title: Treg CD4+CD25+ activated day7

status: Public on Dec 19 2013

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) 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 manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5. (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Treg CD4+CD25+ activated day7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using RNAeasy Kit (Qiagen, Germany)

treatment_protocol: Peripheral blood mononuclear cells were isolated from human buffy coat using Biocoll (Biochrom, Berlin, Germany) separating solution. 100 ml of buffy coat was diluted with 100 ml phosphate buffered saline buffer (PBS). 20 ml of the suspension was carefully layered over 20 ml Biocoll separating solution and centrifuged for 25 min at 1800 x rpm. The lymphocyte layer was transferred into a new tube and washed with PBS once. For long term storage 1.2x108 cells were suspended in 2 ml medium (IMDM, 10% FCS, 25µM β-mercaptoethanol, Penicillin/Streptomycin and 10% DMSO) and stored in liquid nitrogen. CD4+ T cells were enriched by autoMACS using the CD4+ T cell isolation Kit (Miltenyi Biotech, Bergisch-Gladbach, Germany). Cells were stained with CD4-, CD25- and CD127-antibodies for 15 min at 4°C and washed with FACS buffer. Cell sorting of CD4+CD25- and CD4+CD25highCD127low T cells was performed using a FACS Aria II (BD, Franklin Lakes, USA). Purity was >95 % as controlled by FACS. FACS-sorted lymphocytes were cultivated in RPMI 1640 (Life Technologies, Carlsbad, USA) medium with 1 µg/ml anti-CD3, 1 µg/ml anti-CD28 (both Miltenyi Biotec, Bergisch Gladbach, Germany), 100 U/ml IL2 (eBioscince) and Penicillin/Streptomycin at 37°C, 5% CO2 in an incubator (Thermo Scientific Heracell 150i, Waltham, USA).


title: CD4+CD25- activated day7 5µM 5-Aza

type: RNA

country: Germany

molecule: total RNA

organism: Homo sapiens

source_name: CD4+CD25- activated day7 5µM 5-Aza

treatment_protocol: Peripheral blood mononuclear cells were isolated from human buffy coat using Biocoll (Biochrom, Berlin, Germany) separating solution. 100 ml of buffy coat was diluted with 100 ml phosphate buffered saline buffer (PBS). 20 ml of the suspension was carefully layered over 20 ml Biocoll separating solution and centrifuged for 25 min at 1800 x rpm. The lymphocyte layer was transferred into a new tube and washed with PBS once. For long term storage 1.2x108 cells were suspended in 2 ml medium (IMDM, 10% FCS, 25µM β-mercaptoethanol, Penicillin/Streptomycin and 10% DMSO) and stored in liquid nitrogen. CD4+ T cells were enriched by autoMACS using the CD4+ T cell isolation Kit (Miltenyi Biotech, Bergisch-Gladbach, Germany). Cells were stained with CD4-, CD25- and CD127-antibodies for 15 min at 4°C and washed with FACS buffer. Cell sorting of CD4+CD25- and CD4+CD25highCD127low T cells was performed using a FACS Aria II (BD, Franklin Lakes, USA). Purity was >95 % as controlled by FACS. FACS-sorted lymphocytes were cultivated in RPMI 1640 (Life Technologies, Carlsbad, USA) medium with 1 µg/ml anti-CD3, 1 µg/ml anti-CD28 (both Miltenyi Biotec, Bergisch Gladbach, Germany), 100 U/ml IL2 (eBioscince) and Penicillin/Streptomycin at 37°C, 5% CO2 in an incubator (Thermo Scientific Heracell 150i, Waltham, USA). 2,5x106 cells were cultured with two different concentrations of 5-Aza-dC (5 µM and 1 µM) or EGCG (5 µM), which were added every other day (both Sigma-Aldrich, St. Louis, USA). Both substances were diluted in 1% DMSO / 99% IMDM medium. Control cells were stimulated with 1% DMSO. After 4 days of incubation, medium was replaced by fresh medium including hypomethylating agents, as required.

tag: cell type


title: CD4+CD25- activated day7 5µM EGCG

source_name: CD4+CD25- activated day7 5µM EGCG

treatment_protocol: Peripheral blood mononuclear cells were isolated from human buffy coat using Biocoll (Biochrom, Berlin, Germany) separating solution. 100 ml of buffy coat was diluted with 100 ml phosphate buffered saline buffer (PBS). 20 ml of the suspension was carefully layered over 20 ml Biocoll separating solution and centrifuged for 25 min at 1800 x rpm. The lymphocyte layer was transferred into a new tube and washed with PBS once. For long term storage 1.2x108 cells were suspended in 2 ml medium (IMDM, 10% FCS, 25µM β-mercaptoethanol, Penicillin/Streptomycin and 10% DMSO) and stored in liquid nitrogen. CD4+ T cells were enriched by autoMACS using the CD4+ T cell isolation Kit (Miltenyi Biotech, Bergisch-Gladbach, Germany). Cells were stained with CD4-, CD25- and CD127-antibodies for 15 min at 4°C and washed with FACS buffer. Cell sorting of CD4+CD25- and CD4+CD25highCD127low T cells was performed using a FACS Aria II (BD, Franklin Lakes, USA). Purity was >95 % as controlled by FACS. FACS-sorted lymphocytes were cultivated in RPMI 1640 (Life Technologies, Carlsbad, USA) medium with 1 µg/ml anti-CD3, 1 µg/ml anti-CD28 (both Miltenyi Biotec, Bergisch Gladbach, Germany), 100 U/ml IL2 (eBioscince) and Penicillin/Streptomycin at 37°C, 5% CO2 in an incubator (Thermo Scientific Heracell 150i, Waltham, USA). 2,5x106 cells were cultured with two different concentrations of 5-Aza-dC (5 µM and 1 µM) or EGCG (5 µM), which were added every other day (both Sigma-Aldrich, St. Louis, USA). Both substances were diluted in 1% DMSO / 99% IMDM medium.


title: Gene expression in Control

status: Public on Dec 31 2013

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

country: Japan

institute: Tohoku University

description: Gene expression in Control

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

organism: Mus musculus

source_name: Pten flox/flox (P15, female) livers

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole livers using Isogen (Nippon Gene).

tag: strain

value: mixed (mainly C57BL/6J, and probably included 129sv and DBA/2)

tag: tissue

value: liver

tag: genotype/variation

value: Control


title: CD4+CD25- activated day7 1µM 5-Aza

source_name: CD4+CD25- activated day7 1µM 5-Aza


title: CD4+CD25- activated day7 Rep.2

source_name: CD4+CD25- activated day7 Rep.2

value: CD4 T cell


title: CD4+CD25- untreated

source_name: PBMC

treatment_protocol: Peripheral blood mononuclear cells were isolated from human buffy coat using Biocoll (Biochrom, Berlin, Germany) separating solution. 100 ml of buffy coat was diluted with 100 ml phosphate buffered saline buffer (PBS). 20 ml of the suspension was carefully layered over 20 ml Biocoll separating solution and centrifuged for 25 min at 1800 x rpm. The lymphocyte layer was transferred into a new tube and washed with PBS once. For long term storage 1.2x108 cells were suspended in 2 ml medium (IMDM, 10% FCS, 25µM β-mercaptoethanol, Penicillin/Streptomycin and 10% DMSO) and stored in liquid nitrogen. CD4+ T cells were enriched by autoMACS using the CD4+ T cell isolation Kit (Miltenyi Biotech, Bergisch-Gladbach, Germany). Cells were stained with CD4-, CD25- and CD127-antibodies for 15 min at 4°C and washed with FACS buffer. Cell sorting of CD4+CD25- and CD4+CD25highCD127low T cells was performed using a FACS Aria II (BD, Franklin Lakes, USA). Purity was >95 % as controlled by FACS. FACS-sorted lymphocytes were cultivated in RPMI 1640 (Life Technologies, Carlsbad, USA) medium Penicillin/Streptomycin at 37°C, 5% CO2 in an incubator (Thermo Scientific Heracell 150i, Waltham, USA).


title: Gene expression in Pten::Keap1-Alb::Nrf2h

source_name: Pten flox/flox::Keap1 flox/flox::Albumin-Cre::Nrf2+/– (P15, female) livers


title: Treg CD4+CD25+ untreated

source_name: Treg CD4+CD25+ untreated

treatment_protocol: Peripheral blood mononuclear cells were isolated from human buffy coat using Biocoll (Biochrom, Berlin, Germany) separating solution. 100 ml of buffy coat was diluted with 100 ml phosphate buffered saline buffer (PBS). 20 ml of the suspension was carefully layered over 20 ml Biocoll separating solution and centrifuged for 25 min at 1800 x rpm. The lymphocyte layer was transferred into a new tube and washed with PBS once. For long term storage 1.2x108 cells were suspended in 2 ml medium (IMDM, 10% FCS, 25µM β-mercaptoethanol, Penicillin/Streptomycin and 10% DMSO) and stored in liquid nitrogen. CD4+ T cells were enriched by autoMACS using the CD4+ T cell isolation Kit (Miltenyi Biotech, Bergisch-Gladbach, Germany). Cells were stained with CD4-, CD25- and CD127-antibodies for 15 min at 4°C and washed with FACS buffer. Cell sorting of CD4+CD25- and CD4+CD25highCD127low T cells was performed using a FACS Aria II (BD, Franklin Lakes, USA). Purity was >95 % as controlled by FACS. FACS-sorted lymphocytes were cultivated in RPMI 1640 (Life Technologies, Carlsbad, USA) medium with  Penicillin/Streptomycin at 37°C, 5% CO2 in an incubator (Thermo Scientific Heracell 150i, Waltham, USA).


title: CD4+CD25- activated day7 Rep1

source_name: CD4+CD25- activated day7 Rep1


title: melanoma_AJCCstageIII_TumourID356

status: Public on Dec 10 2013

city: North Sydney

first: Graham

middle: J.

last: Mann

state: NSW

address: Poche Centre, 40 Rocklands Road

country: Australia

institute: Melanoma Institute Australia

hyb_protocol: Gene expression analysis was performed using the Sentrix Human-6 v3 Expression BeadChips (Illumina, Inc., San Diego, CA, USA), and BeadStation system from Illumina as per manufacturer’s instructions.

data_processing: Quality control was performed on all chips using R/Bioconductor and the lumi package (www.bioconductor.org). Data normalization was performed using a variance-stabilizing transform (VST) and quantile normalization as implemented in the lumi package for R/Bioconductor. To reduce false positives, unexpressed genes (detection p-value >0.01) were removed, reducing the number of probes analysed from 48,802 to 26,085.

label: biotin

source_name: melanoma lymph node, fresh frozen tissue (>80% tumor cell content, <30% necrosis)

label_protocol: cRNA amplification and labelling with biotin were performed using Illumina TotalPrep RNA amplification kit according to the manufacturer’s directions (Ambion, Inc., Austin, TX, USA) with 250ng total RNA as input material.

growth_protocol: Total RNA was extracted from 20-30mg of fresh frozen tissue.

extract_protocol: The RNA was isolated and purified with an RNeasy purification kit (Qiagen RNeasy purification kit- Qiagen Pty Ltd., Clifton Hill, Victoria, Australia) with DNAse I digestion on the column. The quality of the RNA preparations was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). RNA integrity scores were >8 for all samples analyzed.

treatment_protocol: Tissue samples were homogenized using a high-speed agitation polytron blender (Kinematica, Luzern, Switzerland) in the presence of Trizol.

tag: patient age at primary diagnosis (years)

tag: patient sex

value: Male

tag: patient age at stage iii sample banked (years)

tag: survival from stage iii tumour banked (months)

tag: survival from primary melanoma (months)

tag: patient last status

value: Dead Not Melanoma

tag: number of primary melanomas

tag: stage at primary diagnosis 5th edition

value: Stage II


title: melanoma_AJCCstageIII_TumourID387

scan_protocol: Gene expression analysis was performed using the Sentrix Human-6 v3 Expression BeadChips (Illumina, Inc., San Diego, CA, USA), and BeadStation system from Illumina as per manufacturer’s instructions.

value: Female

value: Dead Melanoma


title: melanoma_AJCCstageIII_TumourID360


title: melanoma_AJCCstageIII_TumourID396

value: Alive No Sign of Recurrence


title: melanoma_AJCCstageIII_TumourID351

value: Stage I


title: melanoma_AJCCstageIII_TumourID334


title: melanoma_AJCCstageIII_TumourID350


title: melanoma_AJCCstageIII_TumourID366


title: melanoma_AJCCstageIII_TumourID349

value: Stage Unknown


title: melanoma_AJCCstageIII_TumourID343


title: melanoma_AJCCstageIII_TumourID76


title: melanoma_AJCCstageIII_TumourID394

value: Stage III


title: melanoma_AJCCstageIII_TumourID340


title: melanoma_AJCCstageIII_TumourID288


title: melanoma_AJCCstageIII_TumourID278


title: melanoma_AJCCstageIII_TumourID322


title: melanoma_AJCCstageIII_TumourID5249


title: melanoma_AJCCstageIII_TumourID259


title: melanoma_AJCCstageIII_TumourID333


title: melanoma_AJCCstageIII_TumourID273


title: melanoma_AJCCstageIII_TumourID233


title: melanoma_AJCCstageIII_TumourID194

value: Alive with Melanoma


title: melanoma_AJCCstageIII_TumourID231


title: melanoma_AJCCstageIII_TumourID234


title: melanoma_AJCCstageIII_TumourID242


title: melanoma_AJCCstageIII_TumourID232

value: Dead Cause Unknown


title: melanoma_AJCCstageIII_TumourID237


title: melanoma_AJCCstageIII_TumourID217


title: melanoma_AJCCstageIII_TumourID219


title: melanoma_AJCCstageIII_TumourID277


title: melanoma_AJCCstageIII_TumourID201


title: melanoma_AJCCstageIII_TumourID179


title: melanoma_AJCCstageIII_TumourID196


title: melanoma_AJCCstageIII_TumourID149

value: Alive Status Unknown


title: melanoma_AJCCstageIII_TumourID142


title: melanoma_AJCCstageIII_TumourID173


title: melanoma_AJCCstageIII_TumourID152


title: melanoma_AJCCstageIII_TumourID125


title: melanoma_AJCCstageIII_TumourID139


title: melanoma_AJCCstageIII_TumourID105


title: melanoma_AJCCstageIII_TumourID126


title: melanoma_AJCCstageIII_TumourID172


title: melanoma_AJCCstageIII_TumourID120


title: melanoma_AJCCstageIII_TumourID102


title: melanoma_AJCCstageIII_TumourID100


title: melanoma_AJCCstageIII_TumourID119


title: melanoma_AJCCstageIII_TumourID93


title: melanoma_AJCCstageIII_TumourID94


title: melanoma_AJCCstageIII_TumourID88


title: melanoma_AJCCstageIII_TumourID83


title: melanoma_AJCCstageIII_TumourID64


title: melanoma_AJCCstageIII_TumourID54


title: melanoma_AJCCstageIII_TumourID61


title: melanoma_AJCCstageIII_TumourID74


title: melanoma_AJCCstageIII_TumourID69


title: melanoma_AJCCstageIII_TumourID53


title: melanoma_AJCCstageIII_TumourID49


title: melanoma_AJCCstageIII_TumourID52


title: melanoma_AJCCstageIII_TumourID51


title: melanoma_AJCCstageIII_TumourID62


title: melanoma_AJCCstageIII_TumourID103


title: melanoma_AJCCstageIII_TumourID43


title: melanoma_AJCCstageIII_TumourID45


title: melanoma_AJCCstageIII_TumourID47


title: melanoma_AJCCstageIII_TumourID17


title: melanoma_AJCCstageIII_TumourID25


title: melanoma_AJCCstageIII_TumourID28


title: melanoma_AJCCstageIII_TumourID37


title: melanoma_AJCCstageIII_TumourID36


title: melanoma_AJCCstageIII_TumourID5


title: melanoma_AJCCstageIII_TumourID32


title: melanoma_AJCCstageIII_TumourID30


title: melanoma_AJCCstageIII_TumourID6


title: melanoma_AJCCstageIII_TumourID15


title: melanoma_AJCCstageIII_TumourID16


title: melanoma_AJCCstageIII_TumourID13


title: melanoma_AJCCstageIII_TumourID1


title: melanoma_AJCCstageIII_TumourID66


title: melanoma_AJCCstageIII_TumourID23


title: Tumor 30

status: Public on Nov 01 2013

city: Bethesda

first: Atsushi

last: Terunuma

state: MD

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

country: USA

institute: National Cancer Institute

hyb_protocol: ssDNA was hybridized onto Gene Chip Human Gene 1.0 ST Arrays according to Affymetrix standard protocols (Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip ® Scanner Scanner 3000 as instructed by the manufacture.

data_processing: Expression values were generated by RMA within Affymetrix Expression Console software.

source_name: Human Breast Tumor

label_protocol: 250 ng of RNA was synthesized to cDNA using the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript Expression arrays (Life technologies, Grand Island, NY).  Fragmentation and labeling of the cDNA was carried-out using the GeneChip WT Terminal Labeling Kit (Affymetrix) according to standard protocols.

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen, Carlsbad, CA) as directed by the manufacturer. The quantity and quality of RNA was assessed with a Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: race

value: African-American

tag: age

tag: tissue type

value: Tumor

tag: estrogen receptor status

value: Negative

tag: triple negative tumor

value: No

tag: Stage

value: IIB

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

value: Alive

tag: death due to cancer

tag: neoadjuvant therapy

tag: hormone-therapy

value: Yes

tag: chemotherapy

tag: tumor or normal lhc


title: Tumor 29

value: Positive

value: IIA


title: Tumor 65

value: European-American

value: I


title: Tumor 66


title: Tumor 32

value: Dead


title: Tumor 27

value: IIIA


title: Tumor 25


title: Tumor 67


title: Tumor 24


title: Tumor 26


title: Tumor 60


title: Tumor 63


title: Tumor 28


title: Tumor 21


title: Tumor 62


title: Tumor 55


title: Tumor 64


title: Tumor 23


title: Tumor 54


title: Tumor 49


title: Tumor 61


title: Tumor 56


title: Tumor 17


title: Tumor 51

value: II


title: Tumor 19


title: Tumor 16


title: Tumor 18

value: IIIa


title: Tumor 58


title: Tumor 50


title: Tumor 52


title: Tumor 14


title: Tumor 12


title: Tumor 48

value: IIIB


title: Tumor 11


title: Tumor 46


title: Tumor 47


title: Tumor 09


title: Tumor 08


title: Tumor 45


title: Tumor 10


title: Tumor 36


title: Tumor 38


title: Tumor 39


title: Tumor 41


title: Tumor 05


title: Normal 67

source_name: Human Breast

value: Non-tumor

value: not applicable


title: Tumor 44

value: Tumor


title: Tumor 34

value: Negative


title: Tumor 35

value: No


title: Tumor 42


title: Tumor 04

value: African-American


title: Tumor 43

value: IIB


title: Tumor 57


title: Tumor 06

value: Yes


title: Tumor 02

value: Positive


title: Normal 62


title: Normal 27


title: Tumor 03


title: Normal 66


title: Normal 28


title: Tumor 01

value: IIA

value: Alive


title: Tumor 07


title: Tumor 33

value: European-American


title: Tumor 31


title: Normal 24


title: Normal 65


title: Normal 64


title: Normal 11


title: Normal 51


title: Normal 17


title: Normal 45


title: Normal 63


title: Normal 19


title: Normal 61


title: Normal 50


title: Normal 58


title: Normal 10


title: Normal 49


title: Normal 20


title: Normal 18


title: Normal 08


title: Normal 16


title: Normal 43


title: Normal 26


title: Normal 52


title: Normal 39


title: Normal 48


title: Normal 07


title: Normal 46


title: Normal 23


title: Normal 54


title: Normal 44


title: Normal 12


title: Normal 37


title: Normal 38


title: Normal 06


title: Normal 36


title: Normal 04


title: Normal 35


title: Normal 01


title: Normal 33


title: Normal 05


title: array 26, xenograft, corn oil vehicle

status: Public on Oct 31 2013

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description:
gene expression data from human fetal testis xenografts or unimplanted samples
26_VEH

hyb_protocol: Hybridization was carried out for 17 h at 45C and 60 rpm.  Arrays were washed and stained on Affymetrix Fluidics Station FS450 using Affymetrix Wash/Stain Reagents and the Affymetrix protocol FS450_0007

scan_protocol: Microarrays were scanned using the Affymetrix 3000 7G Scanner.

data_processing: Microarray data were processed in the R software environment (R Core Team 2012), using the RMA algorithm (R package oligo) (Carvalho and Irizarry 2010) for probe-level summarization and pre-processing with ComBat (Leek et al. 2012) for batch correction.  Gene annotation information was joined to the expression data using the hugene10sttranscriptcluster.db package (Li 2013).

source_name: fetal testis sample 21, 16 weeks gestation

label_protocol: 5.5. ug cDNA were labelled using the Affymetrix WT terminal labeling kit, according to the manufacturer's instructions.

growth_protocol: Donor human fetal testis tissue samples originated from spontaneous pregnancy losses, and were donated with full, informed consent.  Hosts were adult male athymic nude mice (Crl:NU(NCr)-Foxn1nu, strain code 490), obtained from Charles River Laboratories (Wilmington, MA, USA) and housed in the Brown University Animal Care Facility under a 12:12 hr light-dark cycle with controlled temperature and humidity.  Mice were given free access to water and Purina Rodent Chow 5001 (Farmer’s Exchange, Framingham, MA, USA).  All animal care protocols were approved by the Brown University Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was extracted using the Qiagen DNA/RNA AllPrep kit, with on-column DNase digestion using the Qiagen RNase-free DNase set.  RNA was further purified by overnight precipitation at -80C in 3 volumes 70% ethanol, with 0.1 volumes sodium acetate.  RNA was pelleted, washed with 75% ethanol, and reconstituted in RNase-free water.

treatment_protocol: Unimplanted samples were snap-frozen immediately.  Remaining tissue was xenografted into castrated male athymic nude mouse hosts.  Hosts were given 20 IU human chorionic gonadotropin 3x/week for four weeks.  During weeks three and four, hosts were given daily oral gavage of vehicle, 500 mg/kg DBP, or 75 mg/kg abiraterone acetate.

tag: tissue

value: testis

tag: gestational age

value: 16 weeks

tag: xenografted into host

value: castrated male athymic nude mouse hosts

tag: host treatment

value: corn oil vehicle


title: Normal 15

tag: race

tag: age

tag: tissue type


title: array 24, xenograft, DBP 500 mg/kg/d

description:
gene expression data from human fetal testis xenografts or unimplanted samples
24_DBP

source_name: fetal testis sample 19, 20 weeks gestation

value: 20 weeks

value: DBP


title: array 22, xenograft, abiraterone 75 mg/kg/d

description:
gene expression data from human fetal testis xenografts or unimplanted samples
22_ABI

source_name: fetal testis sample 25, 20 weeks gestation

value: abiraterone


title: array 30, xenograft, DBP 500 mg/kg/d

description:
gene expression data from human fetal testis xenografts or unimplanted samples
30_DBP

source_name: fetal testis sample 26, 20 weeks gestation


title: array 29, xenograft, corn oil vehicle

description:
gene expression data from human fetal testis xenografts or unimplanted samples
29_VEH


title: array 28, unimplanted

description:
gene expression data from human fetal testis xenografts or unimplanted samples
28_NON

value: control (unimplanted samples were snap-frozen immediately)


title: Normal 02

value: Non-tumor

tag: estrogen receptor status

value: not applicable

tag: triple negative tumor

tag: Stage


title: Normal 22

value: African-American

tag: tumor grade

tag: node status

tag: survival (months)


title: Entopallium_Testo, biological rep6 (SD)

status: Public on Oct 30 2013

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

description:
Entopallium was dissected from cryosections
Can_SD_male_Ento_Testo_6

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing:
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: E26R1204 Genomatix GmbH (http://www.genomatix.de)
SD processed data files (SDm_HVcto_SDm_Ento.xls, SDmTestoHVc_to_SDmTestoEnto.xls), are the significance results obtained by ChipInspector.
The differential expression was analyzed using the group-wise exhaustive analysis i.e., HVc samples group compare to Ento samples group with False Discovery Rate set to zero and 10-significant probe minimum coverage. These result files consist in the table of transcripts and the fold changes for every data combination, also chromosome location (in TGU), Gene ID, Gene Symbol.
The statistic algorithm in ChipInspector is a T-test with a permuted artificial background. It is based on and enhances the original SAM algorithm by Tusher et al. (2001): Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98(9), pp 5116-5121. Exhaustive matching of the experiments introduces a second level of data volume enhancing. This means it is using the complete set of available data points by matching the values from every condition experiment to the values from every control experiment. This gives the results greater confidence and therefore increases the number of values that are recognized as significant (higher number of significant genes with lower FDR) (http://www.genomatix.de).

organism: Serinus canaria

source_name: Entopallium

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult canaries housed in long light cycles in aviaries

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80 C till RNA preparation.

value: adult

tag: light cycle

value: short day

tag: treatment

value: testosterone

value: Entopallium


title: array 27, xenograft, DBP 500 mg/kg/d

description:
gene expression data from human fetal testis xenografts or unimplanted samples
27_DBP


title: array 25, unimplanted

description:
gene expression data from human fetal testis xenografts or unimplanted samples
25_NON


title: array 23, xenograft, corn oil vehicle

description:
gene expression data from human fetal testis xenografts or unimplanted samples
23_VEH


title: array 21, xenograft, 0.3% Tween-20 vehicle

description:
gene expression data from human fetal testis xenografts or unimplanted samples
21_VEH

value: 0.3% Tween-20 vehicle


title: Normal 03

tag: survival event

tag: death due to cancer

tag: neoadjuvant therapy

tag: hormone-therapy

tag: chemotherapy


title: array 20, unimplanted

description:
gene expression data from human fetal testis xenografts or unimplanted samples
20_NON

tag: tissue

tag: gestational age

tag: xenografted into host

tag: host treatment


title: array 18, xenograft, abiraterone 75 mg/kg/d

description:
gene expression data from human fetal testis xenografts or unimplanted samples
18_ABI

source_name: fetal testis sample 23, 20 weeks gestation


title: array 16, unimplanted

description:
gene expression data from human fetal testis xenografts or unimplanted samples
16_NON

source_name: fetal testis sample 18L, 22 weeks gestation

value: 22 weeks


title: array 13, xenograft, 0.3% Tween-20 vehicle

description:
gene expression data from human fetal testis xenografts or unimplanted samples
13_VEH

source_name: fetal testis sample 17/18, 22 weeks gestation

value: testis


title: array 14, xenograft, abiraterone 75 mg/kg/d

description:
gene expression data from human fetal testis xenografts or unimplanted samples
14_ABI


title: array 17, xenograft, 0.3% Tween-20 vehicle

description:
gene expression data from human fetal testis xenografts or unimplanted samples
17_VEH


title: array 19, unimplanted

description:
gene expression data from human fetal testis xenografts or unimplanted samples
19_NON

source_name: fetal testis sample 23L, 20 weeks gestation


title: Entopallium_Testo, biological rep3 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_Ento_Testo_3

tag: age


title: Entopallium_Testo, biological rep4 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_Ento_Testo_4


title: Entopallium_Testo, biological rep1 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_Ento_Testo_1


title: Entopallium_Testo, biological rep2 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_Ento_Testo_2


title: HVc_Testo, biological rep1 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_Testo_2

source_name: HVC

value: HVc


title: Entopallium, biological rep6 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_ENTO_6

value: No treatment


title: HVc_Testo, biological rep4 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_Testo_5


title: HVc_Testo, biological rep5 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_Testo_6


title: HVc_Testo, biological rep2 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_Testo_3


title: HVc_Testo, biological rep3 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_Testo_4


title: Entopallium, biological rep5 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_ENTO_5


title: HVc, biological rep6 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_6


title: HVc, biological rep5 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_5


title: Entopallium, biological rep2 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_ENTO_2


title: HVc, biological rep2 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_2


title: HVc, biological rep4 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_4


title: HVc, biological rep3 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_3


title: Entopallium, biological rep1 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_ENTO_1


title: Entopallium_Testo, biological rep5 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_Ento_Testo_5


title: HVc, biological rep1 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVc_1


title: GM12864_gDNA_HumanOmni2.5-Quad

status: Public on Oct 18 2013

type: genomic

city: Montreal

first: Tomi

last: Pastinen

state: QC

address: 740 Dr Penfield

department: Human & Medical Genetics

country: Canada

institute: McGill University

description: CEU Pedigree #1459 - Father

hyb_protocol: according to manufacturer's instructions

data_processing:
GenomeStudio from Illumina

For convenience, data was compiled based on analysis date into 20 individual sets.

label: Cy3 and Cy5

molecule: genomic DNA

growth_protocol: All cells were obtained from the Coriell Institute for Medical Research (Camden, NJ). The LCLs were grown in T75 flasks in 1X RPMI 1640 Media (invitrogen, Burlington, ON), with 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2. LCL cells were harvested during log growth phase. The Fibroblast primary cell lines were immortalized as previously desribed (Grundberg et al.,  PLoS Genet., 2011), and then grown in medium containing a-MEM (SigmaAldrich) supplemented with 2 mmol/l L-Glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2. At 70%-80% confluence, fibroblast cells were harvested.

extract_protocol: RNA and gDNA were extracted from cell lysates and we applied a cDNA synthesis protocol as previously described in Moros et al., Genome Biology, 2011 (PMID: 21418647).

treatment_protocol: DNA from the cell lysates was extracted using the GenElute DNA Miniprep Kit (SigmaAldrich, Suffolk, UK) according to the protocol provided by the manufacturer and concentrations were determined using the NanoDrop ND-1000.

tag: gender

value: male

value: Lymphoblasts

tag: population

value: CEU

tag: assayed molecule

value: gDNA


title: GM12865_gDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1459 - Mother

scan_protocol: according to manufacturer's instructions

value: female


title: GM12891_gDNA_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandfather

label_protocol: according to manufacturer's instructions


title: GM12878_gDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM19238_gDNA_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother

value: YRI


title: GM19240_gDNA_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM12892_gDNA_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandmother


title: GM18507_gDNA_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM12875_gDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1459 - Maternal Grandmother


title: GM19239_gDNA_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: Entopallium, biological rep4 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_ENTO_4


title: GM12874_gDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1459 - Maternal Grandfather


title: GM12873_gDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1459 - Paternal Grandmother


title: GM12872_gDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1459 - Paternal Grandfather


title: GM12878_IgG_CellSignalling_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother

treatment_protocol: After harvesting, cells were cross-linked with 1% formaldehyde at room temperature for 10 min. Cells were then immediately quenched with glycine for 5 min (125 mM glycine per ml of media), and washed twice with ice-cold PBS. Cells were collected after each wash by centrifugation at 2,000g for 5 min. Cell pellets were flash frozen and stored at -80 °C. Frozen pellets were thawed and cells were lysed in Farnhamlysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors) for 10 min on ice. After centrifugation and wash with 1 ml of RIPA buffer containing 50mM TrisHCl pH8, 150mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS and protease inhibitors, lysates were then diluted with 500 ul of RIPA buffer. Cells were sonicated in non-stick tubes under conditions optimized to yield soluble chromatin fragments in a size range of 100 to 250 base pairs. Chromatin from 40 million cells was sonicated for 10min using a Branson 250 sonicator at 20% power amplitude (pulses: 10 s on and 30 s off). Lysate was cleared by centrifuging at 12,000g for 10 min at 4 °C to eliminate cellular debris. Chromatin was then flash frozen and stored at -80 °C or used immediately for next step. Before each immunoprecipitation, chromatin was pre-cleared with 50 ul of prewashed ProteinA-magnetic beads (Invitrogen; 100-02D) to avoid non-specific binding. Immunoprecipitation was carried out for 12 hours by rotation at 4 °C in 500 ul of chromatin/RIPA buffer supplemented with protease inhibitor cocktails (Roche; 04 693 159 001) and PMSF. We used 10 to 100 million cells and 2 to 20 ?g of the following antibodies for each assay: H3K4me1 (Diagenode; #pAb-037-050), H3K4me1 (Abcam; H3K4me3 (Diagenode; #pAb-003-050), H3K27ac (Abcam; #ab4729), H3K27me3 (Millipore; #07-449), H3K36me3 (Abcam, #ab9050), RNA Pol II (Abcam; ab5131), RNA Pol II (Covance; 8WG16), Normal IgG (Cell Signaling Technology; #2729). After overnight incubation, samples were rotated with 100 ul of prewashed ProteinA-magnetic beads at 4 °C for 1 h. The beads were then collected by brief centrifugation at 2,000g following by use of magnetic rack. Beads were washed five times with 1 ml of LiCl wash buffer (100mM Tris pH7.5, 500mM LiCl, 1% NP-40, 1% sodium deoxycholate) by resuspending the beads and keeping on ice for 10 min. Bound chromatin was eluted from the beads using 200 ul of Elution buffer (50 mMTris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS) by incubation at 65 °C for 1 h with vortex every 15 min followed by centrifugation at 14,000g at room temperature for 3 min. The eluted chromatin and the input sample were incubated at 65 °C overnight after adding 0.2M of NaCl to remove crosslink. Samples were then treated with RNase 37 °C for 30 min and digested with proteinase K at 55 °C for 1 h. Immunoprecipitated DNA was purified using QIAquick PCR Purification Kit (QIAGEN; 28104) and eluted in 30 ul.

value: ChIP DNA


title: Entopallium, biological rep3 (SD)

description:
Entopallium was dissected from cryosections
Can_SD_male_ENTO_3


title: GM12878_H3K27me3_Abcam_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM19238_H3K27me3_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother


title: GM19239_H3K27me3_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: GM12878_H3K36me3_Millipore_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM19240_H3K36me3_Millipore_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM19238_H3K36me3_Millipore_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother


title: GM18507_H3K27me3_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM19239_H3K36me3_Millipore_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: GM18507_H3K36me3_Millipore_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM12875_gDNA_Human1M-Duov3_B


title: GM18500_gDNA_Human1M-Duov3_B

description: YRI Family #004- Daughter


title: GM12865_gDNA_Human1M-Duov3_B

description: CEU Pedigree #1459 - Mother


title: GM19240_H3K27ac_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM12864_gDNA_Human1M-Duov3_B

description: CEU Pedigree #1459 - Father


title: GM19238_H3K27ac_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother


title: GM19239_H3K27ac_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: GM18507_H3K27ac_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM12875_cDNA_Human1M-Duov3_B

treatment_protocol: Approximately 150µg of total RNA was extracted from the cells using the commercially available TRIzol reagent protocol (Invitrogen, Burlington, ON, CA) and subsequently treated with 18 U DNaseI (Ambion Inc., Austin, TX, USA) for 30 min at 37°C and further extracted with phenol/chloroform. High RNA quality was confirmed for all samples using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA) and the concentrations were determined using the NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA). Poly(A) RNA was then isolated using the MicroPoly(A)Purist protocol (Ambion Inc., Austin, Tx, USA) and poly-A enriched RNA quality and quantity was measured using the Agilent 2100 BioAnalyzer and NanoDrop ND-1000, respectively.

value: cDNA


title: GM12874_cDNA_Human1M-Duov3_B


title: GM19240_H3K27me3_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM12873_cDNA_Human1M-Duov3_B


title: GM12874_gDNA_Human1M-Duov3_B


title: GM12872_cDNA_Human1M-Duov3_B


title: GM19240_PolII_Covance_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM12878_PolII_Covance_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM12872_gDNA_Human1M-Duov3_B


title: GM12873_gDNA_Human1M-Duov3_B


title: GM12878_PolII_Abcam_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM18506_gDNA_Human1M-Duov3_B

description: YRI Family #Y009- Son


title: GM12892_gDNA_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandmother


title: GM12891_gDNA_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandfather


title: GM12891_PolII_Abcam_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandfather


title: GM18508_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #Y009- Mother


title: GM12891_PolII_Abcam_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandfather


title: GM19240_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM18507_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM19239_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: GM18508_PolII_Abcam_Human1M-Duov3_B

description: YRI Family #Y009- Mother


title: GM18508_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y009- Mother


title: GM18508_H3K4me1_Abcam_Human1M-Duov3_B

description: YRI Family #Y009- Mother


title: GM12892_PolII_Abcam_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandmother


title: GM18502_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #004- Mother


title: GM12874_PolII_Abcam_HumanOmni2.5-Quad


title: GM12875_PolII_Abcam_HumanOmni2.5-Quad


title: GM18501_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #004- Father


title: GM12878_H3K27ac_Abcam_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM18502_PolII_Abcam_Human1M-Duov3_B

description: YRI Family #004- Mother


title: GM12878_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM18502_H3K4me1_Abcam_Human1M-Duov3_B

description: YRI Family #004- Mother


title: GM18501_H3K4me1_Abcam_Human1M-Duov3_B

description: YRI Family #004- Father


title: GM18507_PolII_Abcam_Human1M-Duov3_B

description: YRI Family #Y009- Father


title: GM18501_PolII_Abcam_Human1M-Duov3_B

description: YRI Family #004- Father


title: GM12872_PolII_Abcam_HumanOmni2.5-Quad


title: GM19238_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother


title: GM12892_PolII_Abcam_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandmother


title: GM12875_H3K4me3_Diagenode_Human1M-Duov3_B


title: GM18502_PolII_Abcam_HumanOmni2.5-Quad

description: YRI Family #004- Mother


title: GM12892_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandmother


title: GM12875_H3K4me1_Abcam_Human1M-Duov3_B


title: GM19239_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: GM19238_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother


title: GM12874_H3K4me1_Abcam_Human1M-Duov3_B


title: GM12875_PolII_Abcam_Human1M-Duov3_B


title: GM12873_PolII_Abcam_HumanOmni2.5-Quad


title: GM18507_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM12874_PolII_Abcam_Human1M-Duov3_B


title: GM18508_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #Y009- Mother


title: GM18501_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #004- Father


title: GM18501_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #004- Father


title: GM18502_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #004- Mother


title: GM12873_H3K4me1_Abcam_Human1M-Duov3_B


title: GM12874_H3K4me3_Diagenode_HumanOmni2.5-Quad


title: GM12872_H3K4me3_Diagenode_Human1M-Duov3_B


title: GM12875_H3K4me3_Diagenode_HumanOmni2.5-Quad


title: GM12873_PolII_Abcam_Human1M-Duov3_B


title: GM12872_H3K4me1_Abcam_Human1M-Duov3_B


title: GM12873_H3K4me3_Diagenode_HumanOmni2.5-Quad


title: GM12872_H3K4me3_Diagenode_HumanOmni2.5-Quad


title: GM12873_H3K4me3_Diagenode_Human1M-Duov3_B


title: GM12872_PolII_Abcam_Human1M-Duov3_B


title: GM12891_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandfather


title: GM19240_H3K4me3_Diagenode_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM12878_H3K4me1_Abcam_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM12874_H3K4me3_Diagenode_Human1M-Duov3_B


title: GM12892_H3K4me1_Abcam_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandmother


title: GM12892_H3K4me3_Diagenode_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandmother


title: GM12892_H3K4me1_Abcam_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandmother


title: GM12891_H3K4me3_Diagenode_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandfather


title: GM12891_H3K4me1_Abcam_Human1M-Duov3_B

description: CEU Family #1463- Maternal Grandfather


title: GM19240_H3K4me1_Abcam_HumanOmni2.5-Quad_2

description: YRI Family #Y117 - Daughter


title: GM18507_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #Y009- Father


title: GM19238_H3K4me1_Abcam_HumanOmni2.5-Quad_2

description: YRI Family #Y117 - Mother


title: GM18507_H3K4me1_Abcam_Human1M-Duov3_B

description: YRI Family #Y009- Father


title: GM19238_H3K4me1_Abcam_HumanOmni2.5-Quad_1

description: YRI Family #Y117 - Mother


title: GM12878_H3K4me3_Diagenode_Human1M-Duov3_B

description: CEU Pedigree #1463 - Mother


title: GM19239_H3K4me1_Abcam_HumanOmni2.5-Quad_2

description: YRI Family #Y117 - Father


title: GM19239_H3K4me1_Abcam_HumanOmni2.5-Quad_1

description: YRI Family #Y117 - Father


title: GM19240_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #Y117 - Daughter


title: GM12878_H3K4me1_Abcam_Human1M-Duov3_B

description: CEU Pedigree #1463 - Mother


title: GM19240_H3K4me1_Abcam_Human1M-Duov3_B_2

description: YRI Family #Y117 - Daughter


title: GM18508_H3K4me1_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y009- Mother


title: GM19239_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #Y117 - Father


title: GM18502_H3K4me1_Abcam_HumanOmni2.5-Quad

description: YRI Family #004- Mother


title: GM19239_H3K4me1_Abcam_Human1M-Duov3_B_2

description: YRI Family #Y117 - Father


title: GM18501_H3K4me1_Abcam_HumanOmni2.5-Quad

description: YRI Family #004- Father


title: GM19238_H3K4me3_Diagenode_Human1M-Duov3_B

description: YRI Family #Y117 - Mother


title: GM19238_H3K4me1_Abcam_Human1M-Duov3_B_2

description: YRI Family #Y117 - Mother


title: GM12891_H3K4me1_Abcam_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandfather


title: GM19239_H3K4me1_Abcam_Human1M-Duov3_B_1

description: YRI Family #Y117 - Father


title: GM19240_H3K4me1_Abcam_HumanOmni2.5-Quad_1

description: YRI Family #Y117 - Daughter


title: GM19238_H3K4me1_Abcam_Human1M-Duov3_B_1

description: YRI Family #Y117 - Mother


title: GM19239_Polll_Abcam_Human1M-Duov3_B

description: YRI Family #Y117 - Father


title: GM12873_H3K4me1_Abcam_HumanOmni2.5-Quad


title: GM12875_H3K4me1_Abcam_HumanOmni2.5-Quad


title: GM12878_cDNA_HumanOmni2.5-Quad

description: CEU Pedigree #1463 - Mother


title: GM19238_Polll_Abcam_Human1M-Duov3_B

description: YRI Family #Y117 - Mother


title: GM12892_cDNA_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandmother


title: GM19240_H3K4me1_Abcam_Human1M-Duov3_B_1

description: YRI Family #Y117 - Daughter


title: GM19240_Polll_Covance_Human1M-Duov3_B

description: YRI Family #Y117 - Daughter


title: GM19240_cDNA_HumanOmni2.5-Quad

description: YRI Family #Y117 - Daughter


title: GM12891_cDNA_HumanOmni2.5-Quad

description: CEU Family #1463- Maternal Grandfather


title: GM19238_cDNA_HumanOmni2.5-Quad

description: YRI Family #Y117 - Mother


title: GM12872_H3K4me1_Abcam_HumanOmni2.5-Quad


title: GM19240_Polll_Abcam_Human1M-Duov3_B

description: YRI Family #Y117 - Daughter


title: GM19239_cDNA_HumanOmni2.5-Quad

description: YRI Family #Y117 - Father


title: GM18507_H3K4me1_Abcam_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM12878_PolII_Covance_Human1M-Duov3_B

description: CEU Pedigree #1463 - Mother


title: GM18508_cDNA_HumanOmni2.5-Quad

description: YRI Family #Y009- Mother


title: GM18507_cDNA_HumanOmni2.5-Quad

description: YRI Family #Y009- Father


title: GM18502_cDNA_HumanOmni2.5-Quad

description: YRI Family #004- Mother


title: GM12878_PolII_Abcam_Human1M-Duov3_B

description: CEU Pedigree #1463 - Mother


title: HVc_Testo, biological rep6 (SD)

description:
HVC was dissected from cryosections
Can_SD_male_HVC_Testo_7

value: adult


title: GM18501_cDNA_HumanOmni2.5-Quad

description: YRI Family #004- Father


title: GM12875_cDNA_HumanOmni2.5-Quad


title: GM12874_H3K4me1_Abcam_HumanOmni2.5-Quad


title: GM12874_cDNA_HumanOmni2.5-Quad


title: GM12873_cDNA_HumanOmni2.5-Quad


title: GM12872_cDNA_HumanOmni2.5-Quad


title: GM02555_cDNA_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Mother

value: Fibroblasts

value: Caucasian


title: GM02555_H3K4me3_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Mother


title: GM02555_H3K27me3_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Mother


title: GM02555_gDNA_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Mother


title: GM02555_H3K36me3_Millipore_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Mother


title: GM02456_H3K36me3_Millipore_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM02456_H3K27me3_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM02456_H3K27ac_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM12878_IgG_CellSignalling_Human1M-Duov3_B

description: CEU Pedigree #1463 - Mother


title: GM02456_H3K4me3_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM02455_H3K36me3_Millipore_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Daughter


title: GM02456_cDNA_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM02455_H3K27ac_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Daughter


title: GM02456_gDNA_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM02455_H3K27me3_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Daughter


title: GM02455_H3K4me3_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Daughter


title: GM02455_cDNA_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Daughter


title: GM02317_H3K27ac_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother

value: Caucasian- Irish


title: GM02317_H3K4me1_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother


title: GM02455_gDNA_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Daughter


title: GM02317_H3K27me3_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother


title: GM02317_cDNA_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother


title: GM02316_H3K36me3_Millipore_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM02317_gDNA_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother


title: GM02316_H3K27me3_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM02555_H3K27ac_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Mother


title: GM02316_H3K27ac_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM02316_H3K4me3_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM02316_gDNA_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM02314_H3K27me3_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM02314_H3K27ac_Abcam_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM02316_cDNA_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM02314_H3K36me3_Millipore_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM02456_H3K4me1_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0222 - Father


title: GM02314_H3K4me1_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM02314_gDNA_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM12878_H3K36me3_Millipore_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM12891_H3K4me3_Diagenode_HumanOmni2.5S-8v1_B

description: CEU Family #1463- Maternal Grandfather


title: GM02317_H3K36me3_Millipore_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother


title: GM02314_cDNA_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM12892_H3K4me3_Diagenode_HumanOmni2.5S-8v1_B

description: CEU Family #1463- Maternal Grandmother


title: GM12878_H3K27me3_Abcam_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM12878_H3K27ac_Abcam_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM19240_H3K36me3_Millipore_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM19240_H3K4me3_Diagenode_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM19240_H3K27ac_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM19239_H3K36me3_Millipore_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: GM19239_H3K27me3_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: GM19240_H3K4me1_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM19239_H3K27ac_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: GM12878_H3K4me3_Diagenode_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM19239_H3K4me3_Diagenode_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: GM02316_H3K4me1_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Father


title: GM19238_H3K36me3_Millipore_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM19238_H3K27me3_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM19239_H3K4me1_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: GM19238_H3K4me3_Diagenode_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM19238_H3K4me1_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM12878_H3K4me1_Abcam_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM19238_H3K27ac_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM19240_dscDNA_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM02314_H3K4me3_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Daughter


title: GM02317_H3K4me3_Diagenode_HumanOmni5-4v1_B

description: NIGMS Family #0056 - Mother


title: GM12878_dscDNA_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM12891_gDNA_HumanOmni2.5S-8v1_B

description: CEU Family #1463- Maternal Grandfather


title: GM19239_dscDNA_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: GM19238_dscDNA_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM12878_gDNA_HumanOmni2.5S-8v1_B

description: CEU Pedigree #1463 - Mother


title: GM19238_gDNA_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Mother


title: GM19240_H3K27me3_Abcam_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM19240_gDNA_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Daughter


title: GM19239_gDNA_HumanOmni2.5S-8v1_B

description: YRI Family #Y117 - Father


title: Entopallium, biological rep7 (LD)

status: Public on Aug 22 2013

description:
Can_LD_male_Ento_38
Entopallium was dissected from cryosections

data_processing:
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: E26R1204 Genomatix GmbH (http://www.genomatix.de)
ChipInspector fold changes directly generated from the CEL files (i.e. no normalized data for each sample), performing significance analysis on the single probe level.
The *Ento.txt files (on Series records) contains the differential expression data  analyzed using the group-wise exhaustive analysis: HVc (or RA) samples group compare to Ento samples group with False Discovery Rate set to zero and 10-significant probe minimum coverage. These result files consist in the table of transcripts and the fold changes for every data combination, also chromosome location (in TGU), Gene ID, Gene Symbol. The statistic algorithm in ChipInspector is a T-test with a permuted artificial background. It is based on and enhances the original SAM algorithm by Tusher et al. (2001): Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98(9), pp 5116-5121. Exhaustive matching of the experiments introduces a second level of data volume enhancing. This means it is using the complete set of available data points by matching the values from every condition experiment to the values from every control experiment. This gives the results greater confidence and therefore increases the number of values that are recognized as significant (higher number of significant genes with lower FDR) (http://www.genomatix.de).

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80C till RNA preparation.

value: Entopallium

value: long day


title: Entopallium, biological rep6 (LD)

description:
Can_LD_male_Ento_37
Entopallium was dissected from cryosections


title: ChIP_Endog. Cnp1

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: Cnp1 ChIP DNA from WT cells after 8 hours at 36C

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL.files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Two sample comparisons of immunoprecipitated vs. input samples, quantile normalization (separate) and linear scaling to 100 was applied. Linear probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2007 and Sanger 2004) and reported in BAR files (Fwd and Rev strands).
All result files are also provided in .txt format: Input_2.txt, Input_1 .txt, WT_oe_cnp1_4.txt, WT_oe_Cnp1_3.txt, WT_oe_Cnp1_2.txt, WT_oe_Cnp1_1.txt, WT_Cnp1_2.txt, WT_Cnp1_1.txt
Results file in .BAR and .txt formats were generates using  Affymetrix Tiling Analysis Software (TAS) v1.1. and contains linear values for relative enrichment (ChIP vs. input) for each probe.

organism: Schizosaccharomyces pombe

source_name: ChIP DNA, Cnp1, ENDOGENOUS

label_protocol: A specific sequence tag was attached to immunoprecipitated DNA fragments by PCR using sequenase and random primers (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'). This DNA was amplified using Taq polymerase and a primer recognizing the specific sequence tag (5'-GTTTCCCAGTCACGATC-3') in the precence of 5 mM dUTP. PCR products were purified using Qiaquick PCR purification kit. DNA was fragmented by UDG and APE nuclease treatment and labelled with biotin by Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.  Immunoprecipitation Assay Protocol

growth_protocol: Cells expressing additional CENP-ACnp1 from integrated pREP81-cnp1+ (nmt81-CENP-ACnp1), pREP41-cnp1+ (nmt41-CENP-ACnp1) or cells with integrated empty vector were initially grown in rich medium which contains thiamine to repress the expression of additional CENP-ACnp1. Cells were grown in PMG liquid medium (with thiamine) at 25ºC and shifted to 36ºC in PMG lacking thiamine for 24 h to allow CENP-ACnp1 expression before ChIP analysis.

extract_protocol: Cnp1 was immunoprecipitated from chromatin extracts prepared from mid-logarithmic phase cells after 8 hours at 36C. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine,  and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with anti-Cnp1 serum for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

tag: strain

tag: chip antibody

source_name: ChIP input DNA, WT


title: Entopallium, biological rep3 (LD)

description:
Can_LD_male_Ento_34-38
Entopallium was dissected from cryosections

tag: light cycle


title: Entopallium, biological rep2 (LD)

description:
Can_LD_male_Ento_34
Entopallium was dissected from cryosections


title: Entopallium, biological rep5 (LD)

description:
Can_LD_male_Ento_36
Entopallium was dissected from cryosections


title: Entopallium, biological rep4 (LD)

description:
Can_LD_male_Ento_35
Entopallium was dissected from cryosections


title: Entopallium, biological rep1 (LD)

description:
Can_LD_male_Ento_32
Entopallium was dissected from cryosections


title: ChIP_nmt81-Cnp1

description: Cnp1 ChIP DNA from top5-105 cells after 8 hours at 36C

source_name: ChIP DNA, Cnp1, nmt81 overexpressed


title: RA, biological rep5 (LD)

description:
Can_LD_male_RA_5
RA was dissected from cryosections

source_name: robust nucleus of the arcopallium (RA)

value: robust nucleus of the arcopallium (RA)


title: RA, biological rep4 (LD)

description:
Can_LD_male_RA_4
RA was dissected from cryosections


title: RA, biological rep2 (LD)

description:
Can_LD_male_RA_2
RA was dissected from cryosections


title: RA, biological rep1 (LD)

description:
Can_LD_male_RA_1
RA was dissected from cryosections


title: HVc, biological rep6 (LD)

description:
Can_LD_male_HVC_172
HVC was dissected from cryosections

value: HVC


title: RA, biological rep3 (LD)

description:
Can_LD_male_RA_3
RA was dissected from cryosections


title: HVc, biological rep4 (LD)

description:
Can_LD_male_HVC_5
HVC was dissected from cryosections


title: HVc, biological rep5 (LD)

description:
Can_LD_male_HVC_22
HVC was dissected from cryosections


title: HVc, biological rep3 (LD)

description:
Can_LD_male_HVC_4
HVC was dissected from cryosections


title: GM12892_gDNA_HumanOmni2.5S-8v1_B

description: CEU Family #1463- Maternal Grandmother


title: HVc, biological rep2 (LD)

description:
Can_LD_male_HVC_3
HVC was dissected from cryosections


title: HVc, biological rep1 (LD)

description:
Can LD male HVc_1
HVC was dissected from cryosections


title: wt100GLN-2

status: Public on Jul 01 2013

city: Freising

first: Ulrich

last: Guldener

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the second of four biological replicates and the first of two technical replicates used for this condition in this experiment.

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following NimbleGen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following NimbleGen's standard operating protocol. See www.nimblegen.com.

data_processing: Pre-processing steps including background correction, normalization and summarization of probe intensities were performed by employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003).

organism: Fusarium fujikuroi

source_name: wild-type IMI58289, mycelium, growth medium: 60 mM Gln (100%)

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following NimbleGen's standard operating protocol. See www.nimblegen.com.

growth_protocol: Starting cultures of Fusarium fujikuroi IMI58289 were grown for 72 hours in 100 mL of Darken media (Darken et al., 1959) in 300 mL Erlenmeyer flasks on a rotary shaker at 180 rpm at 28°C. 100 mL of ICI medium (Geissman et al., 1966) in 300 mL Erlenmeyer flasks was inoculated with 500 µL of the starting culture and incubated on a rotary shaker at 180 rpm at 28°C for 72 hours. The mycelium was harvested via Miracloth in a Büchner funnel, frozen in liquid nitrogen and lyophilized before RNA extraction.

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany), and DNA was removed using DNase I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration were measured with a Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: The nitrogen composition of the medium for the different cultures varied (6 mM Gln, 60 mM Gln, 6mM NO3, 120 nM NO3).

tag: genotype

value: wild-type

value: mycelium

tag: growth medium


title: EpiLCs, B (clone #2-4), 36H, rep2

status: Public on Aug 04 2013

city: Kyoto

first: Fumio

last: NAKAKI

address: Yoshidakonoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings.

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1 transgenes, differentiation time 36H

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: Transfected ESCs were maintained under 2i+LIF condition and adapted to a feeder-free condition prior to induction. EpiLC differentiation was performed as reported previously (Hayashi et al., Cell, 2011).

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

treatment_protocol: After 36 hrs of differentiation, cells were harvested and cultured in a Lipidure-Coat 96-well plate (NOF) to be aggregated (started with 2,000 cells/well) in GK15 with 1.5 μg/ml of Dox (Clonetech). After 24 hrs aggregation culture, whole cells from the aggregates were harvested.

value: Male

tag: transgene

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector


title: EpiLCs, Parental clone, 36H, rep2

source_name: EpiLCs induced from BVSCR26rtTA ESCs, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA


title: wt10GLN-2

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the second of two biological replicates and the first of two technical replicates used for this condition in this experiment.

source_name: wild-type IMI58289, mycelium, growth medium: 6 mM Gln (10%)


title: Parental clone +Doxycycline, day1, rep1

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, cultured with doxycycline


title: wt10GLN-1

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the first of two biological replicates and the first of two technical replicates used for this condition in this experiment.


title: EpiLCs, A (clone #8-2), 36H, rep2

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring V5-Tfap2c transgenes, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector,


title: EpiLCs, P14 (clone #7-109), 36H, rep2

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring 3xFLAG-Prdm14 transgenes, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector


title: EpiLCs, BP14A (clone #3-3), 36H, rep2

source_name: EpiLCs induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1, 3xFLAG-Prdm14, V5-Tfap2c transgenes, differentiation time 36H

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA, tetOx8-mCMV-Avi-Blimp1-IRES-beta geo-bGH pA in piggyBac trasposon vector, tetOx8-mCMV-3xFLAG-Prdm14-IRES-beta geo in piggyBac trasposon vector, tetOx8-mCMV-V5-Tfap2c-IRES-beta geo in piggyBac trasposon vector,


title: P14 (clone #7-109) +Doxycycline, day1, rep1

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring 3xFLAG-Prdm14 transgenes, cultured with doxycycline


title: A (clone #8-2) +Doxycycline, day1, rep1

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring V5-Tfap2c transgenes, cultured with doxycycline


title: B (clone #2-4) +Doxycycline, day1, rep1

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1 transgenes, cultured with doxycycline


title: wt100GLN-1

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the first of four biological replicates and the first of two technical replicates used for this condition in this experiment.


title: BP14A (clone #3-3) +Doxycycline, day1, rep1

source_name: Aggregates of EpiLCs on day1, induced from BVSCR26rtTA ESCs, harbouring Avi-Blimp1, 3xFLAG-Prdm14, V5-Tfap2c transgenes, cultured with doxycycline


title: Patient 3, 1 month after start of IFN-beta therapy [miRNA]

status: Public on Apr 24 2013

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: microRNA expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Biotin-labeled RNA were hybridized for 16 h at 45°C on Affymetrix miRNA 2.0 arrays. The microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The raw probe-level signals were converted to expression values using the RMA algorithm with quantile normalization. This resulted in expression levels for 20,706 probesets per chip.

label: Biotin

source_name: Peripheral blood mononuclear cells

label_protocol: Biotinylated RNA were prepared using the FlashTag Biotin HSR RNA labeling kit according to the Affymetrix protocol from 600 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Patient blood samples were taken immediately before first IFN-beta injection as well as one month post therapy initiation.

extract_protocol: Peripheral blood mononuclear cells were separated using isopycnic centrifugation (Ficoll), and total RNA enriched with small RNAs was isolated using the mirVana miRNA isolation kit (Invitrogen) according to the manufacturers' protocols.

treatment_protocol: Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer HealthCare) at standard doses.

tag: diagnosis

value: relapsing-remitting multiple sclerosis

value: female

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up

tag: completed years of ifn-beta therapy


title: Patient 3, before first IFN-beta injection [miRNA]

tag: gender


title: Patient 2, 1 month after start of IFN-beta therapy [miRNA]


title: Patient 1, 1 month after start of IFN-beta therapy [miRNA]

value: clinically isolated syndrome


title: NPSG_Enrichment_Phosphate_Rep3_48042

status: Public on Mar 07 2013

city: Santa Cruz

first: Irina

middle: N

last: Shilova

state: California

address: 1154 High str

department: Ocean Sciences

institute: UC Santa Cruz

description: Phosphate enrichment, replicate 3, 48042

hyb_protocol: NimbleGen for prokaryotic gene expression microarray

data_processing: Raw pair data was normalized using Li-Wong normalization, and gene transcription values were obtained using RMA algorithm

organism: uncultured marine microorganism

source_name: Surface (10m) water for nutrient enrichment experiment was collected at Station ALOHA in the North Pacific Subtropical Gyre on August 22, 2010, during KM1016 cruise on R/V Kilo Moana.

extract_protocol: Modified Ambion RiboPure

treatment_protocol: NPSG surface seawater was incubated with 1.0 micro-mole potassium phosphate for 48h

tag: nutrient

value: potassium phosphate 1.0 micromole

tag: time

tag: volume


title: NPSG_Enrichment_Phosphate_Rep2_48041

description: Phosphate enrichment, replicate 2, 48041

label_protocol: NimbleGen for prokaryotic gene expression microarray


title: Patient 8, before month 2 GA injection

status: Public on Dec 07 2012

description: Gene expression data from a multiple sclerosis patient treated with GA

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 2.1.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each chip yielded mRNA levels of 18,862 human genes.

source_name: Patient 8, before month 2 GA injection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100-200 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Patient blood samples were taken immediately before first GA injection as well as one day, one week, one month and two months post therapy initiation.

extract_protocol: CD14+ monocytes were isolated using magnetic-activated cell sorting (MACS), and monocytes were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocols.

treatment_protocol: Patients were treated with subcutaneous GA (Copaxone, Teva) at standard doses.

tag: disease

value: multiple sclerosis

tag: cell

value: CD14+ monocytes

value: male

tag: age at ga therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss after 5 years

tag: number of relapses during 12-month follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ga therapy


title: Patient 1, before first IFN-beta injection [miRNA]

tag: diagnosis

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: number of relapses during the year prior to treatment


title: NPSG_Enrichment_Iron_Rep2_48037

description: Iron (III) enrichment, replicate 2, 48037

treatment_protocol: NPSG surface seawater was incubated with 2.0 nanomole ferric chloride for 48h

tag: nutrient

value: ferric chloride, 2.0 nanomole

tag: time

tag: volume


title: Patient 8, before month 1 GA injection

source_name: Patient 8, before month 1 GA injection

tag: disease

tag: cell

tag: gender

tag: age at ga therapy onset (baseline blood sampling)

tag: number of relapses during 2-year follow-up


title: Patient 2, before first IFN-beta injection [miRNA]

tag: number of relapses during 1-year follow-up

tag: completed years of ifn-beta therapy


title: NPSG_Enrichment_Iron_Rep1_48033

description: Iron (III) enrichment, replicate 1, 48033


title: Patient 8, before second GA injection

source_name: Patient 8, before second GA injection

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss after 5 years

tag: number of relapses during 12-month follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ga therapy


title: Patient 8, before week 1 GA injection

source_name: Patient 8, before week 1 GA injection

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: number of relapses during the year prior to treatment


title: NPSG_Enrichment_Phosphate_Rep1_48040

description: Phosphate enrichment, replicate 1, 48040

tag: nutrient

tag: time

tag: volume


title: Patient 7, before month 2 GA injection

source_name: Patient 7, before month 2 GA injection

tag: disease

tag: cell

tag: gender

tag: age at ga therapy onset (baseline blood sampling)


title: Patient 8, before first GA injection

source_name: Patient 8, before first GA injection

tag: duration from ms diagnosis to therapy initiation (in months)

tag: number of relapses during 2-year follow-up


title: Patient 7, before month 1 GA injection

source_name: Patient 7, before month 1 GA injection

tag: edss after 5 years

tag: number of relapses during 12-month follow-up


title: Patient 7, before first GA injection

source_name: Patient 7, before first GA injection

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)


title: Patient 7, before second GA injection

source_name: Patient 7, before second GA injection

tag: edss at baseline

tag: completed years of ga therapy


title: Patient 6, before month 2 GA injection

source_name: Patient 6, before month 2 GA injection

tag: edss after 1 year

tag: edss after 2 years


title: Patient 6, before month 1 GA injection

source_name: Patient 6, before month 1 GA injection

tag: number of relapses during the year prior to treatment


title: Patient 5, before second GA injection

source_name: Patient 5, before second GA injection


title: Patient 6, before second GA injection

source_name: Patient 6, before second GA injection


title: Patient 4, before month 1 GA injection

source_name: Patient 4, before month 1 GA injection


title: Patient 5, before month 2 GA injection

source_name: Patient 5, before month 2 GA injection


title: Patient 4, before month 2 GA injection

source_name: Patient 4, before month 2 GA injection


title: Patient 6, before first GA injection

source_name: Patient 6, before first GA injection


title: Patient 4, before week 1 GA injection

source_name: Patient 4, before week 1 GA injection


title: Patient 5, before week 1 GA injection

source_name: Patient 5, before week 1 GA injection


title: Patient 4, before first GA injection

source_name: Patient 4, before first GA injection


title: Patient 4, before second GA injection

source_name: Patient 4, before second GA injection


title: 9.1 CD34

status: Public on Aug 07 2013

city: Los Angeles

first: Peter

middle: W.

last: Laird

address: 1450 Biggy St.

department: USC Epigenome Center

institute: USC/Norris Cancer Center

description: Normal human bone marrow cells

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Background corrected against out-of-band signals and dye bias corrected against Illumina internal controls

label: Cy5 and Cy3

source_name: Bone marrow cells

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: cell type

value: CD34+CD38- cells


title: 9.1 CD3

description: Normal human bone marrow cells

value: CD3+ T cells


title: Patient 3, before week 1 GA injection

source_name: Patient 3, before week 1 GA injection


title: Patient 2, before month 2 GA injection

source_name: Patient 2, before month 2 GA injection


title: Patient 3, before first GA injection

source_name: Patient 3, before first GA injection


title: Patient 3, before second GA injection

source_name: Patient 3, before second GA injection


title: Patient 1, before month 2 GA injection

source_name: Patient 1, before month 2 GA injection


title: Patient 2, before second GA injection

source_name: Patient 2, before second GA injection


title: Patient 2, before month 1 GA injection

source_name: Patient 2, before month 1 GA injection


title: Patient 5, before first GA injection

source_name: Patient 5, before first GA injection


title: Patient 1, before week 1 GA injection

source_name: Patient 1, before week 1 GA injection


title: Patient 3, before month 2 GA injection

source_name: Patient 3, before month 2 GA injection


title: Patient 1, before month 1 GA injection

source_name: Patient 1, before month 1 GA injection


title: Patient 1, before second GA injection

source_name: Patient 1, before second GA injection


title: NgnrGR plusDex plusGem, rep2

status: Public on Dec 06 2012

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

hyb_protocol: Performed by the Washington University Genome Technololgy Access Center.

scan_protocol: Affymetrix GeneChip 3000 used by the Washington University Genome Technololgy Access Center.

data_processing: Result was analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/). Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/) after normalization. The entire experiment (microinjection, RNA extraction, and microarray analysis) was repeated two times and quantitative RT-PCR was used to determine cut-offs (see below). Target genes were determined by comparing microarray and quantitative real-time RT-PCR (qRT-PCR) data. Candidates were preliminarily determined from microarray data based on the following criteria: i) expression, represented by model-based expression indices (MBEI), was increased more than 1.2-fold in DEX-treated groups (E/B > 1.2); ii) MBEI differences were larger than 50 (E-B > 50); and iii) expression was claimed as 'present (P) in at least one sample in each experiment. Genes identified as regulated in both experiments were considered candidates. Genes induced in DEX-treated, beta-galactosidase-injected samples compared with the DEX-untreated, Ngnr1-GR-injected samples were also determined and excluded from analysis as they were regarded as DEX-induced. From Ngnr1 candidate target lists, we used qRT-PCR to determine fold-change cut-off values. We found that candidate genes showing E/B > 1.5 and E-B > 70 for Ngnr1 or E/B > 1.3 consistently showed more than 2-fold induction by qRT-PCR.

organism: Xenopus laevis

source_name: Ectoderm co-injected with RNAs encoding NgnrGR and geminin, with Ngnr1 activity induced by Dex addition

label_protocol: Total RNA (20mg) per sample was used for probe synthesis and hybridization to Affymetrix Xenopus laevis Genome Arrays (Washington University Genome Technology Access Center).

growth_protocol: Both blastomeres of two-cell-stage pigmented embryos were injected with X-Ngnr-GR (10pg) with or without geminin (100pg) RNAs (with embryos injected with beta-galactosidase RNA as controls) and were raised until stages 8–9. Xenopus animal caps (50–60 ectodermal explants) per sample were isolated and raised in 0.7MMR at 25 degrees C.

extract_protocol: Total RNA was prepared with Trizol (Invitrogen) (Washington University Genome Technology Access Center).

treatment_protocol: When sibling embryos were at stages 10–10.5, explants were pretreated with cycloheximide (final concentration 10mg/ml) for 30min and dexamethasone (final 10 mM) was added to induce transcriptional activity of Ngnr-GR as described previously (EMBO J.26(24):5093-5108). Explants were incubated at 25 degrees C for 2.5 hours and frozen in liquid nitrogen (when sibling embryos were at stage 12.0–12.5).

tag: tissue

value: embryonic ectoderm

tag: rna injection

value: Dex-inducible version of Ngnr1 (NgnrGR) and geminin

tag: treatment

value: dexamethasone


title: Patient 1, before first GA injection

source_name: Patient 1, before first GA injection

tag: disease

tag: cell

tag: gender


title: Patient 2, before week 1 GA injection

source_name: Patient 2, before week 1 GA injection

tag: age at ga therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: number of relapses during 2-year follow-up


title: NgnrGR plusDex, rep2

source_name: Ectoderm injected with RNA encoding NgnrGR, and treated with Dex to induce Ngnr-dependent target gene induction

value: Dex-inducible version of Ngnr1 (NgnrGR)


title: NgnrGR, rep 2

source_name: Xenopus ectoderm injected with RNA encoding NgnrGR

value: no dexamethasone


title: NgnrGR plusDex, rep1


title: DNA Methylation Brain (Mouse 25 ng)

status: Public on Jun 10 2013

city: Baltimore

first: Verity

middle: Frances

last: Oliver

address: 400 North Broadway, Smith 3001P

department: Ophthalmology

institute: Johns Hopkins University

hyb_protocol: NimbleGen Hybridization Kit

scan_protocol: Roche MS 200 array scanner

data_processing:
Data was processed according to Irizarry et al, PMID 18316654.
XYS files were created using the NimbleGen DEVA software.

source_name: MBD-enriched DNA from mouse brain_starting DNA 25 ng

label_protocol: NimbleGen Dual-Color DNA Labeling kit

extract_protocol: Eight-week old C57BL/6J male mice (n = 3) (Jackson Laboratories) were euthanized using IsoSol™ (VEDCO) exposure followed by neck dislocation. After euthanasia, mouse eyes were immediately enucleated and placed into 1X PBS buffer. The cornea and lens were discarded and the eyecup placed into 500 µL of 1X Hanks’ Balanced Salt Solution (HBSS, Invitrogen). The eyecup was incubated for 15 min at 37°C and then microdissected in 1X HBSS. Surrounding sclera was removed from the retina, and any remnants of retinal pigment epithelium were removed by gentle scraping. Three samples of 25 mg brain cortex were removed from each mouse. DNA extraction was performed on each sample using the DNeasy Blood and Tissue kit (Qiagen) following the manufacturer’s protocols with addition of RNase A.

tag: strain

value: brain

tag: age

value: 8 weeks

tag: enrichment

value: MBD2b/MBD3L1-enrichment of DNA followed by KLM-PCR (MeKL)

tag: starting dna

value: 25 ng

source_name: Input DNA from mouse brain_starting DNA 10 ng

value: 10 ng


title: HSAEC49-UI

status: Public on Jun 18 2012

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Non-immortalized human small airway epithelial cells

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: SAGM (Small Airway Growth Media, Lonza)

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: cell line

tag: atcc alias

tag: histology

tag: race

value: Caucasian

value: M


title: DNA Methylation Brain (Mouse 50 ng)

source_name: MBD-enriched DNA from mouse brain_starting DNA 50 ng

tag: tissue

value: 50 ng


title: NgnrGR, rep 1

tag: rna injection


title: Patient 5, before month 1 GA injection

source_name: Patient 5, before month 1 GA injection

value: multiple sclerosis

value: CD14+ monocytes

value: female

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 12-month follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ga therapy


title: HSAEC37-KT

source_name: Immortalized human small airway epithelial cells

tag: cell type

tag: age

tag: gender


title: HSAEC49-KT

value: Immortalized human small airway epithelial cells

tag: cell line

tag: atcc alias


title: DNA Methylation Brain (Mouse 2)

source_name: MBD-enriched DNA from mouse 2 brain_starting DNA 250 ng

tag: strain

value: male

tag: enrichment

tag: starting dna

source_name: Input DNA from mouse 2 brain_starting DNA 10 ng


title: HSAEC45-KT

tag: histology

tag: race


title: HSAEC45-UI

value: Non-immortalized human small airway epithelial cells


title: HSAEC38-UI

value: F


title: HSAEC37-UI


title: HSAEC36-UI


title: HSAEC35-UI


title: Patient 2, before first GA injection

source_name: Patient 2, before first GA injection

tag: disease

tag: cell

tag: age at ga therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: number of relapses during 2-year follow-up


title: HSAEC36-KT

tag: cell type

tag: age


title: HSAEC35-KT

tag: cell line

tag: gender


title: HSAEC31-KT

tag: atcc alias


title: HSAEC31-UI


title: DNA Methylation Retina (Mouse 50 ng)

source_name: MBD-enriched DNA from mouse retina_starting DNA 50 ng

tag: strain

tag: tissue

value: retina

tag: enrichment

source_name: Input DNA from mouse retina_starting DNA 10 ng


title: DNA Methylation Retina (Mouse 2)

source_name: MBD-enriched DNA from mouse 2 retina_starting DNA 250 ng

tag: starting dna

source_name: Input DNA from mouse 2 retina_starting DNA 10 ng


title: DNA Methylation Brain (Mouse 10 ng)

source_name: MBD-enriched DNA from mouse brain_starting DNA 10 ng


title: DNA Methylation Retina (Mouse 10 ng)

source_name: MBD-enriched DNA from mouse retina_starting DNA 10 ng


title: HSAEC30-KT

tag: histology

tag: race


title: HSAEC22-UI


title: NgnrGR plusDex plusGem, rep1

source_name: Ectoderm co-injected with RNAs encoding NgnrGR and geminin, with Ngnr1 activity induced by Dex addition

value: embryonic ectoderm

tag: rna injection

value: Dex-inducible version of Ngnr1 (NgnrGR) and geminin

tag: treatment

value: dexamethasone


title: HSAEC24-KT


title: HSAEC24-UI


title: HSAEC30-UI


title: HSAEC18-KT

value: Hispanic


title: HSAEC2-UI


title: HSAEC13-UI


title: DNA Methylation Retina (Mouse 1)

source_name: MBD-enriched DNA from mouse 1 retina_starting DNA 250 ng

value: 8 weeks

value: MBD2b/MBD3L1-enrichment of DNA followed by KLM-PCR (MeKL)

source_name: Input DNA from mouse 1 retina_starting DNA 10 ng


title: HSAEC19-KT

value: Caucasian


title: DNA Methylation Brain (Mouse 3)

source_name: MBD-enriched DNA from mouse 3 brain_starting DNA 250 ng

value: brain

source_name: Input DNA from mouse 3 brain_starting DNA 10 ng

value: 10 ng


title: HSAEC15-KT

value: M


title: HSAEC2-KT


title: HBEC39-KT

source_name: Immortalized human bronchial epithelial cells

growth_protocol: K-SFM (Keratinocyte Serum-Free Media, Gibco)


title: HBEC36-KT

value: Immortalized human bronchial epithelial cells


title: HSAEC22-KT


title: HBEC33-KT


title: HSAEC15-UI

source_name: Non-immortalized human small airway epithelial cells


title: HBEC30-KT


title: HBEC29-KT


title: DNA Methylation Retina (Mouse 25 ng)

source_name: MBD-enriched DNA from mouse retina_starting DNA 25 ng

value: 25 ng


title: HBEC35-KT


title: HBEC34-KT


title: HSAEC1-UI

value: Black


title: HSAEC1-KT

source_name: Immortalized human small airway epithelial cells


title: HBEC28-KT


title: HBEC37-KT


title: HBEC31-KT


title: HSAEC13-KT

value: Immortalized human small airway epithelial cells


title: HBEC32-KT


title: DNA Methylation Brain (Mouse 1)

source_name: MBD-enriched DNA from mouse 1 brain_starting DNA 250 ng

value: male

source_name: Input DNA from mouse 1 brain_starting DNA 10 ng


title: DNA Methylation Retina (Mouse 3)

source_name: MBD-enriched DNA from mouse 3 retina_starting DNA 250 ng

source_name: Input DNA from mouse 3 retina_starting DNA 10 ng


title: HBEC24-KT

value: F


title: HBEC26-KT


title: HBEC27-KT


title: HBEC18-KT


title: HBEC14-KT


title: HBEC16-KT


title: HBEC17-KT


title: HBEC13-KT


title: HBEC7-KT


title: HBEC11-KT


title: 3,OC12-HSL biological replicate 3 technical replicate 2

status: Public on Nov 23 2010

city: Champenoux

first: Francis

last: Martin

address: Route d'amance

department: EFPA

country: France

institute: INRA

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

hyb_protocol: The nylon filters were pre-incubated in 30 ml of a hybridization solution (5x SSC solution, 5x Denhardt’s solution, 0.5% SDS, 50µg/ml shared salmon sperm DNA) for 4h at 65°C in a HIR10M rotating hybridization incubator (Grant/Boekel, VWR international, Strasbourg, France). Then the filters were incubated in 20 ml of fresh hybridization solution containing the 33P-labelled probe at 65°C for 18h.  The hybridized filters were washed successively for 3x5 min in 2x SSC at room temperature, 2x20 min in 2x SSC containing 0.05% SDS (65°C), 2x20 min in 1x SSC containing 0.1% SDS (65°C) and 2x20 min in 0.1x SSC containing 0.1% SDS (65°C).

scan_protocol: Filters were then wrapped in plastic foils and exposed to a phosphor screen (Eastman Kodak Company, Rochester, NY, USA) for 24h, after which the imaging plate was scanned by a Personal Molecular Imager FX (Bio-Rad Laboratories, Hercules, CA, USA) at a resolution of 50µm per pixel.

data_processing: Phosphorimages of hybridized membranes were analyzed in XDOTREADER (Cose, Paris, France) to obtain raw spot intensity data. After background subtraction, the raw data were normalized by expressing individual spot intensities as a fraction of the sum of all spot intensities in each image and the data were analyzed using Microsoft EXCEL.

organism: Laccaria bicolor S238N-H82

source_name: Mycelium, 14h of incubation

label_protocol: One µg of total RNA was reverse-transcribed using oligo-dT primers with the SMART cDNA synthesis kit (Clontech, Palo alto, CA, USA). Double strand cDNA were then synthesised using the Advantage 2PCR kit (Clontech, Palo alto, CA, USA). Labelling of the cDNA probes was done in the presence of 30µCi 33P dCTP and  30µCi 33P dATP, and random hexamers using the NonaPrimer Kit (Qbiogene, France) according to the manufacturer’s instructions. The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN, Hilden, Germany).

extract_protocol: L. bicolor RNA were extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) as recommended by manufacturer for fungal material

value: 13 days old mycelium grown in vitro on semi-liquid P5 medium


title: HBEC15-KT


title: 3,OC12-HSL biological replicate 3 technical replicate 1


title: 3,OC12-HSL biological replicate 2


title: HBEC12-KT


title: 3,OC12-HSL biological replicate 1 technical replicate 1


title: 3,OC12-HSL biological replicate 1 technical replicate 2


title: Control biological replicate 2

value: Ethyl acetate (mock)


title: Control biological replicate 3


title: HBEC10-KT


title: HBEC6-KT


title: HBEC3-KT


title: Control biological replicate 1

description: The array contains 4992 cDNA. cDNA for which a regulation was observed where further sequenced for identification.


title: HBEC5-KT


title: HBEC4-KT


title: HBEC2-KT