title: genomic DNA from patient cHGA-HGG7


title: genomic DNA from patient cHGA-HGG19

status: Public on Mar 09 2014

type: genomic

city: Montrea

first: Simon

last: Papillon-Cavanagh

state: Quebec

address: 740 Dr Penfield

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: We removed probes with missing values, binding multiple genomic regions, binding targets with known sequence variants (1000 Genomes Project, SNPs with a minor allele frequency ≥ 2/120), or being located on the X or Y chromosomes. The final set contains 309,015 probes

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: mutation

value: WT

tag: tissue

value: glioblastomas


title: genomic DNA from patient GLIOMA 4

source_name: GLIOMA 4


title: genomic DNA from patient GLIOMA 1

source_name: GLIOMA 1

tag: brain region

value: Infratentorial Midline (DIPG)


title: MDA142

status: Public on Feb 10 2014

type: RNA

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

country: USA

institute: Md Anderson Cancer center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were quantile normalized and extracted from GenomeStudio

label: biotin

molecule: total RNA

source_name: Bladder tumor

label_protocol: Biotinylated cRNA were prepared with Illumina RNA amplification kit

extract_protocol: Total RNA was extracted by mirVANA miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer.

tag: cstage

tag: gender

value: male


title: MDA138

value: Male


title: MDA146

value: female


title: genomic DNA from patient cHGA-HGG28


title: MDA135


title: MDA150


title: MDA148


title: MDA147


title: MDA134


title: genomic DNA from patient cHGA-HGG39


title: MDA139


title: MDA131


title: MDA123

value: Female


title: MDA122


title: MDA125


title: MDA117


title: MDA127


title: MDA121


title: MDA115


title: MDA113


title: genomic DNA from patient cHGA-HGG10


title: genomic DNA from patient cHGA-HGG14


title: MDA102


title: MDA100


title: MDA105


title: MDA82


title: MDA88


title: MDA90


title: MDA106


title: MDA107


title: MDA93


title: MDA101


title: MDA96


title: MDA86


title: MDA92


title: MDA98


title: MDA79


title: MDA87


title: MDA78


title: MDA65


title: MDA67


title: MDA44


title: MDA48

tag: fgfr3 mutation (1;yes, 0;no)

tag: ras mutation (1;yes, 0;no)

tag: rb1 mutation (1;yes, 0;no)

tag: p53 mutation (1;yes, 0;no)

tag: age (at specimen collection)

tag: os censor

value: censored

tag: dss censor

tag: survival (mo)


title: MDA75


title: MDA64


title: MDA41

value: cTa


title: MDA56


title: MDA40


title: MDA52


title: Exon array of fIntestine Small. UW (NREMC); Fetal Intestine, Small primary tissue, day 110; DS16559-exon

status: Public on Mar 04 2014

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15263
sample alias: fIntestine_Small.H-23604d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5413

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymterix Gene Chip Scanner 3000

data_processing: Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

tag: disease

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

value: Primary Tissue

value: Fetal Intestine, Small

value: UW

value: fetal

value: day 110


title: MDA36


title: Exon array of fIntestine Large. UW(NREMC); Fetal Intestine, Large primary tissue, day 110; DS16563-exon

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15265
sample alias: fIntestine_Large.H-23604d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5426

value: Fetal Intestine, Large


title: Exon array of fIntestine Large. UW (NREMC); Fetal Intestine, Large primary tissue, day 105; DS16164-exon

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15267
sample alias: fIntestine_Large.H-23524d105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5421

value: day 105


title: MDA62


title: MDA30

value: uncensored


title: MDA28


title: MDA35


title: MDA33


title: MDA34


title: MDA39


title: MDA32


title: MDA37


title: MDA29


title: MDA16


title: MDA14


title: MDA22


title: MDA25


title: MDA21


title: MDA19


title: MDA26


title: MDA18


title: MDA27


title: MDA38


title: MDA12


title: MDA15


title: MDA17


title: MDA10


title: MDA23


title: MDA9


title: MDA11


title: MDA8


title: MDA6


title: MDA7


title: MDA4


title: MDA1


title: MDA5


title: PHIL_FFPE40

hyb_protocol: Standard Illumina whole genome DASL hybridization protocol

data_processing: Quantile normalization in the Linear Models for Microarray Data (LIMMA) package in the R language environment was used to normalize the data

label: whole genome DASL

label_protocol: Standard Illuminal whole genome DASL method

extract_protocol: Total RNA from FFPE was extracted by High Pure miRNA Isolation Kit (Roche). Quality control was performed by NanoDrop ND-1000.


title: MDA2


title: PHIL_FFPE36


title: PHIL_FFPE43


title: PHIL_FFPE42


title: PHIL_FFPE39


title: PHIL_FFPE41


title: PHIL_FFPE38


title: PHIL_FFPE37


title: PHIL_FFPE32


title: PHIL_FFPE34


title: PHIL_FFPE33


title: Exon array of fIntestine Large. UW (NREMC); Fetal Intestine, Large primary tissue, day 103; DS16027-exon

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15269
sample alias: fIntestine_Large.H-23500d103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5409

value: day 103


title: PHIL_FFPE30


title: PHIL_FFPE29


title: PHIL_FFPE26


title: PHIL_FFPE21


title: PHIL_FFPE28


title: PHIL_FFPE24


title: PHIL_FFPE20


title: PHIL_FFPE16


title: PHIL_FFPE11


title: PHIL_FFPE25


title: PHIL_FFPE22


title: PHIL_FFPE31


title: PHIL_FFPE35


title: PHIL_FFPE12


title: PHIL_FFPE8


title: PHIL_FFPE27


title: PHIL_FFPE18


title: PHIL_FFPE4


title: PHIL_FFPE23


title: PHIL_FFPE19


title: PHIL_FFPE17


title: PHIL_FFPE14


title: PHIL_FFPE15


title: PHIL_FFPE13


title: PHIL_FFPE7


title: PHIL_FFPE9


title: PHIL_FFPE5


title: PHIL_FFPE10


title: PHIL_FFPE1


title: MDA_FFPE80

tag: histology tur

value: urothelial

tag: pstage

tag: cystectomy histology

value: urothelial and cis

tag: nac

value: yes-MVAC/A

tag: age (at diagnosis)

tag: race

value: Caucasian

value: M


title: PHIL_FFPE6

tag: cstage


title: MDA_FFPE54

value: no

tag: gender

value: censored


title: MDA_FFPE55

value: focal micropapillary

value: Black


title: MDA_FFPE50


title: MDA_FFPE41

value: Hispanic


title: MDA_FFPE33

value: F


title: PHIL_FFPE2


title: MDA_FFPE52

value: squamous diff


title: MDA_FFPE42


title: MDA_FFPE37

value: micropapillary

value: urothelial signet ring features


title: MDA_FFPE38


title: MDA_FFPE57


title: MDA_FFPE49


title: MDA_FFPE46


title: PHIL_FFPE3


title: MDA_FFPE48


title: MDA_FFPE36

value: micropapillary/focal glandular


title: MDA_FFPE45

value: uncensored


title: MDA_FFPE44

value: micropapillary/focal squamous


title: MDA_FFPE53

value: urothelial


title: MDA_FFPE40


title: MDA_FFPE34


title: MDA_FFPE47


title: MDA_FFPE43


title: MDA_FFPE39


title: MDA_FFPE51


title: MDA_FFPE32


title: MDA_FFPE56


title: MDA_FFPE31

value: urothelial focal glandular

value: White


title: MDA_FFPE30

value: urothelial, focal glandular


title: MDA_FFPE35

value: Caucasian

value: M


title: MDA_FFPE26

value: focal glandular

value: no

value: Asian

value: censored


title: MDA_FFPE16

value: F


title: MDA_FFPE29

value: squamous diff


title: MDA_FFPE8


title: MDA_FFPE12


title: MDA_FFPE27

value: micropapillary


title: MDA_FFPE25


title: MDA_FFPE17

value: sarcomatoid diff

value: Black


title: MDA_FFPE7


title: MDA_FFPE18


title: MDA_FFPE3


title: MDA_FFPE22


title: MDA_FFPE20


title: MDA_FFPE11

value: uncensored


title: MDA_FFPE21


title: MDA_FFPE9


title: MDA_FFPE23


title: MDA_FFPE28


title: MDA_FFPE19

value: Hispanic


title: MDA_FFPE5

value: urothelial


title: MDA_FFPE13


title: MDA_FFPE2


title: MDA_FFPE10


title: MDA_FFPE14


title: MDA_FFPE6


title: MDA_FFPE1


title: MDA_FFPE24

value: lymphoepithelioma, focal glandular


title: MDA_FFPE15

value: urothelial ?sarc diff


title: MDA_FFPE4


title: Transformant yeast 1 M sorbitol 60 min rep1

status: Public on Feb 01 2014

city: Braunschweig

first: Anna

last: Buschart

address: Inhoffenstr. 7

department: BiSA

country: Germany

institute: Helmholtz-Centre for Infection Research

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix GeneChip Yeast Genome 2.0 Arrays for 16 hours at 45°C. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the mini_euk2v3_FS450 protocol (Affymetrix).

scan_protocol: Image analysis was performed using a GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix).

data_processing: Raw intensities were RMA (robust multi-array average) normalized using the affy package of Bioconductor/R.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae expressing C. albicans Nik1p, sorbitol, 60 min

label_protocol: 500 ng of total RNA were used for biotin labeling according to the 3´ IVT Express Kit (Affymetrix).

growth_protocol: S. cerevisiae transformants were maintained in SD-ura (0.67% yeast nitrogen base without amino acids, 2% glucose, nucleosides and amino acids according to Rose, M. D., Winston, F., and Hieter, P. (1990) Methods in Yeast Genetics: A Laboratory Course Manual, Revised Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, without uracil) at 30°C.

extract_protocol: Cells were disrupted using glass beads (425-600 µm, Sigma) in the presence of lysis buffer (Qiagen RLT). RNA was isolated using RNeasy columns (Qiagen) according to the manufacturer's protocol.

treatment_protocol:
Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h, and functional analysis of the recombinant strain was carried out in SG-ura.
Cultures were treated with 1 M sorbitol.

tag: strain

tag: expression vector

tag: treatment

value: 1 M sorbitol

tag: duration of treatment

value: 60 min


title: Transformant yeast 1 M sorbitol 15 min rep1

source_name: S. cerevisiae expressing C. albicans Nik1p, sorbitol, 15 min

value: 15 min


title: Transformant yeast untreated 60 min rep1

source_name: S. cerevisiae expressing C. albicans Nik1p, untreated, 60 min

treatment_protocol:
Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h, and functional analysis of the recombinant strain was carried out in SG-ura.
Cultures were untreated.


title: Transformant yeast 10 µg/ml fludioxonil 60 min rep2

source_name: S. cerevisiae expressing C. albicans Nik1p, fludioxonil, 60 min

treatment_protocol:
Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h, and functional analysis of the recombinant strain was carried out in SG-ura.
Cultures were treated with 10 µg/ml fludioxonil.

value: 10 µg/ml fludioxonil


title: Transformant yeast 1 M sorbitol 30 min rep1

source_name: S. cerevisiae expressing C. albicans Nik1p, sorbitol, 30 min

value: 30 min


title: Transformant yeast 1 M sorbitol 30 min rep2


title: Transformant yeast 1 M sorbitol 60 min rep2


title: Transformant yeast 10 µg/ml fludioxonil 60 min rep1


title: Transformant yeast untreated 30 min rep1

source_name: S. cerevisiae expressing C. albicans Nik1p, untreated, 30 min


title: Transformant yeast  untreated 15 min rep1

source_name: S. cerevisiae expressing C. albicans Nik1p, untreated, 15 min


title: Transformant yeast 10 µg/ml fludioxonil 15 min rep2

source_name: S. cerevisiae expressing C. albicans Nik1p, fludioxonil, 15 min


title: Transformant yeast 10 µg/ml fludioxonil 30 min rep1

source_name: S. cerevisiae expressing C. albicans Nik1p, fludioxonil, 30 min


title: Transformant yeast untreated 60 min rep2


title: Transformant yeast 10 µg/ml fludioxonil 15 min rep1


title: Transformant yeast 10 µg/ml fludioxonil 30 min rep2


title: Transformant yeast 1 M sorbitol 15 min rep2


title: before EMT, biological rep3

status: Public on Jan 01 2014

city: San Francisco

first: Megan

last: Salt

state: California

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

description: Gene expression data from H358-GFP expressing cells after 12d 100nM 4OHT treatment

hyb_protocol: RNA was hybridized according to standard Affymetrix protocol on Human Gene 1.0 ST arrays by the Gladstone Institute Genomics Core

scan_protocol: Human Gene 1.0 ST Arrays were scanned on an Affymetrix GeneChip Scanner 3000 by the Gladstone Institute Genomics Core according to Affymetrix protocols.

data_processing: Data was analyzed by the Gladstone Genomics Core facility. The RMA algorithm was used.

source_name: Cells expressing GFP treated with 4OHT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by the Gladstone Institute Genomics Core

growth_protocol: Cells were grown in RPMI-1640 media supplmented with 10% FBS and were passaged every 3-4 days.

extract_protocol: Total RNA was extracted using a Qiagen RNEasy kit according to manufacturer's protocol, including optional Dnase treatment.

treatment_protocol: 100nM 4-hydroxytamoxifen (4OHT) was added to cultures for 12 days and replenished after each passage

tag: cell type

value: NSCLC cell line

tag: cell line

value: GFP


title: after EMT, biological rep3

description: Gene expression data from H358-TwistER expressing cells after 12d 100nM 4OHT treatment

source_name: Cells expressing TwistER treated with 4OHT

value: TwistER


title: after EMT, biological rep1


title: Transformant yeast untreated 15 min rep2


title: HCP3 N2 EEMB Hybridization Rep.2 array

status: Public on Oct 30 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing: ChIP-chip normalization standard MA2C:JL:2 protocol. ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190

label: Cy3-monofunctional dye(1-)

organism: Caenorhabditis elegans

source_name: OD00079_HCP3_N2_EEMB channel_1

growth_protocol: Worm_embryo_growth_and_harvest_vRG1. Synchronized worm cultures were grown at 20 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG1. Fixed embryos were suspended in 5 volumes of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (30 % power setting for 3 min; 40 % power setting for 1 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at ? 80 °C.
Worm_chromatin_immunoprecipitation_vRG1. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ?l.  Then 35 ?l 30 % sarcosyl (1 % final) and 20 ?l 5 % Na-deoxycholate (0.1 % final) were added.  50 ?l of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples.  100 ?l antibody/bead suspension (5?g antibody pre-bound to 50 ?l Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated over night at 4 °C.  Beads were washed with 2 × 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Immunocomplexes were eluted with 50 ?l Elution buffer for 15 min at 67 °C.  Eluates were incubated over night at 65 °C to reverse cross-links, then treated with proteinase K (0.44 mg/ml) at 37 °C for 2 h.  Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation.  After digestion with RNAse A (0.33 mg/ml) for 2h at 37 °C, DNA was purified using the Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1. ChIP and input DNA was blunt ended with T4 polymerase for 20 min at 12 °C and purified by phenol/chloroform extraction and EtOH precipitation. Annealed oligonucleotide linkers (oligo 1: gcggtgacccgggagatctgaattc; oligo 2: gaattcagatc) were ligated to the DNA fragments over night at 16 °C. The ligated DNA was precipitated with EtOH, disolved in 10 mM Tris-HCl pH 8, and amplified with a Taq/Pfu polymerase mix using oligo 1. For a detailed protocol see http://www.modencode.org/.

tag: developmental stage

value: Early Embryo

tag: genotype

value: wild type

tag: Sex

value: mixed Male and Hermaphrodite population

label: Cy5-monofunctional dye(1-)

source_name: OD00079_HCP3_N2_EEMB channel_2


title: HCP3 N2 LTEMB Hybridization Rep.2 array

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;channel ch1 is input DNA;
channel ch2 is input DNA;

source_name: OD00079_HCP3_N2_LTEMB channel_1

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

value: Late Embryos

value: Hermaphrodite

source_name: OD00079_HCP3_N2_LTEMB channel_2


title: HCP3 N2 LTEMB Hybridization Rep.1 array


title: before EMT, biological rep2


title: after EMT, biological rep2


title: HCP3 N2 EEMB Hybridization Rep.1 array


title: control oral epithelium 2

status: Public on Nov 08 2013

city: Umeå

first: Karin

last: Danielsson

address: Byggnad 6M

department: Medicalbiosciences

country: Sweden

institute: Umeå University

description: laser microdissected epithelium

hyb_protocol: standard Illumina hybridization protocol

data_processing: Data were normalized and background corrected  in Limma Neqc

source_name: human oral epithelium

label_protocol: Biotinylated cRNA was prepared with the TargetAmp-Nano labeling kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted by the use of trizol reagent,followed by clean up with Qiagen Rneasy mini kit as described in protocol included in the kit. Quality was assed by the use of Agilent Bioanalyzer

value: male

tag: tissue

value: oral epithelium


title: control oral epithelium 4

description: laser microdissected epithelium

value: female


title: seq-SDQ3866_MRE11_FEM2_AD_ChIP_Rep1

status: Public on Aug 28 2013

type: SRA

description: ChIP DNA; Antibody information listed below: official name: MRE-11 SDQ3866;target name: MRE-11;host: Rabbit;antigen: DTMVEDLDEGDEPAHDESEDIIKILVATDIHCGYGENKANIHMDAVNTFEEVLQIATEQKVDMILLGGDLFHENNPSREVQHRVTQLLRQYCLNGNPIAL;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3866;short description: An Affinity purified Rabbit Polyclonal antibody to MRE-11 obtained from SDI (MRE-11 SDQ3866)

library_source: genomic

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10

growth_protocol: Worm_adult_growth_and_harvest_vHP2.  Synchronized cultures of worms were grown until gravid in 400 mL batches.  Gravid adults were isolated through sucrose floatation, and frozen into pellets in liquid nitrogen with EBS (250 mM HEPES (pH 7.5), 1180 mM NaCl, 480 mM KCl, 20 mM EDTA, 5 mM EGTA, sucrose (final 340 mM) and protease/phosphatase inhibitors.  The pellets were stored at -80°C.

extract_protocol:
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (1 hour of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection .
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Germline containing young adult


title: before EMT, biological rep1


title: control oral epithelium 5

description: laser microdissected epithelium


title: control oral epithelium 3

description: laser microdissected epithelium


title: control oral epithelium 7

description: laser microdissected epithelium


title: control oral epithelium 6

description: laser microdissected epithelium


title: OCI-LY1_H3K9Ac_INPUT

status: Public on Aug 05 2013

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

description:
INPUT-seq matching OCI-Ly1 H3K9Ac
qseq files unavailable, as this study took several years: OCI-LY1_H3K9Ac_INPUT_qseq.tar

data_processing:
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis.  Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser.
ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.
.
mRNA-seq: Burrows-Wheeler alignment (BWA) algorithm was used to map paired reads using a 3-tiered hierarchal alignment first to a contaminant reference (containing adapter flanks, mitochondrial DNA and ribosomal DNA), then to the reference genome (human hg18), and finally to a junction database (which contains sequence which spans the boundaries between all concurrent exons as indicated by the annotation file). Gene expression values were calculated for each transcript (RPKM, reads per kilobase of exon per million mapped reads) by normalizing the number of bases aligned in a gene by the adjusted gene size (gene size minus any base that overlaps with other genes) and to the bases aligned to exons.

source_name: Human DLBCL cell line

growth_protocol: DLBCL cell lines OCI-Ly1 and OCI-Ly7 were grown in medium containing 90% Iscoveâs (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine, CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA).

extract_protocol:
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture's instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 3'ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.

treatment_protocol: OCI-Ly1 cells were transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen)

tag: chip antibody

value: none (INPUT)


title: control oral epithelium 1

description: laser microdissected epithelium


title: OCI-LY1_H3K4me3_INPUT

description:
INPUT-seq matching OCI-Ly1 H3K4me3
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me3_INPUT_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me3_INPUT_lane2_qseq.tar


title: OCI-LY1_H3K4me3_CHIP

description:
ChIP-seq in OCI-Ly1 against H3K4me3
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me3_CHIP_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me3_CHIP_lane2_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me3_CHIP_lane3_qseq.tar


title: OCI-LY1_H3K4me1_INPUT

description:
INPUT-seq matching OCI-Ly1 H3K4me1 ChIP
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me1_INPUT_qseq.tar


title: OCI-LY1_RNApolII_CHIP

description:
ChIP-seq in OCI-LY1 against RNA polymerase II
qseq files unavailable, as this study took several years: OCI-LY1_RNA_PolII_CHIP_qseq.tar
INPUT-seq matching OCI-LY1 ChIP against RNA polymerase II is same sample as INPUT-seq matching OCI-LY1 BCOR ChIP

value: RNA polymerase II


title: OCI-LY1_H3K4me1_CHIP

description:
ChIP-seq in OCI-LY1 against H3K4me1
qseq files unavailable, as this study took several years: OCI-LY1_H3K4me1_CHIP_qseq.tar


title: OCI-LY1_H3K27Ac_CHIP

description:
ChIP-seq in OCI-LY1 against H3K27Ac
qseq files unavailable, as this study took several years: OCI-LY1_H3K27Ac_CHIP_qseq.tar


title: OCI-LY1_H3K27Ac_INPUT

description:
INPUT-seq matching OCI-Ly1 H3K27Ac
qseq files unavailable, as this study took several years: OCI-LY1_H3K27Ac_INPUT_qseq.tar


title: Transformant yeast untreated 30 min rep2


title: OCI-LY1_H3K9Ac_CHIP

description:
ChIP-seq in OCI-LY1 against H3K9Ac
qseq files unavailable, as this study took several years: OCI-LY1_H3K9Ac_CHIP_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K9Ac_CHIP_lane2_qseq.tar


title: OCI-LY1_H3K27me3_INPUT

description:
INPUT-seq matching H3K27me3 ChIP
qseq files unavailable, as this study took several years: OCI-LY1_H3K27me3_INPUT_qseq.tar


title: OCI-LY1_H3K36me3_INPUT

description:
INPUT-seq matching H3K36me3 ChIP
qseq files unavailable, as this study took several years: OCI-LY1_H3K36me3_INPUT_qseq.tar


title: OCI-LY1_H3K36me3_CHIP

description:
ChIP-seq in OCI-LY1 against H3K36me3
qseq files unavailable, as this study took several years: OCI-LY1_H3K36me3_CHIP_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K36me3_CHIP_lane2_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K36me3_CHIP_lane3_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K36me3_CHIP_lane3_qseq.tar


title: OCI-LY1_H3K27me3_CHIP

description:
ChIP-seq in OCI-LY1 against H3K27me3
qseq files unavailable, as this study took several years: OCI-LY1_H3K27me3_CHIP_qseq.tar


title: OCI-LY1_H3K79me2_INPUT

description:
INPUT-seq matching H3K79me2 ChIP
qseq files unavailable, as this study took several years: OCI-LY1_H3K79me2_INPUT_qseq.tar


title: OCI-LY1_BCL6_N-3_rep1_INPUT

description:
INPUT-seq matching OCI-LY1 ChIP against BCL6 (N3-antibody) REPLICATE 1
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_INPUT_qseq.tar


title: OCI-LY1_H3K79me2_CHIP

description:
ChIP-seq in OCI-LY1 against H3K79me2
qseq files unavailable, as this study took several years: OCI-LY1_H3K79me2_CHIP_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_H3K79me2_CHIP_lane2_qseq.tar


title: OCI-LY1_BCL6_N-3_rep1_CHIP

description:
ChIP-seq in OCI-LY1 against BCL6 (N3-antibody) REPLICATE 1
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_CHIP_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_CHIP_lane2_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_CHIP_lane3_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_CHIP_lane4_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_CHIP_lane5_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_BCL6_N3_REP1_CHIP_lane6_qseq.tar

value: BCL6 (N3-antibody)


title: ChIP-Seq analysis of WCE in human CD3 cells; DNA_Lib 840

status: Public on Jul 18 2013

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 840
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14631
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.14741
****************
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: GSM1112804_BI.CD3_Primary_Cells.Input.24.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 840.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD3 Primary Cells, Donor 24, 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.17213
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,714,481
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.032
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9633
IROC_PERCENTILE: 59
POISSON_SCORE: 0.0617
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112804_BI.CD3_Primary_Cells.Input.24.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 840.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD3 Primary Cells, Donor 24, 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.17396
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD3 Input 24 40
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells ChIP-Seq Input Donor 24 Library DNA_Lib 840 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,714,481
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.032
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9633
IROC_PERCENTILE: 59
POISSON_SCORE: 0.0617
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Bulk lymphocytes were purified from cord blood and further selected by flow cytometry; DNA_Lib 840

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 265

tag: sample common name

value: CD3 Primary Cells

value: presumed normal

tag: disease

tag: markers

value: Unknown

value: Primary Cell

value: FHCRC

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K27ac in human kidney cells; DNA_Lib 1046

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1046
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14626
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
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: GSM1112799_BI.Adult_Kidney.H3K27ac.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1046.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Kidney H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adult Kidney, Donor 153, 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.17255
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,263,008
FINDPEAKS_SCORE: 0.259
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3222
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.992
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3724
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112799_BI.Adult_Kidney.H3K27ac.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1046.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adult Kidney, Donor 153, 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.17438
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AK H3K27ac 53 46
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K27ac Donor 153 Library DNA_Lib 1046 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,263,008
FINDPEAKS_SCORE: 0.259
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3222
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.992
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3724
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Primary kidney tissue; DNA_Lib 1046

value: Adult Kidney

tag: sra sample accession

value: Surgery

value: NL kidney,right kidney resection for RCC

value: Caucasian

value: Male

value: Primary Tissue

value: Kidney

value: MGH

value: 50.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of WCE in human Duodenum smooth muscle cells; DNA_Lib 993

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 993
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14616
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9762
****************
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: GSM1112789_BI.Duodenum_Smooth_Muscle.Input.Donor_174_REMC_28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 993.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Duodenum Smooth Muscle, Donor Donor 174 REMC 28, 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.17275
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,711,845
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9486
IROC_PERCENTILE: 49
POISSON_SCORE: 0.0901
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112789_BI.Duodenum_Smooth_Muscle.Input.Donor_174_REMC_28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 993.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor Donor 174 REMC 28, 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.17458
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: DSM Input 74 93
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle ChIP-Seq Input Donor 174 REMC 28 Library DNA_Lib 993 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,711,845
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9486
IROC_PERCENTILE: 49
POISSON_SCORE: 0.0901
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Smooth muscle from wall of duodenum obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 993

value: Duodenum Smooth Muscle

value: NL smth muscle,  ddnum rmvd as part of whipple operation  because of autoimmune pancreatitis (type1)

value: Smooth Muscle

value: Duodenum

value: Donor 174 REMC 28

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human hippocampus middle cells; DNA_Lib 1061

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1061
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14627
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
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: GSM1112800_BI.Brain_Hippocampus_Middle.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1061.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Brain Hippocampus Middle, Donor 149, 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.17325
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,354,604
FINDPEAKS_SCORE: 0.0259
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1131
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.7464
IROC_PERCENTILE: 17
POISSON_SCORE: 0.2542
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112800_BI.Brain_Hippocampus_Middle.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1061.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 149, 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.17508
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BHM H3K27me3 49 61
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K27me3 Donor 149 Library DNA_Lib 1061 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,354,604
FINDPEAKS_SCORE: 0.0259
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1131
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.7464
IROC_PERCENTILE: 17
POISSON_SCORE: 0.2542
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 1061

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD evident at demise

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K27ac in human cingulate gyrus cells; DNA_Lib 1052

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1052
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14640
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM1112813_BI.Brain_Cingulate_Gyrus.H3K27ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1052.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Cingulate Gyrus, Donor 112, 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.17201
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,173,472
FINDPEAKS_SCORE: 0.2537
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.3187
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9816
IROC_PERCENTILE: 21
POISSON_SCORE: 0.4089
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112813_BI.Brain_Cingulate_Gyrus.H3K27ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1052.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 112, 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.17384
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BCG H3K27ac 12 52
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K27ac Donor 112 Library DNA_Lib 1052 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,173,472
FINDPEAKS_SCORE: 0.2537
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.3187
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9816
IROC_PERCENTILE: 21
POISSON_SCORE: 0.4089
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: human post mortem brain region from a non Alzheimer's donor; DNA_Lib 1052

value: Brain, Cingulate Gyrus

value: post-mortem

value: Cingulate Gyrus

value: Female

value: brain

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human chondrogenic dif cells; DNA_Lib 995

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 995
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14621
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
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: GSM1112794_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 995.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, 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.17283
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,863,529
FINDPEAKS_SCORE: 0.6662
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.6636
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9992
IROC_PERCENTILE: 86
POISSON_SCORE: 0.71
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112794_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 995.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, 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.17466
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CfBMDMSC H3K27ac 58 95
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 58 Library DNA_Lib 995 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,863,529
FINDPEAKS_SCORE: 0.6662
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.6636
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9992
IROC_PERCENTILE: 86
POISSON_SCORE: 0.71
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; DNA_Lib 995

value: healthy

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: cell/nuclei lysis


title: ChIP-Seq analysis of H3K27ac in human angular gyrus cells; DNA_Lib 1054

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1054
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14634
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8183
****************
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: GSM1112807_BI.Brain_Angular_Gyrus.H3K27ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1054.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Angular Gyrus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Angular Gyrus, Donor 112, 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.17220
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,245,325
FINDPEAKS_SCORE: 0.3235
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3816
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9878
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4617
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1112807_BI.Brain_Angular_Gyrus.H3K27ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1054.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Angular Gyrus, Donor 112, 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.17403
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BAG H3K27ac 12 54
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K27ac Donor 112 Library DNA_Lib 1054 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,245,325
FINDPEAKS_SCORE: 0.3235
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3816
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9878
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4617
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: human post mortem brain region from a non Alzheimer's donor; DNA_Lib 1054

value: Brain, Angular Gyrus

value: post-mortem

value: Angular Gyrus

value: Primary Tissue

value: Rush University Medical Center

value: Branson


title: ChIP-Seq analysis of H3K27ac in human kidney cells; DNA_Lib 1055

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1055
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14633
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
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: GSM1112806_BI.Adult_Kidney.H3K27ac.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1055.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Kidney H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adult Kidney, Donor 27, 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.17317
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,347,275
FINDPEAKS_SCORE: 0.2544
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3039
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9921
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3759
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112806_BI.Adult_Kidney.H3K27ac.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1055.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adult Kidney, Donor 27, 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.17500
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AK H3K27ac 27 55
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K27ac Donor 27 Library DNA_Lib 1055 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,347,275
FINDPEAKS_SCORE: 0.2544
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3039
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9921
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3759
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Primary kidney tissue; DNA_Lib 1055

value: Adult Kidney

value: surgery

value: "normal, renal cell CA (clear cell type)"

value: white

value: Male

value: kidney

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug


title: ChIP-Seq analysis of H3K27ac in human mid frontal lobe cells; DNA_Lib 1051

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1051
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14637
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM1112810_BI.Brain_Mid_Frontal_Lobe.H3K27ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1051.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Mid Frontal Lobe, Donor 112, 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.17310
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,884,493
FINDPEAKS_SCORE: 0.2952
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3651
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9861
IROC_PERCENTILE: 28
POISSON_SCORE: 0.434
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112810_BI.Brain_Mid_Frontal_Lobe.H3K27ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1051.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 112, 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.17493
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BMFL H3K27ac 12 51
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K27ac Donor 112 Library DNA_Lib 1051 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,884,493
FINDPEAKS_SCORE: 0.2952
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3651
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9861
IROC_PERCENTILE: 28
POISSON_SCORE: 0.434
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: human post mortem brain region from a non Alzheimer's donor; DNA_Lib 1051

value: Brain, Mid Frontal Lobe

value: Mid Frontal Lobe

value: Female

value: brain

value: cell/nuclei lysis

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human colonic mucosa cells; DNA_Lib 1045

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1045
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14629
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
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: GSM1112802_BI.Colonic_Mucosa.H3K27ac.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1045.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Colonic Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Colonic Mucosa, Donor 32, 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.17311
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,182,289
FINDPEAKS_SCORE: 0.4
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4449
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9958
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4897
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112802_BI.Colonic_Mucosa.H3K27ac.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1045.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Colonic Mucosa, Donor 32, 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.17494
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CM H3K27ac 32 45
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K27ac Donor 32 Library DNA_Lib 1045 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,182,289
FINDPEAKS_SCORE: 0.4
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4449
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9958
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4897
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Primary colonic mucosal tissue; DNA_Lib 1045

value: Colonic Mucosa

value: surgery

value: "normal mucosa, adeno. CA of Cecum"

value: mucosa

value: Primary Tissue

value: colon

value: Branson


title: ChIP-Seq analysis of WCE in human CD25- IL17+ Th17 stim cells; DNA_Lib 2280

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2280
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14630
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13317
****************
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: GSM1112803_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2280.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17219
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,513,933
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0278
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112803_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2280.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17402
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CCIPsT Input 32 80
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2280 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,513,933
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0278
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2280

value: normal

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27ac in human chondrogenic dif cells; DNA_Lib 1000

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1000
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14613
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5932
****************
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: GSM1112786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1000.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.17285
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,629,674
FINDPEAKS_SCORE: 0.6098
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6283
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.998
IROC_PERCENTILE: 73
POISSON_SCORE: 0.6549
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1000.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.17468
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CfBMDMSC H3K27ac 60 00
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 60 Library DNA_Lib 1000 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,629,674
FINDPEAKS_SCORE: 0.6098
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6283
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.998
IROC_PERCENTILE: 73
POISSON_SCORE: 0.6549
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; DNA_Lib 1000

value: healthy

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human BM-MSC cells; DNA_Lib 999

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 999
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14625
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5950
****************
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: GSM1112798_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 999.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.17295
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,369,571
FINDPEAKS_SCORE: 0.7487
FINDPEAKS_PERCENTILE: 99
HOTSPOT_SCORE: 0.7346
HOTSPOT_PERCENTILE: 99
IROC_SCORE: 0.9998
IROC_PERCENTILE: 98
POISSON_SCORE: 0.7691
POISSON_PERCENTILE: 99
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112798_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 999.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.17478
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BMDMSC H3K27ac 60 99
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 60 Library DNA_Lib 999 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,369,571
FINDPEAKS_SCORE: 0.7487
FINDPEAKS_PERCENTILE: 99
HOTSPOT_SCORE: 0.7346
HOTSPOT_PERCENTILE: 99
IROC_SCORE: 0.9998
IROC_PERCENTILE: 98
POISSON_SCORE: 0.7691
POISSON_PERCENTILE: 99
MAXIMUM_REPLICATE_CORRELATION: 0.95

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source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; DNA_Lib 999

value: BM-MSC

value: Unknown

value: Branson