title: NWBC4_replicate3

city: Philadelphia

first: Jaroslav

last: Jelinek

state: PA

address: 3307 North Broad St

department: Fels Institute

institute: Temple University

description: Biological replicate 4 of 4.

data_processing:
Sequencing tags were mapped to SmaI sites in the human genome (hg18) and signatures corresponding to methylated (starting with CCGGG…) and unmethylated (starting with GGG…) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor calculated based on observed and expected methylation of spiked-in standards.
The value of c for each sample: AML 2.352, CB1 1.911, CB2 2.164, HEL 2.762, K562 2.225, NWBC1_replicate1 1.152, NWBC1_replicate2 1.204, NWBC2_replicate1 2.028, NWBC2_replicate2 1.205, NWBC3 1.748, NWBC4_replicate1 2.137, NWBC4_replicate2 0.858, NWBC4_replicate3 1.352.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data files are tab-delimited text files that contain the methylation values. The columns of these files are: SmaI_ID (SmaI site ID), Chrom (chromosome of the SmaI site), Pos (position of the SmaI site), MetReads (observed number of tags corresponding to methylated CpG, sm), UnmetReads (observed number of tags corresponding to unmethylated CpG, u), Methylation (corrected methylation value).

source_name: healthy white blood cells from adult blood

extract_protocol:
DNA isolation: Red blood cells (RBCs) were lysed in the RBC lysis solution containing 155 mM ammonium chloride, 10 mM potassium bicarbonate and 1 mM EDTA. White blood cells (WBCs) were isolated as a pellet by centrifugation. The WBC pellet was then lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA).

Five micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels of 0, 25, 50, 75, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

value: adult blood

value: healthy white blood cells


title: RRBS hematopoietic progenitor cells Promyelocyte_310511

status: Public on Nov 08 2012

type: SRA

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

library_source: genomic

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
Off-Line Basecaller (OLB) was used for bcl to qseq conversion
Illumina paired-end adapter sequences were removed using Cutadapt version 0.9.3
Reads were mapped using Bismark version 0.5
Methylation calls from Bismark were extracted with a modified methylation_extractor script which removed 3’-MspI-sites
The extracted methylation data was further analyzed in R/Bioconductor with the BiSeq package
Genome_build: hg19 for human samples and mm9 for mouse samples
Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using R/Bioconductor with help of the BiSeq package. Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.

molecule: genomic DNA

organism: Homo sapiens

source_name: Generated in vitro from CD34+ above

extract_protocol: 0.3 – 1 µg of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with 5mC-methylated Illumina paired end sequencing adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 220 bps insert size were gel-purified (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). Each library was sequenced on a separate lane using an Illumina HiScanSQ instrument with version 2.5 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.

tag: disease state

value: Healthy donor cells

tag: Sex

value: m

tag: age

tag: sample pairs


title: RRBS remission bone marrow APL_6

source_name: Density centrifuged bone marrow

value: Remission bone marrow


title: RRBS hematopoietic progenitor cells CD34_300611

source_name: Peripheral blood after G-CSF stimulation


title: RRBS lin- pMIGR transduced day 5

organism: Mus musculus

source_name: lin- mouse bone marrow

value: pMIGR transduced lin- BM cells day 5

tag: strain

value: f

value: 12-week old


title: NWBC2_replicate2

country: USA

description: Biological replicate 2 of 4.

tag: tissue

tag: cell type


title: ChiP-Seq REST APL blast

source_name: APL bone marrow blasts

extract_protocol: ChIP-seq: Cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as previously described (Dietrich et al, PLOS Genetics 2012). Briefly, formaldehyde fixed chromatin was sonicated in IP buffer (IP buffer =2 volume SDS Buffer : 1 volume Triton Dilution Buffer; SDS Buffer-  100mM NaCl  50mM Tris-Cl, pH8.1, 5mM EDTA, pH 8.0, 0.2% NaN3, 2% SDS; Triton Dilution Buffer- 100mM Tris-Cl, pH 8.6, 100mM NaCl, 5mM EDTA, pH 8.0, 0.2% NaN3, 5.0% Triton X-100) using Branson Sonifier (4 cycles of 30 sec each at 20% amplitude). 15ug DNA (sonicated chromatin) was used for each ChIP in IP buffer. Antibodies used: Rabbit IgG (DAKO), rabbit anti-REST (Millipore, 07-579), anti-SUZ12 (Rabbit monoclonal, Cell signaling). Samples were incubated with antibodies overnight at 40C and immunocomplexes were precipitated with protein A-sepharose beads with 3 hr rotation at 40C. After subsequent washes the samples were decrosslinked overnight at 650C (shaking) in 1%SDS, 0.1M NaHCO3. Finally, ChIP DNA was purified using Qiagen PCR purification kit. The ChIPs were validated at REST and Polycomb target genes by qPCR. ChIP DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. The libraries were prepared using “ChIP seq DNA sample preparation kit” from Illumina following manufacturer’s instructions. Individual samples were run in a single lane on HiSeq2000 (Illumina). Basecalls were performed using on-instrument real time analysis (RTA). Mapping was performed with bowtie allowing for <=2 mismatches and only including reads that were mapped to a single position to hg18. The number of reads in 100 bp sections of the genome were counted genome-wide. A normal distribution was fitted to the counts, and the distribution with the least root-mean-square deviation was used as model for the background in the datasets. Thresholds were set so that windows that scored positive had p-values < 0.001 compared to the background distribution. A ChIP-sequenced IgG-control was used as a negative control and handled in the same way. Only windows scoring positive for REST or Suz12, but not IgG, were included for downstream analysis. Also windows where the positive signal (normalized to dataset size) did not exceed the negative signal (normalized to dataset size) at least threefold were omitted from downstream analysis. Datasets were analyzed this way four times in 25 bp shifts, thereby reducing the number of regions that scored negative due to a division of the reads into neighboring sections. Overlapping positive windows and positive windows within 100bp for REST and 500bp for Suz12 of each other were merged. The position of the border was refined by shifting the window in one bp steps until the window scored positive (without scoring positive in the negative control sample) starting at a distance of one window-size from the regions border. Genomic positions were transferred to hg19 using the UCSC liftover tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver).

value: Primary diagnosis


title: RRBS hematopoietic progenitor cells CD34_010611


title: NWBC2_replicate1

description: Biological replicate 2 of 4.


title: RRBS hematopoietic progenitor cells CD34_260511


title: RRBS hematopoietic progenitor cells CD34_190511


title: RRBS lin- PML_RAR transduced day 5

value: PML-RAR transduced lin- BM cells day 5


title: RRBS lin- hematopoietic progenitor cells

value: lin- BM cells


title: RRBS remission bone marrow APL_5894


title: RRBS primary diagnosis APL_8452

tag: pml transcript

value: Long

tag: flt3-itd status

value: negative

tag: sanz score risk group

value: Low


title: RRBS PML-RARa Knock-in mice mm_34_PML-RAR_gr1

source_name: Gr1+ sorted mouse bone marrow

value: Gr1+ bone marrow

tag: genotype/variation

value: PML-RARa (+/-)

value: 6-months pre-leukemic


title: CB1

description: Biological replicate 1 of 2.

source_name: healthy white blood cells from cord blood

value: cord blood


title: CB2

description: Biological replicate 2 of 2.

value: healthy white blood cells


title: RRBS primary diagnosis APL_3

value: Short


title: NWBC4_replicate2

description: Biological replicate 4 of 4.

value: adult blood


title: RRBS PML-RARa Knock-in mice mm_31_PML-RAR_gr1


title: RRBS primary diagnosis APL_8

value: unclear


title: RRBS Wildtype mice mm_14752_control_gr1

value: wt


title: RRBS Wildtype mice mm_14786_control_gr1

value: m


title: RRBS primary diagnosis APL_11

value: f


title: RRBS primary diagnosis APL_1

value: Primary diagnosis


title: RRBS primary diagnosis APL_15

value: Intermediate


title: RRBS Wildtype mice mm_14749_control_gr1


title: RRBS primary diagnosis APL_19

value: positive

value: High


title: RRBS primary diagnosis APL_9882

value: Long


title: RRBS primary diagnosis APL_7717

value: negative


title: RRBS primary diagnosis APL_10759


title: RRBS primary diagnosis APL_2


title: Dyak_WPP_RNAseq_3

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

description: Sample 9

library_source: transcriptomic

data_processing:
Sequencing data are mapped to  the genome as well as the annotated exon-exon conjunctions using Bowtie, allowing 2 mismatches.
Only uniquely mapped reads were used to generate the read counts and RPKM values for each gene following the methods described in Mortazavi et al 2008 Nature Methods paper.
Genome_build: dm3, droSim1, droYak2
Supplementary_files_format_and_content: tab delimited file including read counts and RPKM values for each gene (abundance measurements)

molecule: total RNA

organism: Drosophila yakuba

source_name: Whole animal white prepupa

growth_protocol: The three sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval.

extract_protocol:
Total RNA samples are isolated using Trizol Chroloform, followed by QIAGEN column purification.
RNA seq libraries are prepared using standard Illumina single end RNA seq library protocol

tag: developmental stage

value: white prepupa


title: RRBS lin- PML_RAR transduced day 10

value: PML-RAR transduced lin- BM cells day 10

value: 12-week old


title: RRBS primary diagnosis APL_8503

value: Low


title: Dyak_WPP_RNAseq_2

description: Sample 8


title: Dyak_WPP_CTCF_Input_1

data_processing:
Alignment: Sequence reads were obtained and mapped to multiple drosophila genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the QuEST 2.0 algorithm (http://mendel.stanford.edu/SidowLab/downloads/quest/)

source_name: white prepupae

growth_protocol: The four sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

value: white prepupae

tag: fraction

value: input


title: RRBS primary diagnosis APL_14


title: RRBS primary diagnosis APL_9

value: Short


title: Dyak_WPP_RNAseq_1

description: Sample 7


title: RRBS primary diagnosis APL_7

value: unclear


title: Dsim_WPP_RNAseq_3

description: Sample 6

organism: Drosophila simulans


title: RRBS PML-RARa Knock-in mice mm_33_PML-RAR_gr1

value: Gr1+ bone marrow

value: PML-RARa (+/-)

value: 6-months pre-leukemic


title: Dsim_WPP_RNAseq_2

description: Sample 5


title: RRBS primary diagnosis APL_10892

value: Primary diagnosis

value: f


title: Dsim_WPP_RNAseq_1

description: Sample 4


title: RRBS primary diagnosis APL_10545

value: m


title: RRBS primary diagnosis APL_5

value: positive


title: Dsim_WPP_CTCF_Input_2


title: Dmel_WPP_RNAseq_3

description: Sample 3

organism: Drosophila melanogaster


title: Dmel_WPP_RNAseq_2

description: Sample 2


title: Dsim_WPP_CTCF_Input_1


title: Dmel_WPP_RNASeq_1

description: Sample 1


title: Dmel_WPP_CTCF_Input_1


title: Dmel_WPP_CTCF_Input_2


title: NWBC4_replicate1

description: Biological replicate 4 of 4.

value: adult blood

value: healthy white blood cells


title: NWBC3

description: Biological replicate 3 of 4.


title: NWBC1_replicate2

description: Biological replicate 1 of 4.


title: NWBC1_replicate1

description: Biological replicate 1 of 4.


title: K562

source_name: K562 cell line

tag: cell line

value: leukemia cells


title: Dmel_WPP_CTCF_ChIPSeq_1, 2 and 3

tag: antibody name

value: CTCF-C

tag: antibody manufacturer

value: Renkawitz Lab

tag: antibody lot/batch#

tag: antibody catalog

value: Custom

value: ChIP


title: Dyak_WPP_CTCF_ChIPSeq_1, 2 and 3

value: white prepupae


title: HEL

source_name: HEL cell line

value: HEL


title: AML

source_name: acute myeloid leukemia bone marrow

value: acute myeloid leukemia bone marrow


title: 0.5% OCI-Ly8_99.5% HEK293 [RNA-seq]

status: Public on Nov 07 2012

city: Aalborg

first: Maria

middle: Bro

last: Kloster

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg Hospital

description: Kidney/lymphoma

data_processing:
Illumina pipeline software version 1.3 used for image analysis and base calling, omitting chyasity filtering otherwise default settings were used.
Data was imported into the CLC Genomics workbench 4.5 and sequence error corrected by the SAGEScreen method.
The first 17 bp of the tag sequences were extracted from the output file according to the second adaptor containing the identification key for each sample.
The unique tags were sorted and counted for each sample using the CLC Genomics Workbench 4.5 and exported to .txt files. These text files were imported into Bioconductor.
Each unique tag sequence was annotated by mapping the reads with the anchoring NlaIII
Genome_build: Each unique tag sequence was annotated by mapping the reads with the anchoring NlaIII restriction site to the ENSEMBL Homo Sapiens cDNA reference transcriptome (release 63) downloaded from ftp://ftp.ensemble.org on both the coding and non-coding strands using Bowtie version 0.12.7. The following settings were used –v1 allowing Bowtie to accept a maximum of one mismatch.
Supplementary_files_format_and_content: tag-seq_processed.txt

source_name: Kidney/lymphoma

growth_protocol: OCI-Ly8 was maintained in RPMI-1640 medium including 10% foetal bovine serum. HEK293 was maintained in Eagle’s Minimum Essential Medium including 10% foetal bovine serum. Both cell lines were in a CO2 incubater at 37°C and 5% CO2 atmosphere.

extract_protocol: 2 μg of total RNA was incubated with magnetic Oligo-(dT)25 beads to capture the polyadenylated RNA fraction. Total RNA was reverse transcribed into double-stranded cDNA using the SuperScript II kit (Invitrogen). The double-stranded cDNA was digested with the restriction enzyme NlaIII (New England Biolabs) to generate cDNA fragments from the most 3´ CATG to the poly(A) tail. A biotinylated adaptor containing the recognition site for the restriction enzyme MmeI was linked to the 5´end of the digested double stranded cDNA. tags of 17 bp of double stranded cDNA were released from the Oligo-(dT)25 beads by MmeI (New England Biolabs). Tags were purified from a polyacrylamide gel by phenol-chloroform extraction and bound to Streptavindin beads. A second adapter containing an identification key of 3 bp unique for each sample was ligated to the tags. The adaptor-ligated tags from all samples were pooled and amplified by PCR. The PCR products were purified by excision from a 6% polyacrylamide gel (Invitrogen), followed by elution, ethanol precipitation and resuspension (Illumina). Adaptor-ligated tags from all samples were sequenced in an individual lane of a flow cell by the Solexa/Illumina Whole Genome Sequencer 1G analyzer, according to manufrakturer´s instruction.

treatment_protocol: Cell lines were harvest in the exponential phase. Cells were sorted directly into RNAlater in different cellular concentrations using the FACSAria II cell sorter.

tag: dilutions of the malignant b-cell line

value: 0.5% malignant


title: 10% OCI-Ly8_90% HEK293 [RNA-seq]

description: Kidney/lymphoma

value: 10% malignant


title: 5% OCI-Ly8_95% HEK293 [RNA-seq]

description: Kidney/lymphoma

value: 5% malignant


title: 0% OCI-Ly8_100% HEK293 [RNA-seq]

description: Kidney

source_name: Kidney

value: Normal


title: 1% OCI-Ly8_99% HEK293 [RNA-seq]

description: Kidney/lymphoma

value: 1% malignant


title: 100% OCI-Ly8_0% HEK293 [RNA-seq]

description: lymphoma

source_name: lymphoma

value: 100% malignant


title: 30% OCI-Ly8_70% HEK293 [RNA-seq]

description: Kidney/lymphoma

value: 30% malignant


title: Dmel_WPP_CTCF_Input_3

value: input


title: WT17-ab

city: Derio

first: Rosa

last: Barrio

address: Bizkaia Technology Park

country: Spain

institute: CIC bioGUNE

data_processing:
Illumina RTA 1.5.35.0 & Illumina RTA 1.9.35
SCS_2.5 & SCS_2.9
Aligment with BOWTIE
Differential Expression by Deseq
GO with FatiGO tool
Genome_build: d_melanogaster_fb5_22
Supplementary_files_format_and_content: DE comparisons of the groups considered in the present study. The included fields are:
Id: gene ID
baseMean: mean expression level (at the base scale) as a joint estimate from both conditions
baseMeanA: mean expression level (at the base scale) as an estimate for condition A
baseMeanB: mean expression level (at the base scale) as an estimate for condition B
foldChange: fold change from the first to the second condition
log2FoldChange: the logarithm (to basis 2) of the fold change
pval: significance of this fold change
padj: p values, adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR)
resVarA: the ratio of the single gene estimates for the base variance to the fitted value in condition A
resVarB: the ratio of the single gene estimates for the base variance to the fitted value in condition B

source_name: Pool of 50 embryos

growth_protocol: Standard Drosophila Husbandry protocols

extract_protocol: mRNA Sequencing Sample Preparation (Illumina Inc.)

treatment_protocol: No treatment

tag: Stage

value: early stage 16 (13-14 hours of egg development at 25°C)

tag: genotype

value: Oregon R (sall+/+)


title: He17-ab

value: heterozygous Df(2L)32FP-5/+ (sall+/-)


title: He17-c


title: Ho17-b


title: Ho17-c


title: He16-c


title: Ho16-c


title: Ho17-a


title: 20% OCI-Ly8_80% HEK293 [RNA-seq]

description: Kidney/lymphoma

value: 20% malignant


title: WT16-ab


title: HCF1_CHIP-seq

city: South San Francisco

first: Jinfeng

last: Liu

state: CA

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

data_processing:
Reads were first filtered to keep only those with >70% of bases having Phred quality score of 20 or better.
The filtered reads were mapped to Mus musculus genome revision 9 (mm9) by GSNAP, allowing maximum of two mismatches.
ChIP-seq enrichment regions (peaks) were called using MACS 1.4
Genome_build: mm9
Supplementary_files_format_and_content: BED files for peaks called by MACS 1.4

source_name: bone marrow progenitors

growth_protocol: Bone marrow derived macrophages were differentiated using L929 conditioned media as per standard protocol

extract_protocol: ChIP and input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3' ends.  Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel.  The adaptor-ligated libraries were amplified for 18 cycles.  The resulting DNA libraries were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.  DNA libraries then were sequenced on the Illumina Genome Analyzer II.

treatment_protocol: Cells were not treated further.

tag: strain

value: BAP1 WT

value: bone marrow derived macrophages

tag: passage

value: Primary cells

tag: chip antibody

value: anti-HCF1 [Bethyl Laboratories, catalog# A301-399A]


title: WT16-c


title: Input_CHIP-seq

tag: cell type

value: none (input control)


title: OGT1_CHIP-seq

value: anti-OGT1 [Sigma, catalog# 06264]


title: BAP1 flag_CHIP-seq

value: BAP1-3X Flag Tagged KI

value: anti-FLAG [Sigma, catalog# A2220]


title: tog25_RNASeq

city: Beijing

first: Dong

last: Wang

address: No.1 West Beichen Road,Chaoyang District

department: Institute of Genetics and Developmental Biology

country: China

institute: Chinese Academy of Sciences and National Center for Plant Gene Research

description: Oryza sativa L. ssp. indica

data_processing:
Illumina Casava1.7 software used for basecalling.
Dirty raw reads were removed from the raw sequence data using a Perl script programmed by BGI Tech. Filter steps were: 1.Remove reads which containing adaptors. 2. Remove reads in which unknown bases are more than 5%. 3. Remove low quality reads (more than half of the bases' qualities are less than 5). 4.Obtain clean reads.
Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009). Mismatches no more than 2 bases were allowed in the alignment. Total base number for each sample should no less than that in the contract. Proportions of clean reads mapped back to genome and genes provide an overall assessment of the sequencing.
The calculation of Unigene expression used RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008).
Differentially expressed genes were analyzed referring to "The significance of digital gene expression profiles" (Audic S, Genome Research), and then subjected to GO functional enrichment analysis.
Genome_build: RAP-DB Rice Genome Annotation: IRGSP/RAP build 5
Supplementary_files_format_and_content: Tab-delimited .txt files include RPKM values for each sample.

organism: Oryza sativa Indica Group

source_name: Leaf blades

growth_protocol: Four-day old Zhongxian 3037 and tog1 seedlings were both divided into two groups and grown in growth chambers (12L:12D cycle at 80% humidity) at 25 ℃ and 30 ℃ respectively for further 18 days.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen).
Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina HiSeq™ 2000.

treatment_protocol: For each sample, leaf blades of the fourth leaves were collected, pooled into 100 mg and frozen in liquid nitrogen. Four samples in total were obtained, including Zhongxian 3037 at 25 ℃ and 30 ℃ and tog1 at 25 ℃ and 30 ℃.

tag: variety

value: Zhongxian 3037

value: tog1 mutant

tag: grown temperature

value: 22-day-old seedling

tag: tissue

value: Leaf blades


title: Ho16-a


title: tog30_RNASeq

description: Oryza sativa L. ssp. indica

tag: genotype/variation

tag: developmental stage


title: Dsim_WPP_CTCF_ChIPSeq_1, 2 and 3

value: white prepupae

value: CTCF-C

value: Renkawitz Lab

value: Custom

tag: fraction

value: ChIP


title: WT48 Rep1

status: Public on Nov 06 2012

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: RNA-seq from polyA+_RNA

data_processing: Data were obtained using the Illumina Genome Analyzer CASAVA Pipeline

molecule: polyA RNA

organism: Schizosaccharomyces pombe

growth_protocol: Cultures were grown to mid-log phase in yeast extract with supplements medium (YES; MP Biomedicals, Solon, OH) at 30˚C

extract_protocol: Libraries were prepared according to Illumina's instructions

value: WT


title: WT25_RNASeq

description: Oryza sativa L. ssp. indica

value: wild type


title: WT30_RNASeq

description: Oryza sativa L. ssp. indica


title: zfs1delta50 Rep2

description: RNA-seq from polyA+_RNA

value: zfs1 null mutant


title: WT17-c

value: early stage 16 (13-14 hours of egg development at 25°C)

value: Oregon R (sall+/+)


title: WT47 Rep1

description: RNA-seq from polyA+_RNA


title: WT48 Rep2

description: RNA-seq from polyA+_RNA


title: zfs1delta49 Rep1

description: RNA-seq from polyA+_RNA


title: WT47 Rep2

description: RNA-seq from polyA+_RNA


title: CG4747 female replicate 2 input

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

data_processing:
Illumina base-calling pipeline
aligned to dm3 using bowtie (-t 1 -k 1)
smoothed enrichment calculated using SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/), get.smoothed.enrichment.mle() method with bandwidth of 300bp, step of 30bp and tag shift of 25bp.
Genome_build: dm3 (BDGP rel5)
Supplementary_files_format_and_content: WIG files showing smoothed enrichment estimates (MLE) on log2 scale

source_name: Female larvae

extract_protocol:
Lysates were clarified from sonicated larvae and protein-DNA complexes were isolated with antibody.
300 ng of DNA was used for ChIP-seq library preparation.  DNA amplification was performed using the NEBNext ChIP-seq library prep master mix set for Illumina (NEB) and Illumina Truseq adapter indexes (Illumina) with minor modifications.  One µl of 1:25 dilution of each Illumina Truseq adapter index oligo was used per 300 ng ChIP DNA.  Adapter ligated products were PCR amplified for 12 cycles.  Purified DNA was sequenced on the Illumina Hiseq platform.


title: CG4747 female replicate 1 input


title: CG4747 female replicate 2 IP

value: PAP antibody (Sigma P1291)


title: CG4747 male replicate 2 input

source_name: Male larvae


title: CG4747 female replicate 1 IP


title: He16-ab

value: heterozygous Df(2L)32FP-5/+ (sall+/-)


title: CG4747 male replicate 2 IP


title: CG4747 male replicate 1 IP


title: non antibody control ChIPseq

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

data_processing:
Bed: Sequence reads were mapped to the ASM294v1 NCBI assembly of the S.pombe genome using Bowtie (version 0.12.7) with default parameters.
Wig: RPM (read per million) counts were  calculated from the alignment files and wig files were created with a custom script.
Genome Build:
7-PG.bed: ASM294v1
7-PG.rpm.wig: ASM294v1

source_name: Fission yeast cells

growth_protocol: Cells in YEA + 2% glucose were collected in log phase

extract_protocol: ChIP assays were performed as described previously [Zhu et al., 2006]. RNA Polymerase II CTD antibody is CTD(4H8) (Abcam, ab5408).   Libraries were prepared according to Illumina's instructions.DNA-end was repaired to overhang a 3‟-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.

treatment_protocol: No

tag: develomental stage

value: No

tag: tap tag

value: No TAP tag


title: USC_ChIPSeq_H1-hESC_YY1_UCDavis

city: Davis

first: Henriette

last: O'Geen

address: 1 Shields Avenue

institute: UC Davis

description: Control library ID: wgEncodeEH001751

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina read sequences were aligned to the reference human genome (hg18) using BWA (Li and Durbin 2009).
FindPeaks 4.0.15 (Fejes et al. 2008) was subsequently used to detect enrichment peaks at an FDR of 0.01.
Genome_build: hg18
Supplementary_files_format_and_content: bw format for aligned sequences, .peaks for list of called peaks, wig file

source_name: H1-hESC (WiCell Research Institute WA01)

growth_protocol: Human embryonic stem cells (hESCs) were obtained from Cellular Dynamics as part of a large batch of cells prepared for the ENCODE Consortium and the RoadMap Epigenome Consortium. Cell growth and crosslinking conditions can be found at http://www.genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol: Chromatin was isolated following the Farnham lab protocol (http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf). The YY1ChIP assay was performed using 5x107 cells according to O'Geen et al. 2010 (PMC3019231) except that StaphA cells were blocked only with BSA before use and the pre-clearing step was omitted. ChIP and Input samples (10% of the amount of chromatin used per ChIP) were purified using the QIAquick PCR purification kit (QIAGEN) according to manufacturer’s instructions and purified eluates were dissolved in 50uls of water. ChIP libraries were created and sequenced as described previously (Harris et al. 2010)  by the DNA Technologies Core Facility at the University of California-Davis (http://genomecenter.ucdavis.edu/dna_technologies/). Illumina read sequences were aligned to the reference human genome (hg18) using BWA (Li and Durbin 2009). FindPeaks 4.0.15 (Fejes et al. 2008) was subsequently used to detect enrichment peaks at an FDR of 0.01.

value: human embryonic stem cells

tag: karyotype

value: normal

tag: cell lineage

value: inner cell mass, sex:M

value: YY1 (Santa Cruz Biotechnology, sc-1703X)


title: Input_DNA

status: Public on Nov 05 2012

city: Manchester

first: Xi

last: Chen

address: Michael Smith Building, Dover Street

department: Faculty of Life Sciences

country: United Kingdom

institute: The University of Manchester

description: Sample 3

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed through the bundled Solexa image extraction pipeline.
ChIP-seq reads were aligned to the hg18 genome assembly using MAQ with default parameters.
The reads were aligned allowing a maximum of 2 mismatches,and reads aligning to multiple locations were discarded.
Before peak calling, reads aligned to mitochondrial genome were discarded.
Peaks were called by MACS (ver. 1.4.1) using default parameters, except that the bandwidth was set as 400.
Genome_build: hg18
Supplementary_files_format_and_content: BED file contained the uniquely mapped reads and summit position of peaks with FDR less than 10%.

growth_protocol: Cells were maintained in DMEM with 10% FCS

extract_protocol: ChIP DNA was amplified as described (Schmidt, D. et al. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 48, 240–248.)

treatment_protocol: Cells were harveted for ChIP at 10 hours after double thymidine block (16 hours in 2 mM Thymidine, 12 hours in fresh media, 16 hours in 2 mM thymidine).

tag: cell line

value: Osteosarcoma


title: FOXM1_ChIP-seq_rep2

description: Sample 2

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: FOXM1_ChIP-seq_rep1

description: Sample 1

tag: passage


title: KU

city: Münster

first: Rüdiger

middle: J

last: Paul

address: Schlossplatz 8

department: Institut für Zoophysiologie

data_processing:
Sequencing quality determination with Illumina GA Pipeline
Filtering: Remove reads with adaptors, remove reads in which unknown bases are more than 10%, remove low quality reads
Alignment to reference sequence using soap2, no more than 2 mismatches are allowed in the alignment
Calculation of gene expression levels by using the RPKM (Reads Per kb per Million reads) method
Genome_build: Wormbase release WS223
Supplementary_files_format_and_content: tab-delimited .txt with unique reads number, gene lenth, gene coverage and RPKM-values for annotated genes in KU25 and N2

organism: Caenorhabditis elegans

source_name: worm total lysates

growth_protocol: Worms were grown on NGM at 20°C with E. coli OP50 as food source

extract_protocol:
Total RNA-isolation was carried out with RNAiso-G, a modified Guanidin-isothiocyanate/phenol RNA-extraction method, and a subsequent cleanup with RNeasy® mini kit and on-column DNAseI treatment
mRNA was purified using oligo-(dT)-magnetic beads, and first and second strand cDNA-synthesis was carried out using random hexamer primers. Samples were ligated with sequencing adaptors and sequenced with Illumina HiSeq2000 with a minimum 10 Megareads per sample and a sequencing quality of more than 98% clean reads

treatment_protocol: Worms were incubated on NGM plates in sealed plastic bags for 5 hours at 35°C in a thermostate controlled waterbath

tag: strain

value: KU25; pmk-1 deletion mutant

tag: genotype

value: pmk-1(km25) IV

tag: age

value: young adult


title: WT

value: N2 Bristol; wildtype

value: wild type


title: ada2sas3jhd2_H3K4me3_ChIPSeq

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

data_processing:
Image analysis, base-calling and error calibration was performed using Illumina’s Genome analysis pipeline
Reads were aligned using Burrows-Wheeler Aligner
Aligned reads were imported into SeqMonk
Duplicate reads removed
Reads mapping to longer than 500bp were discarded
Read quantitation performed using a wiggle plot with 1 base pair probes
Data normalized to reflect bulk levels of K4me3 present in each strain
Data track exported as Bedgraph file
Genome_build: S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
Supplementary_files_format_and_content: Bedgraph files, scores represent read quantitation

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast strains were grown to midlog and crosslinked with 1% formaldehyde for 15 minutes

extract_protocol:
Cells were lysed by bead beating and mononucleosomes were generated through Mnase digestion
Library construction for the Illumina platform was prepared using a custom procedure for paired-end sequencing (Illumina). Briefly, 2-10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. The resulting material was then amplified using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5' AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3'], where "NNNNNN" corresponds to unique hexamer barcodes. PCR amplification was performed as follows: denaturation at 98°C for 60 seconds; 8 cycles of (98°C, 30 seconds; 65°C, 30 seconds; 72°C, 30 seconds), and a final extension at  72°C for 5 minutes. An aliquot of each library was run on an Agilent High Sensitivity chip (Agilent) to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200-600 bp size range were selected on an 8% Novex TBE PAGE gel (Invitrogen). The pooled libraries were diluted to 15 nM. Libraries were sequenced on the Hiseq2000 (SBSxx) platform. The hexamer barcode was sequenced using the following primer [5' GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 3']. Image analysis, base-calling and error calibration was performed using Illumina's Genome analysis pipeline.

treatment_protocol: 1% formaldehyde crosslinking

tag: antibody

value: H3K4me3 (Abcam, mAbcam1012, lot 1152779)

value: logarithmic


title: jhd2_H3K4me3_ChIPSeq


title: RELISH_SAMPLE1

city: Cologne

first: Mirka

last: Uhlirova

address: Zülpicher Str. 47a

department: Institute For Genetics

institute: CECAD, University of Cologne

data_processing: Using the Illumina HiSeq 2000 instrument, 76 bp of sequence were read from one DNA end. Image analysis and base calling were done with the Illumina RTA software at runtime. The amount of data from raw FastQ files ranged between 25.87 and 39.33 million reads per sample. The sequences were mapped to the Drosophila genome assembly (version BDGP R5/dm3, April 2006) using Tophat, v.1.3.2 (Trapnell, 2009). The alignment output was processed using Cufflinks, v.1.1.0 (Trapnell, 2010), and the current UCSC annotation of the Drosophila genome (dm3). A single per-gene FPKM value provided by Cufflinks was used for the analysis rather than taking into account expression values for all isoforms of a particular gene. We included all genes for which FPKM of two replicates differed in the same direction from both control replicates at least 5% but did not exceed 6-fold between the two duplicates. To look for genes that were differentially expressed under the respective conditions, the average of the two duplicates was calculated.

source_name: whole larvae, y w, atf3[76];;rel[E20]/+

growth_protocol: Drosophila melanogaster was cultured at 25°C on a diet consisting of 0.8% (w/v) agar, 8% cornmeal, 1% soymeal, 1.8% dry yeast, 8% malt extract and 2.2% sugar-beet syrup, and was supplemented with 0.625% propionic acid and 0.15% Nipagin.

extract_protocol: Sequencing libraries were generated according to the Illumina protocol for total RNA library preparation and loaded to Illumina flow cells (Illumina, San Diego, USA).

value: 3rd instar larvae

tag: gender

value: male

tag: tissue

value: whole body

tag: sample type

value: experimental


title: FOXO_SAMPLE2

source_name: whole larvae, y w, atf3[76];;dfoxo[25J13]/+

tag: developmental stage


title: ATF3[76]_SAMPLE2

source_name: whole larvae, y w, atf3[76]


title: FOXO_SAMPLE1


title: ATF3[76]_SAMPLE1


title: RELISH_SAMPLE2


title: ada2sas3_H3K4me3_ChIPSeq

tag: genotype/variation


title: YW_SAMPLE2

source_name: whole larvae, y w

value: y w

value: control


title: CG4747 male replicate 1 input

tag: chip antibody


title: YW_SAMPLE1


title: Mediator subunit Med7 ChIPseq

data_processing:
Bed: Sequence reads were mapped to the ASM294v1 NCBI assembly of the S.pombe genome using Bowtie (version 0.12.7) with default parameters.
Wig: RPM (read per million) counts were  calculated from the alignment files and wig files were created with a custom script.
Genome Build:
8-IgG.bed: ASM294v1
8-IgG.rpm.wig: ASM294v1

tag: develomental stage

value: No

tag: tap tag

value: has TAP tag

value: Mediator subunit Med7 antibody [conjugated with beads (IgG Sepharose 6 Fast Flow from GE healthcare, 17-0969-01, Lot# 10026538)]


title: RNA Polymerase II CTD domain  ChIPseq

data_processing:
Bed: Sequence reads were mapped to the ASM294v1 NCBI assembly of the S.pombe genome using Bowtie (version 0.12.7) with default parameters.
Wig: RPM (read per million) counts were  calculated from the alignment files and wig files were created with a custom script.
Genome Build:
1-4H8.bed: ASM294v1
1-4H8.rpm.wig: ASM294v1

value: No TAP tag

value: RNA Polymerase II CTD antibody [CTD(4H8) (Abcam, ab5408)]


title: WCE 25mM sodium bicarbonate

status: Public on Nov 04 2012

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: input pH 7.4 ChIP-seq

data_processing:
bowtie alignment -m1 -5 4 --strata --best -v2
value < 1.0 E-4 was chosen to give False Discovery Rate (FDR) less than 1%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization. Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 50-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.
peak calling described in Ferrari et al. 2012 Genome Research
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: WCE 25mM sodium bicarbonate

growth_protocol: Cells were routinely cultured in DMEM (Cellgro) that was supplemented with 10% FBS (Hyclone) and 1X antibiotic/antimycotic (Gibco).  Cells were passaged every 2-3 days.

extract_protocol: Nugen Ovation Ultralow Library system

treatment_protocol: Cells were plated in 10-cm dishes and allowed to attach overnight.  The following day the culture medium was replaced with DMEM (Sigma #D5030 supplemented with glucose, glutamine and pyruvate) with either 25 mM or 3 mM sodium bicarbonate which resulted in a medium pH of 7.4 and 6.5, respectively.  After 4 hours of incubation at 37oC in 5% CO2, cells were fixed with formaldehyde and harvested for ChIP.

tag: agent

value: 25mM sodium bicarbonate

tag: cell line

value: HeLa


title: WCE 3mM sodium bicarbonate

description: input pH 6.5 ChIP-seq

source_name: WCE 3mM sodium bicarbonate

value: 3mM sodium bicarbonate


title: mRNA 25mM sodium bicarbonate

description: mRNA-seq pH 7.4

data_processing:
Alignment of mRNA-seq reads was performed using default parameters of Tophat.
Aligned reads were converted to sam format and SAMMate software6 was used to determine the transcript RPKM (reads per kilobase of exon per million of reads).
Genome_build: hg19
Supplementary_files_format_and_content: bed, RPKM.txt

source_name: mRNA 25mM sodium bicarbonate

extract_protocol: Total RNA was extracted from HeLa cells grown in 25 or 3 mM sodium bicarbonate using Qiagen easy RNA kit. Maximum amount of RNA was used to start the library preparation according to the manufacturer's instructions (Illumina). Libraries were sequenced using Illumina HIseq-2000 to obtain 50 bp-long reads. Nugen Ovation Ultralow Library system

treatment_protocol: Cells were plated in 10-cm dishes and allowed to attach overnight.  The following day the culture medium was replaced with DMEM (Sigma #D5030 supplemented with glucose, glutamine and pyruvate) with either 25 mM or 3 mM sodium bicarbonate which resulted in a medium pH of 7.4 and 6.5, respectively.


title: mRNA 3mM sodium bicarbonate

description: mRNA-seq pH 6.5

source_name: mRNA 3mM sodium bicarbonate


title: H4K16ac 25mM sodium bicarbonate

description: H4K16ac pH 7.4 ChIP-seq

data_processing:
bowtie alignment -m1 -5 4 --strata --best -v2
value < 1.0 E-4 was chosen to give False Discovery Rate (FDR) less than 1%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization. Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 50-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.
peak calling described in Ferrari et al. 2012 Genome Research
Genome_build: hg19
Supplementary_files_format_and_content: bed, wig

source_name: H4K16ac 25mM sodium bicarbonate

value: H4K16ac active motif (39167)


title: H4K16ac 3mM sodium bicarbonate

description: H4K16ac pH 6.5 ChIP-seq

source_name: H4K16ac 3mM sodium bicarbonate


title: ATF3[A]_SAMPLE2

source_name: whole larvae, y w, atf3[76];;atf3[A]/+


title: ATF3[A]_SAMPLE1


title: 9_3_d FAIRE-seq

status: Public on Nov 02 2012

city: Daejeon, Seoul

first: kwoneel

last: kim

address: Gwahangno, Yuseong gu

country: South Korea

institute: KAIST

data_processing:
Raw data processing was carried out by means of Illumina data pipeline (ELAND and CASAVA). To identify the peaks of the reads, we ran F-seq with the default parameters. Small-sized peaks (< 15 bp) were extended in both directions such that all the peaks are 15 bp long at least. To identify all possible open chromatin regions (OCRs), we merged the extended peak positions of the 96 yeast strains by using BEDTools. Overlapping peaks were merged into a single peak.
Genome build: sacCer2

source_name: yeast extract

growth_protocol: We obtained the BY-RM cross strains from the original authors (Science 296, 752-755 & PNAS 102, 1572-1577). Each yeast strain was grown with 200ml YPD medium in conical flask and incubated under shaking condition at 200 rpm overnight to 1.5 of the value of A600.

extract_protocol:
High-throughput sequencing of the 96 FAIRE libraries was performed on eight lanes of a single flow cell of HiSeq 2000 with 100 bp run length. Illumina’s Multiplexing Sample Preparation Oligonucleotide Kit was used to sequence twelve samples in each lane.
library_strategy: FAIRE-seq

treatment_protocol: The yeast cell was fixed by 37% formaldehyde (final 1%) for 20 minutes at room temperature. To stop fixation, 2.5M glycine (final 125 mM) was added and mixed swirling for 5 minutes at room temperature. The fixed cell was harvested by centrifugation at 3000 rpm for 5 minutes, and the pellet cells was rinsed twice with 10ml cold PBS and stored at -70ºC after removing all supernatant. Fixed cell was re-suspended in 300ul ChIP lysis buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1% Triton-X 100, 0.1% Sodium deoxycholate, 1mM EDTA) and protease inhibitor (Roche Inc. #1697498) per 0.12g of cells. Glass bead (425-600 micron diameter, Sigma #G8772) was added an equal volume to each sample and mixed 5 times 30 seconds by vortex mixer with 30 second incubation on ice. Then glass beads were filtered by puncture bottom of tube with a 20-26G needle and centrifugation. The samples were sonicated for 20 cycles (30 seconds ON and 30 seconds OFF) using a Bioruptor sonicator. DNA isolation was done by adding an equal volume of phenol-chloroform (Amresco. AMR-0883-2, phenol : chloroform : isoamyl alcohol 25:24:1), vortexing vigorously for 30 seconds and centrifuged at 13000 rpm for 10 minutes at 4ºC. The aqueous phase was isolated and the stored in a separate tube. The DNA was precipitated by addition of sodium acetate (final 0.3M) and two times the volume of 95% ethanol and incubated at -20ºC overnight. The precipitate was centrifuged at 13000 rpm for 20 minutes at 4ºC. Then the pellet was washed with 70% ethanol and dried at room temperature. The pellet was resuspended in dH2O with the addition of RNase A (final 100ug/mL), and then incubated at 37ºC for 2 hours. DNA fragments of 100-350 bp were eluted from 2% agarose gel.

value: BY4716xRM11_1a segregant


title: 9_6_d FAIRE-seq


title: 9_4_d FAIRE-seq


title: 9_7_d FAIRE-seq


title: 9_5_d FAIRE-seq


title: WT_H3K4me3_ChIPSeq

value: WT

value: H3K4me3 (Abcam, mAbcam1012, lot 1152779)

value: logarithmic


title: 8_5_b FAIRE-seq


title: 8_6_c FAIRE-seq


title: 8_4_c FAIRE-seq


title: 9_1_d FAIRE-seq


title: 8_7_b FAIRE-seq


title: 8_2_d FAIRE-seq


title: 9_2_d FAIRE-seq


title: 8_1_a FAIRE-seq


title: 7_7_c FAIRE-seq


title: 8_3_a FAIRE-seq


title: 7_6_c FAIRE-seq


title: 7_5_d FAIRE-seq


title: 7_8_d FAIRE-seq


title: 7_2_c FAIRE-seq


title: 7_4_c FAIRE-seq


title: 7_1_d FAIRE-seq


title: 6_3_c FAIRE-seq


title: 6_6_d FAIRE-seq


title: 6_2_b FAIRE-seq


title: 5_5_d FAIRE-seq


title: 6_7_d FAIRE-seq


title: pha-degradome

city: Tainan

first: Feng-Ming

last: An

address: No. 59, Silaya Blvd., Sinshi Dist.

department: Biotechnology Center in Southern Taiwan

country: Taiwan

institute: Academia Sinica

description: degradome sequencing

data_processing: Raw data were processed by removing the adaptor/acceptor sequences, contaminants and low quality reads. The final dataset containing reads of orchid degrading RNA fragment sequences were used for this study.

organism: Phalaenopsis aphrodite subsp. formosana

source_name: leaf, stalk, flower bud, flower, tetraploid WT

growth_protocol: Seedlings of Phalaenopsis aphrodite subsp. formosana (M1624) were purchased from Chain Port Orchid Co., Ltd (Chengde Village, Taiwan) and grown in 2.5 in. diameter plastic pots filled with sphagnum moss in an environment-controlled greenhouse, at a constant temperature of 28ºC for 7-8 months.

extract_protocol: Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extraction was freshly prepared using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. About 50 μg of leaves with or without low temperature treatment, stalks and flower buds were taken separately and then mixed. Two hundred μg of total RNA was passed though polyA column using the Oligotex kit (Qiagen). The 5'-RNA adapter containing a Mme I recognition site was ligated by T4 RNA ligase and further reverse transcribed to amplify the templates. After digesting with Mme I then ligated to a 3'-double DNA adapter, the products were amplified by additional PCR cycles and gel-purified for Illumina sequencing.

treatment_protocol: Plants comprising the untreated group were subsequently grown at 32°C/27°C (light/dark) to inhibit phase transition. Low ambient temperature treatment was carried out at 24°C/18°C (light/dark) for two months to complete phase transition. Leaves with or without low temperature treatment were collected at 0.5 month intervals from zero to two months. Stalks and flower buds were only present in the low temperature treatment group. Stalks were collected at 1.5 and 2 months, while flower buds were collected at 3.5 months.

value: leaf, stalk, flower bud, flower

tag: treatment

value: low temperature


title: 4_4_d FAIRE-seq


title: 5_1_d FAIRE-seq


title: 4_1_c FAIRE-seq


title: 3_3_d FAIRE-seq


title: 3_4_d FAIRE-seq


title: 3_1_d FAIRE-seq


title: 26_1_d FAIRE-seq


title: 25_3_d FAIRE-seq


title: 24_1_d FAIRE-seq


title: 26_2_d FAIRE-seq


title: 25_1_d FAIRE-seq


title: 23_5_d FAIRE-seq


title: 22_2_d FAIRE-seq


title: 23_3_d FAIRE-seq


title: 6_4_d FAIRE-seq


title: 21_2_d FAIRE-seq


title: 21_3_d FAIRE-seq


title: 21_1_d FAIRE-seq


title: 2_6_d FAIRE-seq


title: 20_4_c FAIRE-seq


title: 20_3_c FAIRE-seq


title: 2_3_d FAIRE-seq


title: 2_5_d FAIRE-seq


title: 3_5_d FAIRE-seq


title: 2_2_d FAIRE-seq


title: 2_4_a FAIRE-seq


title: 25_4_d FAIRE-seq


title: 19_3_c FAIRE-seq


title: 19_4_b FAIRE-seq


title: 19_2_c FAIRE-seq


title: 19_1_c FAIRE-seq


title: 18_4_c FAIRE-seq


title: 18_6_d FAIRE-seq


title: 18_2_d FAIRE-seq


title: 17_5_b FAIRE-seq


title: 18_1_d FAIRE-seq


title: 17_4_a FAIRE-seq


title: 17_1_a FAIRE-seq


title: 16_1_d FAIRE-seq


title: Input DNA

first: Keyan

last: Salari

address: Gray/Bigelow Rm 1102, 55 Fruit Street

institute: Massachusetts General Hospital

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the unmasked human genome (hg18) using the Illumina Genome Analyzer Pipeline (ELAND Extended).
Peaks: Peak detection was performed with the QuEST algorithm (Valouev et al. Nat Methods 2008)

source_name: colorectal cancer cells

growth_protocol: COLO-320 cells were maintained at 37C in media of RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol: For chromatin immunoprecipitation, approximately 5 x 10^7 cells were fixed in 1% formaldehyde, and chromatin was sheared by sonication for 15 alternating on-off cycles of 30 seconds using a Bioruptor (Diagenode). Sheared chromatin from approximately 1 x 10^6 cells was used for each ChIP assay. ChIP was performed using two independent antibodies against human CDX2: a rabbit polyclonal antibody (Cell Signaling) and a mouse monoclonal antibody (Biogenex CDX2-88). ChIP and input DNA were prepared into libraries and sequenced using a Genome Analyzer IIx (Illumina), according to manufacturer protocols.


title: 20_2_d FAIRE-seq


title: CDX2 ChIP-seq Cell Signaling Ab

description: Chromatin IP against CDX2

value: CDX2 Ab

tag: chip antibody manufacturer

value: Cell Signaling


title: CDX2 ChIP-seq Biogenex Ab

description: Chromatin IP against CDX2

value: CDX2 Ab (clone CDX2-88)

value: Biogenex


title: 15_4_d FAIRE-seq


title: 15_6_c FAIRE-seq


title: 14_6_d FAIRE-seq


title: 14_5_b FAIRE-seq


title: 14_4_a FAIRE-seq


title: 14_3_d FAIRE-seq


title: 14_1_b FAIRE-seq


title: 14_2_c FAIRE-seq


title: 13_5_c FAIRE-seq


title: 13_4_a FAIRE-seq


title: RH_str_H3K9me3_combined_fastq.txt.gz

first: Richard

middle: G.

last: Hunter

state: Massachusetts

address: 100 William Morrissey Blvd.

department: Psychology

institute: University of Massachusetts Bo

data_processing:
Trim to 50bp/average q-score 75% bases over q25
Alignment to rn4 with BWA (v0.5.9-r16)
Peak calling with SICER v1.1 (only uniquely aligning (XT:A:U) reads)
Annotation to genomics features - BEDTools 2.14.2
Alignment to repeats - software provided from:  Daniel S Day, Lovelace J Luquette, Peter J Park and Peter V Kharchenko. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biology (In press). doi:10.1186/gb-2010-11-6-r69
Heatmaps using Cluster3.0 and Java Treeview
Genome_build: rn4
Supplementary_files_format_and_content: all wig files are generated from unique (XT:A:U) reads using IGVtools with 100bp extension and 25bp windowing

organism: Rattus norvegicus

source_name: hippocampus

growth_protocol: Male Sprague-Dawley Rats were purchased from Charles River Laboratories and housed under standard ALAAC and NIH approved conditions, with ad libitum food and water and a 12/12 hr light dark cycle for 2 weeks prior to the experiments described under 'treatment protocol' below.

extract_protocol:
2 month old male Sprague-Dawley rats were restrained for 30 minutes, allowed to recover for one hour and then sacrificed and their hippocampi were extracted and processed using standard methods (See Hunter et al PNAS 2012) for ChIP Sequencing using the Cell Signalling H3K9me3 antibody.
After ChIP for H3K9me3, DNA treated with RNAase A and Proteinase K to remove extraneous material, it was then cleaned using Qiagen spin columns.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Sprague-Dawley

value: hippocampus

value: male

tag: condition

value: stressed

value: Cell Signaling #9754 - Anti H3K9me3


title: 13_2_c FAIRE-seq

tag: strain


title: RH_cnt_H3K9me3_combined_fastq.txt.gz

value: stress-free


title: 13_3_b FAIRE-seq


title: 13_1_a FAIRE-seq


title: 12_2_b FAIRE-seq


title: RH_input_fastq_prefilter.txt.gz

value: none, input


title: 12_1_d FAIRE-seq

value: BY4716xRM11_1a segregant


title: 11_3_b FAIRE-seq


title: 11_1_a FAIRE-seq


title: 10_4_d FAIRE-seq


title: 15_3_b FAIRE-seq


title: 10_3_c FAIRE-seq


title: 18_3_d FAIRE-seq


title: 10_2_d FAIRE-seq


title: 11_2_d FAIRE-seq


title: miRNA-seq_CS_ZT16

city: Waltham

first: Stefan

last: Pescatore

address: 415 South Street

department: Biology

institute: Brandeis University / HHMI

data_processing:
The first 20 bases of fasta formatted reads were mapped to the Drosophila melanogaster genome (dm3) with SeqMap (Jiang et al 2008) using the following command allowing up to two mismatches in the alignment: seqmap-1.0.12-linux-64 2 sequence.fa Dm_all_seqs.fa sequence.seqmap.out /match_shorter_probes /cut:1,20
Reads mapping to miRNA genomic locations were scanned for the presence of the entire mature miRNA sequence.  Drosophila miRNA genomic locations were downloaded from www.mirbase.org.  Read counts were normalized to the total number of mapped reads per sample.  Cycling miRNAs were identified as described (Wijnen et al 2005).
wig files were generated using custom-written perl scripts for purpose of visualization.
Genome_build: dm3
Supplementary_files_format_and_content: wig files generated using custom-written perl scripts are provided for visualization on Genome Browsers.

source_name: Drosophila head

growth_protocol: Adult flies were kept in constant 12 hr:12 hr light:dark conditions for 3 days before collection

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) as suggested by the supplier. Small RNA sequencing libraries were essentially prepared as described in (Seitz et al., 2008) with one exception: The 2S rRNA was depleted by hybridizing to a DNA oligonucleotide followed by RNaseH treatment. Following depletion of 2S rRNA, 19 to 29 nucleotide long RNAs were gel purified and adapters were ligated at 3’ and 5’ end using Rnl2 [(1-249) Ho et al., 2004] and T4 RNA ligase (Ambion) respectively. RNA was PCR amplified using primers corresponding to the adapters and the PCR products were gel purified on a 2% agarose gel.

treatment_protocol: Flies were collected at specified time point and frozen on dry ice, heads were removed.

value: Canton S

value: adult

value: head

tag: circadian time point

tag: molecule subtype

value: Small RNAs 18-20 nucleotides in length, 2s rRNA depleted


title: miRNA-seq_CS_ZT12

tag: age


title: miRNA-seq_CS_ZT4


title: miRNA-seq_CS_ZT8


title: miRNA-seq_CS_ZT20


title: 1_5_c FAIRE-seq


title: miRNA-seq_CS_ZT0


title: 1_4_d FAIRE-seq


title: 1_3_d FAIRE-seq


title: 1_1_d FAIRE-seq


title: RM11_1a FAIRE-seq


title: Digital Genomic Footprinting assay of Fetal Intestine, Small; DGF.DS17317

status: Public on Nov 01 2012

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14555
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027348_UW.Fetal_Intestine_Small.Digital_Genomic_Footprinting.H-23769.DGF.DS17317.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17317.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Intestine Small, Donor H-23769, Library DGF.DS17317 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15148
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 357,862,675
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4001
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.3777
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9921
IROC_PERCENTILE: 45
POISSON_SCORE: 0.4441
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027348_UW.Fetal_Intestine_Small.Digital_Genomic_Footprinting.H-23769.DGF.DS17317.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17317.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Fetal Intestine Small, Donor H-23769, Library DGF.DS17317 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15159
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FIS DGF 69 17
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Digital Genomic Footprinting Donor H-23769 Library DGF.DS17317 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 357,862,675
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4001
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.3777
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9921
IROC_PERCENTILE: 45
POISSON_SCORE: 0.4441
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Fetal  primary tissue, day 108; DGF.DS17317

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Intestine, Small

tag: molecule

value: genomic DNA

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: Male

value: Digital Genomic Footprinting

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Kidney, Left; DNase.DS21344

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21344
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14447
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14446
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027347_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24626.DNase.DS21344.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21344.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-24626, Library DNase.DS21344 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17595
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,011,228
FINDPEAKS_SCORE: 0.4599
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4423
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9925
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5066
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1027347_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24626.DNase.DS21344.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21344.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Left, Donor H-24626, Library DNase.DS21344 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17549
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKL DNase 26 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-24626 Library DNase.DS21344 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,011,228
FINDPEAKS_SCORE: 0.4599
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4423
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9925
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5066
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Fetal Kidney, Left primary tissue, day 87; DNase.DS21344

value: Fetal Kidney, Left

value: day 87

value: Chromatin Accessibility


title: BY4716 FAIRE-seq

growth_protocol: We obtained the BY-RM cross strains from the original authors (Science 296, 752-755 & PNAS 102, 1572-1577). Each yeast strain was grown in 200ml YPD medium and incubated with shaking at 200 rpm overnight to an A600 value of 1.5.

treatment_protocol: The yeast cells were fixed by 37% formaldehyde (final 1%) for 20 minutes at room temperature. To stop fixation, 2.5M glycine (final 125 mM) was added and mixed swirling for 5 minutes at room temperature. The fixed cells were harvested by centrifugation at 3000 rpm for 5 minutes, and the pellet cells were rinsed twice with 10ml cold PBS and stored at -70ºC after removing all supernatant. The fixed cells were resuspended in ChIP lysis buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1% Triton-X 100, 0.1% Sodium deoxycholate, 1mM EDTA) containing protease inhibitor (Roche Inc. #1697498). 300ul of ChIP lysis buffer was used for 0.12g of fixed cells. For disruption of cells, the same volume of glass beads (425-600 micron diameter, Sigma #G8772) was added to each sample and five repetitions of 30-second vortexing and 30-second incubation on ice were carried out. Cells were selectively filtered by spinning at 1000G for 3 minutes at 4ºC after piercing to the bottom of the tube using a 20-26G needle. The samples were then sonicated for 20 cycles (30 seconds ON and 30 seconds OFF) using a Bioruptor sonicator at a “high” mode. DNA isolation was done by the addition of an equal volume of phenol-chloroform (Amresco. AMR-0883-2, phenol : chloroform : isoamyl alcohol 25:24:1), vortexing vigorously for 30 seconds, and spinning at 13000 rpm for 10 minutes at 4ºC. The aqueous phase was isolated and stored in a separate tube. The DNA was precipitated by addition of sodium acetate (final 0.3M) and the 2x volume of 95% ethanol and then incubated at -20ºC for 2 hours. The precipitate was centrifuged at 13000 rpm for 20 minutes at 4ºC. The pellet was washed with 70% ethanol and dried at room temperature. The pellet was resuspended in dH2O and treated with RNaseA (final 100ug/mL), followed by incubation at 37ºC for 2 hours. DNA fragments of 100-350 bp were eluted from 2% agarose gel.


title: Digital Genomic Footprinting assay of Fetal Thymus; DGF.DS20341

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20341
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14546
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11269
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027351_UW.Fetal_Thymus.Digital_Genomic_Footprinting.H-24409.DGF.DS20341.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS20341.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Thymus, Donor H-24409, Library DGF.DS20341 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15151
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 329,108,296
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3576
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.3393
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3707
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027351_UW.Fetal_Thymus.Digital_Genomic_Footprinting.H-24409.DGF.DS20341.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS20341.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Fetal Thymus, Donor H-24409, Library DGF.DS20341 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15162
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FT DGF 09 41
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Digital Genomic Footprinting Donor H-24409 Library DGF.DS20341 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 329,108,296
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3576
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.3393
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3707
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Fetal Thymus primary tissue, day 113; DGF.DS20341

value: Fetal Thymus

value: day 113

value: Female


title: Chromatin accessibility assay of Fetal Kidney, Right; DNase.DS21340

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21340
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14332
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14331
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027346_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24626.DNase.DS21340.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21340.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-24626, Library DNase.DS21340 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17603
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,603,694
FINDPEAKS_SCORE: 0.5336
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5238
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9944
IROC_PERCENTILE: 72
POISSON_SCORE: 0.5795
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1027346_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24626.DNase.DS21340.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21340.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Right, Donor H-24626, Library DNase.DS21340 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17557
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKR DNase 26 40
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-24626 Library DNase.DS21340 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,603,694
FINDPEAKS_SCORE: 0.5336
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5238
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9944
IROC_PERCENTILE: 72
POISSON_SCORE: 0.5795
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Fetal Kidney, Right primary tissue, day 87; DNase.DS21340

value: Fetal Kidney, Right


title: Digital Genomic Footprinting assay of Fetal Muscle, Arm; DGF.DS17765

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17765
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14550
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8512
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17765.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Muscle Arm, Donor H-23914, Library DGF.DS17765 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15153
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 207,283,076
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5236
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5407
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9884
IROC_PERCENTILE: 18
POISSON_SCORE: 0.5557
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17765.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Fetal Muscle Arm, Donor H-23914, Library DGF.DS17765 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15164
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA DGF 14 65
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm Digital Genomic Footprinting Donor H-23914 Library DGF.DS17765 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 207,283,076
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5236
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5407
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9884
IROC_PERCENTILE: 18
POISSON_SCORE: 0.5557
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Fetal Muscle, Arm primary tissue, day 91; DGF.DS17765

value: Fetal Muscle, Arm

value: day 91


title: Chromatin accessibility assay of Fetal Lung, Right; DNase.DS21328

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21328
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14324
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14323
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027344_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24626.DNase.DS21328.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21328.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-24626, Library DNase.DS21328 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17621
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,289,720
FINDPEAKS_SCORE: 0.6261
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.609
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.995
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6235
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM1027344_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24626.DNase.DS21328.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21328.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Right, Donor H-24626, Library DNase.DS21328 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17575
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FLR DNase 26 28
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-24626 Library DNase.DS21328 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,289,720
FINDPEAKS_SCORE: 0.6261
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.609
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.995
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6235
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: Fetal Lung, Right primary tissue, day 87; DNase.DS21328

value: Fetal Lung, Right

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass


title: Chromatin accessibility assay of Fetal Lung, Left; DNase.DS21334

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21334
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14328
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14327
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027345_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24626.DNase.DS21334.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21334.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-24626, Library DNase.DS21334 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17616
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,264,420
FINDPEAKS_SCORE: 0.667
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6539
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9956
IROC_PERCENTILE: 87
POISSON_SCORE: 0.6511
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1027345_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24626.DNase.DS21334.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21334.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-24626, Library DNase.DS21334 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17570
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FLL DNase 26 34
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-24626 Library DNase.DS21334 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,264,420
FINDPEAKS_SCORE: 0.667
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6539
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9956
IROC_PERCENTILE: 87
POISSON_SCORE: 0.6511
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Fetal Lung, Left primary tissue, day 87; DNase.DS21334

value: Fetal Lung, Left

value: Primary Tissue

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Placenta; DNase.DS21111

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21111
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14300
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14299
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027343_UW.Fetal_Placenta.ChromatinAccessibility.H-24608.DNase.DS21111.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21111.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Placenta, Donor H-24608, Library DNase.DS21111 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17614
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,738,721
FINDPEAKS_SCORE: 0.3054
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.2964
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.989
IROC_PERCENTILE: 15
POISSON_SCORE: 0.3756
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1027343_UW.Fetal_Placenta.ChromatinAccessibility.H-24608.DNase.DS21111.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21111.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Placenta, Donor H-24608, Library DNase.DS21111 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17568
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FP DNase 08 11
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta DNase Hypersensitivity Donor H-24608 Library DNase.DS21111 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,738,721
FINDPEAKS_SCORE: 0.3054
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.2964
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.989
IROC_PERCENTILE: 15
POISSON_SCORE: 0.3756
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Fetal Placenta primary tissue, day 85; DNase.DS21111

value: Fetal Placenta

value: day 85

value: Male

value: Qiagen minElut