title: 4sU_DCs_6h_RNASeq

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description:
RNA Sequencing of 4sU labeled RNA
L_6_lane8
library selection: 4sU

data_processing: Reads were aligned to the mouse mm9 reference genome using the TopHat aligner.

source_name: Dendritic cells

growth_protocol: 6-8 week old female C57BL/6J mice were obtained from the Jackson Laboratories. Bone marrow dendritic cells (BMDCs) were collected from femora and tibiae and plated on non-tissue culture treated plastic dishes in RPMI medium (Gibco, Invitrogen), supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, MEM non-essential amino acids, HEPES, sodium pyruvate, β-mercaptoethanol, and GM-CSF (15 ng/μL; Peprotech). At day 5, floating CD11c+ cells were sorted on the autoMACS separator with the CD11c (N418) MicroBeads kit (Myltenyi Biotec). CD11c+ cells where re-plated at a concentration of 106 cells/ml and stimulated 16 hours post sorting.

extract_protocol:
Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen), and sample quality was tested on a 2100 Bioanalyzer (Agilent). We used 20 μg total RNA (80 ng/μL final) for the biotinylation reaction. 4sU-labeled RNA was biotinylated using EZ-Link Biotin-HPDP (Pierce) dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL and stored at -80°C. Biotinylation was carried out in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2 h at room temperature. Unbound Biotin-HPDP was removed by chloroform / isoamylalcohol (24:1) extraction using MaXtract (high density) tubes (Qiagen). Next, a 1/10 volume of 5M NaCl and an equal volume of isopropanol were added, and RNA was precipitated at 20,000g for 20 min. The pellet was washed with an equal volume of 75% ethanol and precipitated again at 20,000g for 10 min. The pellet was re-suspended in 100 μL RNAse-free water. Biotinylated RNA was captured using Dynabeads MyOneTM Streptavidin T1 beads (Invitrogen). 50 μL Dynabeads were washed twice in washing solution A (100 mM NaOH, 50 mM NaCl) and once in washing solution B (100 mM NaCl) and re-suspended in 100 μL 2x washing buffer (2M NaCl, 10mM Tris pH 7.5 1mM EDTA, 0.1% Tween20). Biotinylated RNA was incubated with 100 μL of washed Dynabeads with rotation for 15 min at room temperature. The beads were magnetically fixed and washed 3 times with 1x Dynabeads washing buffer. For recovery of unlabeled preexisting RNA, the flow-through of the first wash was collected. Labeled RNA was eluted by the addition of 100 μL of freshly prepared 100 mM dithiothreitol (DTT). RNA was recovered from the washing fractions and eluates using the RNeasy MinElute Spin columns (Qiagen).
We prepared the 4sU-Seq libraries using the ‘control (non–strand-specific)’ protocol previosly described in Levin et. A. Nature Methods, 2010, with the following modification: after DNase treatment, we did not isolate polyA+ RNA, but used the entire RNA sample. Libraries were analyzed on Illumina GAII system, generating ~30-35 million paired-end reads per sample. Average insert size (distance between two paired reads): 77.44, stdev: 4404.6.

treatment_protocol: LPS (rough, ultra-pure E.coli K12 strain LPS) was purchased from Invivogen (San Diego, CA) and used at 100 ng/μl concentration. For metabolic labeling of RNA, 4-thiouridine (Sigma) was added to a 150 μM final concentration 45 min prior to RNA extraction.

value: Dendritic cell

tag: stimulation

value: LPS

tag: time after stimulation

value: 6 hours

tag: 4su labeling time

value: 45 min


title: 4sU_DCs_5h_RNASeq

status: Public on Apr 24 2011

type: SRA

description:
RNA Sequencing of 4sU labeled RNA
L_5_lane7
library selection: 4sU

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type

value: 5 hours


title: 4sU_DCs_4h_RNASeq

description:
RNA Sequencing of 4sU labeled RNA
L_4_lane1
library selection: 4sU

value: 4 hours


title: STAT5A_control_ChIPSeq (human)

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: NIH

description: Chromatin IP against STAT5A

library_source: genomic

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) and the mouse (Febrary, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

molecule: genomic DNA

organism: Homo sapiens

source_name: T cell

growth_protocol: CD4+ cells were preactivated by anti-CD3/anti-CD28 for 48 hrs

extract_protocol: Th1 cells or preactivated cells were cross-linking with formaldehyde. Formaldehyde-treated nuclear lysates were subjected to immunoprecipitation with antibodies specific for STAT1 (Santa Cruz),STAT4  (R&D Systems), STAT5A (R&D Systems), STAT5b (R&D Systems) or normal rabbit serum at 4°C overnight. After deproteination and reversal of cross-links, amounts of selected DNA sequences were assessed by CHIP-Seq

treatment_protocol: cells were rest two days, and non-treated for 1 hrs

value: T cell

tag: antibody

tag: treatment

value: control


title: 4sU_DCs_3h_RNASeq

description:
RNA Sequencing of 4sU labeled RNA
L_3_lane3
library selection: 4sU

value: 3 hours


title: STAT5B_IL2_ChIPSeq (human)

description: Chromatin IP against STAT5B

treatment_protocol: cells were rest two days, and stimulated with IL-2 for 1 hrs


title: STAT4_IL12_ChIPSeq (human)

description: Chromatin IP against STAT4

treatment_protocol: cells were rest two days, and stimulated with IL-12 for 1 hrs


title: 4sU_DCs_1h_RNASeq

description:
RNA Sequencing of 4sU labeled RNA
L_1_lane2
library selection: 4sU

value: 1 hours


title: STAT5A_IL2_ChIPSeq (human)

description: Chromatin IP against STAT5A


title: STAT4_control_ChIPSeq (human)

description: Chromatin IP against STAT4


title: STAT5B_control_ChIPSeq (human)

description: Chromatin IP against STAT5B


title: STAT5A_IL2_ChIPSeq (mouse)

description: Chromatin IP against STAT5A

treatment_protocol: cells were rest o/n, and stimulated with IL-2 for 1 hrs


title: STAT1_control_ChIPSeq (human)

description: Chromatin IP against STAT1


title: 4sU_DCs_0h_RNASeq

description:
RNA Sequencing of 4sU labeled RNA
L_0_lane6
library selection: 4sU

value: 0 hours


title: STAT1_IFNg_ChIPSeq (human)

description: Chromatin IP against STAT1

treatment_protocol: cells were rest two days, and stimulated with IFNg for 1 hrs

value: IFNg


title: mES_RNA_Seq_shRNA2863

status: Public on Apr 21 2011

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

country: China

institute: Fudan Univ, Shanghai, China

description:
mRNA-seq
cDNA reverse transcribed from the total mRNA of Tet1 shRNA2863-treated cells

data_processing: We used Off-Line Basecaller software (Illumina v1.8) to analyze images and call bases, and used the CASAVA package (Illumina v1.6) to generate read sequences and align to mm9. Since the DNA fragment size in our library is mainly from 200-300bp, we then extended the sequence to 250bp downstream of the 5' end of reads and converted the sorted file into bed format.

source_name: ES cells, Tet1 shRNA2863

growth_protocol: E14 ES cells were feeder-free cultured.

extract_protocol: DNA was end repaired using the End-It DNA End-repair kit (Epicentre), and purified with the QiaQuick PCR purification kit. DNA was treated with Klenow exo- (NEB) in NEB buffer 2 with 1mM ATP. After incubating at 37oC for 50min, the "A" base added DNA was purified with the QiaQuick PCR purification kit. Illumina adapters were ligated using quick T4 DNA ligase. The final DNA was purified with the QiaQuick PCR purification kit and amplified using Illumina sequencing primers for 16-18 cycles.

treatment_protocol: E14 ES cells were infected with Tet1 shRNA2863 containing lentivirus and harvested after 4-days selection with puromycin. Total RNA was extracted using TRIzol reagent (Invitrogen) and genomic DNA was removed by DNaseI digestion. The mRNA was further purified using Dynabeads mRNA purification kit (Invitrogen) and used to synthesize the first strand cDNA using ImPro-IITM Reverse Transcription System (Promega). The second strand cDNA was generated using DNA Pol I (Invitrogen) and the final double-stranded DNA (dsDNA) was purified using QIAquick PCR purification kit (Qiagen) and quantified by Qubit fluorometer (Invitrogen). 300 ng of dsDNA of each sample was fragmented by sonication and used to generate the sequencing library.

tag: cell line

value: mouse embryonic stem (MES) cells

tag: shrna treatment

value: Tet1 shRNA2863


title: mES_RNA_Seq_shRNA3387

description:
mRNA-seq
cDNA reverse transcribed from the total mRNA of Tet1 shRNA3387-treated cells.

source_name: ES cells, Tet1 shRNA3387

treatment_protocol: E14 ES cells were infected with Tet1 shRNA3387 containing lentivirus and harvested after 4-days selection with puromycin. Total RNA was extracted using TRIzol reagent (Invitrogen) and genomic DNA was removed by DNaseI digestion. The mRNA was further purified using Dynabeads mRNA purification kit (Invitrogen) and used to synthesize the first strand cDNA using ImPro-IITM Reverse Transcription System (Promega). The second strand cDNA was generated using DNA Pol I (Invitrogen) and the final double-stranded DNA (dsDNA) was purified using QIAquick PCR purification kit (Qiagen) and quantified by Qubit fluorometer (Invitrogen). 300 ng of dsDNA of each sample was fragmented by sonication and used to generate the sequencing library.

value: Tet1 shRNA3387


title: mES_5hmC_TET1_shRNA2863

description:
hMeDIP-seq
hMeDIPed genomic DNA.

source_name: ES cells, Tet1 shRNA2863, hMeDIP

treatment_protocol: E14 ES cells were infected with Tet1 shRNA2863 containing lentivirus and harvested after 4-days selection with puromycin.Genomic DNA was purified and sonicated. Illumina adapters were ligated before hMeDIP. 5µg of adapter-ligated DNA was denatured and incubated with 5µl of 5hmC antibody (Active Motif) at 4oC overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols.

value: rabbit anti-5hmC antibody

tag: antibody vendor

value: Active Motif

tag: antibody catalog number

tag: antibody lot number


title: mES_Input_Luc_shRNA

description:
hMeDIP-seq
Input.

source_name: ES cells, Luc shRNA, input

treatment_protocol: E14 ES cells were infected with Luc shRNA containing lentivirus and harvested after 4-days selection with puromycin.Genomic DNA was purified and sonicated. Illumina adapters were ligated before hMeDIP. 5µg of adapter-ligated DNA was denatured and incubated with 5µl of 5hmC antibody (Active Motif) at 4oC overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols.

value: Luc shRNA


title: TET1_CpG_Methylation_bisulfite_sequencing

description:
CpG DNA methylation.

library strategy: USER-S1-Ligation
library selection: padlock capture

data_processing: Reads were aligned to captured target sequences. CpG methylation levels were extracted from mapped reads. The resulting values are real numbers ranging from 0 to 1, which correspond to completely unmethylated and completely methylated, respectively.

source_name: J1 ES cells, Tet1 siRNA

growth_protocol: J1 ES cells were co-cultured with MEF feeder cells in standard ES cell medium.

extract_protocol: A library of 55,000 long oligonucleotides was designed to capture the transcription start sites of 908 genes on mouse chromosomes X and Y, 114 imprinted genes, 493 miRNA genes and 88 additional targets. The oligonucleotide library was PCR-amplified and converted into functional padlock probes through a series of enzymatic reactions as described previously (Zhang et al., 2009). The genomic DNA was purified using the DNeasy kit (Qiagen), and bisulfite conversion was performed with the EZ-Methylation Gold kit (Zymo Research). Target capture was performed on 200ng of bisulfite-converted DNA with 100x excess of padlock probes. The detailed protocol is described in the reference: Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotech, 2009, 27, 353-360 (PMID 19330000).

treatment_protocol: J1 ES cells were transfected with control siRNA or Tet1 siRNA and harvested four days after transfection. The genomic DNA was purified, and bisulfite conversion was performed with the EZ-Methylation Gold kit (Zymo Research).

tag: sirna treatment

value: Tet1 siRNA


title: mES_5hmC_Luc_shRNA

description:
hMeDIP-seq
hMeDIPed genomic DNA.

source_name: ES cells, Luc shRNA, hMeDIP


title: mES_Input_TET1_shRNA2863

description:
hMeDIP-seq
Input.

source_name: ES cells, Tet1 shRNA2863, input


title: 773_PES_454

city: St Paul

first: Sam

last: Yang

state: MN

address: 411 Upper Buford Circle

department: ARS

institute: USDA

data_processing: The initial base calling and quality filtering of the Illumina GA-II image data was performed using the default parameters of the Illumina GA Pipeline GERALD stage (www.illumina.com). Further filtering based on the read size (size≥75bp) was performed using custom written code. The velvet algorithm with k-mer 61 (Zerbino and Birney, 2008) was used for de novo assembly of the Solexa GA-II EST reads. The alfalfa gene index (MSGI1.0) was built by combining the de novo assembled Illumine reads (132,153 sequences) with 454 sequences (341,984 sequences), and the Sanger ESTs available from GenBank (12,371 sequences) following the method previously described (Quackenbush, 2001, Yang et al., 2006). For digital gene expression analysis, the raw digital gene expression counts were measured by quantifying the number of Illumina GA-II reads that were mapped to the reference sequences (MSGI1.0 or Mt3.0 cds) using bowtie program (Langmead et al., 2009) with best-match option with at most 3 nucleotide mismatches allowed (-v 3 --best). The raw digital gene expression counts were normalized using the RPKM (reads/Kb/Million) method previously described (Mortazavi et al., 2008; Nagalakshmi et al., 2008). To identify differentially expressed genes, an expression profile matrix was built representing the digital gene expression count for each gene in each library, then imported into the DEGSeq program (Wang et al., 2009). A MA-plot-based method with random sampling model in a DEGSeq program was used to identify genes differentially expressed in each pair-wise comparison (p<0.001, FDR<0.025, ≥2-fold difference).

organism: Medicago sativa

source_name: post_elongation stem internodes

growth_protocol: Alfalfa [Medicago sativa (L) subsp. sativa] genotypes 708 and 773 were selected from a population (UMN 3097) created by mixing seeds from six commercial alfalfa cultivars (5312, Rushmore, Magnagraze, Wintergreen, Windstar and WL 325HQ) as previously described [Yang et al. BMC Genomics, 2010]. Stems of genotype 708 consistently exhibited higher cellulose and lower lignin concentrations in cell walls compared to stems of genotype 773. Cell wall concentration in stems of the two genotypes did not differ. Two subsequent replicated field studies demonstrated that these differences in cell wall composition in stems were environmentally stable (Figure 1). Genotypes 708 and 773 were grown in the greenhouse and ES and PES internodes were harvested as previously described [Yang et al. BMC Genomics, 2010]. Cell wall analysis was also performed as previously described [Yang et al. BMC Genomics, 2010].

extract_protocol: Total RNA was purified from three replicates of elongating and post-elongation stem internodes of genotypes 708 and 773 using the CTAB based protocol previously described [38]. Contaminating genomic DNA was removed from each RNA sample using the DNA-free™ kit following the manufacturer’s recommendations (www.ambion.com).  An equal amount of total RNA was pooled from each replicate for each stem tissue sample. RNA samples were quantified using Quant-iT™ RiboGreen® RNA Reagent (www.invitrogen.com) and the RNA integrity was checked with RNA6000 Nano Assay using the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA). cDNA library preparation and sequencing reactions were conducted in the Biomedical Genomics Center, University of Minnesota. Illumina library prep, clustering and sequencing reagents were used throughout the process following the manufacturer’s recommendations (www.illumina.com). Briefly, mRNAs were purified using poly-T oligo-attached magnetic beads and then fragmented. The first and the second strand cDNAs were synthesized and end repaired. Adaptors were ligated after adenylation at the 3’-ends.  After gel purification, cDNA templates were enriched by PCR. cDNA libraries were validated using a High Sensitivity Chip on the Agilent2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA). The cDNA library was quantified using PicoGreen Assay and by qPCR. The samples were clustered on a flow cell using the cBOT. After clustering, the samples were loaded on the Illumina GA-II machine.  The samples were sequenced using a single read with 76 cycles. Initial base calling and quality filtering of the Illumina GA-II image data were performed using the default parameters of the Illumina GA Pipeline GERALD stage (www.illumina.com). Further filtering for homopolymers and the read size <75bp was performed using custom written code.

tag: developmental stage

value: post_elongation stem internodes

tag: tissue

value: stem internode

tag: genotype


title: mES_5hmC

description:
hMeDIP-seq
hMeDIPed genomic DNA.

source_name: ES cells, hMeDIP

treatment_protocol: Genomic DNA was purified from E14 cells and sonicated. Illumina adapters were ligated before hMeDIP. 5µg of adapter-ligated DNA was denatured and incubated with 5µl of 5hmC antibody (Active Motif) at 4oC overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols.


title: mES_TET1

description:
ChIP-seq
Chromatin IP against Tet1.

source_name: ES cells, Tet1 ChIP

growth_protocol: J1 ES cells were cultured with MEF feeder cells.

treatment_protocol: J1 ES cells were harvested and treated with formaldehyde. The cross-linked chromatin was sonicated and used for ChIP.

value: rabbit polyclonal antibody against mouse Tet1 (made in-house)


title: mES_TET1_CXXC_mut2

description:
ChIP-seq
Genomic DNA bound by Tet1 CXXC mutant2.

source_name: ES cells, Tet1 CXXC mutant2

treatment_protocol: 2 μg of purified and sonicated E14 mouse embryonic stem cell (mESCs) genomic DNA were incubated with 2 μg of Tet1 CXXC mutant2 for 1h at room temperature in the binding buffer (50 mM Tris pH 7.4, 5mM MgCl2, 1mM DTT, 3% Glycerol, 0.1% Triton, 1mM EDTA, and 200mM NaCl). The protein bound DNA was purified and followed by deep sequencing.


title: 773_ES_454

source_name: elongating stem internodes

treatment_protocol: Alfalfa [Medicago sativa (L) subsp. sativa] genotypes 708 and 773 were selected from a population (UMN 3097) created by mixing seeds from six commercial alfalfa cultivars (5312, Rushmore, Magnagraze, Wintergreen, Windstar and WL 325HQ) as previously described [Yang et al. BMC Genomics, 2010]. Stems of genotype 708 consistently exhibited higher cellulose and lower lignin concentrations in cell walls compared to stems of genotype 773. Cell wall concentration in stems of the two genotypes did not differ. Two subsequent replicated field studies demonstrated that these differences in cell wall composition in stems were environmentally stable (Figure 1). Genotypes 708 and 773 were grown in the greenhouse and ES and PES internodes were harvested as previously described [Yang et al. BMC Genomics, 2010]. Cell wall analysis was also performed as previously described [Yang et al. BMC Genomics, 2010].

value: elongating stem internodes


title: Control_CpG_Methylation_bisulfite_sequencing

source_name: J1 ES cells, control siRNA

value: control siRNA


title: 708_PES_Illumina


title: 708_ES_Illumina


title: N28_initial_library

status: Public on Apr 28 2011

city: Worcester

first: Scot

last: Wolfe

state: MA

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

library_source: other

data_processing: The sequences from each B1H experiment were labeled using a barcode.  The raw reads were parsed and assigned to the appropriate data set, based on the barcode sequence.  Only reads that matched the expected constant region, or 'barcode' exactly were considered.  N's correspond to randomized positions.  In the case of samples bp_48hrs_10μM_IPTG_0mM_3-AT_plates and 28bp_48hrs_10μM_IPTG_5mM_3-AT_plates, mismatches were allowed at the second position only, which was expected to be a ligated 'T'.  In the case of the N28_initial_library, the last two positions of the expected sequence ('GC'), or 'barcode,' were allowed allowed to be mismatches.

molecule: other

organism: synthetic construct

source_name: B1H randomized library

extract_protocol: A prey library containing a 28bp long randomized region was used for this selection.  A prey library containing a 6bp long randomized region immediately adjacent to the consensus site for finger 1 was used for most of the other selections.  After each selection, all of the cells were scraped off the plate.  The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.  The PCR products from different experiments were digested with different restriction enzymes  in the first step of uniquely encoding sequences from different experiments.  The restriction enzyme fragments were then barcoded, pooled and sequenced using a Illumina Genome Analyzer IIx machine.  See the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed for each selection.

tag: iptg concentration (μm)

tag: 3-at concentration (mm)

tag: duration of experiment (hours)


title: TET1_CH_Methylation_bisulfite_sequencing

description:
Non-CpG DNA methylation.

library strategy: USER-S1-Ligation
library selection: padlock capture


title: Control_CH_Methylation_bisulfite_sequencing


title: mES_TET1_CXXC

description:
ChIP-seq
Genomic DNA bound by Tet1 CXXC.

source_name: ES cells, Tet1 CXXC

treatment_protocol: 2 μg of purified and sonicated E14 mouse embryonic stem cell (mESCs) genomic DNA were incubated with 2 μg of Tet1 CXXC for 1h at room temperature in the binding buffer (50 mM Tris pH 7.4, 5mM MgCl2, 1mM DTT, 3% Glycerol, 0.1% Triton, 1mM EDTA, and 200mM NaCl). The protein bound DNA was purified and followed by deep sequencing.


title: 773_PES_Illumina


title: 773_ES_Illumina


title: mES_TET1_CXXC_mut1

description:
ChIP-seq
Genomic DNA bound by Tet1 CXXC mutant1.

source_name: ES cells, Tet1 CXXC mutant1

treatment_protocol: 2 μg of purified and sonicated E14 mouse embryonic stem cell (mESCs) genomic DNA were incubated with 2 μg of Tet1 CXXC mutant1 for 1h at room temperature in the binding buffer (50 mM Tris pH 7.4, 5mM MgCl2, 1mM DTT, 3% Glycerol, 0.1% Triton, 1mM EDTA, and 200mM NaCl). The protein bound DNA was purified and followed by deep sequencing.


title: GLIB_5hmC+BGT biol rep1

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

description:
hmC-pulldown by GLIB method
instrument: Helicos HeliScope

data_processing:
alignment: Quality filtered reads were aligned to the mouse genome (mm9) using Helicos open source aligner IndexDP Genomic available at the Open Source HeliSphere
peaks: After balancing the number of reads between treatment and control (+BGT and âBGT) by random sampling, enriched regions were calculated by enrichment of treatment reads using a local background model estimated from control reads employing the statistical software MACS.  Enriched regions with a false discovery rate of less than 5% were defined as peaks. Data from both biological replicates were pooled for the analysis shown in this spreadsheets.

source_name: V6.5 ES cells

growth_protocol: ES cells cultured in presence of LIF

extract_protocol: DNA extracted by cell lysis and phenol chloroforme extraction. Sonicated with Covaris S2 to target size 200-400bp

treatment_protocol: Samples were treated with 20ng BGT per 1ug DNA at 30C for 3hr (50mM HEPES pH 8.0, 25 mM MgCl2, 50 uM UDPG for 3 hr at 30C), then oxidized with 23mM Sodium periodate 16hr at 22C in 0.1M Sodium Phosphate pH 7.0. Periodate was quenched by the addition of 46mM Sodium Sulfite at room temperature for 10 minutes, then exchanged into 1xPBS and incubated with 2mM Aldehyde Reactive Probe (Invitrogen) for 1hr at 37C. DNA was then precipitated with M280 Streptavidin Dynabeads (Invitrogen) and eluted by incubation with 95% Formamide 10mM EDTA for 5 minutes. The eluted DNA was chilled, diluted with an equal volume of water, and ethanol precipitated.

tag: biological replicate

value: First

tag: sample prep

value: hmC-pulldown by GLIB method

tag: instrument model

value: Helicos HeliScope


title: GLIB_5hmC-BGT biol rep 2

description:
neg control for GLIB method
instrument: Helicos HeliScope

treatment_protocol: Samples were treated with 0ng BGT per 1ug DNA (negative control) at 30C for 3hr (50mM HEPES pH 8.0, 25 mM MgCl2, 50 uM UDPG for 3 hr at 30C), then oxidized with 23mM Sodium periodate 16hr at 22C in 0.1M Sodium Phosphate pH 7.0. Periodate was quenched by the addition of 46mM Sodium Sulfite at room temperature for 10 minutes, then exchanged into 1xPBS and incubated with 2mM Aldehyde Reactive Probe (Invitrogen) for 1hr at 37C. DNA was then precipitated with M280 Streptavidin Dynabeads (Invitrogen) and eluted by incubation with 95% Formamide 10mM EDTA for 5 minutes. The eluted DNA was chilled, diluted with an equal volume of water, and ethanol precipitated.

value: Second

value: neg control for GLIB method


title: CMS_Input biol rep 1

description:
neg control forhmC mapping by anti-CMS antisera
instrument: Illumina HiSeq, Illumina Genome Analyzer II

data_processing:
alignment: Quality filtered reads were aligned to the mouse genome (mm9) using Bowtie
peaks: After balancing the number of reads between treatment and control (+CMS IP vs. CMS input) by random sampling, enriched regions were calculated by enrichment of treatment reads using a local background model estimated from control reads employing the statistical software MACS.  Enriched regions with a false discovery rate of less than 5% were defined as peaks. Both biological replicates were pooled in the analysis uploaded to GEO.

extract_protocol: Extracted DNA by cell lysis and phenol chloroform extraction. Sonicated with Covaris S2 to target size 150bp. DNA library was prepared using an Illumina Genomic DNA Sample Prep Kit. Briefly, DNA fragments were end-repaired with nucleotide triphosphate mix free of dATP and ligated with cytosine-methylated adapters. Adapter-ligated fragments were treated with sodium bisulfite (Qiagen). DNA was treated with sodium periodate, the precipiated with anti-CMS antisera for 5hmC maping

treatment_protocol: Adapter-ligated fragments were treated with sodium bisulfite (Qiagen). 1% of bisulfite treated fragments were saved as input and 99% were denatured in 0.4 M NaOH, 10 mM EDTA at 95C for 10 min, then neutralized by adding an equal volume of cold 2 M ammonium acetate (pH 7.0). The denatured DNA fragments were incubated with anti-CMS antiserum (generated in house) in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4C, then incubated with pre-equilibrated protein G beads overnight at 4C (beads were pre-washed twice with PBS, 0.1% BSA and once with 1x IP buffer). The beads were then washed with 1x IP buffer three times at 4C and digested with 0.3mg/ml proteinase K in 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5% SDS at 50C for 3 h. DNA fragments were purified by sequential extraction with phenol: chloroform: isoamyl alcohol (25:24:1) and chloroform: isoamyl alcohol (24:1) followed by precipitation with 2 volumes of ethanol containing 400 mM NaCl and 25ug linear polyacrylamide. The input and immunoprecipitated samples were enriched by 4-6 cycles PCR using Pfu TurboCx hotstart DNA polymerase (Stratagene). The reaction products were purified using AMPure XP (Beckman) to remove primer dimers. Completed libraries were quantified using the Qubit system (Invitrogen).


title: GLIB_5hmC-BGT biol rep 1


title: CMS_Input biol rep 2

value: neg control forhmC mapping by anti-CMS antisera

value: Illumina HiSeq, Illumina Genome Analyzer II


title: GLIB_5hmC+BGT biol rep2


title: mES_RNA_Seq_control1

description:
mRNA-seq
cDNA reverse transcribed from the total mRNA of scramble shRNA-treated cells

source_name: ES cells, scramble shRNA

treatment_protocol: E14 ES cells were infected with Scr shRNA containing lentivirus and harvested after 4-days selection with puromycin. Total RNA was extracted using TRIzol reagent (Invitrogen) and genomic DNA was removed by DNaseI digestion. The mRNA was further purified using Dynabeads mRNA purification kit (Invitrogen) and used to synthesize the first strand cDNA using ImPro-IITM Reverse Transcription System (Promega). The second strand cDNA was generated using DNA Pol I (Invitrogen) and the final double-stranded DNA (dsDNA) was purified using QIAquick PCR purification kit (Qiagen) and quantified by Qubit fluorometer (Invitrogen). 300 ng of dsDNA of each sample was fragmented by sonication and used to generate the sequencing library.

tag: cell type

value: mouse embryonic stem (MES) cells

value: scramble shRNA


title: CMS_IP biol rep 2

description:
hmC mapping by anti-CMS antisera
instrument: Illumina HiSeq, Illumina Genome Analyzer II

value: hmC mapping by anti-CMS antisera


title: mES_Input_for_TET1

description:
ChIP-seq
Input.

source_name: ES cells, input

tag: antibody


title: mES_Input_for_5hmC

description:
hMeDIP-seq
Input.

tag: cell line


title: CMS_IP biol rep 1


title: MeDIP

description:
MeDIP
instrument: Helicos HeliScope

data_processing:
alignment: Quality filtered reads were aligned to the mouse genome (mm9) using Helicos open source aligner IndexDP Genomic available at the Open Source HeliSphere
peaks: After balancing the number of reads between treatment and control (MeDIP and GLIB negative control files glib_d_1_ctrl.fa, glib_e_1_ctrl.fa, glib_e_2_ctrl.fa, glib_e_3_ctrl.fa) by random sampling, enriched regions were calculated by enrichment of treatment reads using a local background model estimated from control reads employing the statistical software MACS.  Enriched regions with a false discovery rate of less than 5% were defined as peaks. The MeDIP was normalized against the GLIB -BGT samples to make the 5hmC and 5mC mappings directly comparable.

treatment_protocol: 4 ug of genomic DNA (20 uL) was combined with 30 uL TE and 40 uL 1M NaOH, 25 mM EDTA. The samples were boiled for 10 min at 95C, then quenched by adding 100 uL 2 M ammonium acetate pH 7.0. The samples were then chilled on ice. After 10 min, 250 uL TE, 50 uL 10x IP buffer (100 mM sodium phosphate pH 7.0, 1.4 M NaCl, 0.5% Triton X-100), and 10 uL monoclonal anti-5-methylcytosine antibody (Calbiochem, cat number: NA81, lot number: D00099896) were added to each sample. The samples were then rotated at 4C for 2 h, the beads were collected with a magnetic rack, and washed 3x with 700 uL 1x IP buffer at room temperature using a rotating platform. The beads were then suspended in 70 ug of Proteinase K and incubated for 3 h at 50C on a shaking (800 rpm) heat block, and the DNA was extracted with phenol-chloroform, followed by ethanol precipitation.

value: Only

value: MeDIP


title: RNAseq from primary human CD4+ T-cells

status: Public on Apr 19 2011

city: Stanford

first: Anton

last: Valouev

state: CA

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

description:
CD4_RNAseq
mRNA purified from primary human CD4+ T-cells

data_processing: All sequence reads were aligned using SOLiD pipeline to human hg18 reference genome using the first 25 bps and allowing for up to two mismatches. RNA-Seq data was processed using custom scripts to obtain RPKM values for each gene isoform based on hg19 RefSeq annotation.

source_name: primary CD4+ T-cells

growth_protocol: Cells were obtained from donor buffy coat and purified using sucrose gradient and Ig-beads

extract_protocol: Trizol-extracted RNA was used for poly-A purification using Qiagen Oligotex kit. RNA-seq SOLiD sequencing library was constructed from 100ng of poly-A RNA using SOLiD whole-transcriptome analysis kit

value: CD4+ T-cells


title: In vitro reconstituted nucleosome cores_2

description:
Invitrosomes_2
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification

source_name: granulocytes

extract_protocol: Naked genomic DNA isolated from neutrophil granulocytes from our in vivo studies was sheared by sonication using a Covaris sonicator and separated on a 1% UltraPure Agarose (Invitrogen) gel run at 100 V for 1 hour. A smear of fragments with lengths from 850-2000 base pairs (the bulk of the sheared DNA) was isolated and extracted from the gel using the QIAquick Gel Extraction Kit (Qiagen). The ends of the sheared DNA fragments were repaired as described below and then were assembled with recombinant Xenopus histones into nucleosomes as described in# at a 1.1:1 molar ratio of DNA to histone octamer such that on average one nucleosome would occupy 850 bp of DNA.  Specifically 4.9ug of DNA and 0.80ug of octamer were reconstituted in a total volume of 200ul.

value: Granulocytes


title: In vitro reconstituted nucleosome cores_5

description:
Invitrosomes_5
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification


title: Granulocyte nucleosome cores_10

description:
Gran_TC_cores_10
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification

source_name: primary granulocytes (mostly neutrophils)

extract_protocol: The ends of isolated mononucleosome core DNAs (Granulocyte neutrophils) were processed by treating 0.3 ug - 0.5 ug of the DNA samples with T4 polynucleotide kinase (New England Biolabs) at 37oC for 2.5 hours followed by ethanol precipitation and subsequent treatment with T4 DNA polymerase (New England Biolabs) in the presence of dNTPs for 15 min at 12oC.  After purification using either the QIAquick Gel Extraction Kit as described above or the QIAquick PCR Purification Kit (Qiagen), linkering of previously annealed duplexes AF-SJ-47 (5' OH-CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT 3’) / AF-SJ-48 (5' Pi-ATCACCGACTGCCCATAGAGAGGAAAGCGGAGGCGTAGTGGTT 3’) and AF-SJ-49 (5' OH-CTGCCCCGGGTTCCTCATTCTCT 3’) / AF-SJ-50 (5' Pi-AGAGAATGAGGAACCCGGGGCAGTT 3’) to the samples was accomplished by T4 DNA ligase during a 6.5-hour room-temperature incubation.  The ligation reactions were separated on a 2% agarose gel, and the relevant band isolated as described above.  Amplification of the linkered libraries was accomplished with 8 (granulocyte mononucleosome library), 10 (CD4+ lymphocytes, CD8+ lymphocytes and genomic control libraries) or 12 (in vitro library) cycles of polymerase chair reaction (PCR) using primers AF-SJ-47 (SOLiD P1 primer) and AF-SJ-49 (SOLiD P2 primer) with subsequent separation and purification using a 2% agarose gel and the QIAquick Gel Extraction Kit as described above. The number of cycles used in the PCR amplification were monitored and selected as described in (Gu and Fire Chromosoma 2009).


title: Micrococcal nuclease treated control genomic DNA_3

description:
Mnase_control_3
Purified human genomic DNA lightly treated with micrococcal nuclease

extract_protocol: For control libraries, genomic DNA (20 ug) from human neutrophil granulocytes in 0.34 M sucrose/Buffer A/1X BSA (New England Biolabs) /1mM CaCl2 was digested with 200 units of micrococcal nuclease (Roche) (0.4 units/ul final concentration) in a total volume of 500ul for 10 minutes at 23oC.  The digestion was stopped by addition of 10ul 0.5M EDTA, followed by ethanol precipitation. The digested DNA was run on a 2.5% agarose gel and the smear of DNA fragments from 135bp-225bp was excised from the gel and purified using the QIAquick Gel Extraction Kit (Qiagen) as noted above.


title: RNAseq from primary human CD8+ T-cells_1-3

description:
CD8_RNAseq_1
mRNA purified from primary human CD8+ T-cells

source_name: primary CD8+ T-cells

value: CD8+ T-cells


title: Micrococcal nuclease treated control genomic DNA_2

description:
Mnase_control_2
Purified human genomic DNA lightly treated with micrococcal nuclease


title: In vitro reconstituted nucleosome cores_1

description:
Invitrosomes_1
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification


title: In vitro reconstituted nucleosome cores_4

description:
Invitrosomes_4
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification


title: In vitro reconstituted nucleosome cores_3

description:
Invitrosomes_3
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification


title: Micrococcal nuclease treated control genomic DNA_1

description:
Mnase_control_1
Purified human genomic DNA lightly treated with micrococcal nuclease


title: In vitro reconstituted nucleosome cores_6

description:
Invitrosomes_6
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification


title: Granulocyte nucleosome cores_9

description:
Gran_TC_cores_9
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_8

description:
Gran_TC_cores_8
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_7

description:
Gran_TC_cores_7
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_5

description:
Gran_TC_cores_5
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_3

description:
Gran_TC_cores_3
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: CD8+ T-cell nucleosome cores_4

description:
CD8_TC_cores_4
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification

extract_protocol: The ends of isolated mononucleosome core DNAs (C8+ T-cells) were processed by treating 0.3 ug - 0.5 ug of the DNA samples with T4 polynucleotide kinase (New England Biolabs) at 37oC for 2.5 hours followed by ethanol precipitation and subsequent treatment with T4 DNA polymerase (New England Biolabs) in the presence of dNTPs for 15 min at 12oC.  After purification using either the QIAquick Gel Extraction Kit as described above or the QIAquick PCR Purification Kit (Qiagen), linkering of previously annealed duplexes AF-SJ-47 (5' OH-CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT 3’) / AF-SJ-48 (5' Pi-ATCACCGACTGCCCATAGAGAGGAAAGCGGAGGCGTAGTGGTT 3’) and AF-SJ-49 (5' OH-CTGCCCCGGGTTCCTCATTCTCT 3’) / AF-SJ-50 (5' Pi-AGAGAATGAGGAACCCGGGGCAGTT 3’) to the samples was accomplished by T4 DNA ligase during a 6.5-hour room-temperature incubation.  The ligation reactions were separated on a 2% agarose gel, and the relevant band isolated as described above.  Amplification of the linkered libraries was accomplished with 8 (granulocyte mononucleosome library), 10 (CD4+ lymphocytes, CD8+ lymphocytes and genomic control libraries) or 12 (in vitro library) cycles of polymerase chair reaction (PCR) using primers AF-SJ-47 (SOLiD P1 primer) and AF-SJ-49 (SOLiD P2 primer) with subsequent separation and purification using a 2% agarose gel and the QIAquick Gel Extraction Kit as described above. The number of cycles used in the PCR amplification were monitored and selected as described in (Gu and Fire Chromosoma 2009).


title: Granulocyte nucleosome cores_2

description:
Gran_TC_cores_2
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_1

description:
Gran_TC_cores_1
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_6

description:
Gran_TC_cores_6
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: RNAseq from primary human Granulocytes_1-3

description:
Gran_RNAseq_1
mRNA purified from primary human Granulocytes

source_name: primary granulocytes


title: CD8+ T-cell nucleosome cores_2

description:
CD8_TC_cores_2
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: CD8+ T-cell nucleosome cores_1

description:
CD8_TC_cores_1
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: CD4+ T-cell nucleosome cores_2

description:
CD4_TC_cores_2
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification

extract_protocol: The ends of isolated mononucleosome core DNAs (CD4+ T-cells) were processed by treating 0.3 ug - 0.5 ug of the DNA samples with T4 polynucleotide kinase (New England Biolabs) at 37oC for 2.5 hours followed by ethanol precipitation and subsequent treatment with T4 DNA polymerase (New England Biolabs) in the presence of dNTPs for 15 min at 12oC.  After purification using either the QIAquick Gel Extraction Kit as described above or the QIAquick PCR Purification Kit (Qiagen), linkering of previously annealed duplexes AF-SJ-47 (5' OH-CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT 3’) / AF-SJ-48 (5' Pi-ATCACCGACTGCCCATAGAGAGGAAAGCGGAGGCGTAGTGGTT 3’) and AF-SJ-49 (5' OH-CTGCCCCGGGTTCCTCATTCTCT 3’) / AF-SJ-50 (5' Pi-AGAGAATGAGGAACCCGGGGCAGTT 3’) to the samples was accomplished by T4 DNA ligase during a 6.5-hour room-temperature incubation.  The ligation reactions were separated on a 2% agarose gel, and the relevant band isolated as described above.  Amplification of the linkered libraries was accomplished with 8 (granulocyte mononucleosome library), 10 (CD4+ lymphocytes, CD8+ lymphocytes and genomic control libraries) or 12 (in vitro library) cycles of polymerase chair reaction (PCR) using primers AF-SJ-47 (SOLiD P1 primer) and AF-SJ-49 (SOLiD P2 primer) with subsequent separation and purification using a 2% agarose gel and the QIAquick Gel Extraction Kit as described above. The number of cycles used in the PCR amplification were monitored and selected as described in (Gu and Fire Chromosoma 2009).


title: CD4+ T-cell nucleosome cores_4

description:
CD4_TC_cores_4
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: CD4+ T-cell nucleosome cores_3

description:
CD4_TC_cores_3
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: CD4+ T-cell nucleosome cores_1

description:
CD4_TC_cores_1
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Granulocyte nucleosome cores_4

description:
Gran_TC_cores_4
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: CD8+ T-cell nucleosome cores_3

description:
CD8_TC_cores_3
Nucleosome-bound DNA isolated by micrococcal-treatment of chromatin, followed by gel purification


title: Two-step_purification_AGO4-associated_sRNAs_seedling

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: smRNA sequencing data of AGO4-associated smRNAs in seedlings, two-step purification

data_processing: Adapters were removed by Perl script, if a hit with at most 1 mismatch to the first 4-nt of the adapter sequence could be found. After adapter removal, only 19-28 nt reads were aligned to the Arabidopsis thaliana genome (TAIR9) using C program. The small RNAs with perfect genomic matches are used for further analysis.

organism: Arabidopsis thaliana

source_name: TSP seedling

growth_protocol: Flowers were collected from 6-week-old plants grown on soil in a growth chamber under 12 hr light/12 hr dark at 21°C. Leaves and roots were harvested from 4-week-old plants grown hydroponically under 12 hr light/12 hr dark at 21°C in the MGRL medium. Seedlings were grown on MS plates in a growth chamber under 16 hr light/8 hr dark at 21°C.

extract_protocol: For two-step purification of AGO/smRNA complexes, cleared extracts were fractioned on Superdex 200 10/300 columns (Akta-FPLC, GE) and further immunoprecipitated. After size-fractionation, total RNA or RNA recovered from the purified AGO-smRNA complexes were ligated to 3'² adapter (AppTCGTATGCCGTCTTCTGCTTG-L) and 5'² adapter (rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC) sequentially. The ligated products were amplified by RT-PCR and used for Illumina's deep sequencing.

value: seedling

tag: smrna

value: AGO4-associated small RNAs


title: Two-step_purification_AGO4-associated_sRNAs_leaf

description: smRNA sequencing data of AGO4-associated smRNAs in leaves, two-step purification

source_name: TSP leaf

value: leaf


title: IP_AGO1-associated_sRNAs_flower

description: smRNA sequencing data of AGO1-associated smRNAs in flowers, IP

source_name: IP flower

value: flower

value: AGO1-associated small RNAs


title: Two-step_purification_AGO1-associated_sRNAs_leaf

description: smRNA sequencing data of AGO1-associated smRNAs in leaves, two-step purification


title: Two-step_purification_AGO1-associated_sRNAs_seedling

description: smRNA sequencing data of AGO1-associated smRNAs in seedlings, two-step purification


title: Two-step_purification_AGO1-associated_sRNAs_flower

description: smRNA sequencing data of AGO1-associated smRNAs in flowers, two-step purification

source_name: TSP flower


title: Two-step_purification_AGO4-associated_sRNAs_flower

description: smRNA sequencing data of AGO4-associated smRNAs in flowers, two-step purification


title: Two-step_purification_AGO1-associated_sRNAs_root

description: smRNA sequencing data of AGO1-associated smRNAs in roots, two-step purification

source_name: TSP root

value: root


title: IP_AGO1-associated_sRNAs_root

description: smRNA sequencing data of AGO1-associated smRNAs in roots, IP

source_name: IP root


title: Th2_rep2

status: Public on Apr 16 2011

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

country: United Kingdom

institute: University of Warwick

description: Biological replicate 2 of 2.

data_processing: Reads were mapped to mm9 with Bowtie -m 1 --best -strata --solexa1.3-quals

molecule: polyA RNA

source_name: Th2 cells

growth_protocol: Murine CD4+CD62L+ splenocytes were activated for 5 days with anti-CD3/CD28 in the presence of 10 ng/ml IL-4 and 2 ug/ml anti-IFN-g, followed by 3 days of resting.

extract_protocol: Poly(A)+ RNA was isolated from cells using the Oligotex Direct mRNA kit (Qiagen), followed by 1st and 2nd strand synthesis using the JustcDNA kit (Stratagene), followed by sonication, followed by library preparation using the Illumina ChIP-seq sample prep kit.

tag: strain

value: T helper cell type 2 (Th2)


title: Th2_rep1

description: Biological replicate 1 of 2.


title: WT-flower

description: smRNA sequencing data of total smRNAs in flowers

source_name: total flower

value: total small RNAs


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17785

status: Public on Apr 14 2011

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17785
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7049
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7048
****************
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: GSM701531_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23941.DS17785.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17785.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23941, Library DS17785 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.7701
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,181,717
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3414
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3407
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9959
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3757
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM701531_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23941.DS17785.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17785.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Large, Donor H-23941, Library DS17785 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.7755
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 4
BROWSER_TRACK_NAME: FIL DNase 41 85
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23941 Library DS17785 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,181,717
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3414
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3407
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9959
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3757
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal  primary tissue, day 120; DS17785

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Intestine, Large

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 120

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of CD4 Primary Cells; DS17881

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17881
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7019
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018
****************
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: GSM701539_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17881.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17881.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD4 Primary Cells, Donor RO 01701, Library DS17881 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.7693
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,073,018
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5922
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6006
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9858
IROC_PERCENTILE: 7
POISSON_SCORE: 0.5629
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701539_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17881.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17881.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD4 Primary Cells, Donor RO 01701, Library DS17881 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.7747
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 4
BROWSER_TRACK_NAME: CD4 DNase 36 81
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17881 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,073,018
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5922
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6006
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9858
IROC_PERCENTILE: 7
POISSON_SCORE: 0.5629
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: flow sorted CD4+ Cells, year 37; DS17881

value: CD4 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic


title: Chromatin accessibility assay of Fetal Stomach; DS17878

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17878
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7169
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7168
****************
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: GSM701538_UW.Fetal_Stomach.ChromatinAccessibility.H-23964.DS17878.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17878.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-23964, Library DS17878 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.7692
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,730,264
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4188
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4253
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9909
IROC_PERCENTILE: 24
POISSON_SCORE: 0.488
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701538_UW.Fetal_Stomach.ChromatinAccessibility.H-23964.DS17878.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17878.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-23964, Library DS17878 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.7746
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 4
BROWSER_TRACK_NAME: FS DNase 64 78
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-23964 Library DS17878 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,730,264
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4188
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4253
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9909
IROC_PERCENTILE: 24
POISSON_SCORE: 0.488
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal  primary tissue, day 98; DS17878

value: Fetal Stomach

value: day 98


title: Chromatin accessibility assay of CD8 Primary Cells; DS17885

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17885
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7036
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035
****************
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: GSM701540_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01701.DS17885.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17885.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD8 Primary Cells, Donor RO 01701, Library DS17885 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.7695
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,666,428
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6247
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6249
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9917
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5757
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM701540_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01701.DS17885.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17885.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD8 Primary Cells, Donor RO 01701, Library DS17885 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.7749
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 4
BROWSER_TRACK_NAME: CD8 DNase 36 85
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17885 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,666,428
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.6247
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6249
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9917
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5757
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: flow sorted CD8+ Cells, year 37; DS17885

value: CD8 Primary Cells

value: genomic DNA


title: Chromatin accessibility assay of Fetal Lung, Left; DS17835

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: DS17835
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7240
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7239
****************
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: GSM701534_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23964.DS17835.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17835.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23964, Library DS17835 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.7682
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,524,426
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5098
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.5317
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9965
IROC_PERCENTILE: 74
POISSON_SCORE: 0.5299
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM701534_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23964.DS17835.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17835.hg19.level.2.release.4
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-23964, Library DS17835 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.7736
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 4
BROWSER_TRACK_NAME: FLL DNase 64 35
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23964 Library DS17835 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,524,426
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5098
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.5317
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9965
IROC_PERCENTILE: 74
POISSON_SCORE: 0.5299
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal  primary tissue, day 98; DS17835

value: Fetal Lung, Left

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

value: Primary Tissue

value: UW


title: Chromatin accessibility assay of Fetal Renal Cortex; DS17804

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17804
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7112
****************
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: GSM701532_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23941.DS17804.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17804.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-23941, Library DS17804 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.7678
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,779,200
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4472
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4447
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9933
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5097
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM701532_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23941.DS17804.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17804.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-23941, Library DS17804 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.7732
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 4
BROWSER_TRACK_NAME: FRC DNase 41 04
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-23941 Library DS17804 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,779,200
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4472
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4447
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9933
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5097
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Fetal  primary tissue, day 120; DS17804

value: Fetal Renal Cortex

value: fetal

value: day 120

value: Female

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Muscle, Back; DS17850

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17850
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7286
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7285
****************
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: GSM701536_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23964.DS17850.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17850.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-23964, Library DS17850 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.7686
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,794,042
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5136
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5135
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9942
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5606
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701536_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23964.DS17850.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17850.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-23964, Library DS17850 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.7740
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 4
BROWSER_TRACK_NAME: FMB DNase 64 50
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-23964 Library DS17850 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,794,042
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5136
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5135
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9942
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5606
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 98; DS17850

value: Fetal Muscle, Back

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: WT-seedling

description: smRNA sequencing data of total smRNAs in seedlings

source_name: total seedling

tag: tissue

value: seedling

value: total small RNAs


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS17848

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17848
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7250
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7249
****************
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: GSM701535_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23964.DS17848.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17848.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-23964, Library DS17848 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.7685
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,640,881
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4411
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4374
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9924
IROC_PERCENTILE: 31
POISSON_SCORE: 0.5052
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM701535_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23964.DS17848.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17848.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-23964, Library DS17848 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.7739
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 4
BROWSER_TRACK_NAME: FMA DNase 64 48
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-23964 Library DS17848 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,640,881
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4411
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4374
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9924
IROC_PERCENTILE: 31
POISSON_SCORE: 0.5052
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Fetal  primary tissue, day 98; DS17848

value: Fetal Muscle, Arm

value: day 98


title: Chromatin accessibility assay of Fetal Thymus; DS17875

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17875
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7181
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7180
****************
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: GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17875.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-23964, Library DS17875 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.7691
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,577,108
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2815
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2823
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.318
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17875.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-23964, Library DS17875 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.7745
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 4
BROWSER_TRACK_NAME: FT DNase 64 75
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23964 Library DS17875 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,577,108
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2815
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2823
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.318
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal  primary tissue, day 98; DS17875

value: Fetal Thymus

value: genomic DNA


title: Two-step_purification_AGO4-associated_sRNAs_root

description: smRNA sequencing data of AGO4-associated smRNAs in roots, two-step purification

value: root

value: AGO4-associated small RNAs


title: Chromatin accessibility assay of CD14 Primary Cells; DS17889

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17889
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6963
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6962
****************
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: GSM701541_UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17889.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD14 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD14 Primary Cells, Donor RO 01701, Library DS17889 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.7698
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,198,925
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4007
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4013
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3974
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM701541_UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17889.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD14 Primary Cells, Donor RO 01701, Library DS17889 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.7752
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 4
BROWSER_TRACK_NAME: CD14 DNase 36 89
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17889 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,198,925
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4007
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4013
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3974
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD14+ Cells, year 37; DS17889

value: CD14 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Male

value: Hispanic


title: WT-root

description: smRNA sequencing data of total smRNAs in roots

source_name: total root


title: Chromatin accessibility assay of Fetal Muscle, Trunk; DS17827

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17827
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7253
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7252
****************
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: GSM701533_UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-23941.DS17827.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17827.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Trunk, Donor H-23941, Library DS17827 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.7681
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,394,158
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5237
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5188
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9941
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5627
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701533_UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-23941.DS17827.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17827.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Trunk, Donor H-23941, Library DS17827 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.7735
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 4
BROWSER_TRACK_NAME: FMT DNase 41 27
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-23941 Library DS17827 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,394,158
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5237
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5188
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9941
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5627
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 120; DS17827

value: Fetal Muscle, Trunk

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

value: Primary Tissue

value: UW

value: fetal

value: day 120

value: Female

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17763

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17763
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7063
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7062
****************
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: GSM701530_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23914.DS17763.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17763.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23914, Library DS17763 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.7699
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,085,147
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4514
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.4493
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9978
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4837
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701530_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23914.DS17763.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17763.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Small, Donor H-23914, Library DS17763 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.7753
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 4
BROWSER_TRACK_NAME: FIS DNase 14 63
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23914 Library DS17763 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,085,147
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4514
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.4493
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9978
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4837
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 91; DS17763

value: Fetal Intestine, Small

value: genomic DNA

value: day 91

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)