title: E20 embryo, biological rep. 2

description:
microRNA expression during parotid acini terminal differentiation
E20_31b

source_name: Rat embryo day E20 (parotid acini total RNA)


title: E20 embryo, biological rep. 1

status: Public on Jan 27 2015

type: RNA

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

country: USA

institute: University of Louisville

description:
microRNA expression during parotid acini terminal differentiation
E20 9b

data_processing:
raw CT values were normalized to the median value on the plate
Fold/Change work sheet lists LogFoldChanges in expression between time points measured

label: SYBR green

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Exiqon’s Universal cDNA Synthesis Kit was used per the manufacturer instructions and combined with exicon's SYBR green master mix

extract_protocol: RNAqueous micro kit from Ambion was used per the manufacturer instructions

tag: strain background

value: Sprague Dawley

tag: genotype/variation

value: albino

tag: age

tag: cell type

value: acinar cells from the parotid


title: E20 embryo, biological rep. 3

description:
microRNA expression during parotid acini terminal differentiation
E20_33a


title: P5 postnatal, biological rep. 1

description:
microRNA expression during parotid acini terminal differentiation
P5 11b

source_name: Rat embryo day P5 (parotid acini total RNA)


title: LSD2-KD3

status: Public on Jan 31 2015

city: Kumamoto

first: Shinjiro

last: Hino

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GCS3000 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling, and baseline transformed to the median of all 5 samples. GeneSpring GX12 software was used for summarization by MAS5.0 algorithm and baseline transformation (median shift).

label: biotin

organism: Homo sapiens

source_name: HepG2 cells introduced with siRNA-3 against LSD2

label_protocol: GeneChip 3' IVT Express Kit.

growth_protocol: HepG2 cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified Eagle's Medium (DMEM) (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum and penicillin/streptomycin.

extract_protocol: After cultured for 3 to 4 days, semiconfluent cells were harvested for RNA extraction using RNeasy kit.

treatment_protocol: For the knockdown experiments, specific siRNAs were introduced to the cells using RNAiMAX reagent (Invitrogen) when the cells were approximately 50% confluent.

tag: cell line

value: hepatic cells line

tag: sirna


title: Cont2

description: Technical replicate of Cont1.

source_name: HepG2 cells introduced with siRNA against GL3


title: HCC_C34

status: Public on Jan 24 2015

type: genomic

city: Suwon

first: Jaeyoun

last: Cheong

address: 164 Worldcup-ro

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: For hybridization, labeled DNA was mixed with Cot-1 DNA (50 mg, Gibco BRL, Gaithersburg, MD, USA) and ethanol precipitated. The precipitated DNA was dissolved in 40 µl hybridization mix. The probe mixture was denatured at 75 ◦C for 5 min and incubated at 37 ◦C for 60 min for blocking of repetitive sequences. The arrays were prehybridized with salmon sperm DNA to reduce non-specific back-ground staining. The probe mixture was applied to the array. The arrays were placed in a moist chamber at 37 ◦C for 72 h for hybridization. The array slides were washed twice in 2 × standard saline citrate (2 ×SSC), 50% formamide, pH 7.0, at 45 ◦C. Then the array slides were washed well in phosphate buffer with 0.1% NP-40, pH 8.0, in 2 × SSC at room temperature.

scan_protocol: After hybridization, the slides were scanned on a GenePix 4000A scanner (Axon Instruments, Union City, CA, USA) and the 16-bit TIFF images were captured using GenePix Pro 5.0 software. The fluorescence images were analyzed using a software (MacViewer, Macrogen Inc.) optimized for analysis of the array. The fluorescence spots were defined using the automatic grid feature and adjusted manually.

data_processing: Then the ratio of the green:red channel of each clone was calculated and all CGH ratios were converted to log base 2 (log2 ratios). The clones with log2 ratios that exceeded ± 0.25 were considered gain and loss of the copy number.  Because the chromosomal region showing high-level gain often contain an important oncogene, the high-level gain was marked and defined a log2 (green/red) ratio >1.0 as an amplification.  In order to define chromosomal regions with DCNAs, the adaptive weights smoothing (AWS) procedure with the gain and loss analysis of DNA (GLAD) algorithm was applied to the ratio data.

molecule: genomic DNA

source_name: liver cancer tissue

label_protocol: Test DNA and reference DNA (Promega, Madison, WI) were labeled with Cy3 and Cy5-dCTP, (Perkin-Elmer Life Science), respectively, with a random primer labelling kit (BioPrime, DNA Labelling System, Invitrogen Co.).

extract_protocol: genomic DNAs from frozen liver cancer tissues were extracted using the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion, Grand Island, NY) following the manufacturer’s protocol, and the DNA concentrations were measured by Nanodrop (Thermo-Fisher, Wilmington, DE).

tag: gender

value: female

tag: age (yrs)

tag: etiology

value: Hepatitis B

tag: tumor stage (muicc)

source_name: human normal cell (reference)

tag: reference provider

value: Promega Co.


title: Cutaneous lesion 3

status: Public on Feb 01 2015

city: Marseille

first: Pablo

last: Oliveira

state: PACA

address: 27, bd Jean Moulin

country: France

institute: INSERM

description: Transcription profilling

hyb_protocol: 1.5 µg of cRNACy3 was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent, following the manufacturer’s instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized hybridized (65° C for 17 hours) to the SurePrint G3 Human Gene Expression v2 microarray (G4851B; Agilent Technologies), which comprises 50,599 biological features. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with 37° C GE Wash buffer 2, and then dried immediately by brief centrifugation.

scan_protocol: The slides were scanned immediately after washing on the SureScan Microarray Scanner (Agilent Technologies). Subsequently, the images were converted into expression values using the Feature Extraction software (version 9.5.3; Agilent Technologies).

data_processing: The scanned images were converted into expression values using the Feature Extraction software (version 9.5.3; Agilent Technologies). Data were quantile-normalized with GeneSpring GX software (Agilent Technologies).

source_name: Cutaneous lesion (L. braziliensis) 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Eight lesion biopsies from patients infected with L. braziliensis (from the border of the ulcers, before treatment) and 8 normal skin samples from uninfected donors were collected and immediately stored in RNAlater solution (Life Technologies). Tissue (20 mg) was placed in microtubes containing 1.4 mm-diameter ceramic beads (CK14; Bertin Technologies) and 350 µL of RTL lysis buffer (Qiagen) supplemented with 3.5 µL of b-mercaptoethanol (Sigma-Aldrich). Complete disruption of the tissue was achieved with a Precellys 24 homogenizer (Bertin Technologies). We added 400 µL of Trizol reagent (Life Technologies) and 150 µL of chloroform (Sigma-Aldrich) and the tubes were then vigorously vortexed and incubated for 5 minutes at room temperature. The aqueous phase was recovered, mixed with 500 µL of 70% ethanol, and the RNA was purified using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. The recovered RNA was quantified by spectrophotometric analysis (NanoVue Plus Spectrophotometer; GE Life Sciences) and its integrity was assessed with a 2100 Bioanalyzer (Agilent Technologies). All 16 samples included in the gene expression profiling experiment were suitable for microarray analysis, in terms of RNA quality [RNA Integrity Number (RIN) ≥ 8.0].

tag: tissue

value: skin


title: Cont1


title: DF_aerosol_rep2

city: Munich

first: Sebastian

last: Oeder

address: Biedersteinerstr. 29

department: Center for Allergy and Environment (ZAUM)

country: Germany

institute: Technische Universität München

description: Gene expression in BEAS-2B cells after 4h on-line exposure to complete DF combustion aerosol

hyb_protocol: Hybridisation to Sure Print G3 Human Gene Expression Microarrays (8x60k) was erformed according to the manufacturers protocol  (Agilent, Waldbronn, Germany).

scan_protocol: Scanning was performed according to the manufacturers protocol  (Agilent, Waldbronn, Germany).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

source_name: BEAS-2B, 4h, DF, aerosol, replicate 2

label_protocol: Total RNA was Cy3-labeled according to the manufacturers protocol  (Agilent, Waldbronn, Germany).

growth_protocol: Human immortalized bronchial epithelial cells BEAS-2B (ATCC® CRL-9609™; http://www.lgcstandards-atcc.org/Products/All/CRL-9609.aspx) were cultured in Bronchial Epithelial Growth Medium (BEGM, Lonza Inc., Walkersville, MD) supplemented with 100 units/ml penicillin/streptomycin and on plates that were pre-coated with 0.01 mg/ml fibronectin, 0.03 mg/ml bovine collagen Type 1 and 0.01 mg/ml BSA.

extract_protocol: Total RNA was extracted using the AllPrep RNA/Protein Kit (Qiagen, Hilden, Germany).

treatment_protocol: In a fully automatic Air-liquid-interface exposure chamber cell cultures grown on porous membrane inserts, which supply the nutrient medium, are exposed directly to diluted aerosol from combustion sources (Fig. S2). The aerosol is humidified by steam injection to 85 % relative humidity and temperature is controlled to 37°C. The flow rate is 100 ml/min.

tag: fuel type

value: Diesel Fuel

tag: aerosol

value: complete aerosol


title: HCC_C35


title: P5 postnatal, biological rep. 2

description:
microRNA expression during parotid acini terminal differentiation
P5 15b


title: HCC_C45


title: HCC_C38

value: male


title: DeltaBcLAE1_r2

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays. It is the second of four deltaBcLAE1 biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed by PartnerChip (http://www.partnerchip.fr/) using NimbleScan.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS website (http://anais.versailles.inra.fr/).

organism: Botrytis cinerea

source_name: Botrytis cinerea B0510_deltaBcLAE1

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: Conidial suspensions of wild type B05.10 and mutant strains deltaBcVEL1 and deltaBcLAE1 were spread onto solid grape juice medium with cellophane overlays, and incubated for 48 h.

extract_protocol: Total RNA was extracted according to the total RNA isolation protocol described by Reid et al. (2006), but with 10M rather than 8M LiCl, and resuspended in RNAse/DNAse-free water. The total RNA was then treated with a DNA-freeTM kit to remove any trace of DNA (Ambion – Applied Biosystems).

tag: genotype

value: Mutant deltaBcLAE1


title: HCC_C44


title: HCC_C37

value: unknown


title: HCC_C31


title: HCC_C29


title: HCC_C39


title: HCC_C41


title: LSD2-KD1

source_name: HepG2 cells introduced with siRNA-1 against LSD2


title: HCC_C42


title: HCC_C40


title: HCC_C32


title: HCC_C43


title: HCC_C36


title: HCC_C33

value: alcohol


title: HCC_C30


title: HCC_C2


title: HCC_C5


title: HCC_C17


title: HCC_C1


title: HCC_C15


title: HCC_C16


title: HCC_C4


title: HCC_C20

value: Hepatitis C


title: HCC_C3


title: HCC_C18


title: HCC_C6


title: HCC_C19


title: HCC_C10


title: HCC_C13


title: HCC_C22


title: HCC_C12


title: HCC_C11


title: HCC_C21


title: HCC_C7


title: HCC_C26


title: HCC_C27


title: HCC_C14


title: HCC_C23


title: HCC_C9


title: NOR_C24

source_name: liver tissue, non-tumor


title: HCC_C24


title: NOR_C25


title: HCC_C28


title: HCC_C25


title: HCC_C8


title: NOR_C20


title: NOR_C19


title: NOR_C22


title: NOR_C18


title: NOR_C13


title: NOR_C23


title: NOR_C17


title: NOR_C14


title: NOR_C15


title: Disease 18

status: Public on Jan 17 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Disease

data_processing: Raw data were loaded on GenEx Pro version 5.4.3.710 from MultiD.  After interplate calibration, data was tested for outliers with cutoff SD (cycles) = 0.25 and Grubbs test was performed with confidence level = 0.95. All outliers were deleted as recommended. Values above Cq > 37 were treated as background. All non-numerical values were replaced and miRNAs with ≥ 75% missing values, both within biological replicates and altogether, were removed from analysis. Missing values within biological replicates were generated by imputing while missing values were assigned a maximum of Cq = 38.

source_name: plasma

label_protocol: First strand cDNA synthesis was performed from 2 ml of RNA (in 10 ml reactions) using the miRCURY universal cDNA synthesis kit per manufacturer instructions (Exiqon, Copenhagen).  The spike-in synthetic RNAs were used as above to monitor the efficiency of the RNA extraction and cDNA synthesis.  The cDNA was diluted 1:20 in nuclease free water and qPCR was performed as above and samples that did not meet quality control thresholds were omitted. Comprehensive miRNA expression profiling was completed using the Exiqon miRNome platform (human panels I+II, V3) as above on 20 disease samples (10 localized, 10 metastatic) and 15 healthy controls to identify reference miRNAs in human OS plasma samples.

extract_protocol: Plasma preparation and RNA extraction are described above, with the exception that 250 ul of human plasma was passed through a 0.22 micron filter and a total volume of 200 ul was used for RNA extraction.  The organic extraction was up-scaled and 100 ul of Qiazol reagent and 200 ul of chloroform were used.  RNA was extracted from the aqueous phase using the Qiagen miRNeasy kit as per manufacturer instructions and eluted in 50 µl of nuclease free water.

tag: disease state

value: osteosarcoma

tag: os type

value: localized


title: Disease 19

description: Disease

value: metastatic


title: NOR_C4


title: NOR_C1


title: NOR_C7


title: NOR_C9


title: NOR_C10


title: Disease 20

description: Disease


title: NOR_C11


title: NOR_C8


title: NOR_C3


title: NOR_C6


title: NOR_C12


title: NOR_C16


title: NOR_C2


title: Disease 17

description: Disease


title: Disease 16

description: Disease


title: Disease 14

description: Disease


title: Disease 13

description: Disease


title: NOR_C21


title: Disease 2

description: Disease


title: Disease 5

description: Disease


title: Disease 6

description: Disease


title: Disease 4

description: Disease


title: Disease 10

description: Disease


title: Disease 7

description: Disease


title: Disease 12

description: Disease


title: Disease 15

description: Disease


title: Disease 9

description: Disease


title: Disease 8

description: Disease


title: Control 13

description: control

value: healthy


title: Control 15

description: control


title: Control 10

description: control


title: Control 9

description: control


title: Control 3

description: control


title: Control 4

description: control


title: Control 8

description: control


title: Control 6

description: control


title: Control 11

description: control


title: Control 12

description: control


title: Control 14

description: control


title: Disease 3

description: Disease


title: Control 7

description: control


title: Disease 11

description: Disease


title: Control 2

description: control


title: Disease 1

description: Disease


title: EBNA3A_rep2

status: Public on Jan 06 2015

type: SRA

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

description: ChIP-seq

library_source: genomic

data_processing:
Raw reads were mapped onto the hg18 version of the human genome with Bowtie 1.0.0 (-k 1 -m 1)
Mapped reads were reads into SPP 1.10.1, and local tag anomalies were removed with remove.local.tag.anomalies
Input normalized wig files were produced using get.smoothed.tag.density with default parameters
Genome_build: hg18
Supplementary_files_format_and_content: data for replicates of EBNA3A ChIP-Seq wig file normalized to the input.

source_name: Lymphoblast Cell Lines

growth_protocol: Cells were grown in RPMI media supplemented witth 10% FetalPlex, 2 mM glutamine, penicillin and streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde. After wash with PBS, the cells were lyzed in ChIP lysis buffer. Lysates were sonicated and cleared by centrifugation. After pre-clear with protein A beads, HA antibody (ab9100, Abcam) was incubated with the lysate overnight at 4°C. Protein A was used to capture the protein DNA complex. The eluted protein DNA complexes were reverse crosslinked and DNA was purified by a Qiagen PCR purification column.
Libraries were prepared using ChIP-Seq Library Prep Reagent Set for Illumina from NEB. Briefly, DNA was end-repaired. 3' A base was added and ligated to adaptors. After PCR amplification, DNA was purified and analyzed with Illumina HiSeq.

value: EBV-infected B Lymphocytes

value: HA-tagged EBNA3A

tag: chip antibody

value: Anti-HA

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: EBNA3A_rep1

description: ChIP-seq

tag: cell type

tag: genotype/variation


title: Control 1

description: control


title: NOR_C5

tag: gender

value: Promega Co.


title: Control 5

description: control


title: Human Fetal Brain (9007217098_R06C01)

status: Public on Dec 19 2014

city: London

first: Jon

last: Mill

address: De Crespigny Park

department: Institute of Psychiatry

country: United Kingdom

institute: King's College London

hyb_protocol: Standard Illumina 450K  Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Genome Studio followed by WateRmelon.  Normalized beta values generated via the Dasen method of the WateRmelon package.

source_name: Brain

label_protocol: Standard Illumina 450K Protocol

extract_protocol: Genomic DNA was extracted and purified from brain samples using a standard phenol/chloroform extraction

tag: days post-conception

value: M


title: Human Fetal Brain (9007217098_R04C01)

value: F


title: Human Fetal Brain (9007217098_R02C01)


title: Human Fetal Brain (9007217098_R03C01)


title: Human Fetal Brain (9007217090_R02C02)


title: Human Fetal Brain (9007217098_R05C01)


title: Human Fetal Brain (9007217077_R04C01)


title: Human Fetal Brain (9007217098_R01C01)


title: Human Fetal Brain (9007217090_R04C02)


title: Human Fetal Brain (9007217077_R04C02)


title: Human Fetal Brain (9007217098_R06C02)


title: Human Fetal Brain (9007217098_R03C02)


title: Human Fetal Brain (9007217090_R04C01)


title: Human Fetal Brain (9007217090_R03C01)


title: Human Fetal Brain (9007217098_R04C02)


title: Human Fetal Brain (9007217098_R02C02)


title: Human Fetal Brain (9007217090_R03C02)


title: Human Fetal Brain (9007217098_R05C02)


title: Human Fetal Brain (9007217098_R01C02)


title: Human Fetal Brain (9007217090_R01C02)


title: Human Fetal Brain (9007217077_R06C01)


title: Human Fetal Brain (9007217090_R05C01)


title: Human Fetal Brain (9007217090_R06C02)


title: Human Fetal Brain (9007217090_R02C01)


title: Human Fetal Brain (9007217077_R05C01)


title: Human Fetal Brain (9007217090_R05C02)


title: Human Fetal Brain (9007217090_R01C01)


title: Human Fetal Brain (9007217077_R05C02)


title: Human Fetal Brain (9007217090_R06C01)


title: Human Fetal Brain (9007217077_R06C02)


title: Human Fetal Brain (9007217077_R02C02)


title: Human Fetal Brain (9007217077_R02C01)


title: Human Fetal Brain (9007217076_R06C01)


title: Human Fetal Brain (9007217076_R04C01)


title: Human Fetal Brain (9007217054_R05C01)


title: Human Fetal Brain (9007217076_R02C02)


title: Human Fetal Brain (9007217054_R02C01)


title: Human Fetal Brain (9007217054_R05C02)


title: Human Fetal Brain (9007217054_R04C02)


title: Human Fetal Brain (9007217076_R05C01)


title: Human Fetal Brain (9007217054_R01C02)


title: Human Fetal Brain (9007217054_R06C02)


title: Human Fetal Brain (9007217054_R02C02)


title: Human Fetal Brain (9007217054_R04C01)


title: Human Fetal Brain (9007217076_R01C01)


title: Human Fetal Brain (9007217076_R06C02)


title: Human Fetal Brain (9007217077_R01C01)


title: Human Fetal Brain (9007217076_R03C01)


title: Human Fetal Brain (9007217076_R02C01)


title: Human Fetal Brain (9007217054_R03C01)


title: Human Fetal Brain (9007217076_R04C02)


title: Human Fetal Brain (9007217054_R06C01)


title: Human Fetal Brain (9007217054_R03C02)


title: Human Fetal Brain (9007217076_R05C02)


title: Human Fetal Brain (9007217076_R01C02)


title: Human Fetal Brain (9007217053_R06C01)


title: Human Fetal Brain (9007217054_R01C01)


title: Human Fetal Brain (9007217077_R03C01)


title: Human Fetal Brain (9007217053_R05C02)


title: Human Fetal Brain (9007217053_R06C02)


title: Human Fetal Brain (9007217076_R03C02)


title: Human Fetal Brain (9007217053_R05C01)


title: Human Fetal Brain (9007217053_R04C02)


title: Human Fetal Brain (9007217053_R01C02)


title: Human Fetal Brain (9007217053_R04C01)


title: Human Fetal Brain (9007217047_R06C01)


title: Human Fetal Brain (9007217053_R01C01)


title: Human Fetal Brain (9007217047_R05C02)


title: Human Fetal Brain (9007217053_R03C02)


title: Human Fetal Brain (9007217053_R03C01)


title: Human Fetal Brain (9007217047_R03C02)


title: Human Fetal Brain (9007217053_R02C02)


title: Human Fetal Brain (9007217047_R01C01)


title: Human Fetal Brain (9007217047_R01C02)


title: Human Fetal Brain (9007217043_R06C01)


title: Human Fetal Brain (9007217043_R05C02)


title: Human Fetal Brain (9007217043_R03C01)


title: Human Fetal Brain (9007217043_R04C01)


title: Human Fetal Brain (9007217043_R05C01)


title: Human Fetal Brain (9007217043_R02C02)


title: Human Fetal Brain (9007217023_R06C02)


title: Human Fetal Brain (9007217023_R06C01)


title: Human Fetal Brain (9007217043_R03C02)


title: Human Fetal Brain (9007217043_R01C02)


title: Human Fetal Brain (9007217047_R05C01)


title: Human Fetal Brain (9007217043_R02C01)


title: Human Fetal Brain (9007217047_R03C01)


title: Human Fetal Brain (9007217053_R02C01)


title: Human Fetal Brain (9007217043_R01C01)


title: Human Fetal Brain (9007217023_R05C02)


title: Human Fetal Brain (9007217043_R04C02)


title: Human Fetal Brain (9007217023_R04C02)


title: Human Fetal Brain (8963311115_R06C02)


title: Human Fetal Brain (9007217023_R02C02)


title: Human Fetal Brain (9007217023_R02C01)


title: Human Fetal Brain (9007217023_R05C01)


title: Human Fetal Brain (9007217023_R03C02)


title: Human Fetal Brain (9007217023_R04C01)


title: Human Fetal Brain (8963311115_R05C02)


title: Human Fetal Brain (8963311115_R04C01)


title: Human Fetal Brain (9007217023_R01C02)


title: Human Fetal Brain (8963311115_R04C02)


title: Human Fetal Brain (8963311093_R05C02)


title: Human Fetal Brain (8963311115_R06C01)


title: Human Fetal Brain (8963311093_R05C01)


title: Human Fetal Brain (8963311115_R01C01)


title: Human Fetal Brain (8963311115_R03C01)


title: Human Fetal Brain (8963311115_R02C01)


title: Human Fetal Brain (8963311093_R06C02)


title: Human Fetal Brain (8963311115_R03C02)


title: monocyte, replicate 2

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

hyb_protocol: After hybridization of the cRNA on the custom- designed array, the chips were washed according to the manufacturer’s protocol.

scan_protocol: The chips were then scanned by using a G2505C scanner (Agilent Technologies) at the resolution of 5 µm.

data_processing: The raw expression values were bakground corrected using the normexp method, and quantile normalized, using the limma package in an R statistical environment.

organism: Sus scrofa

source_name: monocyte

label_protocol: Each RNA sample (50 ng) was amplified and cyanin 3 (Cy3)- labeled, the complementary RNA (cRNA) was checked for quality on Nanodrop and Agilent 2100 Bioanalyzer. Subsequently, the cRNA (600 ng) was fragmented and used for hybridization on custom- designed Agilent porcine arrays.

extract_protocol: Total RNA from cell sorted subsets were extracted using the Arcturus PicoPure RNA Isolation Kit and checked for quality with an Agilent 2100 Bioanalyzer using RNA 6000 Nano or Pico Kits. All RNA samples had a RNA integrity number (RIN) above 8.5. When insufficient total RNA amounts for hydridization were obtained (< 50 ng), the RNA from the sorted cell subsets of distinct animal were mixed. RNA amplification and labeling was performed using the one-color Low Input Quick Amp Labeling kit.

treatment_protocol: 8mm biopsies punches were obtained from conventional Large White pigs  and incubated overnight at 4°C in complete RPMI plus 2mg/ml Dispase. The next day biopsies, still in dispase, were incubated 2h at 37°C allowing the separation of dermis and epidermis. Epidermis and dermis were then incubated separately overnight at 37°C in complete RPMI. Collagenase D was added at 1mg/ml on dermis cultures. Biopsies were filtered on 100µm pores-nylon filters and cells were then processed for FACS staining. For DC sorting, 800 punch skin biopsies were digested as described  200 to 400.106 dermal cells and 30 to 60.106 epidermal cells were FACS-stained for CD172a, CD163, MHC-II and DAPI. Live, DAPI negative, MHC-IIlow/CD172apos/CD163high macrophages, MHC-IIhigh/CD172apos/CD163pos DDC, MHC-IIhigh/CD172apos/CD163low DDC, MHC-IIhigh/CD172aneg/CD163neg DDC from the dermis and MHC-IIhigh/CD172apos/CD163neg Langerhans cells from the epidermis were cell sorted on a MoFlo ASTRIOS.

value: peripheral blood

tag: cell population

value: monocyte


title: Human Fetal Brain (8963311093_R06C01)


title: Human Fetal Brain (8963311093_R04C02)


title: Human Fetal Brain (8963311115_R01C02)


title: Human Fetal Brain (8963311093_R03C02)


title: Human Fetal Brain (8963311115_R02C02)


title: Human Fetal Brain (8963311093_R02C02)


title: Human Fetal Brain (8963311093_R01C01)


title: Human Fetal Brain (9007217023_R03C01)


title: B lymphocyte, replicate 3

source_name: B lymphocyte

value: B lymphocyte


title: Human Fetal Brain (8963311093_R01C02)


title: Human Fetal Brain (8963311093_R03C01)


title: monocyte, replicate 1


title: B lymphocyte, replicate 2


title: Human Fetal Brain (8963311093_R02C01)


title: Human Fetal Brain (8963311065_R06C01)


title: Human Fetal Brain (8963311065_R06C02)


title: B lymphocyte, replicate 1


title: Human Fetal Brain (8963311065_R04C02)


title: Human Fetal Brain (8963311065_R03C02)


title: Human Fetal Brain (8963311065_R04C01)


title: Human Fetal Brain (8963311065_R02C02)


title: Human Fetal Brain (8963311065_R02C01)


title: Human Fetal Brain (8963311065_R05C01)


title: Human Fetal Brain (8963311065_R05C02)


title: Human Fetal Brain (8963311048_R05C01)


title: Human Fetal Brain (8963311048_R06C02)


title: Human Fetal Brain (8963311065_R03C01)


title: Human Fetal Brain (8963311065_R01C01)


title: Human Fetal Brain (8963311048_R06C01)


title: Human Fetal Brain (8963311048_R04C01)


title: Human Fetal Brain (8963311065_R01C02)


title: Human Fetal Brain (8963311048_R03C01)


title: Human Fetal Brain (8963311048_R01C02)


title: Human Fetal Brain (8963311048_R05C02)


title: Human Fetal Brain (8963311042_R06C01)


title: Human Fetal Brain (8963311042_R04C01)


title: Human Fetal Brain (8963311042_R05C02)


title: Human Fetal Brain (8963311048_R04C02)


title: Human Fetal Brain (8963311042_R03C02)


title: Human Fetal Brain (8963311042_R06C02)


title: Human Fetal Brain (8963311042_R04C02)


title: Human Fetal Brain (8963311048_R02C02)


title: Human Fetal Brain (8963311048_R02C01)


title: Human Fetal Brain (8963311048_R01C01)


title: Human Fetal Brain (8963311048_R03C02)


title: Human Fetal Brain (8963311042_R03C01)


title: MeDIP_parental_rep2

status: Public on Dec 03 2014

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
MeDIP and Input reads derived from parental v6.5 mESC and Tet2 kd mESC and mapped against mm9 as previously described [Pastor et al. Nature 2011, PMID 21552279] by discarding all reads that map to multiple positions in the genome. The obtained mapping results (b ed files) were converted to bam files using the bedToBam function of bedtools. Mapping results from replicates were pooled. Reads that map to the same genomic position were replaced by one representative.
In order to identify genome wide differentially hydroxymethylated regions (DHMRs) in parental v6.5 compared to Tet1, or Tet2 kd, respectively, we calculated library size normalized differential coverage of the CMS-IP data at genome wide 300 bp windows by employing a developmental version (v1.9.10) of the Bioconductor package MEDIPS (extend=200, uniq=F, window_size=300, BSgenome=BSgenome.Mmusculus.UCSC.mm9, diff.method = edgeR, p.vale = 1e-5), and adjacent significant windows with the same direction of 5hmC change were merged.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with mapped read alignments available on the sample records due to absence of available raw data files. Result tables contain counts, rpkm, log2FC, and p-values at genome wide 300 bp windows as returned by the MEDIPS software for Tet2 kd mESC vs. V6.5mESC

organism: Mus musculus

source_name: parental V6.5 mES cells

growth_protocol: Mouse embryonic stem cells were cultured in Knockout D-MEM with 15% ES-qualified FBS (Gemini Bio-products), 2 mM L-glutamine with 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 units/ml penicillin/streptomycin and 1000 U/ml ESGRO® (LIF; Chemicon).

extract_protocol:
not provided
libraries were prepared followed by the instruction provied by illumina Truseq DNA library preperation kit

treatment_protocol: Cells stably depleted of Tet1 and Tet2 were obtained by electroporating V6.5 mESC with pSUPER-puro-Tet1shRNA or pSUPER-puro-Tet2shRNA (320V, 250F). Cells were selected by 1.5 ug/ml puromycin for 7-10 days on puromycin-resistant mitomycine C-inactivated SNL76/7-4 feeder cells. Individual clones were picked and propagated in the absence of puromycin if the passage number was less than 10, or maintained in 1 ug/ml puromycin if the passage number was longer than 10. Tet1 and Tet2 mRNA expression in individual clones was evaluated by qPCR.

tag: knockdown

tag: dna enrichment

value: MeDIP

tag: biological replicate

tag: cell line

value: mES


title: MeDIP_Tet2kd_Input_rep1

source_name: Tet2kd mES cells

value: Tet2 kd

value: none, input


title: Human Fetal Brain (8963311042_R05C01)


title: Human Fetal Brain (8963311042_R02C02)


title: Human Fetal Brain (8963303135_R05C02)


title: Human Fetal Brain (8963311042_R02C01)


title: Human Fetal Brain (8963311042_R01C02)


title: 013-123-0049-Day 84-SRT2104-1000 mg

status: Public on Nov 12 2014

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Nugen Pico-DoubleAmp

hyb_protocol: using WT-Ovation Pico RNA Amplification system (Nugen).

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: skin biopsies

label_protocol: Double amplification

growth_protocol: Skin biopsies were snap-frozen in liquid nitrogen and stored at −80°C until used.

extract_protocol: RNA was extracted using the Qiagen RNeasy Fibrous Tissue Mini Kit (QIAGEN, Valencia, CA) and double amplified

tag: patient

tag: time

value: Day 84

tag: treatment

tag: histological response

value: Non-Responder

tag: batch


title: Human Fetal Brain (8963303135_R04C02)


title: Human Fetal Brain (8963303135_R06C01)


title: Human Fetal Brain (8963311042_R01C01)


title: Human Fetal Brain (8963303135_R05C01)


title: 013-118-0004-Day 84-Placebo

description: Nugen Pico-DoubleAmp

value: Placebo

value: Responder


title: 013-118-0004- Day 1-Placebo

description: Nugen Pico-DoubleAmp

value: Day 1


title: Human Fetal Brain (8963303135_R06C02)


title: Human Fetal Brain (8963303135_R04C01)


title: 013-118-0029- Day 1-SRT2104-500 mg

description: Nugen Pico-DoubleAmp


title: 013-123-0049- Day 1-SRT2104-1000 mg

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303135_R03C02)


title: 013-118-0006-Day 84-SRT2104-250 mg

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303135_R01C01)


title: Human Fetal Brain (8963303124_R05C01)


title: 013-118-0029-Day 84-SRT2104-500 mg

description: Nugen Pico-DoubleAmp


title: 013-122-0048- Day 1-SRT2104-1000 mg

description: Nugen Pico-DoubleAmp


title: 013-121-0031- Day 1-Placebo

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R06C02)


title: 013-121-0031-Day 84-Placebo

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R06C01)


title: Human Fetal Brain (8963303124_R04C01)


title: 013-118-0003-Day 84-SRT2104-250 mg

description: Nugen Pico-DoubleAmp


title: 013-121-0026-Day 84-Placebo

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303135_R01C02)


title: 013-122-0048-Day 84-SRT2104-1000 mg

description: Nugen Pico-DoubleAmp


title: Epididymal fat in C57BL/6J mice under standard chow

status: Public on Oct 02 2014

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

description: Sample 7

library_source: transcriptomic

data_processing: The obtained data were mapped to mouse genome sequence and annotated (bowtie-0.12.7).

source_name: Epididymal fat

growth_protocol: Male C57BL/6J (Charles River Laboratories Japan, Yokohama, Japan) mice were housed in cages and maintained on a 12-hour light-dark cycle. STD (NMF; Oriental Yeast) and HFHS chow (D12331; Research Diet, New Brunswick, NJ) were used, the mice were sacrificed at 20 weeks of age.

extract_protocol:
Total RNAs were isolated from serum and various tissues by using QIAamp Circulating Nucleic Acid Kit and miRNeasy Mini kit (Qiagen, Hilden, Germany), respectively.
Total RNAs were subjected to Illumina TruSeq Small RNA Sample Preparation protocol (Illumina, San Diego, CA), including 3’- and 5’- adapter ligation, reverse transcription, PCR amplification, and pooled gel purification to generate a library product.

tag: strain

tag: tissue

value: Epididymal fat

tag: age

value: 20 weeks

value: male


title: Human Fetal Brain (8963303124_R03C02)

value: M


title: 013-117-0007- Day 1-Placebo

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R02C01)


title: 013-118-0002-Day 84-SRT2104-250 mg

description: Nugen Pico-DoubleAmp


title: 013-118-0003- Day 1-SRT2104-250 mg

description: Nugen Pico-DoubleAmp


title: 013-121-0026- Day 1-Placebo

description: Nugen Pico-DoubleAmp


title: 013-118-0002- Day 1-SRT2104-250 mg

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R01C02)

value: F


title: 013-117-0022-Day 84-SRT2104-500 mg

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R02C02)


title: 013-117-0007-Day 84-Placebo

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R05C02)


title: Human Fetal Brain (8963303124_R03C01)


title: Human Fetal Brain (8963303135_R02C01)


title: 013-117-0022- Day 1-SRT2104-500 mg

description: Nugen Pico-DoubleAmp


title: Human Fetal Brain (8963303124_R01C01)


title: Human Fetal Brain (8963303135_R02C02)


title: 013-118-0006- Day 1-SRT2104-250 mg

description: Nugen Pico-DoubleAmp


title: Matched Control Group [cv000852 3months]

status: Public on Feb 24 2014

city: Windber

first: Darrell

last: Ellsworth

state: PA

address: 620 Seventh St.

institute: Windber Research Institute

description: Gene Expression Data from a matched Control Group participant

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C onGeneChip® Human Genome U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: scanned on a GeneChip® Scanner 3000.

data_processing: Partek® Genomics Suite v6.5 (Partek Incorporated) was used to analyze gene expression data from the 378 CEL files, which all passed standard QC assessment. Duplicate blood samples collected at each time point from 7 random participants indicated high repeatability of the microarray data (average Pearson correlation of normalized intensities was 0.992 + 0.006, range 0.969-0.996). Paired t-tests identified 9 genes that were excluded from further analysis because they showed significant differences in expression among duplicate samples based on a false discovery rate (FDR) adjusted P-value <0.05

label: Biotin

source_name: Blood - PaxGene

label_protocol: double-stranded cDNA (1 ug) labeled with biotin-11-UTP using MessageAmp™ II aRNA Amplification System (Ambion)

extract_protocol: Qiagen PAXgene™ Blood RNA System

treatment_protocol: Participants were enrolled on an ongoing basis in a lifestyle intervention that consisted of four components: 1) a very low fat vegetarian diet (<10% of calories from fat); 2) 180 minutes/week of moderate aerobic exercise; 3) one hour of stress management each day; and 4) weekly group support sessions (40). Clinical staff met with patients twice each week during the first 12 weeks to orient participants to the program and maximize adherence. The remainder of the program was primarily self-directed but included ongoing weekly stress management and group support sessions.

tag: group

value: Matched Control Group

value: Female

tag: cad

value: No

tag: diabetes

tag: 1 year weight loss (%)


title: Matched Control Group [cv000942 1year]

tag: gender

value: Yes


title: Matched Control Group [cv000840 baseline]

value: Male


title: LPS-ERRα+/+ BMDM

status: Public on Jun 17 2014

city: Daejeon

first: Jae-Min

last: Yuk

address: Jung-Gu Munhwa dong

department: Department of Microbiology

institute: College of Medicine, Chungnam National University

hyb_protocol: Each 1,650ng of Cy3-labeled cRNA was fragmented at 60°C for 30 min (Agilent Gene Expression Hybridization Kit) and then hybridized to mouse whole genome 4 × 44K oligo microarray v2 slide (Agilent Technologies Inc.) at 65°C for 17 h. After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) using default parameters (protocol GE1-1105_Oct12 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: High-quality RNA samples were processed for genome-wide transcript expression using Agilent Mouse GE 4 × 44K V2 microarrays (Agilent Technologies Inc.). The Low Input Quick Amp Labeling Kit (Agilent Technologies Inc.) was used for labeling and hybridization. The sample was labeled with the aid of T7 RNA polymerase in the presence of Cy3-CTP. The Cy3-labeled cRNAs were purified using RNeasy MiniElute Cleanup kit (Qiagen). The yield and label incorporation efficiencies were measured with the aid of a spectrophotometer (NanoDrop Lite, Thermo Fisher Scientific, Inc).

growth_protocol: BMDMs were differentiated for 5-7 days in medium containing macrophage colony-stimulating factor. The culture medium consisted of Dulbecco's modiﬁed Eagle's medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1 mM sodium pyruvate, 50 U/mL penicillin, 50 μg/mL streptomycin, and 5×10 5 M 2-mercaptoethanol.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: BMDMs from ERRα +/+ and ERRα -/- mice were incubated with LPS (100 ng/mL)

tag: strain background

tag: genotype/variation

value: ERRα+/+

value: 6-8 wks

tag: cell type

value: bone marrow-dereived macrophages (BMDM)

tag: treated with

value: 100 ng/ml LPS


title: Matched Control Group [cv000941 baseline]


title: Matched Control Group [cv000941 3months]


title: PBS-ERRα+/+ BMDM

value: PBS (solvent control)


title: LPS-ERRα-/- BMDM

value: ERRα-/-


title: Matched Control Group [cv000840 3months]


title: Matched Control Group [cv000909 1year]


title: Matched Control Group [cv000765 3months]


title: Matched Control Group [cv000852 1year]


title: Matched Control Group [cv000942 3months]


title: Matched Control Group [cv000840 1year]


title: Matched Control Group [cv000852 baseline]


title: PBS-ERRα-/- BMDM


title: Matched Control Group [cv000765 baseline]


title: Matched Control Group [cv000909 3months]


title: Matched Control Group [cv000844 baseline]


title: Matched Control Group [cv000844 3months]


title: Matched Control Group [cv000844 1year]


title: Matched Control Group [cv000941 1year]


title: Matched Control Group [cv000909 baseline]


title: Matched Control Group [cv000765 1year]


title: Matched Control Group [cv000942 baseline]


title: Matched Control Group [cv000771 3months]


title: Matched Control Group [cv000743 1year]


title: Matched Control Group [cv000771 1year]


title: Matched Control Group [cv000709 baseline]


title: Matched Control Group [cv000771 baseline]


title: Matched Control Group [cv000743 3months]


title: Matched Control Group [cv000709 3months]


title: Matched Control Group [cv000705 baseline]


title: Matched Control Group [cv000711year]


title: Matched Control Group [cv000743 baseline]


title: Matched Control Group [cv000711 3months]


title: Matched Control Group [cv000705 3months]


title: Matched Control Group [cv000700 1year]


title: Matched Control Group [cv000700 3months]


title: Matched Control Group [cv000709 1year]


title: Matched Control Group [cv000708 baseline]


title: Matched Control Group [cv000694 baseline]


title: Matched Control Group [cv000693 baseline]


title: Matched Control Group [cv000708 3months]


title: Matched Control Group [cv000705 1year]


title: Matched Control Group [cv000708 1year]


title: Matched Control Group [cv000693 1year]


title: Matched Control Group [cv000694 3months]


title: Matched Control Group [cv000691 3months]


title: Matched Control Group [cv000711 baseline]


title: Matched Control Group [cv000693 3months]


title: Matched Control Group [cv000691 1year]


title: Matched Control Group [cv000694 1year]


title: Matched Control Group [cv000700 baseline]


title: Matched Control Group [cv000691 baseline]


title: Matched Control Group [cv000646 baseline]


title: Matched Control Group [cv000614 1year]


title: Matched Control Group [cv000655 1year]


title: Matched Control Group [cv000646 1year]


title: Matched Control Group [cv000690 1year]


title: Matched Control Group [cv000614 baseline]


title: Matched Control Group [cv000613R 3months]


title: Matched Control Group [cv000595 1year]


title: Matched Control Group [cv000614 3months]


title: Matched Control Group [cv000595 baseline]


title: Matched Control Group [cv000613R 1year]


title: Matched Control Group [cv000690 3months]


title: Matched Control Group [cv000613R baseline]


title: Matched Control Group [cv000612 1year]


title: Matched Control Group [cv000612 3months]


title: Matched Control Group [cv000595 3months]


title: Matched Control Group [cv000612 baseline]


title: Matched Control Group [cv000594 1year]


title: Matched Control Group [cv000655 3months]


title: Matched Control Group [cv000593 1year]


title: Matched Control Group [cv000655 baseline]


title: Matched Control Group [cv000646 3months]


title: Matched Control Group [cv000593 3months]


title: Matched Control Group [cv000594 3months]


title: Matched Control Group [cv000594 baseline]


title: Matched Control Group [cv000690 baseline]


title: Matched Control Group [cv000593 baseline]


title: Matched Control Group [cv000567 baseline]


title: Matched Control Group [cv000567 1year]


title: Matched Control Group [cv000567 3months]


title: Matched Control Group [cv000555 1year]


title: Matched Control Group [cv000568 3months]


title: Matched Control Group [cv000506 3months]


title: Matched Control Group [cv000568 baseline]


title: Matched Control Group [cv000504 3months]


title: Matched Control Group [cv000566 3months]


title: Matched Control Group [cv000506 baseline]


title: Matched Control Group [cv000568 1year]


title: Matched Control Group [cv000565 1year]


title: Matched Control Group [cv000505 baseline]


title: Matched Control Group [cv000555 baseline]


title: Matched Control Group [cv000566 1year]


title: Matched Control Group [cv000565 baseline]


title: Matched Control Group [cv000554 baseline]


title: Matched Control Group [cv000555 3months]


title: Matched Control Group [cv000566 baseline]


title: Matched Control Group [cv000505 3months]


title: Matched Control Group [cv000504 1year]


title: Matched Control Group [cv000565 3months]


title: Matched Control Group [cv000506 1year]


title: Matched Control Group [cv000505 1years]


title: Matched Control Group [cv000502 3months]


title: Matched Control Group [cv000554 1year]


title: Matched Control Group [cv000502 1year]


title: Matched Control Group [cv000496 baseline]


title: Matched Control Group [cv000503 baseline]


title: Matched Control Group [cv000496 3months]


title: Matched Control Group [cv000495 1year]


title: Matched Control Group [cv000503 3months]


title: Matched Control Group [cv000504 baseline]


title: Matched Control Group [cv000502 baseline]


title: Matched Control Group [cv000496 1year]


title: Matched Control Group [cv000493 1year]


title: Matched Control Group [cv000493 baseline]


title: Matched Control Group [cv000495 3months]


title: Matched Control Group [cv000503 1year]


title: Matched Control Group [cv000492 baseline]


title: Matched Control Group [cv000494 1year]


title: Matched Control Group [cv000493 3months]


title: Matched Control Group [cv000495 baseline]


title: Matched Control Group [cv000494 baseline]


title: Matched Control Group [cv000491 baseline]


title: Matched Control Group [cv000491 1year]


title: Matched Control Group [cv000494 3months]


title: Matched Control Group [cv000492 1year]


title: Matched Control Group [cv000461 1year]


title: Matched Control Group [cv000491 3months]


title: Matched Control Group [cv000463 baseline]


title: Matched Control Group [cv000463 3months]


title: Matched Control Group [cv000461 3months]


title: Matched Control Group [cv000492 3months]


title: Matched Control Group [cv000458 1year]


title: Matched Control Group [cv000462 3months]


title: Matched Control Group [cv000463 1year]


title: Matched Control Group [cv000459 1year]


title: Matched Control Group [cv000462 1 year]


title: Matched Control Group [cv000461 baseline]


title: Matched Control Group [cv000554 3months]


title: Matched Control Group [cv000457 baseline]


title: Matched Control Group [cv000455 3months]


title: Matched Control Group [cv000459 baseline]


title: Matched Control Group [cv000462 baseline]


title: Matched Control Group [cv000441 3months]


title: Matched Control Group [cv000457 1year]


title: Matched Control Group [cv000458 3months]


title: Matched Control Group [cv000459 3months]


title: Matched Control Group [cv000457 3months]


title: Matched Control Group [cv000441 baseline]


title: Matched Control Group [cv000441 1year]


title: Matched Control Group [cv000455 1year]


title: Matched Control Group [cv000458 baseline]


title: Matched Control Group [cv000455 baseline]


title: Matched Control Group [cv000440 1year]


title: Matched Control Group [cv000394 1years]


title: Matched Control Group [cv000400 3months]


title: Matched Control Group [cv000440 3months]


title: Matched Control Group [cv000400 1year]


title: Matched Control Group [cv000394 3months]


title: Matched Control Group [cv000400 baseline]


title: Matched Control Group [cv000402 1year]


title: Matched Control Group [cv000398 baseline]


title: Matched Control Group [cv000402 3months]


title: Matched Control Group [cv000390 3moths]


title: Matched Control Group [cv000398 1year]


title: Matched Control Group [cv000398 3months]


title: Matched Control Group [cv000402 baseline]


title: Matched Control Group [cv000389 3months]


title: Matched Control Group [cv000384 baseline]


title: Matched Control Group [cv000389 1year]


title: Matched Control Group [cv000385 1year]


title: Matched Control Group [cv000394 baseline]


title: Matched Control Group [cv000390 1year]


title: Matched Control Group [cv000389 baseline]


title: Matched Control Group [cv000380 1year]


title: Matched Ornish Participant [cv000931 baseline]

description: Gene Expression Data from a matched Ornish program participant

value: Matched Ornish Participant


title: Matched Control Group [cv000390 baseline]


title: Matched Control Group [cv000380 baseline]


title: Matched Ornish Participant [cv000931 1year]


title: Matched Ornish Participant [cv000928 1year]


title: Matched Control Group [cv000377 3months]


title: Matched Ornish Participant [cv000928 3month]


title: Matched Ornish Participant [cv000931 3month]


title: Matched Control Group [cv000377baseline]


title: Matched Control Group [cv000380 3months]


title: Matched Control Group [cv000385 baseline]


title: Matched Control Group [cv000384 1year]


title: Matched Control Group [cv000374 baseline]


title: Matched Ornish Participant [cv000918 3month]


title: Matched Ornish Participant [cv000918 1year]


title: Matched Control Group [cv000384 3months]


title: Matched Ornish Participant [cv000928 baseline]


title: Matched Control Group [cv000377 1year]


title: Matched Ornish Participant [cv000900 1year]


title: Matched Ornish Participant [cv000886 3month]


title: Matched Ornish Participant [cv000882 3month]


title: Matched Ornish Participant [cv000918 baseline]


title: Matched Ornish Participant [cv000884 baseline]


title: Matched Ornish Participant [cv000882 1year]


title: Matched Ornish Participant [cv000886 1year]


title: Matched Ornish Participant [cv000879 baseline]


title: Matched Ornish Participant [cv000886 baseline]


title: Matched Ornish Participant [cv000827 3month]


title: Matched Ornish Participant [cv000884 3month]


title: Matched Ornish Participant [cv000825 baseline]


title: Matched Ornish Participant [cv000825 3month]


title: Matched Ornish Participant [cv000900 3month]


title: Matched Ornish Participant [cv000827 baseline]


title: Matched Ornish Participant [cv000825 1year]


title: Matched Control Group [cv000374 1year]


title: Matched Ornish Participant [cv000884 1year]


title: Matched Ornish Participant [cv000879 3month]


title: Matched Ornish Participant [cv000882 baseline]


title: Matched Ornish Participant [cv000900 baseline]


title: Matched Ornish Participant [cv000810 1year]


title: Matched Ornish Participant [cv000827 1year]


title: Matched Ornish Participant [cv000823 1year]


title: Matched Ornish Participant [cv000810 baseline]


title: Matched Ornish Participant [cv000879 1year]


title: Matched Ornish Participant [cv000823 3month]


title: Matched Ornish Participant [cv000823 baseline]


title: Matched Ornish Participant [cv000777 3month]


title: Matched Ornish Participant [cv000780 3month]


title: Matched Ornish Participant [cv000810 3month]


title: Matched Ornish Participant [cv000775 1year]


title: Matched Ornish Participant [cv000775 3month]


title: Matched Ornish Participant [cv000750 3month]


title: Matched Ornish Participant [cv000750 baseline]


title: Matched Ornish Participant [cv000703 1year]


title: Matched Control Group [cv000440 baseline]


title: Matched Ornish Participant [cv000781 baseline]


title: Matched Ornish Participant [cv000775 baseline]


title: Matched Ornish Participant [cv000750 1year]


title: Matched Ornish Participant [cv000777 baseline]


title: Matched Ornish Participant [cv000780 baseline]


title: Matched Ornish Participant [cv000751 3month]


title: Matched Ornish Participant [cv000777 1year]


title: Matched Ornish Participant [cv000697 baseline]


title: Matched Ornish Participant [cv000751 baseline]


title: Matched Ornish Participant [cv000703 3month]


title: Matched Ornish Participant [cv000781 1year]


title: Matched Ornish Participant [cv000780 1year]


title: Matched Ornish Participant [cv000751 1year]


title: Matched Control Group [cv000385 3months]


title: Matched Ornish Participant [cv000781 3month]


title: Matched Control Group [cv000374 3months]


title: Matched Ornish Participant [cv000703 baseline]


title: Matched Ornish Participant [cv000687 3month]


title: Matched Ornish Participant [cv000697 1year]


title: Matched Ornish Participant [cv000665 baseline]


title: Matched Ornish Participant [cv000670 3month]


title: Matched Ornish Participant [cv000613 1year]


title: Matched Ornish Participant [cv000621 3month]


title: Matched Ornish Participant [cv000668 1year]


title: Matched Ornish Participant [cv000687 baseline]


title: Matched Ornish Participant [cv000670 1year]


title: Matched Ornish Participant [cv000670 baseline]


title: Matched Ornish Participant [cv000621 1year]


title: Matched Ornish Participant [cv000613 3month]


title: Matched Ornish Participant [cv000613 baseline]


title: Matched Ornish Participant [cv000663 3month]


title: Matched Ornish Participant [cv000669 1year]


title: Matched Ornish Participant [cv000668 3month]


title: Matched Ornish Participant [cv000621 baseline]


title: Matched Ornish Participant [cv000687 1year]


title: Matched Ornish Participant [cv000663 baseline]


title: Matched Ornish Participant [cv000668 baseline]


title: Matched Ornish Participant [cv000589 baseline]


title: Matched Ornish Participant [cv000665 3month]


title: Matched Ornish Participant [cv000589 3month]


title: Matched Ornish Participant [cv000669 3month]


title: Matched Ornish Participant [cv000665 1year]


title: Matched Ornish Participant [cv000669 baseline]


title: Matched Ornish Participant [cv000589 1year]


title: Matched Ornish Participant [cv000697 3month]


title: Matched Ornish Participant [cv000663 1year]


title: Matched Ornish Participant [cv000588 1year]


title: Matched Ornish Participant [cv000588 3month]


title: Matched Ornish Participant [cv000581 1year]


title: Matched Ornish Participant [cv000583 3month]


title: Matched Ornish Participant [cv000583 baseline]


title: Matched Ornish Participant [cv000437 baseline]


title: Matched Ornish Participant [cv000532 baseline]


title: Matched Ornish Participant [cv000529 3month]


title: Matched Ornish Participant [cv000580 3month]


title: Matched Ornish Participant [cv000434 baseline]


title: Matched Ornish Participant [cv000580 1year]


title: Matched Ornish Participant [cv000537 3month]


title: Matched Ornish Participant [cv000581 3month]


title: Matched Ornish Participant [cv000434 3month]


title: Matched Ornish Participant [cv000537 1year]


title: Matched Ornish Participant [cv000437 3month]


title: Matched Ornish Participant [cv000529 baseline]


title: Matched Ornish Participant [cv000437 1year]


title: Matched Ornish Participant [cv000432 3month]


title: Matched Ornish Participant [cv000432 1year]


title: Matched Ornish Participant [cv000532 1year]


title: Matched Ornish Participant [cv000534 baseline]


title: Matched Ornish Participant [cv000534 1year]


title: Matched Ornish Participant [cv000581 baseline]


title: Matched Ornish Participant [cv000580 baseline]


title: Matched Ornish Participant [cv000532 3month]


title: Matched Ornish Participant [cv000534 3month]


title: Matched Ornish Participant [cv000430 3month]


title: Matched Ornish Participant [cv000529 1year]


title: Matched Ornish Participant [cv000588 baseline]


title: Matched Ornish Participant [cv000537 baseline]


title: Matched Ornish Participant [cv000432 baseline]


title: Matched Ornish Participant [cv000428 3month]


title: Matched Ornish Participant [cv000352 3month]


title: Matched Ornish Participant [cv000430 1year]


title: Matched Ornish Participant [cv000352 baseline]


title: Matched Ornish Participant [cv0003711year]


title: Matched Ornish Participant [cv000352 1year]


title: Matched Ornish Participant [cv000342 baseline]


title: Matched Ornish Participant [cv000430 baseline]


title: Matched Ornish Participant [cv000434 1year]


title: Matched Ornish Participant [cv000371baseline]


title: Matched Ornish Participant [cv000341basleline]


title: Matched Ornish Participant [cv0003413month]


title: Matched Ornish Participant [cv000583 1year]


title: Matched Ornish Participant [cv000342 3month]


title: Matched Ornish Participant [cv000342 1year]


title: Matched Ornish Participant [cv000310 baseline]


title: Matched Ornish Participant [cv000309 baseline]


title: Matched Ornish Participant [cv000304 baseline]


title: Matched Ornish Participant [cv000310 1year]


title: Matched Ornish Participant [cv000310 3month]


title: Matched Ornish Participant [cv000304 1year]


title: Matched Ornish Participant [cv000428 1year]


title: Matched Ornish Participant [cv0003411year]


title: Matched Ornish Participant [cv000306 baseline]


title: Matched Ornish Participant [cv000308 baseline]


title: Matched Ornish Participant [cv000428 baseline]


title: Matched Ornish Participant [cv000304 3month]


title: Matched Ornish Participant [cv000306 1year]


title: Matched Ornish Participant [cv000371 3month]


title: Matched Ornish Participant [cv000307 1years]


title: Matched Ornish Participant [cv000309 1year]


title: Matched Ornish Participant [cv000307 3month]


title: Matched Ornish Participant [cv000299 baseline]


title: Matched Ornish Participant [cv000307 baseline]


title: Matched Ornish Participant [cv000309 3month]


title: Matched Ornish Participant [cv000306 3month]


title: Matched Ornish Participant [cv0003011year]


title: Matched Ornish Participant [cv000301 3month]


title: Matched Ornish Participant [cv000303 3month]


title: Matched Ornish Participant [cv000301baseline]


title: Matched Ornish Participant [cv000296 3month]


title: Matched Ornish Participant [cv000303 baseline]


title: Matched Ornish Participant [cv000299 1year]


title: Matched Ornish Participant [cv000298 3month]


title: Matched Ornish Participant [cv000308 1year]


title: Matched Ornish Participant [cv000308 3month]


title: Matched Ornish Participant [cv000295 3month]


title: Matched Ornish Participant [cv000303 1year]


title: Matched Ornish Participant [cv000296 1year]


title: Matched Ornish Participant [cv000297 3month]


title: Matched Ornish Participant [cv0002971year]


title: Matched Ornish Participant [cv000297baseline]


title: Matched Ornish Participant [cv000296 baseline]


title: Matched Ornish Participant [cv000299 3month]


title: Matched Ornish Participant [cv000295 baseline]


title: Matched Ornish Participant [cv000298 1year]


title: Matched Ornish Participant [cv000292 3month]


title: Matched Ornish Participant [cv000295 1year]


title: Matched Ornish Participant [cv000298 baseline]


title: Matched Ornish Participant [cv0002911year]


title: Matched Ornish Participant [cv000292 1year]


title: Matched Ornish Participant [cv000288 baseline]


title: Matched Ornish Participant [cv000288 3month]


title: Matched Ornish Participant [cv000291baseline]


title: Matched Ornish Participant [cv0002913month]


title: Matched Ornish Participant [cv000290 1year]


title: Matched Ornish Participant [cv000290B 3month]


title: Matched Ornish Participant [cv000288 1year]


title: M_GMCSF_sLPS_IFNg_72h [5342595020_I]

status: Public on Feb 13 2014

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Macrophage

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2-transformed and normalized using quantile normalization with Partek Genomics Suite

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: initial differentiation

value: GM-CSF

tag: activation stimuli

value: sLPS+IFNg

tag: donor


title: Matched Ornish Participant [cv000290 baseline]


title: Matched Ornish Participant [cv000292 baseline]


title: M_GMCSF_sLPS_72h [4958478044_L]

description: Macrophage

value: sLPS

tag: time


title: M_GMCSF_sLPS_72h [4958478044_I]

description: Macrophage


title: M_GMCSF_sLPS_IFNg_72h [5342595020_G]

description: Macrophage


title: M_GMCSF_sLPS_72h [4958478033_E]

description: Macrophage


title: M_GMCSF_sLPS_72h [4958478033_C]

description: Macrophage


title: M_GMCSF_sLPS_IC_72h [4950679045_F]

description: Macrophage

value: sLPS+IC


title: M_GMCSF_sLPS_72h [4958478044_E]

description: Macrophage


title: M_GMCSF_sLPS_72h [4950679013_D]

description: Macrophage


title: M_GMCSF_sLPS_IC_72h [4676163025_K]

description: Macrophage


title: M_GMCSF_sLPS_IC_72h [4676163025_B]

description: Macrophage


title: M_GMCSF_sLPS_IFNg_72h [5342595001_A]

description: Macrophage


title: M_GMCSF_sLPS_72h [4676163025_G]

description: Macrophage


title: M_GMCSF_sLPS_72h [4958478044_B]

description: Macrophage


title: JOCK mouse model, Stroma (CID) 6

status: Public on Jan 07 2014

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used. 'signal' a measure of the ratio of transcript abundance of the sample versus a universal RNA reference.

label: Alexa Fluor 647

source_name: JOCK mouse model, prostate stroma

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: Generation and genotyping of transgenic mice has been previously described: JOCK1 (Freeman, Gangula, et al. 2003), Pro-Cat are assayed the same as Ubi-Cat mice (Shahi et al. 2012).

extract_protocol: Total RNA was isolated using the CapSure® Macro LCM caps (Applied Biosystems LCM0211) and amplified using Arcturus™ RiboAmp® PLUS (Applied Biosystems KIT0501. Amplified RNA was then labeled using the Invitrogen cDNA labeling system (L1015-06) and hybridized to the Agilent Whole Mouse Genome Oligo (4×44) Microarray (G4122) chip for analysis.

treatment_protocol: Mice were treated biweekly starting at 6 weeks of age by intraperitoneal injections of AP20187 (aka, a Chemical Inducer of Dimerization, or CID; Ariad Pharmaceuticals, Cambridge, MA) at 2 mg/kg in drug diluent (16.7% propanediol, 22.5% PEG400, 1.25% TWEEN 80). Note: JOCK1 mice data for 40 and 60 weeks were obtained from previous experiments where treatment began at 12 weeks of age.

tag: mouse model

value: JOCK

value: Stroma

tag: treatment

value: CID at 2 mg/kg

label: Alexa Fluor 555

source_name: mouse, universal reference RNA

tag: sample type

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: JOCK mouse model, Stroma (CID) 1

tag: tissue


title: JOCK mouse model, Stroma  (no CID) 1

source_name: JOCK mouse model, prostate stroma mouse model, control

value: control


title: JOCK mouse model, Epithelium  (no CID) 2

source_name: JOCK mouse model, prostate epithelium mouse model, control

value: Epithelium


title: JOCK mouse model, Epithelium  (CID) 5

source_name: JOCK mouse model, prostate epithelium

value: treated


title: JOCK mouse model, Epithelium  (CID) 3


title: Procat.JOCK mouse model, Stroma (CID) 5

source_name: Procat.JOCK mouse model, prostate stroma,treated


title: JOCK mouse model, Stroma (CID) 2


title: Procat.JOCK mouse model, Epithelium (no CID) 1

source_name: Procat.JOCK mouse model, prostate epithelium,untreated

value: untreated


title: Procat.JOCK mouse model, Stroma (no CID) 3

source_name: Procat.JOCK mouse model, prostate stroma,untreated


title: Procat.JOCK mouse model, Stroma (no CID) 1


title: JOCK mouse model, Epithelium  (CID) 6


title: Procat.JOCK mouse model, Epithelium (no CID) 2


title: Procat.JOCK mouse model, Epithelium (CID) 3

source_name: Procat.JOCK mouse model, prostate epithelium,treated


title: JOCK mouse model, Epithelium  (CID) 4


title: Procat.JOCK mouse model, Stroma (no CID) 2


title: JOCK mouse model, Epithelium  (CID) 8


title: Procat.JOCK mouse model, Stroma (CID) 6


title: JOCK mouse model, Epithelium  (no CID) 1


title: JOCK mouse model, Stroma (CID) 5


title: JOCK mouse model, Epithelium  (CID) 7


title: Procat.JOCK mouse model, Epithelium (no CID) 3


title: JOCK mouse model, Stroma  (no CID) 2

source_name: JOCK mouse model, prostate stroma mouse model


title: JOCK mouse model, Stroma (CID) 4


title: Procat.JOCK mouse model, Stroma (CID) 7


title: Procat.JOCK mouse model, Epithelium (CID) 1


title: Ubicat-JOCK mouse model, Stroma (CID) 3

source_name: Ubicat-JOCK mouse model, prostate stroma

value: Ubicat-JOCK


title: Procat.JOCK mouse model, Epithelium (CID) 2


title: JOCK mouse model, Stroma (CID) 3


title: Ubicat-JOCK mouse model, Stroma (CID) 4


title: Ubicat-JOCK mouse model, Stroma (CID) 1


title: Procat mouse model, Stroma (CID) 8

source_name: Procat mouse model, prostate stroma

value: Procat


title: Ubicat-JOCK mouse model, Stroma (CID) 2


title: Procat mouse model, Stroma (CID) 6


title: Procat mouse model, Stroma (CID) 1


title: Procat mouse model, Stroma (CID) 2


title: SDQ0810_KNL2 L2 LTemb Hybridization Rep.1 array

status: Public on Oct 30 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ0810 KNL-2;target name: KNL-2;host: Rabbit;antigen: YTLRAPKSQNGEPITPIRFTRGHDNGGAKKVFIFEQTPVRKQGPIASSTPQQKQRLADGANNQIPPTQKSQDSVQAVQPPPPRPAARNAQFASDADLFAV;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: KNL2 Q0810;reference: PMID: 22495302;short description: An affinity purified rabbit polyclonal antibody to KNL-2 obtained from SDI (KNL2 Q0810). A.A. 207 - A.A. 306 was used as the immunogen;channel ch1 is input DNA;
channel ch2 is input DNA;

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

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

data_processing: ChIP-chip normalization standard MA2C:JL:2 protocol. ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS220

label: Cy5-monofunctional dye(1-)

organism: Caenorhabditis elegans

source_name: SDQ0810_KNL2_N2_LTemb channel_1

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

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

tag: strain

tag: developmental stage

value: Late Embryos

tag: genotype

value: wild type

tag: Sex

value: Hermaphrodite

label: Cy3-monofunctional dye(1-)

source_name: SDQ0810_KNL2_N2_LTemb channel_2


title: SDQ0804_HCP3 N2 LTEMB Hybridization Rep.1 array

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ0804 HCP-3;target name: HCP-3;host: Rabbit;antigen: TSAAGVNDLIDILNQYKKELEDDAANDYTEAHIHKIRLVTGKRNQYVLKLKQAEDEYHARKEQARRRASSMDFTVGRNS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: HCP3 Q0804;reference: PMID: 22495302;short description: An affinity purified rabbit polyclonal antibody to HCP-3 obtained from SDI (HCP3-Q0804). A.A. 40 - A.A. 118 was used as the immunogen;channel ch2 is input DNA;

source_name: SDQ0804_HCP3_N2_LTEMB channel_1

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

source_name: SDQ0804_HCP3_N2_LTEMB channel_2


title: Ubicat-JOCK mouse model, Epithelium (CID) 1

source_name: Ubicat-JOCK mouse model, prostate epithelium


title: SDQ0803_KNL2 L2 LTemb Hybridization Rep.1 array

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ0803 KNL-2;target name: KNL-2;host: Rabbit;antigen: YTLRAPKSQNGEPITPIRFTRGHDNGGAKKVFIFEQTPVRKQGPIASSTPQQKQRLADGANNQIPPTQKSQDSVQAVQPPPPRPAARNAQFASDADLFAV;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: KNL2 Q0803;reference: PMID: 22495302;short description: An affinity purified rabbit polyclonal antibody to KNL-2 obtained from SDI (KNL2 Q0803);channel ch1 is input DNA;
channel ch2 is input DNA;

source_name: SDQ0803_KNL2_N2_LTemb channel_1

source_name: SDQ0803_KNL2_N2_LTemb channel_2


title: Ubicat-JOCK mouse model, Epithelium (CID) 2

source_name: mouse, universal reference RNA


title: Ubicat-JOCK mouse model, Epithelium (CID) 4


title: Procat mouse model, Stroma (CID) 4


title: Procat mouse model, Epithelium (CID) 7

source_name: Procat mouse model, prostate epithelium


title: Ubicat-JOCK mouse model, Epithelium (CID) 3


title: SDQ0804_HCP3 N2 LTEMB Hybridization Rep.2 array

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ0804 HCP-3;target name: HCP-3;host: Rabbit;antigen: TSAAGVNDLIDILNQYKKELEDDAANDYTEAHIHKIRLVTGKRNQYVLKLKQAEDEYHARKEQARRRASSMDFTVGRNS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: HCP3 Q0804;reference: PMID: 22495302;short description: An affinity purified rabbit polyclonal antibody to HCP-3 obtained from SDI (HCP3-Q0804). A.A. 40 - A.A. 118 was used as the immunogen;channel ch1 is input DNA;
channel ch2 is input DNA;


title: Procat mouse model, Epithelium (CID) 2


title: Procat mouse model, Stroma (CID) 3


title: Procat mouse model, Epithelium (CID) 6


title: Procat mouse model, Stroma (CID) 7


title: Procat mouse model, Epithelium (CID) 8


title: Procat mouse model, Epithelium (CID) 4


title: Procat mouse model, Epithelium (CID) 1


title: Procat mouse model, Epithelium (CID) 5


title: MBD3_f_-_iPSC

status: Public on Sep 12 2013

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: MBD3flox/- mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming.

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Matlab affyRMA command, with MoGene_1_0-st-v1.r3.cdf annotation file.

source_name: MBD3flox/- iPSC

label_protocol: 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: N2B2715% KSR 2i/LIF mouse ESC media on mouse irradiated DR4 MEF cells.

extract_protocol: mRNA was extracted by TRIZOL reagent (Invitrogen) according to manufacturer's instructions.

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction.

value: MBD3flox/- transgenic for DOX inducible OSKM reprogramming

value: Embryonic Fibroblast Cells (MEF)

tag: stage in reprogramming

value: iPSC


title: Procat mouse model, Epithelium (CID) 3


title: MBD3_-_-_ES

description: MBD3-/- mouse Embryonic Stem Cell (ESC).

source_name: MBD3-/- ES

value: Embryonic Stem Cell (ESC)

value: ES


title: MBD3_f_-_MEF

source_name: MBD3flox/- MEF

value: Before DOX induction


title: MBD3_-_-_MEF

description: MBD3-/- mouse Embryonic Fibroblast Cells (MEF).

source_name: MBD3-/- MEF

value: MEF


title: EPN_930_2

status: Public on Aug 30 2013

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

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.

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 17,664 genes.

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

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 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Recurrent

value: brain tumor (ependymoma)


title: seq-SDQ2356_MRE11_FEM2_AD_ChIP_Rep1

status: Public on Aug 28 2013

description: ChIP DNA; Antibody information listed below: official name: SDQ2356-MRE11;target name: MRE-11;host: Rabbit;antigen: NYASGSEDEVANSDEEMGSSISRHSKQPTTRGRGRGARGAGASRETTRGRSNKVVSTRQIDSDGFEIINDSPSPPPASRSTRGKARGKSAPSKKRDLSFF;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2356

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

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

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

value: Germline containing young adult


title: EPN_821_2


title: seq-SDQ4713_HIM3_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HIM-3 SDQ4713;target name: HIM-3;host: Rabbit;antigen: KFVDTDNTKQMFASTIKKLHRCIKKMEPLPQGSDASFRVSYTEKAPKDYTPEGYLLSPMFYTLNQDIRKASIGIVCGGHHKIQMLAASQYLKQDFDLDKT;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4713;short description: An Affinity purified Rabbit Polyclonal antibody to HIM-3 obtained from SDI (HIM-3 SDQ4713)

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

extract_protocol:
Worm extract was made from adult worms.  Frozen worm popcorn was ground up in a mixer mill.  Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection .
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: MBD3_f_-_4day_DOX

source_name: MBD3flox/- 4 days after dox induction

tag: genotype/variation

value: 4 days after DOX induction


title: WT_4day_DOX

description: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming.

source_name: WT 4 days after dox induction

value: MBD3+/+ transgenic for DOX inducible OSKM reprogramming

tag: cell type


title: MBD3_f_-_8day_DOX

source_name: MBD3flox/- 8 days after dox induction

value: 8 days after DOX induction


title: WT_11day_DOX

source_name: WT 11 days after dox induction

value: 11 days after DOX induction


title: WT_MEF

source_name: WT MEF


title: seq-SDQ0811_RAD51_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: SDQ0811-RAD51;target name: RAD-51;host: Rabbit;antigen: MGQSWGYEGIAKRSLCTHKWLYNLNLHSINLFLPIESKMSAQASRQKKSDQEQRAADQALLNAAIEDNAMEQDENFTVIDKLESSGISSGDISKLKEAGY;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ0811

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

extract_protocol:
Worm extract was made from adult worms.  Frozen worm popcorn was ground up in a mixer mill.  Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: seq-SDQ0811_RAD51_FEM2_AD_ChIP_Rep1


title: EPN_246_2


title: EPN_459_2


title: EPN_507_2


title: EPN_691_2


title: EPN_483_2


title: seq-SDQ0811_RAD51_FEM2_AD_Input_Rep2

description: input DNA


title: EPN_811_2


title: EPN_364_2


title: EPN_195_2