarized files were used to generate the chromatin state model using standard parameters. In each analysis models up to 30 states were evaluated and we chose the model with the maximum number of non-redundant states.
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.narrowPeak: list of Pu.1 peaks called by MACS2; *_peaks.broadPeak:list of hPTM peaks called by MACS; *.bw: bigwig files; *_segments.bed: segmentation file of the Chromatin state models generated by ChromHMM. Segmentation files are available on the series record.

extract_protocol:
Approximately 10x10^6 of untreated or stimulated (1h and 4h with LPS) RAW cells were used for each experiment. Cells were crosslinked with 0.75% formaldehyde for 10 min at RT and chromatin was sonicated as described previously (Soldi et. Al, 2013). Each chromatin input was immunoprecipitated with 10 g of antibody. beads were washed in Buffer A (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 0.1% SDS, 1% Triton-100, 150 mM NaCl), Buffer B (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 0.1% SDS, 1% Triton-100, 300 mM NaCl) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and de-crosslinked overnight at 65°C. DNA was then purified by Qiaquick columns (QIAGEN) and quantified with Picogreen.
Library preparation for Illumina sequencing (HiSeq 2000) was carried out using a described protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013). The purified DNA libraries were quantified both with a 2100 Bioanalyzer (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 10 nM.

value: macrophage; Abelson murine leukemia virus transformed

tag: treatment

value: 4 hour LPS

tag: antibody

value: H3K79me2 (Abcam ab3594)


title: H3.3-HA ChIP-seq ES cells 4dRA 1hr DOX

source_name: H3.3-HA ChIP-seq ES cells 4dRA 1hr DOX


title: P0143_control


title: P0111_control


title: H3K27me3 ChIP

data_processing:
The reads are aligned with Bowtie2 (standard parameter).
MACS (1.4) is used for peak calling of ATAC, H3K4me3, H3K27ac. Broad peaks of H3K27me3 are called with SICER (W1000, G3000).
Genome_build: mm10
Supplementary_files_format_and_content: Standard BED files of MACS and SICER

source_name: HapES cells (AN3-12)

growth_protocol: Haploid ES cells were grown in standard ES cell medium with serum and LIF. ES cell medium contains of 450 ml DMEM (Sigma D1152); 75 ml FCS  (Invitrogen); 5,5 ml P/S  (Sigma P0781); 5,5 ml NEAA  (Sigma M7145); 5,5 ml LGlu (Sigma G7513); 5,5 ml NaPyr (Sigma S8636); 0,55 ml bME   Merck 805740 (dilute 10 l bME in 2.85 ml PBS for a 1000x stock); and ESGRO Millipore ESG1107 (according to instructions by the manufacturer).

extract_protocol:
ChIP was essentially performed as described previously (Mohn et al., 2008). Briefly, after trypsinization and quenching 25 million Hap ES cells were washed once in PBS before fixing for 7 min by addition of formaldehyde to a final concentration of 1%. Crosslinking was then quenched by addition of 2.5 M glycine (0.125 M final concentration) and cells were then incubated on ice. Crosslinked cells were spun at 600 3 g for 5 min, nuclei were prepared by consecutive washes with Rinse 1 buffer (final: 50 mM HEPES pH 8.0, 140 mM NaCl, 10% glycerol, 0.5% NP40, 0.25% Triton X100, 1 mM EDTA) followed by Rinse 2 buffer (final: 10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Pellets were resuspended in 2 ml total volume of Sonication buffer (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8 with protease inhibitors complete mini (Roche)) and then sonicated with a Covaris E220 sonicator (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 15 minutes). ChIP was perfomed in ChIP buffer (final: 50 mM HEPES/KOH pH 7.5, 300 mM NaCl , 1 mM EDTA, 1 % Triton X100, 0.1 % DOC, 0.1% SDS) with the indicated antibody.
Illumina NEBNext kit

value: embryonic stem

value: H3K27me3 (Diagenode pAb-069-050)


title: H3K27ac ChIP

data_processing:
The reads are aligned with Bowtie2 (standard parameter) to mm10 and dm3. Only mm10 specific reads are taken for peakcalling.
MACS (1.4) is used for peak calling of ATAC, H3K4me3, H3K27ac. Broad peaks of H3K27me3 are called with SICER (W1000, G3000).
Genome_build: mm10
Supplementary_files_format_and_content: Standard BED files of MACS and SICER

value: H3K27ac (Abcam ab4729)


title: P0079_control


title: total_RNA_UT

data_processing:
Both reads alignment on mm9 reference genome and trascripts per million reads (TPM) quantification were done using RSEM-1.17 (PMID: 21816040) using standard settings for aligment and quantification of paired-end RNA-seq
Genome_build: mm9
Supplementary_files_format_and_content: *gene_abundances: standard RSEM output for TPM quantification at gene level

extract_protocol:
Total RNA was extracted from 5x106 cells using RNAeasy kit (Qiagen).
Libraries were then prepared using TruSeq RNA sample preparation Kit (Illumina) after depleting ribosomal RNA

value: untreated


title: H3K27ac_LPS_4h

value: H3K27ac (Abcam 4729)


title: H3K36me2_LPS_4h


title: SB-polyA

description: mutagen mapping by iPCR

data_processing:
Library strategy: iPCR
The sequence is aligned with bowtie against the mm10 genome. A maximum of 3 mismatches (-v 3) is allowed. Only the unique alignments (-m 1) in the best strata are reported.
The insert site is the 5'-end of the read. For samples of the 5' sequencing strategies, the strand gets changed to its opposite.
Insertions which are only 3bp apart, get merged into blocks. Inserts require a coverage of at least 10.
The insertions are intersected with the UCSC RefSeq annotation of all gene features including the intergenic region using BEDtools.
Genome_build: mm10
Supplementary_files_format_and_content: space separated text (chromosome, 0-based insertion site, strand, count, annotation)

value: SB-polyA


title: H3K4me3_LPS_4h

value: H3K4me3 (Active Motif 39159)


title: Input_LPS_4h


title: P0159_control


title: P0175_fail


title: Input_LPS_1h

value: 1 hour LPS


title: P0166_failed


title: Tol2-EGT

description: mutagen mapping by iPCR

value: embryonic stem cells


title: P0156_control


title: SB-EGT

description: mutagen mapping by iPCR

value: SB-EGT


title: H3K79me2_LPS_1h


title: H3K36me3_LPS_4h


title: P0091_fail


title: P0081_control


title: H3K36me3_LPS_1h


title: H3K36me2_LPS_1h


title: H3K4me3 ChIP

value: H3K4me3 (Millipore 05-745R)


title: P0078_fail


title: H3K4me1_LPS_4h

value: H3K4me1 (Abcam 8895)


title: non-selected strain PM diet muscle biological rep10

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software CASAVA version 1.8.2.
Raw reads were processed for quality control using the Trim Galore! software version 0.4.0. This software was used to trim low-quality ends from reads in addition to Illumina adapter removal. Quality trimming was then specified at phred33.
Sequences after QC were filtered for potential contaminating ribosomal RNAs using the Bowtie2 software version 2.2.5. All Oncorhynchus species rRNAs available in GenBank were used to align against, where unaligned reads were output for further usage. The default Bowtie2 parameters were used.
Bowtie2 version 2.2.5 was used for alignment of reads to the rainbow trout transcriptome using the alignment parameters as recommended by eXpress software version 1.5.1.
Alignment files were piped into the eXpress version  1.5.1 software using the default parameters, but including the strand information, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package in R-Bioconductor Release 3.2.
Genome_build: The rainbow trout transcriptome sequences published from Salem et.al., PLoS One, 2015.
Supplementary_files_format_and_content: tab-delimited text files of effective read counts, rounded to the nearest whole number

organism: Oncorhynchus mykiss

source_name: muscle section dorsal to lateral line

extract_protocol:
Tissue samples were excised, flash-frozen in liquid nitrogen and stored at -80°C until usage. Samples were homogenized using a bead-beater with TRIzol reagent per the manufacturer's recommendation for total RNA isolation.
Total RNA was standardized to 1 µg each sample. DNA was removed using Amplification-grade DNase I from Invitrogen. Ribosomal RNAs were reduced using the Ribo-Zero Gold rRNA Removal Kit from Illumina. Sequencing libraries were then prepared using the ScriptSeq v2 RNA-Seq Library Preparation Kit from Illumina. Barcodes used were Illumina TruSeq indexes 1-12.

value: House Creek

value: muscle

tag: diet

value: PM


title: non-selected strain PM diet muscle biological rep9


title: ATACseq

data_processing:
Library strategy: ATAC-seq
The reads are aligned with Bowtie2 (standard parameter).
MACS (1.4) is used for peak calling of ATAC, H3K4me3, H3K27ac. Broad peaks of H3K27me3 are called with SICER (W1000, G3000).
Genome_build: mm10
Supplementary_files_format_and_content: Standard BED files of MACS and SICER

extract_protocol:
ATACseq was performed similar to protocol by Buenrostro JD et al. (Buenrostro JD et al. Curr. Protoc. Mol. Biol. 109 :1.29.1-21-29.9). Briefly, 50k cells were washed on cold PBS before gentle resuspension in 50 ul of cold lysis buffer (10mMTris-HCl pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). For transposition reaction, nuclei were collected by immediate centrifugation for 15 min at 4 degrees. Supernatant was removed and nuclei were suspended in 50 ul of transposition reaction mixture (25 μl 2x TD buffer (Nextera kit), 2.5 μL TDE1 (Nextera Tn5 Transposes), 22.5 μL nuclease-free water). Transposition reaction was performed at 37 degrees for 30 minutes followed  by DNA purification using Qiagen MinElute Kit.
Illumina NEBNext kit


title: WDHD1_r1881_repl2

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-5. DFilter was run with bs=50, ks=30, refine, nonzero.
Genome_build: hg19

source_name: prostate

growth_protocol: LNCaP cells were cultured in RPMI-1640 supplemented with 10% FBS. Cells were hormone deprived three days before R1881 stimulation.

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Embo Mol Med 2015) For each ChIP, 5-10μg of antibody prebound to protein A or protein G beads was used.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Kapa Biosystems kit,KK8234).

treatment_protocol: Cells were treated with 10nM R1881 or vehicle for 4 hours.

value: Prostate cancer cell line LNCaP

tag: procedure

value: Chromatin IP against WDHD1

value: WDHD1 (m15-104; CDI labs)


title: H3K4me3_LPS_1h

value: macrophage; Abelson murine leukemia virus transformed


title: non-selected strain PM diet muscle biological rep8


title: WDHD1_veh_repl2


title: H3K4me1_LPS_1h


title: Input_UT

description: Segmentation files: RAW264.7_UT_27_segments.bed, RAW264.7_1h_27_segments.bed, RAW264.7_4h_27_segments.bed, and RAW264.7_18_segments.bed


title: WDHD1_veh_repl1


title: non-selected strain PM diet liver biological rep8

source_name: section from whole liver

value: liver


title: WDHD1_r1881_repl1


title: non-selected strain PM diet muscle biological rep7


title: TRIM28_r1881_repl2

value: Chromatin IP against TRIM28

value: TRIM28 (ab10483; Abcam)


title: Pu.1_UT

value: untreated

value: Pu.1 (Santa Cruz sc-352)


title: H3K79me2_UT

value: H3K79me2 (Abcam ab3594)


title: TRIM28_veh_repl2


title: H3K36me3_UT


title: non-selected strain PM diet muscle biological rep6


title: TRIM28_r1881_repl1


title: non-selected strain PM diet liver biological rep7


title: non-selected strain PM diet liver biological rep10


title: H3K27ac_LPS_1h

value: 1 hour LPS

value: H3K27ac (Abcam 4729)


title: non-selected strain PM diet liver biological rep6


title: H3K36me2_UT


title: H3K27ac_UT


title: non-selected strain FM diet muscle biological rep10

value: FM


title: non-selected strain FM diet liver biological rep10


title: H3K4me3_UT

value: H3K4me3 (Active Motif 39159)


title: non-selected strain PM diet liver biological rep9

value: House Creek


title: TLE3_veh_repl2

value: Chromatin IP against TLE3

value: TLE3 (ab94972; Abcam)


title: non-selected strain FM diet muscle biological rep9

value: muscle


title: TLE3_r1881_repl1

value: Prostate cancer cell line LNCaP


title: TLE3_r1881_repl2


title: Nov_2 (BC-PCR)

value: embryonic stem cells

value: 4D pooling

value: BC-PCR


title: HOXB13_r1881_repl3

value: Chromatin IP against HOXB13

value: HOXB13 (sc-66923; Santa Cruz)


title: TLE3_veh_repl1


title: non-selected strain FM diet muscle biological rep8


title: Nov_3 (BC-PCR)


title: non-selected strain FM diet liver biological rep8

value: liver


title: Batch12 (BC-PCR)


title: non-selected strain FM diet muscle biological rep7


title: HOXB13_veh_repl3


title: non-selected strain FM diet liver biological rep7


title: HOXB13_veh_repl2


title: non-selected strain FM diet muscle biological rep6


title: Batch10 (BC-PCR)


title: TRIM28_veh_repl1

value: Chromatin IP against TRIM28

value: TRIM28 (ab10483; Abcam)


title: Batch11 (BC-PCR)


title: non-selected strain FM diet liver biological rep6


title: HOXB13_r1881_repl1


title: HOXB13_veh_repl1


title: Batch9 (BC-PCR)

value: Lenti-EGT


title: H3K4me1_UT

value: macrophage; Abelson murine leukemia virus transformed

value: untreated

value: H3K4me1 (Abcam 8895)


title: Nov_3 (iPCR)

value: inverse PCR


title: non-selected strain FM diet muscle biological rep5

value: House Creek

value: FM


title: non-selected strain FM diet liver biological rep9


title: Nov_2 (iPCR)


title: non-selected strain FM diet liver biological rep5


title: FOXA1_r1881_repl2

value: Chromatin IP against FOXA1

value: FOXA1 (sc-6554; Santa Cruz)


title: FOXA1_veh_repl2

value: Prostate cancer cell line LNCaP


title: Nov_1 (iPCR)

value: embryonic stem cells

value: 4D pooling


title: Batch12 (iPCR)


title: Nov_1 (BC-PCR)

value: BC-PCR


title: non-selected strain FM diet muscle biological rep4

value: muscle


title: Batch11 (iPCR)


title: HOXB13_r1881_repl2

value: Chromatin IP against HOXB13

value: HOXB13 (sc-66923; Santa Cruz)


title: non-selected strain FM diet liver biological rep4

value: liver


title: non-selected strain FM diet muscle biological rep3


title: BRG1_r1881_repl2

value: Chromatin IP against BRG1

value: BRG1 (A300-813A; Bethyl)


title: Batch10 (iPCR)


title: non-selected strain FM diet liver biological rep3


title: BRG1_veh_repl2


title: FOXA1_veh_repl1


title: Batch4 (iPCR)


title: BRG1_r1881_repl1


title: non-selected strain FM diet liver biological rep2


title: Batch2 (iPCR)

value: Retro-EGT


title: ARID1a_r1881_repl2

value: Chromatin IP against ARID1a

value: ARID1a (sc-32761x; Santa Cruz)


title: non-selected strain FM diet muscle biological rep1

value: House Creek


title: Batch1 (iPCR)

value: inverse PCR


title: non-selected strain FM diet muscle biological rep2

value: FM


title: non-selected strain FM diet liver biological rep1


title: BRG1_veh_repl1


title: Batch3 (iPCR)

value: Lenti-EGT


title: ARID1a_veh_repl2

value: Prostate cancer cell line LNCaP


title: RV-A1a screen

description: mutagen mapping by iPCR

value: embryonic stem cells

value: Retrovirus-EGT


title: ARID1a_r1881_repl1


title: Tol2-polyA

description: mutagen mapping by iPCR


title: ARID1a_veh_repl1


title: non-selected strain PM diet liver biological rep5

value: PM


title: non-selected strain PM diet muscle biological rep5

value: muscle


title: AR_veh_repl2

value: Chromatin IP against AR

value: AR (sc-816; Santa Cruz)


title: Lentivirus WPXL

description: mutagen mapping by iPCR

value: Lentivirus WPXL


title: non-selected strain PM diet liver biological rep4

value: liver


title: Piggybac transposon

description: mutagen mapping by iPCR

value: Piggybac transposon


title: non-selected strain PM diet muscle biological rep4


title: non-selected strain PM diet muscle biological rep2


title: non-selected strain PM diet liver biological rep3


title: AR_r1881_repl2


title: Lentivirus-LKO

description: mutagen mapping by iPCR

value: Lentivirus-LKO


title: non-selected strain PM diet muscle biological rep1


title: H2AZ_ChIPseq_PrEC_rep2

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie (version 1.0.1), allowing up to three mismatches. Non-uniquely alignable reads were excluded.
Peaks were called using PeakRanger (version 1.16) with peak size set to broad and with input control set to a pooled control LNCaP or VCaP input.
Bigwig files were generated using a scaling factor of 1,000,000 reads/library size, average fragment length of 300 and duplicates removed.
ChromHMM v.1.10 was used to simultaneously partition the genome of PrEC and LNCaP cell lines into states. The same approach was employed for the VCaP cell line. Redundant states were then collapsed into seven distinct states and manually annotated by comparison to the published ChromHMM model for HMEC cells.
genome_build = hg19
processed data files format and content: bed file format

source_name: Human cell line

extract_protocol: ChIP assays were carried out according to the manufacturer's protocol (Upstate Biotechnology). Briefly, ~ 2 x 10^6 cells were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C. The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibodies specific for Histone H2AZ (Active motif # 39113), acetylated Histone H2AZ (Abcam #ab18262), H3K4Me1 (Active Motif #39297), H3K27ac (Active Motif #39133), H3K9K14ac (Millipore #06-599.) and H3K36Me3 (Abcam ab9050-100). Ten ul of antibody was used for each immunoprecipitation. No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 ul H2O.

value: Primary prostate epithelial cells. Cambrex Bio Science Cat. No. CC-2556

tag: passage number

value: Active Motif Cat #39113


title: LNCaP_NOMe_16hr_1

data_processing:
Raw read pairs were aligned to the human genome (hg19) using bwa-meth, a bisulfite aware wrapper for the bwa-mem aligner.
Read pairs with identical strand, start and end positions were considered PCR duplicates and removed from downstream analysis using MarkDuplicates from the Picard toolset.
BisSNP v0.82.2 was then used to extract the methylation status of each WCG and GCH  site in each sample which was then transformed into a "bigTable" of counts of methylation and coverage.
Nucleosome deplete regions (NDRs) were detected using the findNDRs function of the aaRon R package https://github.com/astatham/aaRon
NDRs were detected by a 100bp sliding window in 20bp increments chi-squared test of GCH methylation versus the genome background with a p-value cutoff of -log10(p)>15,
significant windows overlapped and retained if a minimum 140bp in size.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: NDR bed files contain the -log10 pvalue in the name field (4th column)

value: LNCaP clone FGC (ATCC CRL-1740). Androgen-sensitive human prostate adenocarcinoma cells


title: non-selected strain PM diet liver biological rep2

value: House Creek

tag: tissue


title: Differentiation replicate 5

data_processing:
Reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Mus musculus genome (mm10); a maximum of 6 mismatches were allowed. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC RefSeq mm10). rRNA loci are masked on the genome for downstream analysis. Transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator. The mean FPKM was calculated over the replicates.
Aligned reads were subjected to FPKM measurements with Cufflinks (v1.3.0). Furthermore, only those fragments compatible with UCSC RefSeq annotation (mm10) of genes with at least one protein coding transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator. The mean FPKM was calculated over the replicates.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file (standard Cufflinks output)

extract_protocol:
see www.haplobank.at
Illumina TrueSeq RNA library Prep kit V2

treatment_protocol: RNA was harvested by direct lysis on cell culture dishes using RLT buffer (Qiagen)

tag: lif removal

value: minusLIF 3 days

tag: genotype

value: haploid murine ES cells


title: selected strain FM diet muscle biological rep10

value: ARS-KO

value: FM


title: Differentiation replicate 4


title: LNCaP_NOMe_4hr_2

tag: cell type


title: non-selected strain PM diet liver biological rep1


title: Differentiation replicate 3


title: LNCaP_NOMe_16hr_2


title: selected strain FM diet liver biological rep10


title: H2AZ_ChIPseq_LNCaP_rep2


title: LNCaP_NOMe_4hr_1


title: non-selected strain PM diet muscle biological rep3


title: Lentivirus-EGT

description: mutagen mapping by iPCR

value: embryonic stem cells

value: Lentivirus-EGT


title: Differentiation replicate 2


title: ESC replicate 5

value: ESC medium


title: selected strain FM diet muscle biological rep9

value: muscle


title: LNCaP_NOMe_2hr_2.


title: Retrovirus-GT

description: mutagen mapping by iPCR

value: Retrovirus-GT


title: selected strain FM diet liver biological rep9


title: Retrovirus-EGT

description: mutagen mapping by iPCR

value: Retrovirus-EGT


title: LNCaP_NOMe_2hr_1


title: ESC replicate 4


title: selected strain FM diet muscle biological rep8


title: selected strain FM diet liver biological rep8

value: liver


title: ESC replicate 3


title: ESC replicate 2


title: ESC replicate 1


title: selected strain FM diet liver biological rep7


title: Mdr2+/- Rep 2

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Mdr2+/- Mus musculus sacrificed at Day 10 of life with Total RNA obtained from the Liver, lobe 1

data_processing:
Illumina Hi-Seq 2000
Following trimming of adaptors and barcodes, sequenced reads were aligned to the mm10 genome using TopHat, and quantified in GeneSpring NGS.
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing FPKM, transcript ID, and gene symbol

source_name: Liver, lobe 1

growth_protocol: Mdr2-/- mice were backcrossed into the BALB/c strain.

extract_protocol:
Total RNA was isolated from snap frozen samples from lobe 1 of livers.
RNAseq libraries were prepared with the Illumina TruSeq RNA preparation kit and sequenced on the Illumina Hi-Seq2000.

treatment_protocol: Neonatal mice of different genotypes were kept as littermates and  sacrificed on day 10 of life.

value: BALB/C

tag: time of sacrifice

value: Day 10 of life


title: selected strain FM diet muscle biological rep6


title: Mdr2+/- Rep 1


title: selected strain FM diet liver biological rep6


title: selected strain FM diet muscle biological rep7


title: Mdr2+/+ Rep 2

description: Mdr2+/+ Mus musculus sacrificed at Day 10 of life with Total RNA obtained from the Liver, lobe 1


title: selected strain FM diet muscle biological rep5


title: Differentiation replicate 1


title: selected strain FM diet muscle biological rep4


title: 3T.7 (RNA-seq)

city: Wenzhou

first: Chunming

last: Ding

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

institute: Wenzhou Medical University

data_processing:
paired-end/ single-end 36-base pair (bp) reads were filtered based on qseq score
Reads were the subjected to Illumina RNA-seq pipeline (CASAVA 1.7) for RNA-seq analysis, aligned using Hg19 genome as reference, and all default parameters for alignment
A gene was considered to be differentially expressed between first and third samples when: 1) two-sided Mann Whitney U test p-value less than 0.05; and 2) the ratio of (Average third trimester/Average first trimester) ≥ 2 or ≤0.5.
Genome_build: hg 19
Supplementary_files_format_and_content: Differentially methylated promoters and gene expression (RPKM) between early and late gestational ages

source_name: Third trimester placenta

extract_protocol:
Total RNA was extracted using TRIZOL protocol (Life Technologies). Sequencing library was constructed using Illumina mRNA-Seq Sample Preparation protocol.
Illumina's mRNA-Seq for Gene Expression Analysis

tag: gestational stage

value: Third trimester

value: Placenta


title: Mdr2+/+ Rep 1


title: selected strain FM diet muscle biological rep3


title: 3T.8 (RNA-seq)


title: selected strain FM diet liver biological rep5


title: 3T.6 (RNA-seq)


title: selected strain FM diet liver biological rep3


title: LNCaP_NOMe_EtOH_2

extract_protocol:
Cells were trypsinized and centrifuged for 7 mins at 1000rpm, then washed in ice-cold PBS and resuspended in 1mL ice-cold Nuclei Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA and 1% IGEPAL, plus protease inhibitors) per 5x106 cells and incubated on ice for 10 min. To obtain the nuclei, cells were dounce-homogenized for 15 times and incubated on ice for about 45 min, until single nuclei were visualized under the microscope. Nuclei were recovered by centrifugation at 3000 rpm for 5 min and washed in Nuclei Wash Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1mM EDTA containing protease inhibitors). Freshly prepared nuclei (2x105 cells) were resuspended in 1X M.CviPI reaction buffer (NEB), then treated with 150U of M.CviPI (NEB; 50,000U/mL) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20mM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
50ng of genomic DNA was bisulfite converted using the EZ DNA Methylation Gold kit (Zymo Research, Cat: D5005) following the manufacturer’s protocol. The bisulfite converted DNA was then subjected to library preparation using the EpiCenter kit (now known as the EpiGnome library preparation kit or TruSeq DNA Methylation kit, Illumina, Cat: EGMK81312). In this “post bisulfite conversion” library preparation method, single stranded bisulfite converted DNA was randomly primed to synthesize DNA strands with a specific sequence tag followed by 3’ tagging and PCR amplification using the FailSafe PCR enzyme (Gene Target Solutions,Cat: FSE51100). The PCR was performed for 10 cycles followed by purification using Agencourt AMPure XP beads (Beckman Coulter, Cat: A63881). The purified library was eluted in a final volume of 20ul pure water. Quality of the library obtained was checked using the DNA High sensitivity chip on the Agilent Bioanalyzer. The library was quantified using Qubit and KAPA Biosystems Library quantification kit according to manufacturer’s instructions.

value: LNCaP clone FGC (ATCC CRL-1740). Androgen-sensitive human prostate adenocarcinoma cells


title: 1T.9 (RNA-seq)

source_name: First trimester CVS

value: First trimester

value: CVS


title: selected strain FM diet liver biological rep4


title: selected strain FM diet muscle biological rep2


title: 3T.3 (RNA-seq)


title: 2T.1 (RNA-seq)

source_name: Second trimester CVS

value: Second trimester


title: Mdr2+/- Rep 3


title: selected strain FM diet muscle biological rep1

value: ARS-KO


title: selected strain FM diet liver biological rep2

value: FM


title: LNCaP_NOMe_EtOH_1


title: 1T.8 (RNA-seq)


title: OL5

city: Dresden

first: Michell

middle: M

last: Reimer

state: Saxony

address: Fetscherstrasse 105

department: CRT Dresden

institute: TU Dresden

data_processing:
basecalling: bcl2fastq 2.17.1.14
alignment: Libraries were mapped to GRCz10 with GSNAP (v 2016-09-23); splice site were supported by using Ensembl version 81
fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delimited file from featureCounts (bfx684.GRCz10.e81.txt.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 2 Conditions and their 5 replicates

molecule: polyA RNA

organism: Danio rerio

source_name: adult spinal cord

extract_protocol:
Spinal cord dissection, tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized, their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution (HBSS, Gibco)). For the dissociation of spinal cords into a single cell suspension at room temperature, the tissue was incubated for 3 min with 100 µL 0.25% Trypsin (Sigma; T4549) / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then, tissue digestion was stopped by adding 100 µL of 20% fetal calf serum (Sigma; F0804) in 2 mM CaCl2 and 300 µL HBSS. Afterwards the cell suspension was allowed to sit for 5’ at on ice, before it was applied to a 20 µm (OPCs, Miltenyi Biotec, # 130-101-812) or a 35 µm (OL, Corning, # 352235) cell strainer, respectively. After washing with 9 ml of HBSS, the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed, cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain (Molecular Probes, Invitrogen, V35003) and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates, filled with culture media only, or pre-seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter after excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected after 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection, all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris.
For the RNAseq experiment, the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit - HV from Clontech was used to reverse transcribe the RNA and amplify full-length cDNA according to the user manual. Therefore, 2000 cells from five biological replicates of both lines Tg(olig2:eGFP) and Tg(mbp:GFP) where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. After amplification of cDNA using 12 cycles, the cDNA was sheared to 200bp fragment length with 8-micro TUBE strip in the ultrasonicator Covaris LE220, followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

value: oligodendrocyte


title: OL4


title: 1T.7 (RNA-seq)


title: 1T.5 (RNA-seq)


title: OL3


title: BC_1

city: Regensburg

last: Dresselhaus

address: Universitätsstr. 31

department: Institute of Plant Sciences

institute: Universität Regensburg

description: untreated wildtype plants

data_processing:
Illumina Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.
The quality of sequencing data from the different  RNA-Seq libraries was assessed with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Primer contaminations from the SMARTer Ultra Low RNA Kit were removed with a cutadapt (ver 1.13,http://dx.doi.org/10.14806/ej.17.1.200). Afterwards size and quality trimming was performed using Trimmomatic (ver: 0.32 (Am et al., 2014), ILLUMINACLIP: NexteraPE-PE_SMARTer.fa:2:30:10:2:true TRAILING:26 LEADING:26 MINLEN:25).
For the alignment of mRNA reads, we used STAR 2.5.2a (Dobin A, Bioinformatics 2013, with the option: --outSAMtype BAM   Unsorted      --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 0   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --quantMode TranscriptomeSAM )
Mapped fragments were summarized with Rsubread featureCounts (Liao et al., 2014) using the gene build http://ftp.gramene.org/maizesequence.org/release5b+/zea_mays
Differential Expression analysis was performed with DESeq2(Love et al., 2014)
Genome_build: AGPv3, INSEC Assembly GCA_000005005.5, release 23, ftp://ftp.ensemblgenomes.org/pub/plants/Zea_mays-AGPv3.23.dna.genome.fa
Supplementary_files_format_and_content: .csv, FeatureCounts: Countable of reads per gene, DE_DESeq2_Tissue1_vs_Tissue2.csv, DESeq2 results for all 15 possible comparisons (available in a tar archive on the series record).

organism: Zea mays

source_name: Basal Cell

growth_protocol: Maize plants were grown in a growth chamber at 26°C under illumination of 24000 lux with 16h light/8h dark cycles

extract_protocol:
manual dissection of plant cells was followed by flash freezing of isolated cells in liquid nitrogen.mRNA was extracted from cell samples using the Dynabeads mRNA DIRECT Micro  Kit (Life Technologies). The SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech Laboratories) was used to generate first strand cDNA. Double stranded cDNA was amplified by LD PCR (15 cycles) and purified via magnetic bead clean-up using Agencourt AMPure PCR Purification Kit (Beckman Coulter). The quality of purified cDNA was then measured using the Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA Kit (Agilent Technologies), frozen in liquid nitrogen and stored at −80°C before further usage.
Library preparation was carried out as described by the Adapted Nextera Sample Preparation protocol (Clontech Laboratories) for use with the SMARTer Ultra Low RNA Kit for Illumina Sequencing. 5 ng of input cDNA was tagmented (tagged and fragmented) by the Nextera transposome. Products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems). Equimolar amounts of each library were pooled, and pools thereafter used for cluster generation on the cBot with the Illumina TruSeq PE Cluster v3 and Illumina TruSeq Dual Index Sequencing Primer paired end kits. Sequencing runs were performed on a HiSeq 1000 instrument using the dual indexed 2 x 100 cycles paired end (PE) protocol and the TruSeq SBS v3 reagents according to the Illumina HiSeq 1000 System User Guide.

value: Basal Cell


title: BC_2

description: untreated wildtype plants


title: OL2


title: selected strain PM diet muscle biological rep9

value: PM


title: AC_2

description: untreated wildtype plants

source_name: Apical Cell

value: Apical Cell


title: selected strain PM diet liver biological rep10


title: 3T.4 (RRBS)

data_processing:
paired-end 36-base pair (bp) reads were filtered based on qseq score
reads were aligned to the bisulfite-converted human genome (UCSC Build hg19, GRCh37, Feb 2009) using Bowtie
Differential DNA methylation between 1T and 3T samples were analyzed at single CpG level and at genomic region (CGI and promoters) level.
Average methylation for each core promoter for both 1T and 3T were calculated.
Genome_build: hg 19
Supplementary_files_format_and_content: Differentially methylated promoters and gene expression (RPKM) between early and late gestational ages

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Mini Kit (QIAGEN GmbH, Germany). Library was constructed using modified Illumina RRBS Sample Preparation Protocol.
Illumina's RRBS for Methylation Analysis


title: AC_3

description: untreated wildtype plants


title: selected strain PM diet liver biological rep9


title: 3T.5 (RRBS)


title: 3T.3 (RRBS)


title: OL1


title: selected strain PM diet muscle biological rep8

value: muscle


title: AC_1

description: untreated wildtype plants


title: OPC5

value: oligodendrocyte precursor cell


title: OPC4


title: OPC3


title: selected strain FM diet liver biological rep1

value: liver


title: BC_3

description: untreated wildtype plants


title: 3T.2 (RRBS)

source_name: Third trimester placenta villi

value: Placenta villi


title: Zy24_2

description: untreated wildtype plants

value: Zygote


title: 3T.1 (RRBS)

value: Third trimester


title: selected strain PM diet muscle biological rep10


title: selected strain PM diet liver biological rep8


title: OPC2


title: selected strain PM diet muscle biological rep7


title: Zy24_1

description: untreated wildtype plants


title: Zy12_3

description: untreated wildtype plants


title: OPC1


title: 1T.6 (RRBS)


title: selected strain PM diet liver biological rep7


title: 1T.5 (RRBS)


title: Zy12_1

description: untreated wildtype plants


title: 1T.3 (RRBS)


title: selected strain PM diet muscle biological rep6


title: 1T.4 (RRBS)


title: 1T.1 (RRBS)


title: Zy12_2

description: untreated wildtype plants


title: Zy24_3

description: untreated wildtype plants


title: selected strain PM diet muscle biological rep4


title: 1T.2 (RRBS)


title: selected strain PM diet liver biological rep6


title: EC_3

description: untreated wildtype plants

source_name: Egg Cell

value: egg


title: selected strain PM diet muscle biological rep5


title: selected strain PM diet liver biological rep4


title: selected strain PM diet liver biological rep5


title: SP_2

description: untreated wildtype plants

source_name: Sperm Cell

value: sperm


title: EC_2

description: untreated wildtype plants


title: selected strain PM diet liver biological rep3


title: SP_3

description: untreated wildtype plants


title: EC_1

description: untreated wildtype plants


title: selected strain PM diet muscle biological rep3


title: selected strain PM diet liver biological rep2


title: SP_1

description: untreated wildtype plants