title: AA_137

status: Public on Oct 31 2011

description: Gene expression data from surgical tumor sample of high grade astrocytoma

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 20,722 genes.

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500).
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (high grade astrocytoma)

tag: survival (months)


title: AA_512

type: RNA

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

country: USA

institute: CU Anschutz Medical Campus

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: tissue

tag: genotype


title: Control_biological rep26 11-0081

status: Public on Jan 13 2011

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from normal control

hyb_protocol: Standard Affymetrix

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Gene expression was measured using one patient sample per chip. Image files were captured using an Affymetrix GeneChip Scanner 3000. CEL files were subsequently preprocessed using Robust Multiple-Array Average (RMA) normalization and GeneSpring GX 7.3 software (Agilent Technologies, Palo Alto, CA). All signal intensity-based data were used after RMA normalization, which specifically suppresses all but significant variation among lower intensity probe sets. All chips representing patient samples were then normalized to the respective median values of controls.

source_name: Children ≤ 10 years old

label_protocol: WT-Ovation Pico (NuGen)

extract_protocol: Qiagen extraction from PaxGene whole blood RNA collection tubes

treatment_protocol: standard ICU care for septic shock

value: whole blood

tag: disease state

value: normal control

tag: age (years)

tag: outcome

tag: group


title: Control_biological rep23 11-0077


title: Control_biological rep27 11-0082


title: Control_biological rep25 11-0080


title: HGA_11


title: Control_biological rep28 11-0083


title: Septic Shock_biological rep96 21-0003

description: Gene expression data from septic shock patient

value: septic shock patient

value: Survivor

value: C


title: Septic Shock_biological rep93 20-0003


title: Septic Shock_biological rep66 10-0009


title: Septic Shock_biological rep89 18-0002

value: B


title: Septic Shock_biological rep91 19-0005


title: Septic Shock_biological rep90 19-0001


title: Control_biological rep24 11-0078


title: Septic Shock_biological rep40 01-0088

value: Nonsurvivor


title: Septic Shock_biological rep77 11-0035


title: Control_biological rep2 01-0105


title: Septic Shock_biological rep67 10-0018


title: Septic Shock_biological rep85 15-0017

value: A


title: Septic Shock_biological rep95 21-0001


title: Septic Shock_biological rep75 11-0002


title: Septic Shock_biological rep64 10-0003


title: Control_biological rep8 04-0015


title: Septic Shock_biological rep68 10-0019


title: Septic Shock_biological rep76 11-0007


title: Control_biological rep1 01-0104


title: Septic Shock_biological rep39 01-0086


title: Control_biological rep3 01-0106


title: Septic Shock_biological rep30 01-0047


title: Septic Shock_biological rep38 01-0070


title: Septic Shock_biological rep26 01-0007A


title: Septic Shock_biological rep57 07-0004


title: Septic Shock_biological rep25 01-0080


title: Septic Shock_biological rep24 01-0079


title: Septic Shock_biological rep21 01-0074


title: Septic Shock_biological rep22 01-0077


title: Septic Shock_biological rep20 01-0073


title: Septic Shock_biological rep23 01-0078


title: Septic Shock_biological rep19 01-0072


title: Septic Shock_biological rep16 01-0068


title: Septic Shock_biological rep18 01-0071


title: Septic Shock_biological rep17 01-0069


title: Septic Shock_biological rep15 01-0064


title: Control_biological rep19

value: Whole Blood


title: Septic Shock_biological rep73


title: Septic Shock_biological rep75


title: Septic Shock_biological rep78


title: Septic Shock_biological rep68


title: Control_biological rep13


title: Control_biological rep21


title: Septic Shock_biological rep1 01-0013


title: Septic Shock_biological rep79


title: Septic Shock_biological rep80


title: Septic Shock_biological rep81


title: Septic Shock_biological rep76


title: Control_biological rep16


title: Control_biological rep14


title: Septic Shock_biological rep77


title: Septic Shock_biological rep82


title: Septic Shock_biological rep72


title: Control_biological rep18


title: Septic Shock_biological rep70


title: Septic Shock_biological rep69


title: Septic Shock_biological rep67


title: Control_biological rep15


title: Control_biological rep20


title: Septic Shock_biological rep74


title: Control_biological rep12


title: Septic Shock_biological rep71


title: Septic Shock_biological rep66


title: Septic Shock_biological rep59


title: Septic Shock_biological rep56


title: Control_biological rep9


title: Septic Shock_biological rep61


title: Septic Shock_biological rep60


title: Septic Shock_biological rep52


title: Control_biological rep10


title: Septic Shock_biological rep51


title: Control_biological rep11


title: Septic Shock_biological rep53


title: Septic Shock_biological rep58


title: Septic Shock_biological rep55


title: Septic Shock_biological rep49


title: Septic Shock_biological rep62


title: Septic Shock_biological rep48


title: Septic Shock_biological rep64


title: Septic Shock_biological rep65


title: Septic Shock_biological rep57


title: Septic Shock_biological rep63


title: Septic Shock_biological rep46


title: Septic Shock_biological rep45


title: Septic Shock_biological rep50


title: Septic Shock_biological rep43


title: Septic Shock_biological rep44


title: Septic Shock_biological rep54


title: Septic Shock_biological rep47


title: Septic Shock_biological rep42


title: Control_biological rep8


title: Septic Shock_biological rep38


title: Septic Shock_biological rep30


title: Control_biological rep7


title: Septic Shock_biological rep40


title: Septic Shock_biological rep36


title: Septic Shock_biological rep35


title: Septic Shock_biological rep32


title: Septic Shock_biological rep31


title: Septic Shock_biological rep27


title: Septic Shock_biological rep33


title: Septic Shock_biological rep34


title: Septic Shock_biological rep25


title: Septic Shock_biological rep23


title: Septic Shock_biological rep26


title: Septic Shock_biological rep39


title: Septic Shock_biological rep28


title: Septic Shock_biological rep24


title: Septic Shock_biological rep20


title: Septic Shock_biological rep21


title: Septic Shock_biological rep22


title: Septic Shock_biological rep13


title: Septic Shock_biological rep16


title: Septic Shock_biological rep15


title: Septic Shock_biological rep19


title: Septic Shock_biological rep11


title: Septic Shock_biological rep18


title: Septic Shock_biological rep17


title: Control_biological rep5


title: Control_biological rep1


title: Septic Shock_biological rep12


title: Septic Shock_biological rep10


title: AB9048_H3K36ME1206009_N2_L3 extraction1_array1 channel_1

status: Public on Dec 28 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab9048 H3K36me1:206009;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 monomethylated at K36;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;short description: A rabbit affinity purified antibody to H3K36me1 from abcam (Ab9048 lot #206009). Used for ChIP.;

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

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

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

label: Cy3 dye

molecule: genomic DNA

organism: Caenorhabditis elegans

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:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are 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.

tag: strain

tag: developmental stage

value: L3 Larva

value: wild type

tag: Sex

value: mixed Male and Hermaphrodite population

label: Cy5 dye


title: UP07448_H3K27ME124439_N2_L3 extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: UP07448 H3K27me1:24439;target name: H3K27me1;host: Rabbit;antigen: peptide including monomethyl-lysine 27 of histone H3;clonal: Polyclonal;purified: Affinity;company: Upstate/Millipore;catalog: 07-448;short description: A rabbit polyclonal antibody to H3K27me1 obtained from Upstate (07-448 lot #24439). Used for ChIP.;

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.


title: Control_biological rep2


title: Control_biological rep4


title: Control_biological rep6


title: Septic Shock_biological rep8


title: AB2886_H3K79ME1361912_N2_MXEMB extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB2886 H3K79me1:361912;target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2886;reference: http://www.abcam.com/histone-h3-mono-methyl-k79-antibody-chip-grade-ab2886.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide mono-methylated at K79.;

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ6. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (3 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.

value: Mixed Embryo


title: UP07448_H3K27ME124439_N2_L3 extraction1_array1 channel_1


title: AB2886_H3K79ME1361912_N2_MXEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: AB2886 H3K79me1:361912;target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2886;reference: http://www.abcam.com/histone-h3-mono-methyl-k79-antibody-chip-grade-ab2886.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide mono-methylated at K79.;
channel ch2 is input DNA;


title: AB9048_H3K36ME1206009_N2_L3 extraction2_array1 channel_1


title: Septic Shock_biological rep9


title: Control_biological rep3


title: MP07329_H4K16ACDAM1612187_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MP07329 H4K16ac:DAM1612187;target name: H4K16ac;host: Rabbit;antigen: KLH-conjugated frollowed by Histone H4 corresponding to the N-terminus region at and around acetylated Lys16;clonal: Polyclonal;purified: Crude;company: Millipore;catalog: 07-329;short description: Rabbit serum to H4K16ac from Millipore (07-329 lot #DAM1612187). Used for ChIP. KLH-conjugated frollowed by Histone H4 corresponding to the N-terminus region at and around acetylated Lys16;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen 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. 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_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, 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 according to the NimbleScan v2.4 User?s Guide.

growth_protocol: Worm_embryo_growth_and_harvest_vSS4. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

value: Early Embryo


title: Septic Shock_biological rep5


title: Septic Shock_biological rep7


title: MP07329_H4K16ACDAM1612187_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: MP07329 H4K16ac:DAM1612187;target name: H4K16ac;host: Rabbit;antigen: KLH-conjugated frollowed by Histone H4 corresponding to the N-terminus region at and around acetylated Lys16;clonal: Polyclonal;purified: Crude;company: Millipore;catalog: 07-329;short description: Rabbit serum to H4K16ac from Millipore (07-329 lot #DAM1612187). Used for ChIP. KLH-conjugated frollowed by Histone H4 corresponding to the N-terminus region at and around acetylated Lys16;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen 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. 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.

growth_protocol: Worm_embryo_growth_and_harvest_vSS3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85 % formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: AB15823_H4K8AC487128_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab15823-H4K8ac;target name: H4K8ac;host: Rabbit;antigen: mpdtnstinlslstrvtlaffmslvafaimlgnalvilafvvdknlrhrssyfflnlaisdffvgvisiplyiphtlfewdfgkeicvfwlttdyllcta;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: blank;


title: AB15823_H4K8AC487128_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab15823-H4K8ac;target name: H4K8ac;host: Rabbit;antigen: mpdtnstinlslstrvtlaffmslvafaimlgnalvilafvvdknlrhrssyfflnlaisdffvgvisiplyiphtlfewdfgkeicvfwlttdyllcta;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: blank;
channel ch2 is input DNA;

growth_protocol: Worm_embryo_growth_and_harvest_vSS5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: AB46540_NIGG_N2_MXEMB extraction2_array1 channel_1

status: Public on Dec 22 2010

description:
channel ch1 is input DNA;
channel ch2 is negative control for ChIP; Antibody information listed below:

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vKI1. Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr and then washed by extraction buffer. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. Before immunoprecipitation, 10% of extract was taken and treated with RNase. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/
Worm_LM-PCR_Amplification_for_ChIP-chip_vKI2. ChIP or input DNA was incubated with T4-DNA polymerase followed by T4-polynucleotide kinase to ensure 5?-phospho and 3?-hydroxyl blunt ends. The DNA fragments were ligated to the double-strand DNA linker with 5?-phosphate and then amplified by using primer corresponding to the linker sequences.


title: SDQ4051_LEM2_SP646_MXEMB_SP646 extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below:
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vKI3. Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr and then washed by extraction buffer. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. Before immunoprecipitation, 10% of extract was taken. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with RNase A at room temperature for ? 1 hr then proteinase K at 55C for ? 1 hr. Samples were transferred to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/
Worm_LM-PCR_Amplification_for_ChIP-chip_vKI3 DNA was incubated with End Repair Enzyme mix (Epicentre, Madison) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends. The DNA fragments were ligated with T-over-hanged linker and then amplified by PCR with the longer linker oligonucleotide as a primer.


title: SDQ4051_LEM2_N2_MXEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ4051 LEM2;target name: LEM-2;host: Rabbit;antigen: MVDVEKMSDAELRAELNVRGANVGPVTGTTRSLYEKKLKKLLSGGAKTPARPTVAKPAPKPTPKSAPAPKSPKSPPARRSIPRAAATAANSTINSTFNRS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4051 LEM2;short description: Rabbit antisera against the amino-terminal 100 amino acids of LEM-2 produced at SDI.;


title: Septic Shock_biological rep4


title: SDQ4051_LEM2_SP646_MXEMB_SP646 extraction1_array1 channel_1


title: AB46540_NIGG_N2_MXEMB extraction1_array1 channel_1


title: SDQ3891_LEM2_VC1317_MXEMB extraction1_array1 channel_1


title: Septic Shock_biological rep6


title: AB9051_H4K20ME1104513_N2_L3_1 extraction1_array1

status: Public on Nov 18 2010

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab9051 H4K20me1:104513;target name: H4K20me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H4 mono methylated at K20;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;short description: An affinity purified rabbit antibody to H4K20me1 obtained from Abcam (ab9051 lot #104513). 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 nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are 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 ul 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.


title: HK00013_H3K27ME3:1E7_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00013 H3K27me3:1E7:JL:1;target name: H3K27me3;host: Mouse;antigen: KQLATKAAR(me3-K)SAPATGGVKC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00013;short description: A protein G purified mouse monocloonal antibody agsinst H3K27me3.  Used for ChIP;
channel ch2 is input DNA;


title: AB9051_H4K20ME1104513_N2_L3_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab9051 H4K20me1:104513;target name: H4K20me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H4 mono methylated at K20;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;short description: An affinity purified rabbit antibody to H4K20me1 obtained from Abcam (ab9051 lot #104513). Used for ChIP.;

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.


title: Septic Shock_biological rep2


title: AB8895_H3K4ME1733246_N2_L3_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;antigen: Peptide including dimethyl-lysine 9 of histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.;
channel ch2 is input DNA;


title: AB9045_H3K9ME1291918_N2_L3_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab9045 H3K9me1:291918;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 mono methylated at K9;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9045;short description: A Rabbit affinity purified antibody to H3K9me1 from abcam (ab9045 lot #291918). Used for ChIP.;
channel ch2 is input DNA;


title: AB4729_H3K27AC361571_N2_L3_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab4729 H3K27ac:361571;target name: H3K27ac;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 acetylated at K27;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab4729;short description: A rabbit affinity purified antibody to H3K27ac obtained from Abcam (ab4729 lot#361571). Used for ChIP.;
channel ch2 is input DNA;


title: AB4729_H3K27AC361571_N2_L3_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab4729 H3K27ac:361571;target name: H3K27ac;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 acetylated at K27;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab4729;short description: A rabbit affinity purified antibody to H3K27ac obtained from Abcam (ab4729 lot#361571). Used for ChIP.;


title: HK00013_H3K27ME3:1E7_N2_EEMB extraction1_array1 channel_1


title: MP05858_H4DAM1636076_N2_L3_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: H4;target name: H4;host: Rabbit;antigen: aa17-28;clonal: Monoclonal;purified: Protein A/G;company: Upstate-Millipore;catalog: 05-858;short description: Anti-histone H4 pan;


title: AB9045_H3K9ME1291918_N2_L3_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab9045 H3K9me1:291918;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 mono methylated at K9;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9045;short description: A Rabbit affinity purified antibody to H3K9me1 from abcam (ab9045 lot #291918). Used for ChIP.;


title: ChIP-Seq analysis of H3K36me3 in rectal mucosa cells; Lib:XZ:20100423:28--ChIP:XZ:70100407:17:rectal mucosa:H3K36Me3

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:28--ChIP:XZ:70100407:17:rectal mucosa:H3K36Me3
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM621646_BI.Rectal_Mucosa.H3K36me3.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:28--ChIP:XZ:70100407:17:rectal mucosa:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Rectal Mucosa, Donor 29 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.4721
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2339
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2316
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9787
IROC_PERCENTILE: 69
POISSON_SCORE: 0.5286
POISSON_PERCENTILE: 59

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

ANALYSIS FILE NAME: GSM621646_BI.Rectal_Mucosa.H3K36me3.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:28--ChIP:XZ:70100407:17:rectal mucosa:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 29 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.4995
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 2
BROWSER_TRACK_NAME: RM H3K36me3 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K36me3 Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2339
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2316
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9787
IROC_PERCENTILE: 69
POISSON_SCORE: 0.5286
POISSON_PERCENTILE: 59

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:28--ChIP:XZ:70100407:17:rectal mucosa:H3K36Me3

extract_protocol: Library construction protocol: Single read - Illumina

value: surgery

value: normal mucosa

tag: molecule

value: genomic DNA

tag: disease

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human rectal mucosa cells; Lib:XZ:20100423:32--ChIP:XZ:70100407:21:rectal mucosa:WCE

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:32--ChIP:XZ:70100407:21:rectal mucosa:WCE
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621647_BI.Rectal_Mucosa.Input.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:32--ChIP:XZ:70100407:21:rectal mucosa:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Rectal Mucosa, Donor 29 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.4785
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 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0037
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2383
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM621647_BI.Rectal_Mucosa.Input.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:32--ChIP:XZ:70100407:21:rectal mucosa:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Rectal Mucosa, Donor 29 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.5059
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 2
BROWSER_TRACK_NAME: RM Input 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa ChIP-Seq Input Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0037
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2383
POISSON_PERCENTILE: 54

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:32--ChIP:XZ:70100407:21:rectal mucosa:WCE

value: standard

value: ChIP-Seq Input

value: Input


title: MP05858_H4DAM1636076_N2_L3_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H4;target name: H4;host: Rabbit;antigen: aa17-28;clonal: Monoclonal;purified: Protein A/G;company: Upstate-Millipore;catalog: 05-858;short description: Anti-histone H4 pan;
channel ch2 is input DNA;

value: L3 Larva

value: wild type

value: mixed Male and Hermaphrodite population


title: Septic Shock_biological rep3

description: Gene expression data from septic shock patient

value: Whole Blood

value: septic shock patient

value: Survivor


title: ChIP-Seq analysis of H3K4me3 in human rectal mucosa cells; Lib:XZ:20100423:27--ChIP:XZ:70100407:16:rectal mucosa:H3K4Me3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:27--ChIP:XZ:70100407:16:rectal mucosa:H3K4Me3
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621643_BI.Rectal_Mucosa.H3K4me3.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:27--ChIP:XZ:70100407:16:rectal mucosa:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Rectal Mucosa, Donor 29 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.4789
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3513
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3461
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.998
IROC_PERCENTILE: 34
POISSON_SCORE: 0.455
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM621643_BI.Rectal_Mucosa.H3K4me3.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:27--ChIP:XZ:70100407:16:rectal mucosa:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 29 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.5063
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 2
BROWSER_TRACK_NAME: RM H3K4me3 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K4me3 Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3513
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3461
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.998
IROC_PERCENTILE: 34
POISSON_SCORE: 0.455
POISSON_PERCENTILE: 50

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:27--ChIP:XZ:70100407:16:rectal mucosa:H3K4Me3

value: surgery

value: normal mucosa

value: genomic DNA

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K9ac in human rectal mucosa cells; Lib:XZ:20100423:30--ChIP:XZ:70100407:19:rectal mucosa:H3K9Ac

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:30--ChIP:XZ:70100407:19:rectal mucosa:H3K9Ac
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621636_BI.Rectal_Mucosa.H3K9ac.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:30--ChIP:XZ:70100407:19:rectal mucosa:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Rectal Mucosa, Donor 29 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.4706
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 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1085
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.1351
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9968
IROC_PERCENTILE: 83
POISSON_SCORE: 0.2782
POISSON_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM621636_BI.Rectal_Mucosa.H3K9ac.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:30--ChIP:XZ:70100407:19:rectal mucosa:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Rectal Mucosa, Donor 29 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.4980
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 2
BROWSER_TRACK_NAME: RM H3K9ac 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K9ac Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1085
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.1351
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9968
IROC_PERCENTILE: 83
POISSON_SCORE: 0.2782
POISSON_PERCENTILE: 3

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:30--ChIP:XZ:70100407:19:rectal mucosa:H3K9Ac

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: 12hr ctrl, rep3

status: Public on Nov 20 2010

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: information provided elsewhere

hyb_protocol: Standard Affymetrix Procedures:  50C, 16hrs, 60rpm

scan_protocol: Standard Affymetrix Procedures; GCOS 7G scanner

data_processing: GCOS v1.4 generated MAS5 signal intensities. Microarray data from other researchers studies of planktonic bacteria were used to interpret the data from our own microarrays.  The available MAS5 signal intensity data for all the probes on these microarrays were downloaded from the NIH’s gene expression omnibus (GEO) database and imported into Microsoft Excel along with our own MAS5 signal intensities.  For all of these datasets the probe intensities from each microarray were sorted from highest to lowest and the ranking for each of the loci of interest was taken as an average of the ranking from individual replicates.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa biofilm, grown in drip flow reactor 84hrs, no treatment

label_protocol: Isolated total RNA was reverse-transcribed, fragmented using DNAseI and biotin end-labeled according to Affymetrix’s Prokaryotic Target Labeling Protocol (GeneChip Expression Analysis Technical Manual; November, 2004). 10 µg of RNA was used to produce cDNA, and 4.5 µg of CDNA was fragmented and labeled.

growth_protocol: Biofilms were grown in drip-flow reactors using Pseudomonas Basal Mineral media supplemented with 0.2 g l-1 glucose. The Drip-flow reactors consist of four parallel chambers with polycarbonate covers containing septa for the introduction of media using 22 gauge needles, and a filtered air vent. Media was pumped into the chambers at a flow rate of 60 ml h-1, dripping onto the stainless steel slides (8.5cm x 1.3cm) placed in the chambers. The reactors were placed on a stand inclined at 10º from horizontal to allow PBM to flow down the length of the coupon and drain from the reactor. The reactors were inoculated by adding 1 ml of an overnight culture to 15 ml of fresh PBM covering the slides (inocula OD600 ˜ 0.3) in PBM containing 1 g l-1 glucose. The reactor was sealed by clamping the effluent tubes and the inocula were allowed to sit in the reactor for 18-24h on a level surface. After the inoculation period, the reactor was inclined and flow was initiated. The entire drip-flow reactor was kept in a 37 ºC incubator. Media flowing from outside the incubator was warmed by passing the supply tubing through a grooved aluminum block kept in the incubator.

extract_protocol: Biofilms were scraped directly into 1ml of RNAlater, and dispersed by pipetting repeatedly with a micro-pipette. Recovered biofilms were stored at 4 ºC for one day prior to removal of RNAlater® by centrifugation, followed by freezing of the biofilm cells at -70 ºC until extraction. Biofilm cells were thawed on ice and re-suspended in 300 µl of lysozyme (1mg/ml TE buffer) and divided into 3 aliquots. Each aliquot was sonicated for 15s, and incubated at room temperature for 15 minutes. RNA was extracted with an RNeasy® mini kit with on column DNA digestion with the 3 aliquots being combined on a single column.

treatment_protocol: The biofilms were grown in drip flow reactors for 72hrs or 84hrs.

tag: biofilm type

value: Drip Flow

tag: age

tag: treatment


title: AB8895_H3K4ME1733246_N2_L3_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;antigen: Peptide including dimethyl-lysine 9 of histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.;

value: L3 Larva

value: wild type

value: mixed Male and Hermaphrodite population


title: ChIP-Seq analysis of H3K4me1 in human rectal mucosa cells; Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621639_BI.Rectal_Mucosa.H3K4me1.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Rectal Mucosa, Donor 29 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.4608
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0828
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1858
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9143
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4011
POISSON_PERCENTILE: 5

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

ANALYSIS FILE NAME: GSM621639_BI.Rectal_Mucosa.H3K4me1.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Rectal Mucosa, Donor 29 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.4882
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 2
BROWSER_TRACK_NAME: RM H3K4me1 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K4me1 Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0828
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1858
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9143
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4011
POISSON_PERCENTILE: 5

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1

value: surgery

value: normal mucosa

value: genomic DNA

value: mucosa

value: white

value: Female

value: Histone H3K4me1


title: 0hr ctrl, baseline, rep2

description: information provided elsewhere

source_name: Pseudomonas aeruginosa biofilm, grown in drip flow reactor 72hrs, no treatment


title: WA30634849_H3K27AC_N2_L3_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA306-34849 H3K27ac;target name: H3K27ac;host: Mouse;antigen: 19 end of N amino acids of homo sapiens histone H3.1;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA306-34849;short description: A protein G purified mouse monoclonal antibody to H3K27ac (cat #306-34849) obtained from Wako. Used for ChIP.;
channel ch2 is input DNA;


title: ChIP-Seq analysis of H3K9me3 in human rectal mucosa cells; Lib:XZ:20100423:31--ChIP:XZ:70100407:20:rectal mucosa:H3K9Me3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:31--ChIP:XZ:70100407:20:rectal mucosa:H3K9Me3
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621633_BI.Rectal_Mucosa.H3K9me3.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:31--ChIP:XZ:70100407:20:rectal mucosa:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Rectal Mucosa, Donor 29 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.4669
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0261
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0546
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.7916
IROC_PERCENTILE: 39
POISSON_SCORE: 0.3071
POISSON_PERCENTILE: 22

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

ANALYSIS FILE NAME: GSM621633_BI.Rectal_Mucosa.H3K9me3.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:31--ChIP:XZ:70100407:20:rectal mucosa:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 29 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.4943
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 2
BROWSER_TRACK_NAME: RM H3K9me3 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K9me3 Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0261
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0546
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.7916
IROC_PERCENTILE: 39
POISSON_SCORE: 0.3071
POISSON_PERCENTILE: 22

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:31--ChIP:XZ:70100407:20:rectal mucosa:H3K9Me3

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K9me3


title: WA30634849_H3K27AC_N2_L3_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA306-34849 H3K27ac;target name: H3K27ac;host: Mouse;antigen: 19 end of N amino acids of homo sapiens histone H3.1;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA306-34849;short description: A protein G purified mouse monoclonal antibody to H3K27ac (cat #306-34849) obtained from Wako. Used for ChIP.;


title: 12hr ctrl, rep1

description: information provided elsewhere

value: Drip Flow


title: E0-4_rbCBP

status: Public on Nov 11 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

description:
input CEL file: extracted_0-4h_Input.CEL
input CEL file: extracted_E-0-4h_Input-0-4h_Ctl1.CEL

hyb_protocol: Affymetrix Hybridization Protocol - Hybridizations were performed at the Functional Genomics Facility (FGF) at the University of Chicago.

scan_protocol: Affymetrix Protocol - Scans were performed at the Functional Genomics Facility (FGF) at the University of Chicago.

data_processing:
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks.
.bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

organism: Drosophila melanogaster

label_protocol: Affymetrix Labeling Protocol (TdT labeling)

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB).

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No Treatment

tag: antibody

value: rbCBP

tag: antibody provider

value: Mannervik Lab

tag: antibody lot/batch#

tag: antibody catalog#

tag: fly

value: iso1 (y; bw cn sp)

source_name: input


title: Kc_Kr

description:
input CEL file: extracted_KC167_Input_A.CEL
input CEL file: extracted_KC167_Input_B.CEL

value: White Lab


title: sens_sens-E-4-8h

description:
input CEL file: extracted_sens-E-4-8h_Input-sens-A_Ctl1.CEL
input CEL file: extracted_sens-E-4-8h_Input-sens-B_Ctl2.CEL
input CEL file: extracted_sens-E-4-8h_Input-sens-C_Ctl3.CEL

value: sens

value: Bellen Lab

value: transgenic


title: GFP_sens-E-4-8h

description:
input CEL file: extracted_sens-E-4-8h_Input-sens-A-GFP_Ctl1.CEL
input CEL file: extracted_sens-E-4-8h_Input-sens-B-GFP_Ctl2.CEL
input CEL file: extracted_sens-E-4-8h_Input-sens-C-GFP_Ctl3.CEL

value: GFP


title: E4-8h_sens

description: input CEL file: extracted_ISO1_4-8_Input.CEL


title: E0-8h_jumu

description:
input CEL file: extracted_Input_0-8h_C.CEL
input CEL file: extracted_ISO1_0-8_Input_A.CEL
input CEL file: extracted_ISO1_0-8_Input_B.CEL

value: jumu


title: E0-12_Su(Hw)PG

description: input CEL file: extracted_Su(Hw)PG_E-0-12h_E-0-12h_Input-A-su(hw)_Ctl1.CEL

value: Su(Hw)PG

value: Geyer Lab


title: GFP_7T-E0-4

description:
input CEL file: extracted_7T-E-0-4h_input-0-4h-7T_Ctl2.CEL
input CEL file: extracted_7T-E-0-4h_Input-7T_Ctl1.CEL


title: 0hr ctrl, baseline, rep1

description: information provided elsewhere


title: 0hr ctrl, baseline, rep3

description: information provided elsewhere


title: Septic Shock_biological rep1

tag: tissue

value: Whole Blood

tag: disease state

value: septic shock patient

value: Survivor


title: E0-8h_h

description:
input CEL file: extracted_Input_0-8h_B.CEL
input CEL file: extracted_ISO1_0-8_Input_A.CEL
input CEL file: extracted_ISO1_0-8_Input_B.CEL

value: h


title: ChIP-Seq analysis of H3K27me3 in rectal mucosa cells; Lib:XZ:20100423:29--ChIP:XZ:70100407:18:rectal mucosa:H3K27Me3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:29--ChIP:XZ:70100407:18:rectal mucosa:H3K27Me3
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621650_BI.Rectal_Mucosa.H3K27me3.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:29--ChIP:XZ:70100407:18:rectal mucosa:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Rectal Mucosa, Donor 29 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.4621
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0097
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0651
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.543
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3838
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM621650_BI.Rectal_Mucosa.H3K27me3.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:29--ChIP:XZ:70100407:18:rectal mucosa:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 29 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.4895
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 2
BROWSER_TRACK_NAME: RM H3K27me3 29
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K27me3 Donor 29 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0097
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0651
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.543
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3838
POISSON_PERCENTILE: 25

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100423:29--ChIP:XZ:70100407:18:rectal mucosa:H3K27Me3

value: surgery

value: normal mucosa

value: genomic DNA

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: E0-8h_disco

description:
input CEL file: extracted_E-0-8h_input_0-8h_Ctl1.CEL
input CEL file: extracted_ISO1_0-8_Input_A.CEL
input CEL file: extracted_ISO1_0-8_Input_B.CEL

value: disco

value: White Lab

value: iso1 (y; bw cn sp)


title: E0-8_D

value: D


title: E0-8h_GATAe

value: GATAe


title: E0-8h_hkb

value: hkb


title: 12hr ctrl, rep2

description: information provided elsewhere

value: Drip Flow


title: S2_ctcf_n

description:
input CEL file: extracted_S2-Cells_Input-S2_Ctl2.CEL
input CEL file: extracted_S2-Cells_S2-Mock_Ctl1.CEL

value: CTCF-N

value: Renkawitz Lab


title: ISO1_0-4_cad

description: input CEL file: extracted_ISO1_0-4_Input.CEL

value: cad

value: Reinitz Lab


title: E-0-4h_bks

description: input CEL file: extracted_0-4h_Input.CEL

value: bks

value: Mannervik Lab


title: Kc167_Trl

value: Trl


title: SDQ3582_CBP1_N2_MXEMB_2 extraction2_array1

status: Public on Jul 07 2010

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ3582 CBP1;target name: CBP-1;host: Rabbit;antigen: RYPYAQGGPPPGAQGMPQGYPGVSRGGPTPGQPMGRGAMMNGAMPRSGPMPTQGRPGIPPNQQAMMQPMMTDRQFMQHGQYGQQRPEFMQQYGRPGGYP;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3582 CBP1;
channel ch2 is input DNA;

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 WS180
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 WS180

value: Mixed embryos 20dC

tag: genotype

value: wild type

tag: sex

value: Hermaphrodite


title: SDQ3575_CBP1_N2_MXEMB_1 extraction4_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ3575 CBP1;target name: CBP-1;host: Rabbit;antigen: RYPYAQGGPPPGAQGMPQGYPGVSRGGPTPGQPMGRGAMMNGAMPRSGPMPTQGRPGIPPNQQAMMQPMMTDRQFMQHGQYGQQRPEFMQQYGRPGGYP;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3575 CBP1;
channel ch2 is input DNA;

tag: strain


title: SDQ3582_CBP1_N2_MXEMB_3 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ3582 CBP1;target name: CBP-1;host: Rabbit;antigen: RYPYAQGGPPPGAQGMPQGYPGVSRGGPTPGQPMGRGAMMNGAMPRSGPMPTQGRPGIPPNQQAMMQPMMTDRQFMQHGQYGQQRPEFMQQYGRPGGYP;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3582 CBP1;

tag: developmental stage


title: LPAR109_H4TETRAAC109_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: LPAR109 H4tetraac:109;target name: H4tetraac;host: Rabbit;antigen: Peptide containing the amino terminal region of tetrahymena histone variant hv1 acetylated at multiple lysines;clonal: Polyclonal;purified: Crude;company: LP BIO;catalog: AR109;short description: Rabbit serum to H4 tetra acetyl from LP Bio (AR-109 lot #109). Used for ChIP.;
channel ch2 is input DNA;

data_processing:
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

value: Early Embryo

value: mixed Male and Hermaphrodite population


title: LPAR109_H4TETRAAC109_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: LPAR109 H4tetraac:109;target name: H4tetraac;host: Rabbit;antigen: Peptide containing the amino terminal region of tetrahymena histone variant hv1 acetylated at multiple lysines;clonal: Polyclonal;purified: Crude;company: LP BIO;catalog: AR109;short description: Rabbit serum to H4 tetra acetyl from LP Bio (AR-109 lot #109). Used for ChIP.;


title: AB9051_H4K20ME1104513_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab9051 H4K20me1:104513;target name: H4K20me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H4 mono methylated at K20;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;short description: An affinity purified rabbit antibody to H4K20me1 obtained from Abcam (ab9051 lot #104513). Used for ChIP.;
channel ch2 is input DNA;


title: AB9051_H4K20ME1104513_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab9051 H4K20me1:104513;target name: H4K20me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H4 mono methylated at K20;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;short description: An affinity purified rabbit antibody to H4K20me1 obtained from Abcam (ab9051 lot #104513). Used for ChIP.;


title: SDQ3582_CBP1_N2_MXEMB_1 extraction1_array1


title: SDQ3897_NPP13_N2_MXEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ4094 NPP13;target name: NPP-13;host: Rabbit;antigen: HCRNEEAEIAYGISTHLRLIPTEPDQVTVIVNEFHMVPQKVREVLPDMCLHLMKCLVDHCIRQSTTQANRGANSATTSMFSSSNRYVKQIKAIVLYSATV;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4094 NPP13;


title: SDQ3897_NPP13_N2_MXEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ4094 NPP13;target name: NPP-13;host: Rabbit;antigen: HCRNEEAEIAYGISTHLRLIPTEPDQVTVIVNEFHMVPQKVREVLPDMCLHLMKCLVDHCIRQSTTQANRGANSATTSMFSSSNRYVKQIKAIVLYSATV;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4094 NPP13;
channel ch2 is input DNA;


title: SDQ4094_NPP13_N2_MXEMB_3 extraction3_array1


title: SDQ4051_LEM2_N2_MXEMB_1 extraction4_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ4051 LEM2;target name: LEM-2;host: Rabbit;antigen: MVDVEKMSDAELRAELNVRGANVGPVTGTTRSLYEKKLKKLLSGGAKTPARPTVAKPAPKPTPKSAPAPKSPKSPPARRSIPRAAATAANSTINSTFNRS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4051 LEM2;


title: SDQ3891_LEM2_N2_MXEMB_3 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ3891 LEM2;target name: LEM-2;host: Rabbit;antigen: MVDVEKMSDAELRAELNVRGANVGPVTGTTRSLYEKKLKKLLSGGAKTPARPTVAKPAPKPTPKSAPAPKSPKSPPARRSIPRAAATAANSTINSTFNRS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3891 LEM2;


title: E0-8_Kr-D2

description:
input CEL file: extracted_E-0-8h_input_0-8h_Ctl1.CEL
input CEL file: extracted_E-0-8h_Input-0-8h-D_Ctl2.CEL

value: White Lab

value: iso1 (y; bw cn sp)


title: SDQ3891_LEM2_N2_MXEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ3891 LEM2;target name: LEM-2;host: Rabbit;antigen: MVDVEKMSDAELRAELNVRGANVGPVTGTTRSLYEKKLKKLLSGGAKTPARPTVAKPAPKPTPKSAPAPKSPKSPPARRSIPRAAATAANSTINSTFNRS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3891 LEM2;
channel ch2 is input DNA;


title: SDQ3891_LEM2_N2_MXEMB_2 extraction2_array1


title: AB8896_H3K9ME1104560_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab8896 H3K9me1:104560;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide derived from within residues 1-100 of Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8896;short description: An affinity purified rabbit antibody to H3K9me1 obtained from Abcam (ab8896 lot #104560). Used for ChIP.;
channel ch2 is input DNA;


title: AB4441_H3K9AC_N2_EEMB_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab4441 H3K9ac:360927;target name: H3K9ac;host: Rabbit;antigen: Synthetic peptide:ARTKQTARacKSTG-C conjugated to KLH corresponding to amino acids 1-12 of human Histone H3.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab4441;short description: An affinity purified rabbit polyclonal antibody to H3K9ac from abcam(ab4441 lot #360927). Used for ChIP.;


title: AB4729_H3K27AC361571_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab4729 H3K27ac:361571;target name: H3K27ac;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 acetylated at K27;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab4729;short description: A rabbit affinity purified antibody to H3K27ac obtained from Abcam (ab4729 lot#361571). Used for ChIP.;
channel ch2 is input DNA;


title: AB4441_H3K9AC_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab4441 H3K9ac:360927;target name: H3K9ac;host: Rabbit;antigen: Synthetic peptide:ARTKQTARacKSTG-C conjugated to KLH corresponding to amino acids 1-12 of human Histone H3.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab4441;short description: An affinity purified rabbit polyclonal antibody to H3K9ac from abcam(ab4441 lot #360927). Used for ChIP.;
channel ch2 is input DNA;


title: WA30634849_H3K27AC_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA306-34849 H3K27ac;target name: H3K27ac;host: Mouse;antigen: 19 end of N amino acids of homo sapiens histone H3.1;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA306-34849;short description: A protein G purified mouse monoclonal antibody to H3K27ac (cat #306-34849) obtained from Wako. Used for ChIP.;
channel ch2 is input DNA;


title: AB8895_H3K4ME1733246_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;antigen: Peptide including dimethyl-lysine 9 of histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.;


title: WA30634849_H3K27AC_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA306-34849 H3K27ac;target name: H3K27ac;host: Mouse;antigen: 19 end of N amino acids of homo sapiens histone H3.1;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA306-34849;short description: A protein G purified mouse monoclonal antibody to H3K27ac (cat #306-34849) obtained from Wako. Used for ChIP.;


title: AB9045_H3K9ME1291918_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab9045 H3K9me1:291918;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 mono methylated at K9;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9045;short description: A Rabbit affinity purified antibody to H3K9me1 from abcam (ab9045 lot #291918). Used for ChIP.;


title: AB9045_H3K9ME1291918_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab9045 H3K9me1:291918;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 mono methylated at K9;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9045;short description: A Rabbit affinity purified antibody to H3K9me1 from abcam (ab9045 lot #291918). Used for ChIP.;
channel ch2 is input DNA;


title: MP07030_H3K4ME2DAM1570816_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: MP07030 H3K4me2:DAM157816;target name: H3K4me2;host: Rabbit;antigen: KLH conjugated synthetic peptide (ARTME2KQTAR-GC) corresponding to amino acis 1-8 of human histone H3;clonal: Polyclonal;purified: Crude;company: Upstate/Millipore;catalog: 07-030;short description: Rabbit serum to H3K4me2 from Millipore (07-030 lot # DAM1570816). Used for ChIP.;


title: AB9048_H3K36ME1206009_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab9048 H3K36me1:206009;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 monomethylated at K36;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;short description: A rabbit affinity purified antibody to H3K36me1 from abcam (Ab9048 lot #206009). Used for ChIP.;
channel ch2 is input DNA;


title: AB9048_H3K36ME1206009_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab9048 H3K36me1:206009;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 monomethylated at K36;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;short description: A rabbit affinity purified antibody to H3K36me1 from abcam (Ab9048 lot #206009). Used for ChIP.;


title: OD00079_HCP3_N2_EEMB_3 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: OD00001 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;
channel ch2 is input DNA;


title: OD00079_HCP3_N2_EEMB_2 extraction2_array1

growth_protocol: Worm_embryo_growth_and_harvest_vSS2. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at ?80°C. For a detailed protocol see http://www.modencode.org/.


title: OD00079_HCP3_N2_EEMB_1 extraction1_array1


title: WA30834809_H3K4ME2_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA308-34809 H3K4me2;target name: H3K4me2;host: Mouse;antigen: ART(me2-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA308-34809;short description: A protein G purified mouse monoclonal antibody to H3K4me2 (cat #308-34809) obtained from Waco. Used for ChIP.;
channel ch2 is input DNA;


title: HK00008_H3K9ME26D11_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00008 H3K9me2:6D11;target name: H3K9me2;host: Mouse;antigen: ARTKQTAR(me2-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00008;short description: A protein G purified mouse monoclonal antibody to H3K9me2 (clone 6D11) obtained from Hiroshi Kimura. Used for ChIP.;
channel ch2 is input DNA;


title: WA30834809_H3K4ME2_N2_EEMB_1 extraction1_array1


title: HK00008_H3K9ME26D11_N2_EEMB_1 extraction1_array1


title: AB2621_H3K79ME3361576_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.;
channel ch2 is input DNA;

data_processing:
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180


title: AB2621_H3K79ME3361576_N2_EEMB_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.;


title: AB3594_H3K79ME2346021_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: AB3594 H3K79me2:346021;target name: H3K79me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 di methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab3594;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide di-methylated at K79.;
channel ch2 is input DNA;