title: HPL2 N2 L3 Hybridization Rep.2 array

status: Public on Sep 18 2012

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 ChIP DNA; Antibody information listed below: official name: FP00001 HPL2;target name: HPL-2;host: Rabbit;antigen: C-terminus;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Francesca Palladino;short description: An affinity purified rabbit polyclonal antibody to HPL-2 (C-terminus) obtained from Francesca Palladino was used for ChIP.
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: Cy5 dye

organism: Caenorhabditis elegans

source_name: FP00001_HPL2_N2_L3 channel_1 ChIP DNA

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

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 (20-30 pulses 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_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vIL1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.

tag: strain

tag: developmental stage

value: L3 Larva

tag: genotype

value: wild type

tag: Sex

value: mixed Male and Hermaphrodite population

label: Cy3 dye

source_name: FP00001_HPL2_N2_L3 channel_2 input DNA


title: AB1791 H3 N2 L3 Hybridization Rep.1 extraction1_array1

type: genomic

country: Canada

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  AB1791 H3 rabbit polyclonal antibody;target name: Histone H3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 100 to the C-terminus of Human Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB1791;short description: An affinity purified rabbit polyclonal antibody to H3 obtained from Abcam (H3-AB1791);used for ChIP.

molecule: genomic DNA

source_name: AB1791_H3_N2_L3 channel_1 input DNA

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.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses 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_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vIL1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.

source_name: AB1791_H3_N2_L3 channel_2 ChIP DNA


title: EL720

status: Public on Oct 10 2012

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: PBMC sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged using iScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Color correction, background normalization and quantile normalization were done using the standard protocol suggested in the Bioconductor lumi package.

label: Cy3 and Cy5

organism: Homo sapiens

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA mini kit according to manufacturer's instructions

tag: age (y)

tag: gender

value: Male

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: Low

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: European

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: AB1791 H3 N2 L3 Hybridization Rep.2 extraction2_array1

tag: strain

tag: developmental stage

tag: genotype

tag: Sex


title: EL713

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

value: High

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: Others

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: EL710

description: PBMC sample

tag: age (y)

tag: gender

value: Female

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL705

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

value: c in pg/ml):204

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: EL711

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL719

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; I3 (eye three) stem cells; RNAPrp 24_513980

status: Public on Aug 07 2012

type: RNA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
I3 stem cells were cultured using standard methods in TESR media; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13328
sample alias: 60
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3160

hyb_protocol: As recommended by Affymetrix

scan_protocol: As recommended by Affymetrix

data_processing: Processed data were not provided for this record

label: biotin

molecule: total RNA

label_protocol: As recommended by Affymetrix

growth_protocol: tissue culture

extract_protocol: Cells were lysed and RNA extracted using Qiagen Rneasy kit

treatment_protocol: untreated cultured cells

tag: lineage

value: embrionic stem cell

tag: medium

value: TESR

tag: disease

tag: passage

tag: line

value: hES I3 TESR

tag: batch

value: hES I3 TESR-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Harvard University


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary colonic mucosal tissue; RNAPrp 27_632058

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from colonic mucosa was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13329
sample alias: 41
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354

growth_protocol: Uncultured primary tissue

treatment_protocol: untreated primary tissue

value: surgery

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

value: mucosa

value: white

value: Primary Tissue

value: colon

value: MGH Pathology


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary gastric smooth muscle tissue; GBM_hsKM_REMC5

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from gastric smooth muscle was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7568
sample alias: 37
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346

value: normal smooth muscle

value: smooth muscle

value: stomach


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary skeletal muscle tissue; RNAPrp 28_632062

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from skeletal muscle was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13330
sample alias: 84
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356

value: "NL muscle,... PVD - BKA"

value: Skeletal muscle

value: Female

value: unknown

value: 72 years


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary rectal mucosal tissue; GBM_hsKM_REMC3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from rectal mucosa was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7566
sample alias: 40
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351

value: "normal mucosa, diverticular disease"

value: rectum


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary rectal smooth muscle tissue; GBM_hsKM_REMC4

description:
sample_term_id: NTR_0001404
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from rectal smooth muscle was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7567
sample alias: 39

value: surgery


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; flow sorted CD34+ cells from cord blood; Chuck_Mitch2

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
CD34+ cells were isolated from umbilical cord blood by flow cytometry; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7564
sample alias: 32.0
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2299

growth_protocol: Uncultured primary cells

treatment_protocol: untreated primary cells

value: FHCRC

value: Primary Cell

value: CD34 Primary Cells

tag: markers

value: Unknown

value: not passaged


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary duodenum mucosa tissue; GBM_hsKM_REMC2

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from duodendum mucosa was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7565
sample alias: 83
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882

value: "NL mucosa,... Pancreatitis/IPMN"

value: mucosa

value: white

value: Male

value: Primary Tissue

value: duodenum

value: MGH Pathology

value: 76 years


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; IPS cell line 20b; CE_AM_1013095

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
IPS cells were differentiated in vitro from fibroblasts using standard methods; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7562
sample alias: 66.0
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2298

source_name: IPS cell line 20b; CE_AM_1013095

value: Harvard University

value: Cell Line

value: induced pluripotent cells

value: undifferentiated

value: KSR


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; flow sorted CD19+ cells from cord blood; Chuck_Mitch1

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
CD19+ cells were isolated from umbilical cord blood by flow cytometry; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7563
sample alias: 30.0
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2303

value: FHCRC

value: Primary Cell

value: CD19 Primary Cells

value: Female


title: EL716

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: High

tag: current (low vs. high ses at present)

value: Low

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: European

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL706

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: Others

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary skeletal muscle tissue; RNAPrp 29_632064

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from skeletal muscle was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13331
sample alias: 85
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355

value: surgery

value: "NL muscle,... Osteomylitis - BKA"

tag: disease

value: Skeletal muscle

value: white

value: Male

value: Primary Tissue

value: unknown

value: 54 years


title: EL714

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL717

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; H7 (WA07) embryonic stem cells; CE_AM_1013092

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
WA7 stem cells were cultured using standard methods; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7559
sample alias: 57
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5952

source_name: H7 (WA07) embryonic stem cells; NIH Approval # NIHhESC-10-0061; CE_AM_1013092

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: disease

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; I3(eye three) stem cells; CE_AM_1013091

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
I3 stem cells were cultured using standard methods; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7558
sample alias: 59.0
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2352

source_name: I3(eye three) stem cells; CE_AM_1013091

value: Female


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; flow sorted CD3+ cells from cord blood; GBM_hsKM_REMC

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
CD3+ cells were isolated from umbilical cord blood by flow cytometry; total RNA was isolated and subject to Affymetrix profiling.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6957
sample alias: 29
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6956

treatment_protocol: Untreated primary cells

value: FHCRC

value: Primary Cell

tag: markers


title: EL708

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: Low

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: European

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL701

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

value: High

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: Others

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: ChIP-Seq analysis of H3K27ac in human skeletal mu cells; DNA_Lib 1766

status: Public on Jul 11 2012

type: SRA

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1766
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11692
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM916064_BI.Skeletal_Muscle.H3K27ac.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1766-DNA_Lib 1766.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Skeletal Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Skeletal Muscle, Donor 62, 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.13397
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,950,385
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.5266
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5417
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9968
IROC_PERCENTILE: 43
POISSON_SCORE: 0.6003
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916064_BI.Skeletal_Muscle.H3K27ac.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1766-DNA_Lib 1766.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Skeletal Muscle, Donor 62, 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.13417
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 8
BROWSER_TRACK_NAME: SM H3K27ac 62 66
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K27ac Donor 62 Library DNA_Lib 1766 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,950,385
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.5266
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5417
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9968
IROC_PERCENTILE: 43
POISSON_SCORE: 0.6003
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary skeletal muscle tissue; DNA_Lib 1766

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Skeletal Muscle

value: surgery

value: "NL muscle,... PVD - BKA"

tag: molecule

value: genomic DNA

tag: disease

value: Skeletal muscle

value: white

value: Primary Tissue

value: MGH Pathology

value: 72 years

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

value: Branson


title: ChIP-Seq analysis of H3K27ac in human stomach smooth mu cells; DNA_Lib 1765

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1765
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11693
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM916065_BI.Stomach_Smooth_Muscle.H3K27ac.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1765-DNA_Lib 1765.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Stomach Smooth Muscle, Donor 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.13389
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,225,368
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.247
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2884
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9961
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3489
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916065_BI.Stomach_Smooth_Muscle.H3K27ac.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1765-DNA_Lib 1765.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 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.13409
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 8
BROWSER_TRACK_NAME: SSM H3K27ac 28 65
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K27ac Donor 28 Library DNA_Lib 1765 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,225,368
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.247
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2884
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9961
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3489
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary gastric smooth muscle tissue; DNA_Lib 1765

value: Stomach Smooth Muscle

value: normal smooth muscle

value: smooth muscle

value: Female

value: stomach


title: ChIP-Seq analysis of H3K27me3 in human AdiposeNuclei cells; DNA_Lib 709

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 709
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11683
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM916055_BI.Adipose_Nuclei.H3K27me3.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 709-DNA_Lib 709-DNA_Lib 709.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adipose Nuclei H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Adipose Nuclei, Donor 7, 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.13382
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,689,263
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0122
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0847
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.735
IROC_PERCENTILE: 20
POISSON_SCORE: 0.286
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM916055_BI.Adipose_Nuclei.H3K27me3.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 709-DNA_Lib 709-DNA_Lib 709.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 7, 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.13402
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 8
BROWSER_TRACK_NAME: AN H3K27me3 7 09
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K27me3 Donor 7 Library DNA_Lib 709 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,689,263
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0122
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0847
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.735
IROC_PERCENTILE: 20
POISSON_SCORE: 0.286
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Nuclei derived from crude preps of adipose tissue; DNA_Lib 709

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: abdomen

value: Harvard University

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27ac in human chondrogenic dif  cells; DNA_Lib 1248

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 1248
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11686
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
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: GSM916058_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1248-DNA_Lib 1248.hg19.level.1.release.8
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 57, 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.13392
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,696,104
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.6447
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6349
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6921
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916058_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1248-DNA_Lib 1248.hg19.level.2.release.6
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 57, 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.13412
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 8
BROWSER_TRACK_NAME: CfBMDMSC H3K27ac 57 48
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 1248 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,696,104
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.6447
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6349
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6921
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; DNA_Lib 1248

value: healthy

tag: markers

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: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug


title: ChIP-Seq analysis of H3K27ac in human AdiposeNuclei cells; DNA_Lib 1764

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1764
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11694
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM916066_BI.Adipose_Nuclei.H3K27ac.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1764-DNA_Lib 1764.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adipose Nuclei H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adipose Nuclei, Donor 7, 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.13381
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,591,902
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4468
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.4746
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9976
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5425
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916066_BI.Adipose_Nuclei.H3K27ac.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1764-DNA_Lib 1764.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adipose Nuclei, Donor 7, 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.13401
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 8
BROWSER_TRACK_NAME: AN H3K27ac 7 64
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K27ac Donor 7 Library DNA_Lib 1764 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,591,902
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4468
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.4746
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9976
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5425
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Nuclei derived from crude preps of adipose tissue; DNA_Lib 1764

value: Adipose Nuclei

value: Female

value: Primary Tissue

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: EL704

description: PBMC sample

tag: age (y)

tag: gender

value: Male

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: High

tag: current (low vs. high ses at present)

value: Low

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

value: European

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL703

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: Others

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)


title: ChIP-Seq analysis of H3K9me3 in human colonic mucosa cells; DNA_Lib 368

status: Public on Apr 17 2012

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 368
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9622
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
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: GSM916048_BI.Colonic_Mucosa.H3K9me3.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 368-DNA_Lib 368-DNA_Lib 368-DNA_Lib 368.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Colonic Mucosa, Donor 155, 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.12295
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,942,668
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0252
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1162
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.5218
IROC_PERCENTILE: 15
POISSON_SCORE: 0.2009
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM916048_BI.Colonic_Mucosa.H3K9me3.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 368-DNA_Lib 368-DNA_Lib 368-DNA_Lib 368.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.12342
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 6
BROWSER_TRACK_NAME: CM H3K9me3 55 68
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K9me3 Donor 155 Library DNA_Lib 368 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,942,668
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0252
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1162
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.5218
IROC_PERCENTILE: 15
POISSON_SCORE: 0.2009
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 368

tag: sample alias

value: BioSam 157 REMC 19

tag: sample common name

value: Colonic Mucosa

value: Surgery

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

tag: molecule

value: genomic DNA

tag: disease

value: Caucasian

value: Colon

value: MGH

value: 56.0 Years

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in human colonic mucosa cells; DNA_Lib 369

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 369
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9621
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
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: GSM916047_BI.Colonic_Mucosa.Input.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 369-DNA_Lib 369-DNA_Lib 369-DNA_Lib 369.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Colonic Mucosa, Donor 155, 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.12304
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,107,433
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.0547
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9687
IROC_PERCENTILE: 40
POISSON_SCORE: 0.0778
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM916047_BI.Colonic_Mucosa.Input.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 369-DNA_Lib 369-DNA_Lib 369-DNA_Lib 369.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Colonic Mucosa, Donor 155, 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.12351
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 6
BROWSER_TRACK_NAME: CM Input 55 69
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa ChIP-Seq Input Donor 155 Library DNA_Lib 369 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,107,433
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.0547
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9687
IROC_PERCENTILE: 40
POISSON_SCORE: 0.0778
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 369

value: Female

value: Primary Tissue

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: EL707

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: High

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

value: European

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: ChIP-Seq analysis of H3K4me1 in human colonic mucosa cells; DNA_Lib 363

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 363
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9620
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
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: GSM916046_BI.Colonic_Mucosa.H3K4me1.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 363-DNA_Lib 363-DNA_Lib 363-DNA_Lib 363.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Colonic Mucosa, Donor 155, 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.12283
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,243,914
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.1047
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2145
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9106
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3405
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM916046_BI.Colonic_Mucosa.H3K4me1.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 363-DNA_Lib 363-DNA_Lib 363-DNA_Lib 363.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.12330
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 6
BROWSER_TRACK_NAME: CM H3K4me1 55 63
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K4me1 Donor 155 Library DNA_Lib 363 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,243,914
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.1047
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2145
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9106
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3405
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 363

tag: sample alias

value: BioSam 157 REMC 19

tag: sample common name

value: Colonic Mucosa

value: Surgery

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

tag: molecule

value: genomic DNA

tag: disease

value: Caucasian

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me3 in human colonic mucosa cells; DNA_Lib 366

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 366
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9619
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
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: GSM916045_BI.Colonic_Mucosa.H3K4me3.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 366-DNA_Lib 366-DNA_Lib 366-DNA_Lib 366.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Colonic Mucosa, Donor 155, 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.12298
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,106,373
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1141
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.1558
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9989
IROC_PERCENTILE: 45
POISSON_SCORE: 0.195
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM916045_BI.Colonic_Mucosa.H3K4me3.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 366-DNA_Lib 366-DNA_Lib 366-DNA_Lib 366.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.12345
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 6
BROWSER_TRACK_NAME: CM H3K4me3 55 66
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K4me3 Donor 155 Library DNA_Lib 366 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,106,373
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1141
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.1558
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9989
IROC_PERCENTILE: 45
POISSON_SCORE: 0.195
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 366

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: Protein A-Sepharose 4B

value: cell/nuclei lysis

value: Millipore

value: Histone H3K4me3


title: Normal Muscle individual 2

status: Public on Sep 14 2012

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

hyb_protocol: Hybridization was performed on an illumina air hybridization owen. Slides were washed  and stained using reagents and protocols provided by Illumina.

scan_protocol: Slides were scanned on an Illumina Iscan BeadChip reader, following the protocol provided by illumina for the HumanHT-12_V3_0_R1  BeadChip.

data_processing: Data were extracted from the scan files using Illumina Genome Studio and exported both as raw and preprocessed expression data. Before analysis, the dataset was quantile normalized, local background was not subtracted, and the expression values for the missing bead were imputed using the GenomeStudio imputation algoritm

source_name: Muscle tissue

label_protocol: Biotin labelled cRNA was produced using the Ambion TotalPrep RNA amplification kit

extract_protocol: Total RNA was extracted from muscle biopsies using the Trizol reagent followed by an additional clean up step on Qiagen RNAeasy column, following protocols provided by the manufacturer

tag: individual

tag: tissue

value: deltoid

tag: gender

value: M

tag: disease state

value: Normal Muscle


title: Normal Muscle individual 6

value: quadriceps


title: ChIP-Seq analysis of H3K9ac in human colonic mucosa cells; DNA_Lib 367

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 367
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9618
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
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: GSM916044_BI.Colonic_Mucosa.H3K9ac.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 367-DNA_Lib 367-DNA_Lib 367-DNA_Lib 367.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Colonic Mucosa, Donor 155, 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.12281
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,409,085
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.2221
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.2801
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9968
IROC_PERCENTILE: 89
POISSON_SCORE: 0.3413
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM916044_BI.Colonic_Mucosa.H3K9ac.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 367-DNA_Lib 367-DNA_Lib 367-DNA_Lib 367.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.12328
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 6
BROWSER_TRACK_NAME: CM H3K9ac 55 67
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K9ac Donor 155 Library DNA_Lib 367 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,409,085
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.2221
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.2801
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9968
IROC_PERCENTILE: 89
POISSON_SCORE: 0.3413
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 367

value: BioSam 157 REMC 19

value: Colonic Mucosa

value: Surgery

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

value: genomic DNA

value: Caucasian

value: 0.5 to 3 million cells

value: Abcam

value: Histone H3K9ac

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human Duodenum smooth muscle cells; DNA_Lib 987

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 987
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9610
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: GSM916036_BI.Duodenum_Smooth_Muscle.H3K36me3.Donor_174_REMC_28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 987-DNA_Lib 987.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.12322
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,076,712
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.3341
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3415
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9834
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5453
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM916036_BI.Duodenum_Smooth_Muscle.H3K36me3.Donor_174_REMC_28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 987-DNA_Lib 987.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.12369
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 6
BROWSER_TRACK_NAME: DSM H3K36me3 74 87
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K36me3 Donor 174 REMC 28 Library DNA_Lib 987 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,076,712
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.3341
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3415
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9834
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5453
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Smooth muscle from wall of duodenum obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 987

value: BioSam 309

value: Duodenum Smooth Muscle

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

value: Smooth Muscle

value: Male

value: Primary Tissue

value: Duodenum

value: Donor 174 REMC 28

value: MGH

value: Protein A-Sepharose 4B

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K36me3


title: Normal Muscle individual 4

value: deltoid

value: M

value: Normal Muscle


title: Normal Muscle individual 3

value: quadriceps


title: ChIP-Seq analysis of H3K4me1 in human Duodenum smooth muscle cells; DNA_Lib 988

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 988
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9607
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: GSM916033_BI.Duodenum_Smooth_Muscle.H3K4me1.Donor_174_REMC_28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 988-DNA_Lib 988.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.12294
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,291,333
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3565
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.4185
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9803
IROC_PERCENTILE: 79
POISSON_SCORE: 0.5624
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.78

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

ANALYSIS FILE NAME: GSM916033_BI.Duodenum_Smooth_Muscle.H3K4me1.Donor_174_REMC_28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 988-DNA_Lib 988.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.12341
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 6
BROWSER_TRACK_NAME: DSM H3K4me1 74 88
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K4me1 Donor 174 REMC 28 Library DNA_Lib 988 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,291,333
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3565
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.4185
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9803
IROC_PERCENTILE: 79
POISSON_SCORE: 0.5624
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.78

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source_name: Smooth muscle from wall of duodenum obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 988

value: BioSam 309

value: Duodenum Smooth Muscle

value: Surgery

value: genomic DNA

value: Caucasian

value: 0.5 to 3 million cells

value: Abcam

value: Histone H3K4me1

value: Branson


title: Normal Muscle individual 1


title: Normal Muscle individual 5

value: F