title: Normal left ventricular function, Left Ventricle, sample 5


title: bone marrow-2BE-7days-rep 5

status: Public on Jan 11 2010

type: RNA

city: groton

first: Petra

last: Koza-Taylor

state: CT

address: Eastern Point Road

country: USA

institute: Pfizer

description: B6C3F1 Mouse

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: The microarrays were scanned on a GeneChip Scanner 3000 according to standard procedures.

data_processing: RNA expression data were analyzed using the Affymetrix and lpackages of the Bioconductor suite of microarray analysis tools available for the R statistical environment (Gentleman, 2005; Gentleman et al., 2004; Irizarry et al., 2003; R Development Core Team, 2007).  Robust Microarray Analysis (RMA) background correction and quantile normalization were used to generate microarray expression values.  An overall linear model was fit to the data for all sample groups and specific contrasts of interest were evaluated to generate raw p-values for each probe set on the expression array (Smyth, 2004).  The Benjamini-Hochberg False Discovery Rate (FDR) method was then used to correct for multiple testing effects.  Probe sets were considered to have changed qualitatively in a specific comparison if an adjusted p-value of 0.05 was obtained, their average expression intensity was above 150 in either treatment group, and they had an absolute fold change greater than 1.3.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: bone marrow-2BE-7days

label_protocol: The Affymetrix GeneChip One-Cycle labeling kit was used for labeling according to the manufacturer's protocol.

extract_protocol: RNA from bone marrow was isolated using Paxgene Bone Marrow as described by the manufacturere (Qiagen). RNA from the liver and spleen was isolated using Qiagen mini columns as recomemended by the manufacturer.

tag: tissue

value: Bone Marrow

tag: treatment

value: reduced oxygen

tag: time

value: 7 days

tag: strain


title: spleen-2BE-7days-rep 1

description: B6C3F1 Mouse

value: Spleen


title: spleen-2BE-7days-rep 3

description: B6C3F1 Mouse


title: spleen-vehicle-7days-rep 1

description: B6C3F1 Mouse

value: control


title: Normal left ventricular function, Left Ventricle, sample 8

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Affymetrix Power Tools version 1.0.12. Antigenomic background correction were applied to probe intensities, gene level expression were summarized using the Robust Multichip Average (RMA) method.

organism: Homo sapiens

label_protocol: RNA was labeled by random priming using Affymetrix Whole Transcript and used to probe Affymetrix GeneChip Human Exon 1.0 ST (HuEx) Arrays.

extract_protocol: RNA was extracted with Trizol (Invitrogen) and further purified on RNeasy columns (Qiagen) with on column DNase digestion. RNA quality was checked on an Experion bio-analyzer (Bio-Rad).

tag: clinical diagnosis

value: Normal


title: Normal left ventricular function, Left Ventricle, sample 3


title: DeltaREL+MUPIROCIN vs WT+MUPIROCIN_20min_rep3

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate

hyb_protocol: Fluorescently-labeled cDNAs were resuspended in the manufacturer's salt-based hybridization buffer. Samples were heated for 3 min at 95C, chilled on ice for 3 min, and applied to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed for 5 min in prewarmed (30C) buffers. Buffer 1: 2X SSC, 0.1% SDS; Buffer 2: 1X SSC; Buffer 3: 0.1X SSC.

scan_protocol: Microarray slides were scanned using an Axon GenePix 4200A scanner at gain settings which balanced the channel signals (ratio~0.1). Images were analyzed using GenePix Pro 5.0 software (Molecular Devices).

data_processing: Spots flagged as bad in more than one replicate were removed from further analysis. The Bioconductor marray package was used to perform loess normalization on background-subtracted data. Ribosomal proteins were excluded from the normalization procedure. See associated publication (Kazmierczak, KM et al., Roles of relSpn in Stringent Response, Global Regulation, and Virulence of Serotype 2 Streptococcus pneumoniae D39, submitted) for further details

organism: Streptococcus pneumoniae

source_name: S. pneumoniae D39 mutant (IU1921) treated with mupirocin for 20 min

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2. Culture density OD620~0.1 is defined as (t=0 min)

extract_protocol: Total RNA was extracted after 20 min of mupirocin treatment (t=20 min) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification (RNAeasy mini kit, Qiagen) as described in Robertson et al., J Bact (2002) 184:3508-3520

treatment_protocol: Treated with lithium mupirocin (100 ng per mL) at culture density OD620~0.1 (t=0 min)

tag: serotype

tag: genotype

value: relSpn gene (spd1458) is deleted

source_name: S. pneumoniae D39 (IU1690) treated with mupirocin for 20 min

value: wildtype


title: Japanese Female, NA18951, slide 14

status: Public on Jan 13 2010

type: genomic

city: Seoul

first: Dongwan

last: Hong

address: 28 Yeongeon-dong, Jongno-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Genomic Medicine Institute, Seoul National University College of Medicine

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed using wash buffer I, II (Agilent Inc.).

scan_protocol: Scanned on an Agilent G2505 Scanner.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Immortalized cell line, Japanese female

label_protocol: 1.5ul of genomic DNA fragmented and amplified using random primer. Cy3-dCTP and Cy5-dCTP were incorporated using the BioPrime DNA labelling kit using the manufacturer’s protocol.

growth_protocol: Cell lines were cultured under 10% FBS+standard RPMI media. No antibacterials were used.

extract_protocol: Genomic DNA was extracted using the Gentra DNA extraction kit (Qiagen).

treatment_protocol: Not treated.

tag: population

value: Japanese

tag: gender

value: female

tag: sample source

value: HapMap

tag: sample type

value: test

source_name: NA10851 reference

value: Caucasian

value: male

value: reference


title: Normal left ventricular function, Left Ventricle, sample 2


title: DeltaREL+MUPIROCIN vs WT+MUPIROCIN_20min_rep2

description: Independent biological replicate, dye swap


title: DeltaREL+MUPIROCIN vs WT+MUPIROCIN_20min_rep1

description: Independent biological replicate


title: DeltaREL vs WT_20min_rep3

description: Independent biological replicate

source_name: S. pneumoniae D39 mutant (IU1921), untreated

extract_protocol: Total RNA was extracted at (t=20 min) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification (RNAeasy mini kit, Qiagen) as described in Robertson et al., J Bact (2002) 184:3508-3520

treatment_protocol: No treatment

source_name: S. pneumoniae D39 (IU1690), untreated


title: Normal left ventricular function, Left Ventricle, sample 1


title: bone marrow-2BE-7days-rep 2

description: B6C3F1 Mouse


title: DeltaREL+MUPIROCIN vs DeltaREL_20min_rep2

data_processing: Spots flagged as bad in more than one replicate were removed from further analysis. The Bioconductor marray package was used to perform loess normalization on background-subtracted data. Ribosomal proteins were excluded from the normalization procedure. See associated publication (Kazmierczak, KM et al., Roles of relSpn in Stringent Response, Global Regulation, and Virulence of Serotype 2 Streptococcus pneumoniae D39, submitted) for further details.

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2. Culture density OD620~0.1 is defined as (t=0 min).


title: DeltaREL vs WT_20min_rep2


title: DeltaREL+MUPIROCIN vs DeltaREL_20min_rep3

description: Independent biological replicate


title: bone marrow-2BE-7days-rep 1

description: B6C3F1 Mouse


title: bone marrow-2BE-7days-rep 3

description: B6C3F1 Mouse


title: DeltaREL+MUPIROCIN vs DeltaREL_20min_rep1

description: Independent biological replicate


title: WT+MUPIROCIN vs WT_20min_rep3

description: Independent biological replicate


title: bone marrow-vehicle-7days-rep 3

description: B6C3F1 Mouse

source_name: bone marrow-vehicle-7days


title: bone marrow-vehicle-7days-rep 1

description: B6C3F1 Mouse


title: WT+MUPIROCIN vs WT_20min_rep2


title: liver-2BE-7days-rep 4

description: B6C3F1 Mouse

value: Liver


title: bone marrow-vehicle-7days-rep 2

description: B6C3F1 Mouse


title: bone marrow-vehicle-7days-rep 5

description: B6C3F1 Mouse


title: liver-2BE-7days-rep 3

description: B6C3F1 Mouse


title: liver-2BE-7days-rep 1

description: B6C3F1 Mouse


title: liver-2BE-7days-rep 2

description: B6C3F1 Mouse


title: WT+MUPIROCIN vs WT_20min_rep1

description: Independent biological replicate


title: liver-vehicle-7days-rep 2

description: B6C3F1 Mouse


title: spleen-2BE-4hours-rep 2

description: B6C3F1 Mouse

value: 4 hours


title: liver-vehicle-7days-rep 1

description: B6C3F1 Mouse


title: liver-vehicle-7days-rep 4

description: B6C3F1 Mouse


title: liver-2BE-4hours-rep 2

description: B6C3F1 Mouse


title: liver-2BE-4hours-rep 3

description: B6C3F1 Mouse


title: liver-2BE-7days-rep 5

description: B6C3F1 Mouse


title: liver-2BE-4hours-rep 1

description: B6C3F1 Mouse


title: spleen-2BE-4hours-rep 3

description: B6C3F1 Mouse


title: spleen-vehicle-4hours-rep 4

description: B6C3F1 Mouse


title: spleen-2BE-4hours-rep 1

description: B6C3F1 Mouse


title: liver-vehicle-7days-rep 3

description: B6C3F1 Mouse


title: spleen-vehicle-4hours-rep 3

description: B6C3F1 Mouse


title: liver-2BE-4hours-rep 4

description: B6C3F1 Mouse


title: spleen-vehicle-4hours-rep 1

description: B6C3F1 Mouse


title: spleen-2BE-4hours-rep 4

description: B6C3F1 Mouse


title: liver-vehicle-4hours-rep 3

description: B6C3F1 Mouse


title: bone marrow-vehicle-7days-rep 4

description: B6C3F1 Mouse

value: Bone Marrow


title: CD79A transduced HBL-1 - 48 hrs - repeat 1 - mAdbID:99359

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 99359

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 10.1.1.1). Spot values were normalized using the default linear-lowess normalization.

source_name: Untreated HBL-1 cells

label_protocol:
Cy3 Labeling Protocol
Other: 2 ug total RNA were labeled with Cy3.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

value: blood

tag: cell line

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: CD79A transduced HBL-1 - 48 hr

label_protocol:
Cy5 Labeling Protocol
Other: 2 ug total RNA were labeled with Cy5.

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (CD79A) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 48 hr and then harvested for total RNA.


title: spleen-vehicle-4hours-rep 2

description: B6C3F1 Mouse

value: Spleen


title: liver-vehicle-4hours-rep 2

description: B6C3F1 Mouse

value: control


title: CD79A transduced HBL-1 - 24 hrs - repeat 1 - mAdbID:99358

description: mAdb experiment ID: 99358

source_name: CD79A transduced HBL-1 - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (CD79A) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 24 hr and then harvested for total RNA.


title: alb193_2_replicate (Illumina Mouse WG-6 v2.0)

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

description: Technical replicate

hyb_protocol: 1.5 ug of amplified cRNA was hybridized to each section of the array at 58 degrees Centigrade for 16 hours with rocking according to the Illumina Whole Genome protocol using the IntelliHyb hybriidzation chamber.

scan_protocol: Arrays were scanned using the Illumina BeadStation 500GX scanner with high-resolution upgrade

data_processing: All probes were remapped to current version of mouse coding sequence and regrouped into probe sets corresponding to NCBI genes, using AffyProbeMiner web tool. Resultant library CDF files were imported into R to process the BeadStudio-exported data with RMA method implemented in the affy package.

label: Biotin-labeled target, secondary labeling using streptavidin-conjugated Cy3.

source_name: Liver

label_protocol: 100 ng of total RNA was converted to cdBA and labeled using the Ambion Illumina TotalPrep Amplification Kit.

growth_protocol: Liver-conditional knockout mice for Pdss2, a coenzyme Q biosynthetic pathway gene, were generated as previously described [9].  Briefly, the mutation was targeted to hepatocytes by utilizing mice homozygous for the floxed gene (B6.Pdss2loxP/loxP) crossed with partners that expressed cre under the control of an albumin/cre promoter (B6.Cg-Tg(alb-cre)21 Mgn/J (alb/cre)) obtained from The Jackson Lab.  Animals were sacrificed and liver specimens flash frozen for RNA extraction at 140 to 169 days old.  All procedures were approved by the Institutional Animal Care and Use Committee of both the University of Pennsylvania and The Children’s Hospital of Philadelphia.

extract_protocol: Total RNA from each mouse was isolated by standard Trizol extraction, purified, and combined into a single aliquot from 100 mg flash-frozen liver specimens collected at the time of sacrifice, as previously described for GSE10904.

treatment_protocol: Two B6.alb/cre,Pdss2loxP/loxP mice (one male and one female) were fed standard mouse chow supplemented with probucol (1% wt/vol) from weaning beginning on day of life 44.  Untreated controls consisted of two B6.alb/cre,Pdss2loxP/loxP mice (one male and one female) fed standard mouse chow.

value: Male

tag: age

value: 140 days

tag: mutation

value: Probucol (1% wt/vol)

tag: treatment start age

value: 44 days

value: liver


title: alb187_untreated_male (Illumina Mouse WG-6 v2.0)


title: alb193_treated_male (MoGene-1_0-st)

hyb_protocol: 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45 degrees Centigrade with rotation at 60 RPM according to the Affymetrix standard protocol for Gene arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.

data_processing: All probes were remapped to current version of mouse coding sequence and regrouped into probe sets corresponding to NCBI genes, using AffyProbeMiner web tool. Resultant library CDF files were imported into R to processCEL files  with RMA method implemented in the affy package.

label_protocol: 1 ug of total RNA was processed using a ribosomal RNA reduction step (Invitrogen RiboMinus) and labeled according to the Affymetrix Whole Transcriptome Sense Kit.


title: CARD11 transduced HBL-1 - 48 hrs - repeat 2 - mAdbID:98866

description: mAdb experiment ID: 98866

source_name: CARD11 transduced HBL-1 - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (CARD11) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 48 hr and then harvested for total RNA.


title: BTK transduced HBL-1 - 48 hrs - repeat 1 - mAdbID:98870

description: mAdb experiment ID: 98870

source_name: BTK transduced HBL-1 - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (BTK) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 48 hr and then harvested for total RNA.


title: alb168_untreated_female (Illumina Mouse WG-6 v2.0)

value: Female

value: 169 days


title: alb189_treated_female (Illumina Mouse WG-6 v2.0)


title: alb187_2_replicate (Illumina Mouse WG-6 v2.0)

description: Technical replicate


title: CARD11 transduced HBL-1 - 24 hrs - repeat 1 - mAdbID:99356

description: mAdb experiment ID: 99356

source_name: CARD11 transduced HBL-1 - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (CARD11) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 24 hr and then harvested for total RNA.


title: DeltaREL vs WT_20min_rep1

description: Independent biological replicate

value: relSpn gene (spd1458) is deleted

value: wildtype


title: BTK transduced HBL-1 - 24 hrs - repeat 1 - mAdbID:98869

description: mAdb experiment ID: 98869

source_name: BTK transduced HBL-1 - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (BTK) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 24 hr and then harvested for total RNA.


title: CARD11 transduced HBL-1 - 24 hrs - repeat 2 - mAdbID:98865

description: mAdb experiment ID: 98865


title: CD79A transduced HBL-1 - 48 hrs - repeat 2 - mAdbID:98864

description: mAdb experiment ID: 98864


title: CD79A transduced HBL-1 - 48 hrs - repeat 3 - mAdbID:96977

description: mAdb experiment ID: 96977


title: CARD11 transduced HBL-1 - 48 hrs - repeat 1 - mAdbID:99357

description: mAdb experiment ID: 99357


title: alb189_treated_female (MoGene-1_0-st)


title: alb193_treated_male (Illumina Mouse WG-6 v2.0)


title: alb187_untreated_male (MoGene-1_0-st)


title: CD79A transduced HBL-1 - 24 hrs - repeat 2 - mAdbID:98863

description: mAdb experiment ID: 98863


title: alb193_treated_male (MoEx-1_0-st)

hyb_protocol: 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45 degrees Centigrade with rotation at 60 RPM according to the Affymetrix standard protocol for Exon arrays.


title: alb168_untreated_female (MoGene-1_0-st)


title: liver-vehicle-4hours-rep 1

description: B6C3F1 Mouse


title: alb168_untreated_female (MoEx-1_0-st)


title: alb189_treated_female (MoEx-1_0-st)


title: alb187_untreated_male (MoEx-1_0-st)


title: SYK transduced HBL-1 - 48 hrs - mAdbID:96976

description: mAdb experiment ID: 96976

source_name: SYK transduced HBL-1 - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (SYK) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 48 hr and then harvested for total RNA.


title: CD79A transduced HBL-1 - 24 hrs - repeat 3 - mAdbID:96143

description: mAdb experiment ID: 96143


title: BTK transduced HBL-1 - 24 hrs - repeat 2 - mAdbID:96141

description: mAdb experiment ID: 96141


title: SYK transduced HBL-1 - 24 hrs - mAdbID:96142

description: mAdb experiment ID: 96142

source_name: SYK transduced HBL-1 - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: HBL-1 cells were infected with retroviral vectors expressing various shRNAs (SYK) doxycycline-inducible fashion, selected with puromycin, treated with doxycycline for 24 hr and then harvested for total RNA.


title: BTK transduced HBL-1 - 48 hrs - repeat 2 - mAdbID:96975

description: mAdb experiment ID: 96975


title: VB4 GRA9p

status: Public on Jan 10 2010

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: We conducted a genome-wide transcription analysis in peripheral blood mononuclear cells (PBMCs) from 14 women (9 MS patients and 5 normal controls) followed during their pregnancy. Samples were obtained before pregnancy and at the third, sixth, and ninth month of gestation. Findings were corroborated by real time RT-PCR in a larger cohort of MS patients (n=28) and healthy controls (n=11). Afterwards, we compared expression profiles of patients relapsing during pregnancy (n=23) with those of relapse-free patients (n=5).

hyb_protocol: Twelve ug fragmented cRNA was then used for hybridization. Hybridization and staining were performed as suggested by manufaturer.

scan_protocol: Hybridized Arrays were scanned using an Affymetrix GeneChip 3000 scanner.

data_processing: GeneChip Operating Software (GCOS) (Affymetrix, Santa Clara, CA) was used to generate background-normalized image data (CEL files). Microarray quality controls and statistical validation was done using Bioconductor. The presence of hybridization/construction artifacts was evaluated with the fitPLM function (Bioconductor package affyPLM), and the probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of RMA (Robust Multichip Average) and normalization was done according to the quantiles method.

source_name: Peripheral blood mononuclear cells

label_protocol: Double strand cDNA was synthesized from 1 ug of total RNA using a cDNA Synthesis System (InvitroGen, Basel, Switzerland) with the T7-(T)24 primer. The in vitro-labeling kit (Enzo; Farmingdale, NY) was used to transcribe the cDNA into cRNA in the presence of Biotin-11-CTP and Biotin-16-UTP according to the instructions supplied with the kit.

extract_protocol: PBMCs were isolated from edetic anticoagulated whole blood by centrifugation over LymphoprepTM separation medium (Axis-Shield, Oslo, Norway) and were subjected to RNA extraction using the TriReagent® as instructed by the manufacturer (Ambion, Austin, TX). The time delay from a blood draw to RNA extraction of PBMCs was about 30 minutes.

tag: cell type

value: Peripheral blood mononuclear cells

value: multiple sclerosis specimens at 9th month pregnancy


title: alb193_treated_male (Mouse430_2)

hyb_protocol: 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45 degrees Centigrade with rotation at 60 RPM according to the Affymetrix standard protocol for 3'-focused arrays.

label: biiotin

label_protocol: 1 ug of total RNA was converted to cDNA and labeled using the Ambion MessageAmp Premier RNA Amplification Kit.

tag: tissue


title: 19_LL4 GRA9p


title: DD4 GRA9p


title: 04_CP4 GRA9p


title: alb187_untreated_male (Mouse430_2)

tag: treatment


title: VC4 GRA9n

value: healthy donors at 9th month pregnancy


title: SDC4 GRA9p


title: RP4 GRA9p


title: CF4 GRA9n


title: alb189_treated_female (Mouse430_2)


title: 29_SV4 GRA9n


title: 14_AR4 GRA9p


title: 24_MO4 GRA9n


title: 32 preN

value: healthy


title: 09_MA4 GRA9p


title: alb168_untreated_female (Mouse430_2)


title: Wt_0hTNF_rep2

city: Zurich

first: Karin

last: Rothgiesser

address: Winterthurerstrasse 190

country: Switzerland

institute: Institute of Veterinary Biochemistry and Molecular Biology

description: Gene expression from unstimulated p65(-/-) MEFs genetically complemented with p65 wild type

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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 DNA Microarray-Scanner with Surescan High-Resolution Technology (Agilent Technologies) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, eCtended Dynamic range selected, Dye channel is set to Green, Green PMT XDR Hi is set to 100% and Green PMT XDR Lo to 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_v5_91_0806 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data was normalized with default settings using ‘Rosetta Resolver® Gene Expression Data Management and Analysis System’ (Rosetta Biosoftware).

source_name: p65 wt, unstimulated, replicate 2

label_protocol: RNA was labeled using the ‘Agilent Low RNA Input Linear Amplification Kit PLUS’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Cells were maintained in DMEM supplemented with 10% FCS, 100 units/ml penicillin/streptomycin and non-essential amino acids.

extract_protocol: Total RNA from three biological replicates per sample was isolated at different days using the ‘Total RNA isolation mini kit’ (Agilent Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were starved overnight before either left untreated or stimulated with 30 ng/ml mouse TNFα for 3 hours.

value: Mouse embryonic fibroblasts


title: Wt_0hTNF_rep1

source_name: p65 wt, unstimulated, replicate 1


title: pTV_3hTNF_rep3

description: Gene expression after 3 hours of TNFalpha stimulation from p65(-/-) MEFs genetically complemented with the empty vector

source_name: pTV MEFs, 3h TNF, replicate 3


title: Wt_0hTNF_rep3

source_name: p65 wt, unstimulated, replicate 3


title: 31 preN


title: 21 preN


title: 26 preN


title: 33 preN


title: 06 preMS

value: multiple sclerosis


title: 01 preMS


title: pTV_3hTNF_rep1

source_name: pTV MEFs, 3h TNF, replicate 1


title: pTV_3hTNF_rep2

source_name: pTV MEFs, 3h TNF, replicate 2


title: SF1 preMS


title: KTR_3hTNF_rep3

description: Gene expression after 3 hours of TNFalpha stimulation from p65(-/-) MEFs genetically complemented with p65 KTR mutant (K310/314/315R)

source_name: p65 KTR MEFs, 3h TNF, replicate 3


title: K314/315R_3hTNF_rep2

description: Gene expression after 3 hours of TNFalpha stimulation from p65(-/-) MEFs genetically complemented with p65 K314/315R mutant

source_name: p65 K314/315R MEFs, 3h TNF, replicate 2


title: VC1 preN


title: wt_3hTNF_rep3

description: Gene expression after 3 hours of TNFalpha stimulation from p65(-/-) MEFs genetically complemented with p65 wild type

source_name: p65 wt MEFs, 3h TNF, replicate 3


title: VB1 preMS


title: 11 preMS


title: wt_3hTNF_rep2

source_name: p65 wt MEFs, 3h TNF, replicate 2


title: K314/315R_3hTNF_rep1

source_name: p65 K314/315R MEFs, 3h TNF, replicate 1


title: C. jejuni strain 81116dccR::cm Replicate 3

status: Public on Jan 09 2010

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

description: Technical replicate 3 of 3. C. jejuni strain 81116dccR::cm  grown to stationary phase.

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Scanned on an Axon GenePix4000B scanner at 10nm resolution using GenePix software. Optimize intensities manually. Images were quantified using GenePix software (version 6.0).

data_processing: Fluorescence ratios were calculated after local background was subtracted from spot signals. To compensate for any effect of the amount of template and uneven Cy-dye incorporation, data normalization (centering) was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero using the following equation: ln(Ti ) = ln(Ri /Gi ) - c, where T is the centered ratio, i is the gene index, R and G are the red and green intensities, respectively, and c is the 50th percentile of all red/green ratios.

organism: Campylobacter jejuni subsp. jejuni 81116

source_name: strain 81116dccR::cm

label_protocol: 2 µg of genomic DNA were Cy5-dUTP labeled during random primed synthesis with Klenow fragment.  20 µg of total RNA were labeled during reverse transcription with random primed hexamers to cDNA with Cy3-dUTP using Stratascript (Stratagene, Palo Alto, CA) at 42°C for 16 h.

growth_protocol: Campylobacter were grown under micro-aerobic conditions (5% O2, 10% CO2, and 85% N2) at 42°C on blood agar base II medium.

extract_protocol: Campylobacter genomic DNA was prepared with the Qiagen Dneasy Blood and Tissue kit. Total RNA was extracted from  stationary phase cultures with the RNA-BeeTM kit (Tel-Test, Inc) according to the manufacturer’s specifications.

growth_protocol: Precultures of Campylobacter were grown under micro-aerobic conditions (5% O2, 10% CO2, and 85% N2) at 42°C in Heart Infusion broth (HI) , diluted to an A550 of 0.02 in 5 ml of HI, and incubated on a gyratory shaker (150 rpm) under microaerobic conditions at 42°C to stationary phase (A550 of 1.0-1.4) .


title: C. jejuni strain 81116 wildtype Replicate 3

description: Technical replicate 3 of 3. C. jejuni strain WT81116  grown to stationary phase.

source_name: strain WT 81116


title: SDC1 preMS


title: C. jejuni strain 81116dccR::cm Replicate 2

description: Technical replicate 2 of 3. C. jejuni strain 81116dccR::cm  grown to stationary phase.


title: KTR_3hTNF_rep1

source_name: p65 KTR MEFs, 3h TNF, replicate 1


title: C. jejuni strain 81116dccR::cm Replicate 1

description: Technical replicate 1 of 3. C. jejuni strain 81116dccR::cm  grown to stationary phase.


title: C. jejuni strain 81116 wildtype Replicate 2

description: Technical replicate 2 of 3. C. jejuni strain WT81116  grown to stationary phase.


title: DD1 preMS


title: wt_3hTNF_rep1

source_name: p65 wt MEFs, 3h TNF, replicate 1


title: MDL1 preN


title: C. jejuni strain 81116 wildtype Replicate 1

description: Technical replicate 1 of 3. C. jejuni strain WT81116  grown to stationary phase.


title: RP1 preMS


title: KTR_3hTNF_rep2

source_name: p65 KTR MEFs, 3h TNF, replicate 2


title: leaves PSARK::IPT 300 mL, biological rep3

city: Rehovot

first: Zvi

last: Peleg

address: P.O.Box 12

department: Inst. of Plant Sciences

country: Israel

institute: Hebrew University

description: Gene expression data from Nicotiana leaf RNA hybridized to Affymetrix Tomato Genome Array

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA using quantile normalization and background correction feature using Express Version 1.0.4.

organism: Nicotiana

source_name: Nicotiana leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 3 week old plants were transplanted from growth chamber to greenhouse and water stress treatment imposed for 45 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: control plants (1000 mL per day water per pot); water deficit (300 mL water per day per pot)

value: leaves

tag: genome/variation

value: ~ 10 weeks

tag: environmental factor

value: water stressed


title: Bell_536-1_Col-0_Control_Rep1_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: 2 days, at 4 degrees.  20% bleach solution for 10 minutes, washed 3 x with distilled water.  Arabidopsis thaliana seeds were sterilized in 20% bleach for 10 min and washed with sterilized water for 3 times. Seeds were sown in Petri-dishes containing sterilized media, Murashige and Skoog (MS) basal salt pH 5.7, 1% sucrose and 0.5% phytagel (Sigma, UK). Prior to germination, seeds were stratified at 4oC for 4 days. The plants were grown vertically in the growth room with continual light at 25oC. Autoclaved  25oC average, 25oC day, 25oC night on plates % average, on plates % day, on plates % night Murashige & Skoog basal salt mixture. Modifications: Murashige and Skoog (MS) basal salt pH 5.7, 1% sucrose and 0.5% phytagel (Sigma, UK)  Constant light

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Arabidopsis thaliana

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

extract_protocol: Qiagen RNAeasy kit protocol

tag: developmental stage

value: root

tag: genetic background

tag: wild-type


title: Bell_536-7_35S::RSL4_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: Seeds were stratified at 4oC for 4 days. Arabidopsis thaliana seeds were sterilized in 20% bleach for 10 min and washed with sterilized water for 3 times.  Arabidopsis thaliana seeds were sterilized in 20% bleach for 10 min and washed with sterilized water for 3 times. Seeds were sown in Petri-dishes containing sterilized media, Murashige and Skoog (MS) basal salt pH 5.7, 1% sucrose and 0.5% phytagel (Sigma, UK). Prior to germination, seeds were stratified at 4oC for 4 days. The plants were grown vertically in the growth room with continual light at 25oC.  autoclaved  25oC average, 25oC day, 25oC night on plates % average, on plates % day, on plates % night Murashige & Skoog basal salt mixture. Modifications: Murashige and Skoog (MS) basal salt pH 5.7, 1% sucrose and 0.5% phytagel (Sigma, UK)  Constant light

tag: genetic variation

value: T-DNA knock-out mutation


title: Bell_536-8_35S::RSL4_Rep2_ATH1


title: Bell_536-2_Col-0_Control_Rep2_ATH1


title: leaves PSARK::IPT 1000 mL, biological rep3

value: control


title: Bell_536-4_rsl4-1_Rep2_ATH1


title: leaves PSARK::IPT 300 mL, biological rep1


title: Bell_536-3_rsl4-1_Rep1_ATH1


title: control subject D1, biological replicate 6

city: Paris

first: Véronique

last: Avettand-Fenoel

address: 22 rue Méchain

country: France

institute: INSERM U567

description: Gene expression data from control subject

hyb_protocol: Following fragmentation, 80 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

source_name: Adipose tissue from Control subject

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 1 ug total RNA

extract_protocol: Qiagen extraction of total RNA was performed according to the manufacturer's instructions (RNeasy lipid tissue Mini kit ).

value: Subcutaneous Abdominal Adipose tissue


title: Tiwari_2-10_2x-X-6x-5dap_Rep1_ATH1

description: Seeds stratified and planted in soil and let to grow till flowering. Crosses done at this stage 22C average, 22C day, 22C night 65% average, 65% day, 65% night.

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

value: siliques

value: 5 days after fertilization


title: Tiwari_2-9_4x-X-2x-5dap_Rep1_ATH1


title: control subject C1_2, biological replicate 3


title: control subject C2, biological replicate 5


title: leaves PSARK::IPT 1000 mL, biological rep1


title: Tiwari_2-1_met1-X-2x-1-5dap_Rep1_ATH1


title: control subject A2, biological replicate 1


title: control subject C1, biological replicate 4


title: SF4 GRA9p

description: We conducted a genome-wide transcription analysis in peripheral blood mononuclear cells (PBMCs) from 14 women (9 MS patients and 5 normal controls) followed during their pregnancy. Samples were obtained before pregnancy and at the third, sixth, and ninth month of gestation. Findings were corroborated by real time RT-PCR in a larger cohort of MS patients (n=28) and healthy controls (n=11). Afterwards, we compared expression profiles of patients relapsing during pregnancy (n=23) with those of relapse-free patients (n=5).

source_name: Peripheral blood mononuclear cells


title: Tiwari_2-8_2x-X-4x-5dap_Rep1_ATH1


title: HIV-infected patient K2, biological replicate 7

description: Gene expression data from HIV-infected patient

source_name: Adipose tissue from HIV-infected patient


title: leaves PSARK::IPT 300 mL, biological rep2


title: Tiwari_2-11_6x-X-2x-5dap_Rep1_ATH1


title: leaves PSARK::IPT 1000 mL, biological rep2


title: HIV-infected patient J2, biological replicate 6


title: control subject B2, biological replicate 2


title: Tiwari_2-2_met1-X-2x-2-5dap_Rep2_ATH1


title: leaves WT 300 mL, biological rep1


title: leaves WT 300 mL, biological rep3


title: HIV-infected patient 3, biological replicate 2


title: HIV-infected patient I1, biological replicate 5


title: leaves WT 1000 mL, biological rep2


title: Tiwari_2-4_2x-X-met1-2-5dap_Rep2_ATH1


title: 200 µM (final concentration) of 2,2’-dipyridyl (dip), RyhB2-deleted mutant strain

status: Public on Jan 08 2010

city: Fayetteville

first: Jeong Nam

last: Kim

state: AR

address: 1260 W Maple St. POSC L-115

department: Cell and Molecular Biology

institute: University of Arkansas

hyb_protocol: The generated cDNA was coupled to Cy3 or Cy5 dye (Amersham Biosciences) according to manufacturer's protocol.

scan_protocol: The array slides were scanned on a GenePix 4000B Array Scanner (Axon Instruments). Array data acquisition was performed using TM4 Spotfinder v3.2.1 (http://www.tm4.org/spotfinder.html).

data_processing: TM4 MIDAS v2.21 software was used: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: Wild-Type, Gram-negative Bacteria, 18h incubation in LB media containing 200 µM (final concentration) of 2,2’-dipyridyl (dip)

label_protocol: 10 µg of total RNA were primed with 2 µl of 50 ng Random Hexamers at 65°C for 5 min, then reversed transcribed at 42°C for overnight in the presence of 400 U SuperScript III Reverse Transcriptase (Invitrogen), 500 µM each dATP, dCTP, dGTP, 200 µM dTTP, 1 mM amino allyl-modified dUTP (Sigma), 0.01 M dithiothreitol (DTT) (Sigma), and 40 U RNaseOut (Invitrogen).

extract_protocol: Total RNA extracted using RNeasy mini kit (QIAGEN) following manufacturer's instructions

tag: synonym

value: Salmonella enterica serovar Typhimurium 14028

tag: genotype

source_name: ∆ryhB2, Gram-negative Bacteria, 18h incubation in LB media containing 200 µM (final concentration) of 2,2’-dipyridyl (dip)

value: RyhB2-deletion mutant strain


title: HIV-infected patient H2, biological replicate 4


title: Tiwari_2-3_2x-X-met1-1-5dap_Rep1_ATH1


title: HIV-infected patient 4, biological replicate 3


title: Tiwari_2-6_fis1-X-2x-2-5dap_Rep2_ATH1

value: EMS-induced mutation


title: Tiwari_2-5_fis1-X-2x-1-5dap_Rep1_ATH1


title: leaves WT 1000 mL, biological rep3

value: wildtype


title: Stomach mucosa of H. pylori-negative, patient 19

city: Nagasaki

first: Kayoko

last: Matsushima

address: Sakamoto 1-7-1

department: Gastroenterology and Hepatology

country: Japan

institute: Nagasaki university

description: miRNA expression in H. pylori-negative human stomach mucosa.

hyb_protocol: 100ng of Cy3-labelled RNA  was filtrated　through a colomn and discard the filtrate. The column was added 30μl Nucrease free water and cetrifuzed at 1000xg for 2mins.The labelled samples in a reaction volume of 45μl containing  and 4.5μl of 10x Agilent blocking agent and 22.5μl of 2x Agilent hybridization buffer were incubated at 100Â°C for 5mins.  The samples ware hybridized to Agilent  microRNA Microarrays (G4470A) for 20 hours at 55Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505B). using one color scan setting for 8X15k array slides.

data_processing: Average of gTotalGeneSignal, Data transformation Set measurements less than 0.01 (The negative values) are converted to 0.01, no further processing. To identify miRNAs that were differentially expressed between the H. pylori-negative and -positive groups, supervised analysis was performed using significance analysis of microarrays (SAM, Stanford University, Stanford, CA). Differences in miRNA expressions between the two groups were considered significant if the fold change of expression values was >2.0 and the p value was <0.05 using the t-test.

source_name: Stomach mucosa of H. pylori-negative,patient17

label_protocol: RNAs were directly labeled with Cy3 using T4 RNA ligase (GE Healthcare)

extract_protocol: total RNA including miRNAs was extracted using a commercial kit (mirVana RNA Isolation kit, Applied Biosystems) according to the supplier’s instructions.Quality of total RNA was determined on a Bioanalyzer (Bioanalyzer RNA Nano kit, Agilent), and the RNA was quantified using Nonodrop-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).

treatment_protocol: We excluded patients peformed medications effective against H. pylori during the preceding 3 months, alcohol abuse, drug addiction, and chronic corticosteroid or nonsteroidal anti-inflammatory drug use. None of the subjects had undergone gastrointestinal surgery.

tag: sample type

value: Stomach biopsy tissue


title: Stomach mucosa of H. pylori-negative, patient 17


title: leaves WT 1000 mL, biological rep1


title: Stomach mucosa of H. pylori-negative, patient 16

source_name: Stomach mucosa of H. pylori-negative,patient16


title: 200 µM (final concentration) of 2,2’-dipyridyl (dip), Double (RyhB1 and RyhB2)-deletion mutant strain

source_name: ∆ryhB1&∆ryhB2, Gram-negative Bacteria, 18h incubation in LB media containing 200 µM (final concentration) of 2,2’-dipyridyl (dip)

value: RyhB1/RyhB2-double deletion mutant strain


title: Stomach mucosa of H. pylori-negative, patient 13

source_name: Stomach mucosa of H. pylori-negative,patient13


title: Stomach mucosa of H. pylori-negative, patient 11

source_name: Stomach mucosa of H. pylori-negative,patient11


title: leaves WT 300 mL, biological rep2


title: Stomach mucosa of H. pylori-negative, patient 14

source_name: Stomach mucosa of H. pylori-negative,patient14


title: Stomach mucosa of H. pylori-negative, patient 15

source_name: Stomach mucosa of H. pylori-negative,patient15


title: 200 µM (final concentration) of 2,2’-dipyridyl (dip), RyhB1-deletion mutant strain

source_name: ∆ryhB1, Gram-negative Bacteria, 18h incubation in LB media containing 200 µM (final concentration) of 2,2’-dipyridyl (dip)

value: RyhB1-deletion mutant strain


title: HIV-infected patient 1, biological replicate 1


title: Stomach mucosa of H. pylori-negative, patient 10

source_name: Stomach mucosa of H. pylori-negative,patient10


title: Tiwari_2-7_2x-X-2x-5dap_Rep1_ATH1


title: Stomach mucosa of H. pylori-positive, patient 3

description: miRNA expression in H. pylori-positive human stomach mucosa.

source_name: Stomach mucosa of H. pylori-positive,patient3


title: Stomach mucosa of H. pylori-positive, patient 7

source_name: Stomach mucosa of H. pylori-positive,patient7


title: Stomach mucosa of H. pylori-positive, patient 4

source_name: Stomach mucosa of H. pylori-positive,patient4


title: Stomach mucosa of H. pylori-positive, patient 2

source_name: Stomach mucosa of H. pylori-positive,patient2


title: Stomach mucosa of H. pylori-negative, patient 12

source_name: Stomach mucosa of H. pylori-negative,patient12


title: Stomach mucosa of H. pylori-negative, patient 18


title: Stomach mucosa of H. pylori-positive, patient 9

source_name: Stomach mucosa of H. pylori-positive,patient9


title: Intrascapular brown adipocytes, biological rep 1

city: Aurora

first: Dwight

last: Klemm

state: CO

address: 12700 East 19th Ave., Mail Stop B-133

department: Cardiovascular Pulmonary Research

institute: University of Colorado Denver

description: Gene expression data from intrascapular brown adipocytes.

hyb_protocol: cDNA was hybridized to Affymetrix Mouse 430v2 chips for 16 hours at 45°C in an Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned with a GeneChip 7G Scanner.

data_processing: Data files were imported into Partek Genomics Suite software and normalized using the RMA algorithim.  Principal component analysis was performed on all ~45,000 transcripts.  All data sets were subjected to multiway anova and transcripts whose signal differed between groups by more than 1.25-fold at a p-value less than or equal to 0.05 were selected for further study.  Supervised hierarchial cluster analysis was performed with the k-means algorithim.

source_name: Intrascapular brown adipocytes

label_protocol: RNA was amplified and cDNA was generated using Nugen Ovation RNA Amplification System V2, and the cDNA was labeled with Nugen FL-Ovation cDNA Biotin Module V2.

growth_protocol: White adipocytes were recovered from gonadal white adipose tissue.  Brown adipocytes were isolated from dorsal intrascapular adipose tissue after white adipose tissue was careful removed.  Portions of tissue were suspended in Hank’s Balanced Salt Solution  containing 2 mg/ml collagenase and 4 mg/ml bovine serum albumin (BSA), and agitated for 1 hour at 37°C.  The suspension was filtered through a 200 um sieve, and allowed to stand for 5 minutes to allow the buoyant adipocytes to rise to the top of the solution.  Suspensions were then centrifuged at 500 x g for 5 minutes to pellet the stromal/vascular cells.  The adipocyte layer was recovered and the remaining supernatant was removed by aspiration.

extract_protocol: During FACS approximately 5000 adipocytes were sorted into 100 ul Extraction Buffer (PicoPure RNA Isolation Kit) and incubated at 42°C for 30 minutes.  RNA was purified as directed by the manufacturer’s of the RNA isolation kit, and material from at least 6 sorts were pooled for each sample.  RNA quality and quantity were determined on a Agilent Technologies 2100 Bioanalyzer .

treatment_protocol: Adipocytes were sorted using a Legacy Moflo cell sorter with Summit 4.3 software.  GFP- or LacZ (detected with FDG)-expressing cells were collected with a 530/40 bandpass filter with a voltage of 550.  Sort mode was set to Purify 1. Forward angle light scatter and side light scatter were collected using log scales.

tag: tissue source

value: intrascapular adipose tissue

value: Intrascapular brown adipocytes


title: Gonadal white adipocytes, biological rep 2

description: Gene expression data from gonadal white adipocytes.

source_name: Gonadal white adipocytes

value: gonadal adipose tissue

value: Gonadal white adipocytes


title: Stomach mucosa of H. pylori-positive, patient 8

source_name: Stomach mucosa of H. pylori-positive,patient8


title: Stomach mucosa of H. pylori-positive, patient 5

source_name: Stomach mucosa of H. pylori-positive,patient5


title: Stomach mucosa of H. pylori-positive, patient 6

source_name: Stomach mucosa of H. pylori-positive,patient6


title: Stomach mucosa of H. pylori-positive, patient 1

source_name: Stomach mucosa of H. pylori-positive,patient1


title: S10SG_24h_1

first: Warren

last: Leonard

address: 10 Center Dr

institute: NHLBI/NIH

description: IL-21-induced transcriptional profiling of CD4+ T cells

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization of S10 transformation.

source_name: IL-21 for 24h

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: Splenic CD4+ T cells were sorted with anti-CD4-labeled magnetic beads (Miltenyi) and activated with plate-bound anti-CD3ε (3 μg/ml), soluble anti-CD28 (1 μg/ml), and IL-2 (50 U/ml) for 3 days, rested for 24h.

extract_protocol: Total RNA was extracted from CD4+ T cells with RNeasy Mini Kit (Qiagen) and DNase I treatment (Qiagen).

treatment_protocol: CD4+ T cells were treated with IL-21 for 1h, 6h, and 24h.

value: CD4+ T cells sorted from spleen


title: S10SG_24h_4


title: Intrascapular brown adipocytes, biological rep 2


title: S10SG-1h_2

source_name: IL-21 for 1h


title: Gonadal white adipocytes, biological rep 1


title: LacZ-expressing bone marrow progenitor-derived adipocytes, biological rep2

description: Gene expression data from LacZ-expressing bone marrow progenitor-derived adipocytes.


title: S10SG_6h_3

source_name: IL-21 for 6h


title: S10SG_Ctrl_4

source_name: baseline


title: S10SG-1h_1


title: S10SG_6h_2


title: S10SG_6h_4


title: S10SG_24h_2


title: S10SG_24h_3


title: S10SG_Ctrl_1


title: S10SG_6h_1


title: GFP-expressing bone marrow progenitor-derived adipocytes, biological rep 1

description: Gene expression data from GFP-expressing bone marrow progenitor-derived adipocytes.


title: S10SG-1h_3


title: S10SG_Ctrl_2


title: S10SG_Ctrl_5


title: WT repl4

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Biological replicate 4; individual hippocampus sample from a wild type animal expressing normal levels of PrPc protein derived from diploid dosage of the Prnp gene

hyb_protocol: For each sample, 750 ng of biotinylated cRNA were hybridized in a BeadChip Hyb Chamber with rocking 16 h at 58ºC. The day after, the beadarrays were washed with Illumina proprietary washing solutions in a Hybex waterbath: first with static incubation for 10 min at 55ºC in E1BC solution, followed by 10 rinses by dipping in the same solution and shaking 5 min at 90 rpm in an orbital shaker; the next wash was by dipping 10 times in 100% ethanol and shaking 10 min at 110 rpm in an orbital shaker; this was followed by another wash in E1BC solution with 10 dippings followed by 2 min shaking at 90 rpm. Washed bead arrays were blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer plus streptavidin-Cy3. The fluorescent reagent was washed away with E1BC solution with 10 dippings plus 5 min shaking at 140 rpm. Finally beadarrays were dried by centrifugation 4 min at 275 rcf, followed by scanning in an Illumina Beadstation.

scan_protocol: The Beadscan software was used to control de scanner, generate .tif images and extract the raw data as tabulated text files. Default settings for DirectHyb Gene Expression were used.

data_processing: The raw data was summarized per probe using BeadStudio software Gene Expression module and the summary data file was processed using the PILLA web interface tool (Lozano et al, unpublished), an implementation of the Lumi package (Du et al, 2008) developed within the Bioconductor project in the R statistical programming environment (Gentleman et al, 2004). Data were normalized using the rsn method and vst as the variance stabilization method. The log2 intensities were median centered and log ratios were computed as differences in log2 intensities for each probe. The SAM  (significance analysis of microarrays) two class unpaired comparison test was applied with 300 permutations to detect statistically significant differences in gene expression between each of the three possible comparisons (Tusher et al, 2001).

label: biotin / streptavidin-Cy3

source_name: Wild type hippocampus

label_protocol: For each sample 200 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

growth_protocol: The Prnp -/- mice used in this study were purchased from EMMA (Monterotondo, Italy). Originally described by Büeler et al. in 1992, these mice  showed mixed background with 129/Ola and C57BL/6J. We back-crossed to C57BL/6J  for at least 15 generations to obtain Prnp -/- and control littermates. PrPc overexpressing mice (Tg20) were purchased from EMMA (Monterotondo). These animals were generated by random insertion in Prnp -/- mice described by Marek et al (Fischer et al., 1996).

extract_protocol: Total RNA was extracted using Trizol followed by cleanup with the RNAsy Kit (Qiagen). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN ranging between 8.5 and 10.0.

tag: gender

value: adult male

value: 3-5 months old

tag: weight

tag: status

value: control with normal diploid Prnp gene dose

tag: strain

value: wild type


title: WT repl1

description: Biological replicate 1; individual hippocampus sample from a wild type animal expressing normal levels of PrPc protein derived from diploid dosage of the Prnp gene

tag: age


title: WT repl2

description: Biological replicate 2; individual hippocampus sample from a wild type animal expressing normal levels of PrPc protein derived from diploid dosage of the Prnp gene


title: WT repl3

description: Biological replicate 3; individual hippocampus sample from a wild type animal expressing normal levels of PrPc protein derived from diploid dosage of the Prnp gene


title: S10SG_Ctrl_3

tag: cell type


title: S10SG_6h_5


title: Sg4_ASH1_exp2 input only (DM35B_MR_V02)

city: Piscataway

first: Yuri

middle: B

last: Schwartz

state: NJ

address: 604 Allison Rd

institute: Rutgers University

description: ASH1 ChIP, Biological Rep 1-2

hyb_protocol: Hybridization of labeled DNA was done in 200ul of solution containing 1xMES, 3M TMAC, 40pM oligo B2, 100u/ml sonicated salmon sperm DNA, 0.02% Triton X100 for 18 hours at 45C with 45rpm rotation. Staining and washing was done using EukGE-WS2v4 protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT v2.8.3
The .sgr files were produced with TiMAT v2.8.3 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window.

organism: Drosophila melanogaster

source_name: Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from Sg4 chromatin

label_protocol: 2ug of amplified ChIP product was fragmented with DNAse I  and labeled with TdT by biotin-11-ddATP incorporation

growth_protocol: Sg4 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine

extract_protocol: Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.

tag: cell line

tag: antibody

value: ASH1, rat mAb (Sanchez-Elsner et al., 2006)

tag: dsrna treatment

source_name: DNA isolated from matching input Sg4 chromatin


title: Sg4_H3K27ac (DM35B_MF_V02)

description: H3K27ac ChIP, Biological Rep 1-2

source_name: Anti H3K27ac (Active Motif) ChIP from Sg4 chromatin

value: H3K27ac (Active Motif, cat# 39135)


title: S10SG_24h_5


title: S10SG-1h_4


title: Sg4_TRX_N-ter (DM35B_MR_V02)

description: TRX N-ter ChIP, Biological Rep 1-3

source_name: Anti TRX N-ter (Kuzin et al., 1994) ChIP from Sg4 chromatin

value: TRX N-ter (Kuzin et al., 1994)


title: BG3_H3K27ac_wild_type (DM35B_MR_V02)

description: H3K27ac ChIP, Biological Rep 1-2

source_name: Anti H3K27ac (Active Motif) ChIP from ML-DmBG3-c2 chromatin

growth_protocol: ML-DmBG3-c2 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 10ug/ml insulin, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine

treatment_protocol: Where indicated the cells were treated with 25ug of dsRNA per 1x10^6 cells

source_name: DNA isolated from matching input  ML-DmD23-c4 chromatin


title: BG3_ASH1_wild_type_exp1_replicate_1 (DM35B_MR_V02)

description: ASH1 ChIP, Biological Rep 1

source_name: Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from ML-DmBG3-c2 chromatin

value: ASH1, rabbit pAb (Sanchez-Elsner et al., 2006)


title: BG3_H3K4me3 (DM35B_MR_V02)

description: H3K4me3 ChIP, Biological Rep 1-2

source_name: Anti H3K4me3 (AbCam) ChIP from ML-DmBG3-c2 chromatin

value: H3K4me3 (AbCam, cat# ab8580)


title: BG3_TRX_N-ter_wild_type_exp1 (DM35B_MR_V02)

description: TRX N-ter ChIP, Biological Rep 1-2

source_name: Anti TRX N-ter (Kuzin et al., 1994) ChIP from ML-DmBG3-c2 chromatin


title: BG3_TRX_C-ter_wild_type_exp1 (DM35B_MR_V02)

description: TRX C-ter ChIP, Biological Rep 1-2

source_name: Anti TRX C-ter (Poux et al., 2002) ChIP from ML-DmBG3-c2 chromatin

value: TRX C-ter (Poux et al., 2002)


title: D39 treated with bacitracin 30min.

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1h	203	2.3Cy5
	1j	212	3.2 Cy3
	1k	245	4.1 Cy3
	2h	213	2.9 Cy3
	2i	236	2.2 Cy5
	2k	220	1.7 Cy5
Hybridization	slide number	samples
	176666	1h-2h
	176667	1j-2k
	176668	1k-2i

hyb_protocol: The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519)

scan_protocol: Images were acquired with 4200AL Molecular Devices

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

label: Cy3, Cy5

organism: Streptococcus pneumoniae D39

source_name: samples with AMP

label_protocol:
sample number	concentration	labeling pmol/μl
1h	203	2.3Cy5
1j	212	3.2 Cy3
1k	245	4.1 Cy3
Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: agent

value: bacitracin

tag: time

value: 30 min

source_name: samples without AMP

label_protocol:
sample number	concentration	labeling pmol/μl
2h	213	2.9 Cy3
2i	236	2.2 Cy5
2k	220	1.7 Cy5
aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

value: no antimicrobial peptide


title: BG3_ASH1_wild_type_exp2_replicate_1 (DM35B_MR_V02)

description: ASH1 ChIP, Biological Rep 1


title: BG3_H3K27me3_wild_type (DM35B_MR_V02)

description: H3K27me3 ChIP, Biological Rep 1-2

source_name: Anti H3K27me3 (AbCam) ChIP from ML-DmBG3-c2 chromatin

value: H3K27me3 (AbCam, cat# ab6002)


title: Nisin15

description:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1l	171	3.9 Cy3
	1m		5.5 Cy3
	1n		3.1 Cy5
	1o		3.6 Cy5
	2l		3.5 Cy5
	2m		3   Cy5
	2n		5.7 Cy3
	2o		4.4 Cy3
Hybridization	slide number	samples
	181028	1l-2m
	181029	1m-2l
	181030	1n-2n
	181031	1o-2o

label_protocol:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1l	171	3.9 Cy3
1m		5.5 Cy3
1n		3.1 Cy5
1o		3.6 Cy5

Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

value: Nisin

value: 15 min

label_protocol:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1l	171	3.9 Cy3
2l		3.5 Cy5
2m		3   Cy5
2n		5.7 Cy3
2o		4.4 Cy3
aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).


title: BG3_PC_wild_type_replicate_1-2 (DM35B_MR_V02)

description: PC ChIP, Biological Rep 1-2

source_name: Anti PC (Poux et al., 2001) ChIP from ML-DmBG3-c2 chromatin

value: PC (Poux et al., 2001)


title: BG3_RNA_Pol_II (DM35B_MR_V02)

description: RNA Pol II ChIP, Biological Rep 1-2

source_name: Anti RNA Pol II (Covance) ChIP from ML-DmBG3-c2 chromatin

value: RNA Pol II (clone 8WG16, Covance, cat# MMS-126R)


title: LL37-15 min

description:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1t	174	3.1 Cy5
	1u	80	0.8 Cy5
	1v	178	4.4 Cy3
	2t	154	3.5 Cy3
	2u	141	2.8 Cy3
	2v	151	2.4 Cy5

Hybridization	slide number	samples
	181046	1t-2t
	181047	1u-2u
	181048	1v-2v

label_protocol:
sample number	concentration	labeling pmol/μl
1t	174	3.1 Cy5
1u	80	0.8 Cy5
1v	178	4.4 Cy3
Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

label_protocol:
sample number	concentration	labeling pmol/μl
2t	154	3.5 Cy3
2u	141	2.8 Cy3
2v	151	2.4 Cy5
aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).


title: Nisin30

description:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1p		5.9 Cy3
	1q		4.2 Cy3
	1r		3   Cy5
	1s		4.1 Cy5
	2p		3.7 Cy3
	2q		4.1 Cy3
	2r		3.6 Cy5
	2s		3.2 Cy5
Hybridization	slide number	samples
	181032	1p-2s
	181033	1q-2r
	181034	1r-2p
	181035	1s-2q

label_protocol:
sample number	concentration	labeling pmol/μl
1p		5.9 Cy3
1q		4.2 Cy3
1r		3   Cy5
1s		4.1 Cy5
Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

label_protocol:
sample number	concentration	labeling pmol/μl
2p		3.7 Cy3
2q		4.1 Cy3
2r		3.6 Cy5
2s		3.2 Cy5
aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).


title: D39 treated with bacitracin 15min.

description:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1d	228	4.4 Cy3
	1f	173.4	1.3 Cy5
	1g	175.2	1.6 Cy5
	2d	265.5	2.1 Cy5
	2e	260.6	5.0 Cy3
	2g	350.4	12.4 Cy3
Hybridization	slide number	samples
	176661	1f -  2e
	176662	1g - 2g
	176663	1d - 2d

label_protocol:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)
1d	228	4.4 Cy3
1f	173.4	1.3 Cy5
1g	175.2	1.6 Cy5
Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

label_protocol:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)
2d	265.5	2.1 Cy5
2e	260.6	5.0 Cy3
2g	350.4	12.4 Cy3
aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).


title: LL37-30 min

description:
sample number	concentration	labeling pmol/μl
Labeled cDNA  (ng/ml)	1w	112	1.5 Cy5
	1x	133	2.1 Cy5
	1y	131	3.1 Cy3
	2w	97	1.6 Cy3
	2x	151	3 Cy3
	2y	78	 0.9 Cy5

Hybridization	slide number	samples
	181049	1w-2w
	181050	1x-2x
	181051	1y-2y

label_protocol:
sample number	concentration	labeling pmol/μl
1w	112	1.5 Cy5
1x	133	2.1 Cy5
1y	131	3.1 Cy3
Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

label_protocol:
sample number	concentration	labeling pmol/μl
2w	97	1.6 Cy3
2x	151	3 Cy3
2y	78	 0.9 Cy5
aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).


title: Prnp KO repl1

description: KO biological replicate 1; individual hippocampus sample from a knock out animal lacking PrPc protein expression because of a homozygous deletion of the Prnp gene

source_name: Prnp knock out hippocampus

value: adult male

value: 3-5 months old

value: loss of function of Prnp gene

value: Prnp -/-


title: D23_RNA_Pol_II (DM35B_MF_V02)

description: RNA Pol II ChIP, Biological Rep 1-2

source_name: Anti RNA Pol II (Covance) ChIP from ML-DmD23-c4 chromatin

growth_protocol: ML-DmD23-c4 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 10ug/ml insulin, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine


title: Prnp KO repl2

description: KO biological replicate 2; individual hippocampus sample from a knock out animal lacking PrPc protein expression because of a homozygous deletion of the Prnp gene


title: Prnp KO repl4

description: KO biological replicate 4; individual hippocampus sample from a knock out animal lacking PrPc protein expression because of a homozygous deletion of the Prnp gene


title: Prnp Tg20 repl2

description: Tg20 biological replicate 2; individual hippocampus sample from a transgenic animal overexpressing PrPc protein derived from a 30 exogenous copies of the Prnp gene inserted within a homozygous Prnp deletion background

source_name: Prnp transgenic hippocampus

value: gain of function of Prnp gene


title: Prnp Tg20 repl4

description: Tg20 biological replicate 4; individual hippocampus sample from a transgenic animal overexpressing PrPc protein derived from a 30 exogenous copies of the Prnp gene inserted within a homozygous Prnp deletion background


title: Prnp Tg20 repl3

description: Tg20 biological replicate 3; individual hippocampus sample from a transgenic animal overexpressing PrPc protein derived from a 30 exogenous copies of the Prnp gene inserted within a homozygous Prnp deletion background


title: Prnp Tg20 repl1

description: Tg20 biological replicate 1; individual hippocampus sample from a transgenic animal overexpressing PrPc protein derived from a 30 exogenous copies of the Prnp gene inserted within a homozygous Prnp deletion background


title: D23_TRX_C-ter (DM35B_MF_V02)

description: TRX C-ter ChIP, Biological Rep 1-2

source_name: Anti TRX C-ter (Poux et al., 2002) ChIP from ML-DmD23-c4 chromatin


title: D23_H3K4me3 (DM35B_MF_V02)

description: H3K4me3 ChIP, Biological Rep 1-2

source_name: Anti H3K4me3 (AbCam) ChIP from ML-DmD23-c4 chromatin


title: CpG ODN-5 days-repeat 1 - mAdbID:90141

city: Frederick

first: Dennis

last: Klinman

department: CIP

institute: NCI Frederick

description: mAdb experiment ID: 90141

hyb_protocol: Murine oligonucleotide microarrays were produced by the NCI microarray facility (Gaithersburg, MD). Cy-labeled reference and sample cDNAs (10 microliter each) were combined, de-naturated by heating for 2' at 98 C and mixed with 36 microliter of hybridization solution at 42 C (Ambion, Austin, TX). A low volume active mixing chamber was applied to the microarray via an adhesive gasket (MAUI mixer FL, BioMicro Systems, Salt Lake City, Utah), the hybridization solution containing the sample was added to the array, and was placed for 18 h at 42 C in the base unit of the actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah). Post hybridization, the arrays were washed in 1X SSC/0.05X SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.12906; 3.7492 Temperature: 25.1366

data_processing: BRB Data Processing Protocol: Data were up-loaded to the mAdb database (Microarray Database, a collaboration of CIT/BIMAS and NCI/CCR at the NIH; http://nciarray.nci.nih.gov/) and formatted via the export function for use with BRB ArrayTools. Data from 4 independent experiments/time point and 6 untreated controls were used for all statistical analyses. Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes (21). Analysis was restricted to genes present on >70% of the arrays after filtering.

source_name: Universal Mouse Reference RNA

label_protocol: Cy3 Labeling Protocol: 20 microgram of total RNA (universal reference mouse RNA, Stratagene, La Jolla, CA) was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy3 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol: Strategene UHR RNA Extraction

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: CpG ODN - 5 days

label_protocol: Cy5 Labeling Protocol: 20 microgram of total RNA was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy5 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol: TRIzol Extraction Protocol: Total RNA was extracted from spleens using TRIzol reagent (Invitrogen) as specified by the manufacturer.

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 5 days
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0 hr, 3 hr, 9 hr, 24 hr, 3 days, 5 days, 7 days, 9 days, and 14 days.

value: BALB/c

value: female

tag: tissue

value: spleen


title: D23_ASH1_exp1 (DM35B_MF_V02)

description: ASH1 ChIP, Biological Rep 1-2

source_name: Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from ML-DmD23-c4 chromatin

value: ASH1, rabbit pAb (Sanchez-Elsner et al., 2006)

source_name: DNA isolated from matching input  ML-DmD23-c4 chromatin


title: CpG ODN-9 days-repeat 4 - mAdbID:90253

description: mAdb experiment ID: 90253

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.20414; 3.65154 Temperature: 28.7988

source_name: CpG ODN - 9 days

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 9 days
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0 hr, 3 hr, 9 hr, 24 hr, 3 days, 5 days, 7 days, 9 days, and 14 days.


title: CpG ODN-9 days-repeat 1 - mAdbID:90143

description: mAdb experiment ID: 90143

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.20566; 3.68328 Temperature: 30.0806


title: Prnp KO repl3

description: KO biological replicate 3; individual hippocampus sample from a knock out animal lacking PrPc protein expression because of a homozygous deletion of the Prnp gene


title: D23_PC (DM35B_MF_V02)

description: PC ChIP, Biological Rep 1-2

source_name: Anti PC (Poux et al., 2001) ChIP from ML-DmD23-c4 chromatin


title: D23_E(Z) (DM35B_MF_V02)

description: E(Z) ChIP, Biological Rep 1-2

source_name: Anti E(Z) (Kahn et al., 2006) ChIP from ML-DmD23-c4 chromatin

value: E(Z) (Kahn et al., 2006)


title: CpG ODN-9 days-repeat 2 - mAdbID:90146

description: mAdb experiment ID: 90146

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.20414; 3.65398 Temperature: 28.6462


title: Sg4_H3K9ac (DM35B_MF_V02)

description: H3K9ac ChIP, Biological Rep 1-2

source_name: Anti H3K9ac (Active Motif) ChIP from Sg4 chromatin

value: H3K9ac (Active Motif, cat# 39137)

source_name: DNA isolated from matching input Sg4 chromatin


title: Sg4_H3K27ac (DM35B_MR_V02)

description: H3K27ac ChIP, Biological Rep 1-2

source_name: Anti H3K27ac (Active Motif) ChIP from Sg4 chromatin

value: H3K27ac (Active Motif, cat# 39135)


title: Sg4_RNA_Pol_II (DM35B_MF_V02)

description: RNA Pol II ChIP, Biological Rep 1-2

source_name: Anti RNA Pol II (Covance) ChIP from Sg4 chromatin


title: CpG ODN-5 days-repeat 2 - mAdbID:88954

description: mAdb experiment ID: 88954

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.09488; 3.72234 Temperature: 25.0755


title: Sg4_ASH1_exp1 (DM35B_MF_V02)

description: ASH1 ChIP, Biological Rep 1-2

source_name: Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from Sg4 chromatin


title: CpG ODN-5 days-repeat 4 - mAdbID:89705

description: mAdb experiment ID: 89705

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.15928; 3.72295 Temperature: 27.8527


title: CpG ODN-14 days-repeat 3 - mAdbID:88326

description: mAdb experiment ID: 88326

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.19; 3.45 Temperature: 29.17

source_name: CpG ODN - 14 days

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 14 days
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0 hr, 3 hr, 9 hr, 24 hr, 3 days, 5 days, 7 days, 9 days, and 14 days.


title: CpG ODN-24h-repeat 1 - mAdbID:88558

description: mAdb experiment ID: 88558

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.41; 4.06 Temperature: 29.74

data_processing: Data Processing Protocol: Data were background corrected, flagged values were removed, spots with both signals less than 100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. Only genes present on >70% of the arrays were included in the subsequent analysis.

source_name: CpG ODN - 24 hrs BALB/c WT

extract_protocol: RNA Extraction Protocol: Total RNA was extracted from mice spleens using TRIzol reagent (Invitrogen, Carlsbad, CA) as specified by the manufacturer.

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 24 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: CpG ODN-14 days-repeat 4 - mAdbID:88327

description: mAdb experiment ID: 88327

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.24; 3.62 Temperature: 29.68


title: BG3_H3K27me3_wild_type (Dm35b_MF_v02)

description: H3K27me3 ChIP, Biological Rep 1-2

source_name: Anti H3K27me3 (AbCam) ChIP from ML-DmBG3-c2 chromatin

value: H3K27me3 (AbCam, cat# ab6002)


title: CpG ODN-14 days-repeat 1 - mAdbID:88324

description: mAdb experiment ID: 88324

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.25; 3.58 Temperature: 28.22


title: CpG ODN-7 days-repeat 4 - mAdbID:88323

description: mAdb experiment ID: 88323

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.22; 3.63 Temperature: 28.89

source_name: CpG ODN - 7 days

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 7 days
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0 hr, 3 hr, 9 hr, 24 hr, 3 days, 5 days, 7 days, 9 days, and 14 days.


title: CpG ODN-14 days-repeat 2 - mAdbID:88325

description: mAdb experiment ID: 88325

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.19; 3.59 Temperature: 27.06


title: CpG ODN-7 days-repeat 3 - mAdbID:88322

description: mAdb experiment ID: 88322

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.26; 3.59 Temperature: 28.19


title: Sg4_H3K4me3 (DM35B_MF_V02)

description: H3K4me3 ChIP, Biological Rep 1-2

source_name: Anti H3K4me3 (AbCam) ChIP from Sg4 chromatin

value: H3K4me3 (AbCam, cat# ab8580)


title: CpG ODN-72h-repeat 4 - mAdbID:88318

description: mAdb experiment ID: 88318

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.19; 3.6 Temperature: 27.43

source_name: Universal Mouse Reference RNA

source_name: CpG ODN - 72 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 72 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: CpG ODN-72h-repeat 3 - mAdbID:88317

description: mAdb experiment ID: 88317

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.43; 4.05 Temperature: 28.59


title: CpG ODN-72h-repeat 2 - mAdbID:88316

description: mAdb experiment ID: 88316

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.36; 4.08 Temperature: 27.49


title: BG3_PC_wild_type_replicate_1-2 (Dm35b_MF_v02)

description: PC ChIP, Biological Rep 1-2

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

source_name: Anti PC (Poux et al., 2001) ChIP from ML-DmBG3-c2 chromatin

value: PC (Poux et al., 2001)


title: Sg4_ASH1_exp2 (DM35B_MF_V02)

description: ASH1 ChIP, Biological Rep 1-2

value: ASH1, rat mAb (Sanchez-Elsner et al., 2006)


title: Sg4_TRX_N-ter (DM35B_MF_V02)

description: TRX N-ter ChIP, Biological Rep 1-3

source_name: Anti TRX N-ter (Kuzin et al., 1994) ChIP from Sg4 chromatin

value: TRX N-ter (Kuzin et al., 1994)


title: CpG ODN-72h-repeat 1 - mAdbID:88315

description: mAdb experiment ID: 88315

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.35; 4.04 Temperature: 25.84


title: Sg4_TRX_C-ter_exp2 (DM35B_MF_V02)

description: TRX C-ter ChIP, Biological Rep 1-2

source_name: Anti TRX C-ter (Beisel at al., 2007) ChIP from Sg4 chromatin

value: TRX C-ter (Beisel at al., 2007)


title: BG3_H3K27ac_wild_type (Dm35b_MF_v02)

description: H3K27ac ChIP, Biological Rep 1-2

source_name: Anti H3K27ac (Active Motif) ChIP from ML-DmBG3-c2 chromatin

source_name: DNA isolated from matching input  ML-DmD23-c4 chromatin


title: Sg4_TRX_C-ter_exp1 (DM35B_MF_V02)

description: TRX C-ter ChIP, Biological Rep 1-2

source_name: Anti TRX C-ter (Poux et al., 2002) ChIP from Sg4 chromatin

value: TRX C-ter (Poux et al., 2002)


title: S10SG-1h_5

description: IL-21-induced transcriptional profiling of CD4+ T cells

scan_protocol: Affymetrix GeneChip scanner

source_name: IL-21 for 1h

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

value: CD4+ T cells sorted from spleen


title: CpG ODN-7 days-repeat 2 - mAdbID:88321

description: mAdb experiment ID: 88321

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.24; 3.62 Temperature: 26.91


title: Control ODN-3h-repeat 4 - mAdbID:88314

description: mAdb experiment ID: 88314

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.6; 4.11 Temperature: 34.69

source_name: Control ODN - 3 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture of ODN 1612, 1471
Treatment dose: 400 ug
Treatment time: 3 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of equimolar mixture of ODN 1612, 1471. Spleens were surgical removed under sterile conditions after 3 hours.


title: D23_H3K27ac (DM35B_MF_V02)

description: H3K27ac ChIP, Biological Rep 1-2

source_name: Anti H3K27ac (Active Motif) ChIP from ML-DmD23-c4 chromatin


title: BG3_H3K27ac_lacZ_RNAi (DM35B_MF_V02)

description: H3K27ac ChIP after mock RNAi, Biological Rep 1-2

value: lacZ dsRNA


title: D23_ASH1_exp2 (DM35B_MF_V02)

description: ASH1 ChIP, Biological Rep 1-2

source_name: Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from ML-DmD23-c4 chromatin


title: BG3_H3K27ac_PC_RNAi (DM35B_MF_V02)

description: H3K27ac ChIP after PC RNAi, Biological Rep 1-2

value: PC dsRNA


title: BG3_ASH1_ASH1_RNAi (DM35B_MF_V02)

description: ASH1 ChIP after ASH1 RNAi, Biological Rep 1-2

source_name: Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from ML-DmBG3-c2 chromatin

value: ASH1 dsRNA


title: BG3_ASH1_wild_type_exp1_replicate_2 (DM35B_MF_V02)

description: ASH1 ChIP, Biological Rep 2


title: BG3_H3K27ac_TRX_RNAi (DM35B_MF_V02)

description: H3K27ac ChIP after TRX RNAi, Biological Rep 1-2

value: TRX dsRNA


title: CpG ODN-9 days-repeat 3 - mAdbID:89109

description: mAdb experiment ID: 89109

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.18216; 3.71838 Temperature: 27.0592

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: CpG ODN - 9 days

value: BALB/c

value: female

value: spleen


title: BG3_TRX_N-ter_PC_RNAi (DM35B_MF_V02)

description: TRX N-ter ChIP after PC RNAi, Biological Rep 1-2

source_name: Anti TRX N-ter (Schwartz et al., submitted) ChIP from ML-DmBG3-c2 chromatin

value: TRX N-ter (Schwartz et al., submitted)


title: BG3_ASH1_TRX_RNAi (DM35B_MF_V02)

description: ASH1 ChIP after TRX RNAi, Biological Rep 1-2


title: BG3_ASH1_PC_RNAi (DM35B_MF_V02)

description: ASH1 ChIP after PC RNAi, Biological Rep 1-2


title: BG3_TRX_N-ter_wild_type_exp2 (DM35B_MF_V02)

description: TRX N-ter ChIP, Biological Rep 1-2


title: Control ODN-3h-repeat 3 - mAdbID:88313

description: mAdb experiment ID: 88313

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.61; 4.11 Temperature: 34.78


title: CpG ODN-7 days-repeat 1 - mAdbID:88319

description: mAdb experiment ID: 88319

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.26; 3.59 Temperature: 28.68

source_name: CpG ODN - 7 days


title: BG3_TRX_C-ter_wild_type_exp2 (DM35B_MF_V02)

description: TRX C-ter ChIP, Biological Rep 1-2

source_name: Anti TRX C-ter (Beisel at al., 2007) ChIP from ML-DmBG3-c2 chromatin


title: BG3_ASH1_wild_type_exp2_replicate_2 (DM35B_MF_V02)

description: ASH1 ChIP, Biological Rep 2

value: ASH1, rabbit pAb (Sanchez-Elsner et al., 2006)


title: BG3_H3K27me3_TRX_RNAi (DM35B_MF_V02)

description: H3K27me3 ChIP after TRX RNAi, Biological Rep 1-2

source_name: Anti H3K27me3 (AbCam) ChIP from ML-DmBG3-c2 chromatin

value: H3K27me3 (AbCam, cat# ab6002)


title: BG3_H3K27me3_PC_RNAi (DM35B_MF_V02)

description: H3K27me3 ChIP after PC RNAi, Biological Rep 1-2


title: BG3_TRX_N-ter_ASH1_RNAi (DM35B_MF_V02)

description: TRX N-ter ChIP after ASH1 RNAi, Biological Rep 1-2


title: BG3_H3K27me3_lacZ_RNAi (DM35B_MF_V02)

description: H3K27me3 ChIP after mock RNAi, Biological Rep 1-2


title: Control ODN-3h-repeat 2 - mAdbID:88312

description: mAdb experiment ID: 88312

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.52; 4.07 Temperature: 30.6

source_name: Universal Mouse Reference RNA


title: Control ODN-3h-repeat 1 - mAdbID:88311

description: mAdb experiment ID: 88311

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.46; 4.07 Temperature: 29.96


title: CpG ODN-24h-repeat 3 - mAdbID:88232

description: mAdb experiment ID: 88232

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.22; 3.61 Temperature: 27.55

source_name: CpG ODN - 24 hrs BALB/c WT


title: CpG ODN-9h-repeat 2 - mAdbID:88227

description: mAdb experiment ID: 88227

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.35; 4.04 Temperature: 27.97

source_name: CpG ODN - 9 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 9 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: BG3_TRX_N-ter_TRX_RNAi (DM35B_MF_V02)

description: TRX N-ter ChIP after TRX RNAi, Biological Rep 1-2


title: CpG ODN-3h-repeat 4 - mAdbID:88206

description: mAdb experiment ID: 88206

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.3; 3.59 Temperature: 29.35

source_name: CpG ODN - 3 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 3 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: Untreated-repeat 2 - mAdbID:88207

description: mAdb experiment ID: 88207

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.36; 4.05 Temperature: 27.91

source_name: Untreated BALB/c WT


title: CpG ODN-9h-repeat 4 - mAdbID:88229

description: mAdb experiment ID: 88229

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.39; 4.07 Temperature: 27.76


title: BG3_PC_PC_RNAi (DM35B_MF_V02)

description: PC ChIP after PC RNAi, Biological Rep 1-2

source_name: Anti PC (Poux et al., 2001) ChIP from ML-DmBG3-c2 chromatin

value: PC (Poux et al., 2001)

source_name: DNA isolated from matching input  ML-DmD23-c4 chromatin


title: CpG ODN-3h-repeat 3 - mAdbID:88205

description: mAdb experiment ID: 88205

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.36; 4.05 Temperature: 25.69


title: BG3_PC_wild_type_replicate_3 (DM35B_MF_V02)

description: PC ChIP, Biological Rep 3


title: CpG ODN-9h-repeat 3 - mAdbID:88228

description: mAdb experiment ID: 88228

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.34; 4.05 Temperature: 26.72


title: CpG ODN-24h-repeat 4 - mAdbID:88233

description: mAdb experiment ID: 88233

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.28; 3.59 Temperature: 28.52


title: CpG ODN-24h-repeat 2 - mAdbID:88231

description: mAdb experiment ID: 88231

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.48; 4.08 Temperature: 27.12


title: Untreated-repeat 3 - mAdbID:88174

description: mAdb experiment ID: 88174

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.66; 4.15 Temperature: 35.09


title: Untreated-repeat 1 - mAdbID:88172

description: mAdb experiment ID: 88172

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.29; 4.06 Temperature: 26.94


title: Untreated-repeat 4 - mAdbID:88163

description: mAdb experiment ID: 88163

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.67; 4.15 Temperature: 35.15


title: CpG ODN-9h-repeat 1 - mAdbID:88226

description: mAdb experiment ID: 88226

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.34; 4.05 Temperature: 26.17


title: CpG ODN-3h-repeat 2 - mAdbID:88224

description: mAdb experiment ID: 88224

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.56; 4.13 Temperature: 34.44


title: CpG ODN-3h-repeat 1 - mAdbID:88222

description: mAdb experiment ID: 88222

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100; 100 LaserPower: 3.42; 4.08 Temperature: 30.26


title: BG3_PC_TRX_RNAi (DM35B_MF_V02)

description: PC ChIP after TRX RNAi, Biological Rep 1-2

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G


title: BG3_E(Z) (DM35B_MF_V02)

description: E(Z) ChIP, Biological Rep 1-2

source_name: Anti E(Z) (Kahn et al., 2006) ChIP from ML-DmBG3-c2 chromatin

value: E(Z) (Kahn et al., 2006)


title: Untreated-repeat 6 - mAdbID:88176

description: mAdb experiment ID: 88176

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.23; 3.6 Temperature: 27.79


title: D23_H3K27me3 (DM35B_MF_V02)

description: H3K27me3 ChIP, Biological Rep 1-2

source_name: Anti H3K27me3 (AbCam) ChIP from ML-DmD23-c4 chromatin


title: Untreated-repeat 5 - mAdbID:88175

description: mAdb experiment ID: 88175

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.16; 3.64 Temperature: 25.32