title: seedlings, salt stress, 1h after treatment, replicate A

description: Replicate: A


title: Liver_PCN_PXR_rep5

status: Public on Nov 13 2008

type: RNA

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: Steroltalk V2 slides were washed before hybridization at room temperature 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. Samples were denatured and hybridized in 3xSSC and 0.2% SDS hybridization buffer at 65˚C for 16 hours using humidified hybridization chambers (HybChambers, GeneMachines). After hybridizations slides were washed at room temperature for 5 min in 2xSSC and 0.5% SDS, followed by 5 min in 0.5xSSC, then 5 min in 0.05xSSC and dried by centrifugation.

scan_protocol: Slides were scanned with Affimetrix 428 Array Scanner using Software Jaguar 2.0. Images were analyzed Gene Pix Pro 6.0 (Molecular Devices Corporation). The median feature and local background intensities were extracted together with the estimates of their standard deviation.

data_processing: Features were filtered out according to the following criteria: coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) above 0.5 and foreground to background ratio above 1.5. Saturated features were removed. Log2 ratios were normalized using LOESS fit to spike in control RNAs and housekeeping controls. Filtration and normalization was done in Orange software. Normalized log ratios can be compared across samples.

molecule: total RNA

organism: Mus musculus

source_name: Liver, PCN treated

label_protocol: Firefly luciferase (Promega) was added as an universal reference for microarray experiment. 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol.

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were maintained in 12-hour light/12-hour dark cycle.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). Spectrofotometer (Nanodrop) was used to monitor the quality of RNA. RNAs from 6 replicates were pooled and used for hybridization.

treatment_protocol: Animals were injected i.p. 40mg/kg PCN (5% DMSO in corn oil). After 12h they were sacrificed.

tag: Genetic background

value: PXR deficient

tag: Strain

tag: Gender

value: male

tag: Age

value: 9-12 weeks

tag: Tissue

value: liver

tag: Treatment

value: 40 mg/kg PCN

source_name: Liver, untreated PXR pool

treatment_protocol: Animals were injected i.p. wit vehicle (5% DMSO in corn oil). After 12h they were sacrificed.

value: 5% DMSO in corn oil


title: PBMCs_Control_paired_rep6 (HG-U133B)

status: Public on Nov 14 2008

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

country: USA

institute: Johns Hopkins University

description: PBMC's were isolated from 7 healthy NIH blood bank donors.

hyb_protocol: cRNA was hybridized to Affymetrix Human Genome-U133A and HG-U133B microarray chips according to the manufacturer’s instructions.  GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station Model 400.

scan_protocol: GeneChips were scanned by the HP-Affymetrix GeneArray Scanner using the manufacturer's protocol.

data_processing: The data were analyzed with Microarray Suite version 5 (MAS5) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean (2% trim at bottom and at top) target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Homo sapiens

source_name: PBMCs, Control, Sample 1769

label_protocol: Biotin-labeled cRNA was synthesized using the BioArray High Yield RNA transcript labeling kit (Enzo Life Sciences, Inc., Farmingdale, NY) Affymetrix).

growth_protocol: as described in Wendy T. Watford, et al., Tpl2 kinase regulates T cell interferon gamma production and host resistance to Toxoplasma gondii. Journal of Experimental Medicine.

extract_protocol: Cytokine-stimulated cells were lysed in RNeasy lysis buffer (Qiagen, Valencia, CA) and total RNA was isolated with the Qiagen RNeasy Midi kit using the standard protocol. RNA was purified using Trizol (Invitrogen Life Technologies, Carlsbad, CA) and chloroform, followed by ethanol precipitation.

value: male, Race:Black


title: seedlings, salt stress, 1h after treatment, replicate C

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: Replicate: C

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing: Data were quantile normalized and repetitive probes were deleted (see Laubinger et al., 2008, for details)

organism: Arabidopsis thaliana

source_name: seedling, 7d

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: 1h after transfer to liquid MS with 150mM NaCl, LL, 0.5MS + 1% sucrose, 23°C, 7 days

tag: Arabidopsis (Col)


title: seedlings, ABA treatment, 1h after treatment, replicate A

description: Replicate: A

treatment_protocol: 1h after transfer to liquid MS with 100µM ABA, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: Liver_PCN_PXR_rep3

description: No additional data.


title: Liver_PCN_PXR_rep2

description: No additional data.


title: Liver_PCN_CAR/PXR_rep4

description: No additional data.

value: CAR/PXR deficient

source_name: Liver, untreated CAR/PXR pool


title: Liver_PCN_PXR_rep1

description: No additional data.


title: Liver_PCN_PXR_rep4

description: No additional data.


title: Liver_PCN_CAR/PXR_rep5

description: No additional data.


title: PBMCs_IL12_paired_rep2 (HG-U133B)

source_name: PBMCs, IL12, Sample 546

treatment_protocol: as described in Wendy T. Watford, et al., Tpl2 kinase regulates T cell interferon gamma production and host resistance to Toxoplasma gondii. Journal of Experimental Medicine.

value: female, Race:Caucasian


title: Liver_PCN_PXR_rep6

description: No additional data.


title: Liver_PCN_CAR/PXR_rep6

description: No additional data.


title: Liver_PCN_CAR/PXR_rep3

description: No additional data.


title: Liver_PCN_CAR_rep3

description: No additional data.

value: CAR deficient

source_name: Liver, untreated CAR pool


title: Liver_PCN_CAR_rep4

description: No additional data.


title: Liver_PCN_CAR/PXR_rep1

description: No additional data.


title: Liver_PCN_CAR/PXR_rep2

description: No additional data.


title: PBMCs_Control_paired_rep5 (HG-U133B)

source_name: PBMCs, Control, Sample 635


title: PBMCs_IL12_paired_rep5 (HG-U133B)

source_name: PBMCs, IL12, Sample 635


title: Liver_PCN_CAR_rep6

description: No additional data.


title: Liver_PCN_CAR_rep2

description: No additional data.


title: PBMCs_Control_paired_rep2 (HG-U133B)

source_name: PBMCs, Control, Sample 546


title: Liver_PCN_CAR_rep5

description: No additional data.


title: Liver_PCN_CAR_rep1

description: No additional data.


title: PBMCs_IL12_paired_rep3 (HG-U133B)

source_name: PBMCs, IL12, Sample 1193

value: male, Race:Caucasian


title: Liver_PCN_WT_rep6

description: No additional data.

value: wild type

source_name: Liver, untreated WT pool


title: Liver_PCN_WT_rep5

description: No additional data.


title: Liver_PCN_WT_rep4

description: No additional data.


title: Liver_PCN_WT_rep3

description: No additional data.


title: PBMCs_Control_paired_rep3 (HG-U133B)

source_name: PBMCs, Control, Sample 1193


title: Liver_PCN_WT_rep2

description: No additional data.

source_name: Liver, PCN-treated

source_name: Liver_untreated WT pool


title: PBMCs_Control_paired_rep1 (HG-U133B)

source_name: PBMCs, Control, Sample 541

value: male, Race:Asian


title: PBMCs_Control_paired_rep4 (HG-U133B)

source_name: PBMCs, Control, Sample 2115


title: PBMCs_IL12_paired_rep4 (HG-U133B)

source_name: PBMCs, IL12, Sample 2115


title: PBMCs_IL12_paired_rep1 (HG-U133B)

source_name: PBMCs, IL12, Sample 541


title: seedlings, ABA treatment, 12h after treatment, replicate A

description: Replicate: A

treatment_protocol: 12h after transfer to liquid MS with 100µM ABA, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: Liver_PCN_WT_rep1

description: No additional data.


title: Pima S-7 Fiber 2 DPA (58043)

city: Athens

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

description: Pima S-7 Fiber 2 DPA (58043)

hyb_protocol: Hybridization by NimbleGen

scan_protocol: Scanning by NimbleGen

data_processing: The procedure for spot detection was performed by NimbleGen.  All values of the 42,429 genes with 7 redundant probes per gene were median polished with Tukey's biweight prior to performing a standard mixed linear model (LM) analysis of the data for expression differences between each fiber developmental stage within and between accessions of G. barbadense.

organism: Gossypium barbadense

source_name: Fiber 2 DPA

label_protocol: Labelling by NimbleGen

extract_protocol: Hot-borate / Li precipitation method("Wilkins and Smart, 1996")

tag: Genome

tag: Polyploid level

tag: Tissue & age

value: Fiber 2 DPA

tag: Soil type

value: Bessey Mix

tag: Soil mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: Date planted

tag: Planting location

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

tag: Average temperature (C)

value: 80 daytime - 70 nighttime

tag: Day light regime

value: ambient daylight

tag: Light sources

value: sun and 10 hour day sodium supplemental lighting

tag: Night duration

value: natural

tag: Age at harvest

value: 20 weeks

tag: Developmental stage at harvest

value: Mature plant

tag: Harvest time(hours after daybreak)

tag: Harvested tissue type

value: Fiber

tag: Number of plants harvested


title: Pima S-7 Fiber 20 DPA (58039)

description: Pima S-7 Fiber 20 DPA (58039)

source_name: Fiber 20 DPA

value: Fiber 20 DPA


title: Pima S-7 Fiber 2 DPA (58042)

description: Pima S-7 Fiber 2 DPA (58042)


title: Pima S-7 Fiber 20 DPA (58038)

description: Pima S-7 Fiber 20 DPA (58038)


title: Pima S-7 Fiber 20 DPA (58040)

description: Pima S-7 Fiber 20 DPA (58040)


title: Pima S-7 Fiber 10 DPA (58037)

description: Pima S-7 Fiber 10 DPA (58037)

source_name: Fiber 10 DPA

value: Fiber 10 DPA


title: non-bloodfed female carcass vs. bloodfed female carcass rep 2

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: Agilent

hyb_protocol: Agilent

scan_protocol: AXON

data_processing: GENEPIX

organism: Anopheles gambiae

source_name: non-bloodfed female carcass

label_protocol: Agilent

extract_protocol: QIAGEN

treatment_protocol: dark

tag: female carcass

source_name: bloodfed female carcass

treatment_protocol: 2 hr light


title: K101 Fiber 2 DPA (58034)

description: K101 Fiber 2 DPA (58034)

tag: Genome


title: Pima S-7 Fiber 10 DPA (58036)

description: Pima S-7 Fiber 10 DPA (58036)

tag: Polyploid level


title: Pima S-7 Fiber 2 DPA (58041)

description: Pima S-7 Fiber 2 DPA (58041)

tag: Tissue & age


title: Pima S-7 Fiber 10 DPA (58035)

description: Pima S-7 Fiber 10 DPA (58035)

tag: Soil type


title: K101 Fiber 2 DPA (58032)

description: K101 Fiber 2 DPA (58032)

tag: Soil mix


title: non-bloodfed female carcass vs. bloodfed female carcass rep 3

description: Agilent


title: non-bloodfed female carcass vs. bloodfed female carcass rep 1

description: Agilent

tag: non-bloodfed female carcass


title: K101 Fiber 20 DPA (58031)

description: K101 Fiber 20 DPA (58031)

tag: Date planted

tag: Planting location


title: non-bloodfed female head vs. bloodfed female head rep 3

description: Agilent

source_name: non-bloodfed female head

tag: female head

source_name: bloodfed female head


title: non-bloodfed female head vs. bloodfed female head rep 1

description: Agilent

tag: Adult female head


title: K101 Fiber 20 DPA (58030)

description: K101 Fiber 20 DPA (58030)

tag: Average temperature (C)

tag: Day light regime

tag: Light sources

tag: Night duration


title: K101 Fiber 20 DPA (58029)

description: K101 Fiber 20 DPA (58029)

tag: Age at harvest

tag: Developmental stage at harvest

tag: Harvest time(hours after daybreak)

tag: Harvested tissue type


title: non-bloodfed female head vs. bloodfed female head rep 2

description: Agilent


title: non-light stimulated male head vs. 2 min light stimulated male head at -30 min rep 2

description: Agilent

source_name: non-light stimulated male head

tag: Adult male head


title: T24 THP-1 infection, Microarray #2 second replicate

type: mixed

city: Montreal

first: Sébastien

middle: P

last: Faucher

state: QUEBEC

address: C.P. 6128 Succ. Centre-Ville

department: Microbiology and Immunology

country: Canada

institute: University of Montreal

description: This sample to study the effect of human macrophages phagocytosis on the global transcriptome of EDL933 at different time

hyb_protocol: Dry the probe and then resuspend in 80ul of DIG 37°C for the Cy3 and Cy5 sample. Place the mixed probe at 95°C, 5 min and then chilled on ice 5 min. Depose the mixed probe on the microarray, cover with a cover-slip and place in an corning hybridation chamber.

scan_protocol: Slide was scanned with Scan Array Lite (Perkin-Elmer) using Scan Array Express 2.1 software.

data_processing: After backgroud correction and total intensity normalization, ratio to reference were calculated and log base 2 transformed

organism: Escherichia coli

source_name: 3XSCOTS cDNA 24 h post-infection

label_protocol: Bioprime DNA labeling kit Invitrogen

extract_protocol: TRIzol reagent (Gibco BRL) was used according to the manufacturer instruction. RNA was treated with DNase (Ambion). RNA sample was converted to cDNA in 5 independent reverse-transcription reactions as described previously (Graham, J. 1999. PNAS 96:11554-559). Bacterial transcript were purified from host transcript by using 3 round of the SCOTS procedure (Daigle, F. 2002. Methods Enzymol. 358:108-122).

tag: EDL933 cDNA 24 h post-infcetion of THP-1 human cells

molecule: genomic DNA

source_name: REference genomic DNA

label_protocol: Bioprime DNA labelin kit Invitrogen

extract_protocol: Genomic DNA was extracted by standard phenol-chloroform method (Sambrook, J, Molecular Cloning, 3rd Edition)

tag: EDL933 genomic DNA


title: seedlings, mock control, 12h after treatment, replicate C

description: Replicate: C

source_name: seedling, 7d

treatment_protocol: 12h after transfer to liquid MS, LL, 0.5MS + 1% sucrose, 23°C, 7 days

tag: Arabidopsis (Col)


title: T24 THP-1 infection, Microarray #2 first replicate

source_name: 3XSCOTS cDNA obtained 24 h post-infection

tag: EDL933 cDNA obtained 24h post-infection of THP-1 human cells

source_name: Reference genomic DNA


title: K101 Fiber 10 DPA (58028)

description: K101 Fiber 10 DPA (58028)

tag: Genome

tag: Polyploid level

tag: Tissue & age

tag: Soil type

tag: Soil mix

tag: Date planted

tag: Number of plants harvested


title: seedlings, mock control, 12h after treatment, replicate B

description: Replicate: B


title: non-light stimulated male head vs. non-light stimulated female head rep 2

description: Agilent

source_name: non-light stimulated female head

tag: Adult female head


title: non-light stimulated male head vs. 2 min light stimulated male head at -30 min rep 1

description: Agilent


title: K101 Fiber 10 DPA (58027)

description: K101 Fiber 10 DPA (58027)

tag: Planting location

tag: Average temperature (C)

tag: Day light regime

tag: Light sources

tag: Night duration

tag: Age at harvest


title: T24 THP-1 infection, Microarray #1 second replicate

tag: EDL933 cDNA obtained 24 h post- infection of THP-1 human cells

tag: EDL933 genomic DNA


title: seedlings, mock control, 1h after treatment, replicate B

description: Replicate: B

treatment_protocol: 1h after transfer to liquid MS, LL, 0.5MS + 1% sucrose, 23°C, 7 days

tag: Arabidopsis (Col)


title: non-light stimulated male head vs. non-light stimulated female head rep 3

description: Agilent

tag: Adult male head


title: non-light stimulated male head vs. 2 min light stimulated male head at -30 min rep 3

description: Agilent


title: T8 THP-1 infection, Microarray #2 second replicate

source_name: 3XSCOTS cDNA obtained 8h post-infection

tag: EDL933 8h post THP-1 infection

tag: EDL933 genommic DNA


title: K101 Fiber 2 DPA (58033)

description: K101 Fiber 2 DPA (58033)

tag: Genome

tag: Polyploid level

tag: Tissue & age

tag: Soil type

tag: Developmental stage at harvest

tag: Harvest time(hours after daybreak)

tag: Harvested tissue type


title: T8 THP-1 infection, Microarray #1 second replicate

tag: EDL933 in humans macrophages 8h post-infection


title: T24 THP-1 infection, Microarray #1 first replicate

tag: EDL933 24 h post infection in THP-1 humans cells


title: non-light stimulated male head vs. non-light stimulated female head rep 1

description: Agilent

tag: Adult female head


title: 2 min light stimulated male head at -30 min vs. 2 min light stimulated female head at -30 min rep 1

description: Agilent


title: seedlings, mock control, 12h after treatment, replicate A

description: Replicate: A


title: seedlings, mock control, 1h after treatment, replicate C

description: Replicate: C


title: 2 min light stimulated male head at -30 min vs. 2 min light stimulated female head at -30 min rep 3

description: Agilent


title: T8 THP-1 infection, Microarray #1 first replicate

source_name: 3XSCOTS cDNA obtained after 8h post-infection

tag: EDL933 8h post-infection in THP-1 human cells

source_name: Reference DNA genomic DNA

tag: EDL933 from overnight culture in LB broth


title: T2 THP-1 infection, Microarray #2 first replicate

description: This sample was used as a reference to an experiment of the effect of human macrophages phagocytosis on the global transcriptome of EDL933

source_name: 3XSCOTS cDNA obtained 2h post-infection

tag: EDL933 infection of THP-1 cells, recovered 2h post-infection

growth_protocol: EDL933 from overnight culture in LB broth

tag: EDL933 genomic DNA


title: non-light stimulated female head vs. 2 min light stimulated female head at -30 min rep 2

description: Agilent

tag: adult female head


title: T8 THP-1 infection, Microarray #2 first replicate

tag: EDL933 in THP-1 cells 8h post-infection


title: T2 THP-1 infection, Microarray #2 second replicate

tag: EDL933 infection of THP-1 cells, recovered 2 h post-infection


title: non-light stimulated female head vs. 2 min light stimulated female head at -30 min rep 1

description: Agilent


title: T2 THP-1 infection, Microarray #1 second replicate


title: non-light stimulated vs. 2 min light stimulated  at -30 min rep 3

description: Agilent

source_name: non-light stimulated

tag: adult female

source_name: 2 min light stimulated  at -30 min


title: non-light stimulated female head vs. 2 min light stimulated female head at -30 min rep 3

description: Agilent


title: non-light stimulated vs. 2 min light stimulated  at -30 min rep 2

description: Agilent


title: Cerebellar cortex 40 Control

status: Public on Nov 12 2008

city: Santa Fe

first: Stephen

last: Kingsmore

state: NM

address: 2935 Rodeo Park Drive East

institute: National Center for Genome Resources

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Read Alignment-based gene expression profiling: Reads were aligned to the human genome and RefSeq transcript databases (Pruitt et al., 2005) using the algorithm GMAP (Wu and Watanabe, 2005) and the software system Alpheus (Sugarbaker et al., 2008), with adjustments for short SBS reads (oligomer overlap interval = 3nt, identities > 34/36 or 94%). Only the highest scoring alignment(s) was retained. Reads with a single best alignment or with equally good alignments to alternative transcripts of the same gene were considered uniquely aligned.  Aligned read frequencies (per million aligned reads) were calculated for each sample and gene using Alpheus (Sugarbaker et al., 2008).   read frequencies were log10 transformed prior to evaluation of inter-sample differences.

label: not applicable

molecule: polyA RNA

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 40

label_protocol: not applicable

extract_protocol: Sample preparation: was as previously described (Paz et al., 2006; Bullock et al., In Press).  Cerebellar samples were from 14 patients with a diagnosis of SCZ according to DSM-IV criteria and six controls.  Samples were obtained from the Maryland Brain Collection with the permission of the Maryland Brain Collection Steering Committee.  Permission for the study of brain tissue was provided by families in accordance with the guidelines of the Uniform Anatomical Gift Act.  Approval for the study was obtained from the Institutional Review Board of the University of Maryland.  Cortical areas corresponding to crus I/VIIa of cerebellar hemispheres were dissected at -20 ºC and frozen at -80 ºC, as described (Bullock et al., In Press). The average pH of the samples was 6.6 + 0.17.  Cerebellum specimens were obtained according to NIH guidelines for confidentially and privacy. Genomic DNA and total RNA were isolated from samples using standard techniques (Qiagen, Valencia, CA).

tag: Sample

tag: Diagnosis

value: Control

tag: Age (Years)

tag: Race

value: Caucasian

tag: Death Cause

value: ASCVD

tag: Treatment

tag: Post Mortem Interval

value: 20 hours

tag: Brain pH


title: Cerebellar cortex 2S Control

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 2S

value: 22 hours


title: Cerebellar cortex 17 Control

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 17

value: SAH

value: 19 hours


title: seedlings before treatment, replicate B

description: Replicate: B

treatment_protocol: 0.5MS + 1% sucrose, 23°C, 7 days, before transfer

tag: Arabidopsis (Col)


title: non-light stimulated vs. 2 min light stimulated  at -30 min rep 1

description: Agilent


title: Cerebellar cortex 5 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 5

value: SCZD

value: Intoxication

value: Thioridazine

value: 16 hours


title: Cerebellar cortex 6S Control

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 6S

value: Arrhythmia

value: 17 hours


title: 7B12 Treated 3

city: Zurich

first: Laura

last: Montani

address: Winterthurerstrasse 190

department: Neuromorphology

country: Switzerland

institute: Brain Research Institute - UZH/ETHZ - Zurich

hyb_protocol: The biotinylated cRNA sample (10µg) was fragmented ramdomly to 35-200 bp at 94°C in Fragmentation Buffer (Affymetrix, Santa Clara, CA, US) and mixed in 300µl of Hybridization Buffer containing a hybridization control cRNA and Control Oligo B2 (Affymetrix, Santa Clara, CA, US), 0.1mg/ml herring sperm DNA and 0.5mg/ml acytilated bovina serum albumin in a 2-(4-morpholino)-ethane sulfonic acid (MES), pH 6.7 before hybridization to GeneChip® Rat Expression Array 230 2.0 (Affymetrix, Santa Clara, CA) for 16h at 45°C. The arrays was then washed using a Affymetrix Fluidics Station 450 FS450_0001 protocol.

scan_protocol: An Affymetrix GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Raw data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix, Santa Clara, CA, US). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm. To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm. The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spikein controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).

label: Biotin

organism: Rattus norvegicus

source_name: Hippocampal Slice Cultures, 7B12 (anti Nogo-A antibody) Treated

label_protocol: Total RNA extracted was then reverse-transcribed into cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA, US). The double stranded cDNA was purified with a Sample Clean-Up Module (Affymetrix, Santa Clara, CA, US). The purified double-stranded cDNA was in vitro transcribed in the presence of biotin-labeled nucleotides using and IVT Labeling Kit (Affymetrix, Santa Clara, CA, US). The biotinylated cRNA was purified using a Sample Clean-Up Module (Affymetrix, Santa Clara, CA, US) and its quality and quantity was assessed using a NanoDrop ND 1000 (NanoDrop Technologies, ThermoFisher Scientific, MA, US) and a Bioanalyzer 2100 (Agilent, CA, US).

growth_protocol: Hippocampal slices were cultured as previously described (Stoppini et al., 1991). Briefly, the hippocampus of P7 Wistar rats (bred in house) was dissected and immediately cut into 350 µm thick slices. Slices were separated in ice cold dissecting medium and then 4 slices were placed into a Millicel-CM insert (Millipore, MA, USA) with 1 ml of culture medium and placed into 6 well plates (TPP, Switzerland). Cultures were kept for 26 days at 33ºC, in a 5% CO2 atmosphere.

extract_protocol: 24 cultures were pooled together and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol, with the addition of an on-column DNaseI digestion step to more efficiently remove remaining DNA contamination. Quantity and quality of the extracted RNA were determined using a NanoDrop ND 1000 (NanoDrop Technologies, ThermoFisher Scientific, MA, US) and a Bioanalyzer 2100 (Agilent, CA, US). Only RNA samples with an integrity index > 9.0 have been used.

treatment_protocol: At DIV 21, 7B12 (mouse monoclonal antibody directed against rat aa 763–820 of Nogo-A, produced by Novartis, Basel, Switzerland) was applied at a concentration of 3ug/ml in the culture medium for a period of 5 days (medium was changed every 2 days).

tag: Strain

value: Wistar Age:P7 Tissue:Hippocampus Cultures:Hippocampal slice cultures Time in culture before collection of the samples:26 DIV Number of pooled cultures for this sample:24


title: seedlings, mock control, 1h after treatment, replicate A

description: Replicate: A


title: non-light stimulated vs. 2 hr light stimulated rep 2

description: Agilent

source_name: 2 hr light stimulated


title: seedlings before treatment, replicate A

description: Replicate: A

source_name: seedling, 7d


title: 7B12 Treated 2


title: non-light stimulated vs. 2 hr light stimulated rep 1

description: Agilent

tag: whole adult female mosquito


title: Cerebellar cortex 35 Control

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 35

value: African American

value: Obesity

value: 14 hours


title: Non-adherent cells pool vs. Adherent cells pool

city: Dresden

first: Nael

last: Alakel

address: Fetscherstrasse 74

institute: university hospital Dresden

description: All samples were shipped to Miltenyi Biotec (Bergisch Gladbach, Germany) which performed RNA extraction, RNA quality control, Hybridization of Agilent Whole Genome Oligo Microarrays, Fluorescence signals scanning and data analysis.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver® gene expression data analysis system (Rosetta Biosoftware).

source_name: Non-adherent cells pool

label_protocol: the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Hematopoietic stem cells (HSCs) were suspended in HSC serum-free medium supplemented with 150 ng/ml Fetal Liver Tyrosine Kinase-3 ligand (FLT3-L), 150 ng/ml stem cell factor (SCF) and 50 ng/ml IL-3 for one week

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin® RNA II, Macherey-Nagel)

tag: Non-adherent cells after one HSCs co-culture on MSCs feeder layer

source_name: Adherent cells pool

tag: Adherent cells after one HSCs co-culture on MSCs feeder layer


title: Cerebellar cortex 42 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 42

value: Apendicitis

value: Olanzapine

value: 12 hours


title: Cerebellar cortex 41 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 41

value: Caucasian

value: Suicide

value: Risperidone


title: Cerebellar cortex 36 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 36

value: Embolism

value: Haloperidol

value: 13 hours


title: Cerebellar cortex 5S Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 5S

value: SCZD

value: Tuberculosis

value: Trilafon

value: 21 hours


title: Cerebellar cortex 7S Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 7S

value: Clozapine

value: 7 hours


title: Cerebellar cortex 8S Control

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 8S

value: Control

value: African American

value: Asthma


title: Cerebellar cortex 31 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 31

value: ASCVD

value: Olanzapine

value: 20 hours


title: non-light stimulated vs. 2 hr light stimulated rep 3

description: Agilent

source_name: non-light stimulated


title: K101 Fiber 10 DPA (58026)

description: K101 Fiber 10 DPA (58026)

source_name: Fiber 10 DPA

tag: Genome

tag: Polyploid level

tag: Tissue & age

value: Fiber 10 DPA

tag: Soil type

value: Bessey Mix

tag: Soil mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: Date planted

tag: Planting location

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

tag: Average temperature (C)

value: 80 daytime - 70 nighttime

tag: Day light regime

value: ambient daylight

tag: Light sources

value: sun and 10 hour day sodium supplemental lighting

tag: Night duration

value: natural

tag: Age at harvest

value: 20 weeks

tag: Developmental stage at harvest

value: Mature plant

tag: Harvest time(hours after daybreak)

tag: Harvested tissue type

value: Fiber

tag: Number of plants harvested


title: Cerebellar cortex 39 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 39

tag: Sample

tag: Diagnosis

value: SCZD

tag: Age (Years)

tag: Race

tag: Death Cause

tag: Treatment

value: Clozapine

tag: Post Mortem Interval

value: 14 hours

tag: Brain pH


title: 11C7 Treated 2

source_name: Hippocampal Slice Cultures, 11C7 (anti Nogo-A antibody) Treated

treatment_protocol: At DIV 21, 11C7 (mouse monoclonal antibody directed against rat aa 623–640 of Nogo-A, produced by Novartis, Basel, Switzerland) was applied at a concentration of 3ug/ml in the culture medium for a period of 5 days (medium was changed every 2 days).

tag: Strain

value: Wistar Age:P7 Tissue:Hippocampus Cultures:Hippocampal slice cultures Time in culture before collection of the samples:26 DIV Number of pooled cultures for this sample:24


title: IgG Treated 3

source_name: Hippocampal Slice Cultures, IgG (control) Treated

treatment_protocol: At DIV 21, control monoclonal antibody against wheat auxin was applied as highly purified IgG at a concentration of 3ug/ml in the culture medium for a period of 5 days (medium was changed every 2 days).


title: 11C7 Treated 1


title: Cerebellar cortex 3S Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 3S

value: African American

value: Asphyxia

value: Prolixin

value: 6 hours


title: Cerebellar cortex 2 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 2

value: ASCVD

value: Haloperidol


title: 7B12 Treated 1

source_name: Hippocampal Slice Cultures, 7B12 (anti Nogo-A antibody) Treated


title: IgG Treated 2


title: 11C7 Treated 3


title: IgG Treated 1


title: seedlings before treatment, replicate C

description: Replicate: C

source_name: seedling, 7d

tag: Arabidopsis (Col)


title: Not Treated 1

source_name: Hippocampal Slice Cultures, Not Treated

treatment_protocol: Not treated sample


title: Cerebellar cortex 18 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 18

value: Caucasian

value: Suicide

value: Olanzapine


title: T2 THP-1 infection, Microarray #1 first replicate

source_name: 3XSCOTS cDNA obtained 2h post-infection

tag: EDL933 infection of THP-1 cells, recovered 2h post-infection

source_name: Reference genomic DNA

tag: Genomic DNA from EDL933


title: Cerebellar cortex 11S Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 11S

value: Pneumonia

value: Chlorpromazine

value: 5 hours


title: Cerebellar cortex 1S Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 1S

value: Perphenazine

value: 11 hours


title: RPMI 2A, Microarray #2, first replicate

source_name: 3XSCOTS cDNA obtained in RPMI medium

tag: EDL933 in RPMI medium

tag: EDL933 genomic DNA


title: RPMI 2B, Microarray #2 second replicate

source_name: 3XSCOTS cDNA in RPMI medium

tag: Genomic DNA of EDL933


title: RC94_1

status: Public on Nov 11 2008

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC94

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.

source_name: Human B-cell chronic lymphocytic leukemia patient RC94

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: Legend

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

tag: Sex

value: M; VH status:unmut


title: RC88_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC88

source_name: Human B-cell chronic lymphocytic leukemia patient RC88


title: TS7_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS7

source_name: Human B-cell chronic lymphocytic leukemia patient TS7


title: Not Treated 3

value: Wistar Age:P7 Tissue:Hippocampus Cultures:Hippocampal slice cultures Time in culture before collection of the samples:26 DIV Number of pooled cultures for this sample:24


title: Cerebellar cortex 1 Schizophrenia

source_name: post-mortem crus I/VIIa of cerebellar cortex, sample 1

tag: Sample

value: SCZD

value: African American

value: 12 hours


title: RC89_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC89

source_name: Human B-cell chronic lymphocytic leukemia patient RC89


title: RC87_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC87

source_name: Human B-cell chronic lymphocytic leukemia patient RC87


title: Not Treated 2

source_name: Rattus norvegicus


title: RC5_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC5

source_name: Human B-cell chronic lymphocytic leukemia patient RC5


title: RC84_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC84

source_name: Human B-cell chronic lymphocytic leukemia patient RC84


title: RC81_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC81

source_name: Human B-cell chronic lymphocytic leukemia patient RC81


title: TS12_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS12

source_name: Human B-cell chronic lymphocytic leukemia patient TS12

value: F; VH status:unmut


title: RC7_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC7

source_name: Human B-cell chronic lymphocytic leukemia patient RC7


title: RC92_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC92

source_name: Human B-cell chronic lymphocytic leukemia patient RC92


title: TS3_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS3

source_name: Human B-cell chronic lymphocytic leukemia patient TS3


title: ada2rlr vs. ada2wt (array2)

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

institute: University of Western Ontario

description: Experiment was performed to analyze the effects of a mutant ada2 allele on gene expression. This array is one of three dye-swapped replicates.

hyb_protocol: Hybridization was performed at MOgene LC (St. Louis, MO). Labeled material was fragmented according to the protocol described in the Agilent processing manual and hybridized overnight with the array in a rotating oven at 60 degrees Celsius in an ozone-free environment. Wash conditions used were as outlined in the Agilent processing manual.

scan_protocol: Scanning was performed at MOgene LC (St. Louis, MO) using an Agilent scanner.

data_processing: Data processing was performed at MOgene LC (St. Louis, MO). Feature extraction, normalization and background subtraction of reported values were performed using Agilent software.

organism: Saccharomyces cerevisiae

source_name: Cy3: BY4842(ada2delta) with HA-Ada2_rlr on a URA3 cen plasmid

label_protocol: Labeling was performed at MOgene LC (St. Louis, MO). Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies). 1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.). The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.). All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.

extract_protocol: RNA extraction was performed as described in Mutiu AI, and Brandl CJ (2005) RNA isolation from yeast using silica matrices. J Biomol Tech 16:316-317.

tag: Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.

source_name: Cy5: BY4842(ada2delta) with HA-Ada2_wt on a URA3 cen plasmid


title: RC77_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC77

source_name: Human B-cell chronic lymphocytic leukemia patient RC77


title: ada2wt vs. ada2rlr (array3)

source_name: Cy3: BY4842(ada2delta) with HA-Ada2_wt on a URA3 cen plasmid

source_name: Cy5: BY4842(ada2delta) with HA-Ada2_rlr on a URA3 cen plasmid


title: ada2wt vs. ada2rlr (array1)


title: RPMI 1B, Microarray #1 second replicate

source_name: 3XSCOTS cDNA obtained in RPMI medium

source_name: Reference genomic DNA


title: RPMI 1A, Microarray #1 first duplicate

source_name: 3XSCOTS cDNA obtained in RPMI

tag: Genomic DNA E. coli EDL933


title: RC23_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC23

source_name: Human B-cell chronic lymphocytic leukemia patient RC23


title: RC24_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC24

source_name: Human B-cell chronic lymphocytic leukemia patient RC24


title: RC22_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC22

source_name: Human B-cell chronic lymphocytic leukemia patient RC22


title: GE88_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE88

source_name: Human B-cell chronic lymphocytic leukemia patient GE88


title: GE99_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE99

source_name: Human B-cell chronic lymphocytic leukemia patient GE99


title: GE114_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE114

source_name: Human B-cell chronic lymphocytic leukemia patient GE114


title: RC33_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC33

source_name: Human B-cell chronic lymphocytic leukemia patient RC33


title: RC14_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC14

source_name: Human B-cell chronic lymphocytic leukemia patient RC14


title: GE116_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE116

source_name: Human B-cell chronic lymphocytic leukemia patient GE116


title: GE144_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE144

source_name: Human B-cell chronic lymphocytic leukemia patient GE144


title: GE101_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE101

source_name: Human B-cell chronic lymphocytic leukemia patient GE101


title: RC21_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC21

source_name: Human B-cell chronic lymphocytic leukemia patient RC21


title: RC1_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC1

source_name: Human B-cell chronic lymphocytic leukemia patient RC1


title: GE173_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE173

source_name: Human B-cell chronic lymphocytic leukemia patient GE173


title: GE107_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE107

source_name: Human B-cell chronic lymphocytic leukemia patient GE107


title: TS18_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS18

source_name: Human B-cell chronic lymphocytic leukemia patient TS18

value: F; VH status:mut


title: GE163_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE163

source_name: Human B-cell chronic lymphocytic leukemia patient GE163


title: GE111_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE111

source_name: Human B-cell chronic lymphocytic leukemia patient GE111


title: RC9_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC9

source_name: Human B-cell chronic lymphocytic leukemia patient RC9


title: RC93_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC93

source_name: Human B-cell chronic lymphocytic leukemia patient RC93


title: GE87_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE87

source_name: Human B-cell chronic lymphocytic leukemia patient GE87


title: GE227_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE227

source_name: Human B-cell chronic lymphocytic leukemia patient GE227


title: CS12_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CS12

source_name: Human B-cell chronic lymphocytic leukemia patient CS12


title: GE130_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE130

source_name: Human B-cell chronic lymphocytic leukemia patient GE130


title: TS21_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS21

source_name: Human B-cell chronic lymphocytic leukemia patient TS21


title: GE161_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE161

source_name: Human B-cell chronic lymphocytic leukemia patient GE161


title: RC95_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC95

source_name: Human B-cell chronic lymphocytic leukemia patient RC95


title: RC73_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC73

source_name: Human B-cell chronic lymphocytic leukemia patient RC73


title: RC3_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC3

source_name: Human B-cell chronic lymphocytic leukemia patient RC3

value: M; VH status:mut


title: RC4_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC4

source_name: Human B-cell chronic lymphocytic leukemia patient RC4


title: RC17_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC17

source_name: Human B-cell chronic lymphocytic leukemia patient RC17


title: RC20_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC20

source_name: Human B-cell chronic lymphocytic leukemia patient RC20


title: RC12_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC12

source_name: Human B-cell chronic lymphocytic leukemia patient RC12


title: RC10_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC10

source_name: Human B-cell chronic lymphocytic leukemia patient RC10


title: RC16_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC16

source_name: Human B-cell chronic lymphocytic leukemia patient RC16


title: RC13_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC13

source_name: Human B-cell chronic lymphocytic leukemia patient RC13


title: KMS-34_GWP

type: genomic

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-34

hyb_protocol: Following fragmentation, 90 micrograms of biotin-labeled DNA were hybridized for 16 hr at 49°C on GeneChip® Human Mapping 250K NspI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 250K NspI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Genome-wide DNA profiling was performed on Affymetrix GeneChip® Human Mapping 250k Nsp arrays. To find the corresponding CN values, we firstly extracted the raw data from the CEL files using the Affymetrix packages GTYPE 4.1 and Copy Number Analysis Tool 4.0.1 (Affymetrix, Santa Clara, CA, USA) and the Mapping Array 250k Nsp probe annotations released on July, 12 2007. In order to keep only the raw data and thus to avoid the CN inference facility of the latter software package, the Hidden Markov Model Genomic Smoothing window was set to 0. After the preprocessing, piecewise constant estimates of the underlying local DNA CN variation was calculated using the DNA copy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).

The VALUE column described as "HmmMedianLog2Ratio - Genomic Bandwith Smoothing 0 Mb" is the result displayed by CNAT4.0.1 software (Affymetrix) when applying Hidden Markov Model algorithm. The Log2Ratio is the base-2 logarithm applied to the ratio between the CEL-extracted probe values in our samples and in a dataset of 48 normal samples belonging to HapMap Project and freely available on Affymetrix website http://www.affymetrix.com/support/technical/sample_data/500k_data.affx. The Genomic Smoothing Window was set to zero in order to extract raw data.

source_name: Human Myeloma Cell Line KMS-34

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol starting from 250 nanograms of genomic DNA.

extract_protocol: Genomic DNA extraction was performed using Wizard® Genomic DNA Purification kit according to the manufacturer's instructions (Promega).

treatment_protocol: The Human Myeloma Cell Lines were obtained from DMSZ-German collection of Microorganisms and Cell Culture, Germany (NCI-H929, OPM2, JJN3, RPMI-8226, and KMS-12); or kindly provided by Dr. T. Otsuki, Kawasaki Medical School, Okayama, Japan (KMS-28, KMS-34, KMS-18, KMS-11, KMS-26, KMS-27, KMM-1 and KMS-20); Dr S. Iida, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan (KM4, FR4, and AMO1), and Dr. F. Malavasi, Department of Genetics, University of Torino, Italy (LP-1); or were established in our laboratory (CMA-01, CMA-02 and CMA-03) [Verdelli D et al.; Haematologica 2005, 90: 1541-1548]. They were cultured in Iscove’s modified Dulbecco’s medium supplemented with 10% fetal calf serum at concentrations ranging from 3×105 to 8×105, at 37°C in a 5% CO2 humidified atmosphere. CMA-01, CMA-02 and CMA-03 were cultured in presence of 20U/ml recombinant human IL-6 (R&D System, Minneapolis, MN, USA).

tag: Human Myeloma Cell Line KMS-34


title: GE126_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE126

source_name: Human B-cell chronic lymphocytic leukemia patient GE126


title: KMS-28_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-28

source_name: Human Myeloma Cell Line KMS-28

tag: Human Myeloma Cell Line KMS-28


title: OPM2_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line OPM2

source_name: Human Myeloma Cell Line OPM2

tag: Human Myeloma Cell Line OPM2


title: RPMI-8226_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line RPMI-8226

source_name: Human Myeloma Cell Line RPMI-8226

tag: Human Myeloma Cell Line RPMI-8226


title: KMS-12_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-12

source_name: Human Myeloma Cell Line KMS-12

tag: Human Myeloma Cell Line KMS-12


title: KMS-27_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-27

source_name: Human Myeloma Cell Line KMS-27

tag: Human Myeloma Cell Line KMS-27


title: GE98_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE98

source_name: Human B-cell chronic lymphocytic leukemia patient GE98


title: KMS-18_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-18

source_name: Human Myeloma Cell Line KMS-18

tag: Human Myeloma Cell Line KMS-18


title: GE193_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE193

source_name: Human B-cell chronic lymphocytic leukemia patient GE193


title: KMS-20_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-20

source_name: Human Myeloma Cell Line KMS-20

tag: Human Myeloma Cell Line KMS-20


title: GE93_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE93

source_name: Human B-cell chronic lymphocytic leukemia patient GE93


title: GE140_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE140

source_name: Human B-cell chronic lymphocytic leukemia patient GE140


title: KMS-11_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-11

source_name: Human Myeloma Cell Line KMS-11

tag: Human Myeloma Cell Line KMS-11


title: KMS-26_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMS-26

source_name: Human Myeloma Cell Line KMS-26

tag: Human Myeloma Cell Line KMS-26


title: GE118_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE118

source_name: Human B-cell chronic lymphocytic leukemia patient GE118


title: LP-1_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line LP-1

source_name: Human Myeloma Cell Line LP-1

tag: Human Myeloma Cell Line LP-1


title: GE117_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE117

source_name: Human B-cell chronic lymphocytic leukemia patient GE117


title: JJN3_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line JJN3

source_name: Human Myeloma Cell Line JJN3

tag: Human Myeloma Cell Line JJN3


title: NCI-H929_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line NCI-H929

source_name: Human Myeloma Cell Line NCI-H929

tag: Human Myeloma Cell Line NCI-H929


title: egg chamber BMP loss of function rep2

city: Princeton

first: Stas

last: Shvartsman

state: NJ

address: Carl Icahn Lab

department: Chemical Engineering and LSI Genomics

institute: Princeton University

description: We hand-dissected stage 9-10 egg chambers. Flies were transferred to a fresh cornmeal vial with yeast and incubated at 23C for 24h prior to dissection. Ovaries were hand-dissected in cold PBS and egg chambers at stages 9–10 (defined in Spradling, 1993) were separated from older and younger stages and divided into three groups of equal number egg chambers. To prevent RNA degradation, egg chambers were collected in groups of 20 in the RNA stabilizing buffer (RNeasy Mini Kit, Qiagen, Valencia, CA), over 5 rounds to accumulate a total of 100 egg chambers for each biological replicate (a total of 300 egg chambers from each genetic background).

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Summaries were processed using R, using Bioconductor's affy package and Choe et al. goldenspike package (Choe et al. Genome Biol. 2005, PMID: 15693945)

organism: Drosophila melanogaster

source_name: stage 9-10 egg chambers

label_protocol: 3 μg of total RNA was used in One Cycle Target Labeling for 1st and 2nd strand cDNA synthesis to obtain biotinylated labeled cRNA (Affymetrix GeneChip protocol, Santa Clara, CA).

extract_protocol: Total RNA was extracted with the RNeasy kit (Qiagen)

tag: Genotype

value: CY2-GAL4, UAS-Dad;  Gender:female; Age:6 to 8 days;  Tissue:Ovary


title: egg chamber BMP gain of function rep3

value: CY2-GAL4, UAS-tkv*;  Gender:female; Age:6 to 8 days;  Tissue:Ovary


title: GE115_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE115

source_name: Human B-cell chronic lymphocytic leukemia patient GE115

tag: Legend

tag: Sex


title: egg chamber BMP gain of function rep1


title: AMO1_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line AMO1

source_name: Human Myeloma Cell Line AMO1

tag: Human Myeloma Cell Line AMO1


title: GE110_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE110

source_name: Human B-cell chronic lymphocytic leukemia patient GE110


title: FR4_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line FR4

source_name: Human Myeloma Cell Line FR4

tag: Human Myeloma Cell Line FR4


title: Leishmania major TBP ChIP - early-log promastigotes

city: Seattle

first: Sean

last: Thomas

state: WA

address: WTC East #600, 2211 Elliott Ave

department: Genome Sciences

institute: University of Washington

description: (refer to manuscript)

hyb_protocol: On the Nimblegen hybridization system, the temperature was set to 42C with the cover closed and left alone 3 hours to stabilize. 6ug of labeled sample in 5uL of water was added to 13uL of Nimblegen Hybridization Solution, incubated at 95C for 5 minutes, then placed at 42C for at least 5 minutes until sample loading. The samples were loaded into a NimbleGen X1 Mixer, and hybridized at 42C for 16-20 hours.  The mixers were disassembled in warm Nimblegen Wash Buffer 1, and agitated vigorously for 2 minutes, then washed in Nimblegen Wash Buffer 2 for another minute under vigorous agitation.  After 15 seconds of vigorous agitation in Wash Buffer III, the slides were spun dry for one minute.

scan_protocol: The microarrays were scanned using a with a GenePix 4000B Scanner and associated software.  The arrays were kept in the dark until scanning.  Cy3 was detected using 532nm light and Cy5 was detected using 635nm light. The photomultiplier tube gain settings for each channel were set such that the curves obtained when examining the histograms of Cy3 and Cy5 intensities overlap significantly.

data_processing: The logratio of experimental to control for each microarray probe was taken as the relative enrichment at any given site for the target of the antiserum.

organism: Leishmania major

source_name: TBP antiserum immunoprecipitated input chromatin

label_protocol: 1ug of ChIP sample was added to 40 uL of Random Priming buffer (0.125M Tris pH 7.4, 0.0125M MgCl2, 0.175% B-ME) containing Cy3 or Cy5 labeled 9mers (1 O.D. per 42uL of random priming buffer). The total volume was raised to 80uL with water and heat denatured at 98C for 10 minutes.  20uL of a dNTP/Klenow Master mix (25xdNTP, Klenow 5U/uL) was added to the Random Priming Buffer solution with labeled 9mers, repipeted and incubated at 37C for 2 hours in the dark, after which the reaction was stopped using 10uL 0.5M EDTA. 11.5uL of 5M NaCl was added to each tube, then the reactions were precipitated with the addition of 110uL of isopropanol for 10 minutes at room temperature in the dark. Labeled sample was pelleted at 12k x g for 10 minutes, rinsed with 500uL of 80% cold ethanol, repelleted at 12k x g for 2 minutes, and dried on low heat in a SpeedVac for 5 minutes. Pellets were rehydrated in 25uL of water.

extract_protocol: For each IP, 2.5 ×109 L. major cells were incubated with 1% formaldehyde at 25 °C for 15 min. Next 2.5 ml of 2.5 M glycine was added and incubation continued at 25 °C for an additional 5 min. The cells were pelleted and washed once with 20 ml 1x phosphate buffered saline (PBS), pelleted again and washed once more with 2 ml PBS. After the final pelleting, the cells were resuspended in 400 ul ChIP lysis buffer (50 mM HEPES (pH 7.5), 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate and Complete Protease Inhibitor Tablets [Roche]) and an equal volume of glass beads were added. The sample was shaken continuously for 30 min on a vortex at 4 °C. The lysate was recovered by piercing the bottom of the tube and collecting drops. The samples were sheared on a Misonix Microson model #XL2007 sonicator with 6?10 s pulses at 12 Watts followed by a 15 s pause after each pulse. The lysate was centrifuged at 10,000 rpm for 10 min at 4°C. The supernatant was taken and its protein concentration determined. One mg of protein was used for each immunoprecipitation reaction. One-fortieth of the amount of lysate that would be used for an immunoprecipitation was reverse-crosslinked (65 °C overnight), and the DNA was purified on a Qiagen QiaQuick® spin column and analysed by agarose gel to determine the average genomic fragment size achieved by sonication (300 bp). Antiserum and 50 ul protein A-agarose (equilibrated in lysis buffer) were added to 1 mg of lysate and incubated overnight at 4 °C. Two washes each of the following were then performed, pelleting beads after each wash: 1 ml ChIP lysis buffer (50 mM HEPES pH7.5, 140 mM NaCl, 1% Triton X100, 0.1% sodium deoxycholate, Complete Protease Inhibitor Tablets [Roche]), 1 ml high salt lysis buffer (same as lysis buffer except 500 mM NaCl),1 ml ChIP wash buffer (10 mM Tris?HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Nadeoxycholate, 1 mM EDTA), and 1 ml TE. The beads were mixed with 75 ul of ChIP elution buffer (50 mM Tris?HCl pH 8.0, 1% SDS, 10 mM EDTA) and the sample incubated at 65 °C for 10 min. After centrifuging, the supernatant was taken and the beads were eluted again with 75 ul elution buffer. The supernatants were combined and incubated at 65 °C overnight to reverse-crosslink and the liberated DNA was purified with a Qia-Quick column. Where PCR is used to assay the chromatin, 1 ul is used for each 10 ul reaction.  Chromatin to be used in microarray experiments was first lyophilized, then using the GenomePlex Whole Genome Amplification Kit (Sigma), the lyophilized chromatin was amplified to obtain 4 ug of material

tag: LmjF early-log promastigotes

source_name: Input chromatin


title: egg chamber BMP gain of function rep2


title: KMM1_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KMM1

source_name: Human Myeloma Cell Line KMM1

tag: Human Myeloma Cell Line KMM1


title: CMA-02_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line CMA-02

source_name: Human Myeloma Cell Line CMA-02

tag: Human Myeloma Cell Line CMA-02


title: egg chamber BMP loss of function rep3


title: egg chamber BMP loss of function rep1


title: KM4_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line KM4

source_name: Human Myeloma Cell Line KM4

tag: Human Myeloma Cell Line KM4


title: Leishmania major TBP ChIP - stationary promastigotes

description: (refer to manuscript)

tag: Stationary phase LmjF promastigotes

tag: stationary phase LmjF promastigotes


title: CS3_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CS3

source_name: Human B-cell chronic lymphocytic leukemia patient CS3


title: egg chamber EGFR loss of function rep2

value: CY2-GAL4, UAS-dnEGFR;  Gender:female; Age:6 to 8 days;  Tissue:Ovary


title: Leishmania major acetylH3 ChIP - early-log promastigotes

description: (refer to manuscript)

source_name: acetylH3 antiserum precipitated input chromatin

tag: early-log promastigotes

source_name: H3 antiserum precipitated chromatin


title: egg chamber EGFR gain of function rep3

value: CY2-GAL4, UAS-lambda-Top;  Gender:female; Age:6 to 8 days;  Tissue:Ovary


title: egg chamber wildtype repB2

description: We hand-dissected stage 9-10 egg chambers. Flies were transferred to a fresh cornmeal vial with yeast and incubated at 23C for 24h prior to dissection. Ovaries were hand-dissected in cold PBS and egg chambers at stages 9–10 (defined in Spradling, 1993) were separated from older and younger stages and divided into three groups of equal number egg chambers. To prevent RNA degradation, egg chambers were collected in groups of 20 in the RNA stabilizing buffer (RNeasy Mini Kit, Qiagen, Valencia, CA), over 5 rounds to accumulate a total of 100 egg chambers for each biological replicate (a total of 300 egg chambers from each genetic background). Wildtype replicates B1-B3 were used as the control for the BMP loss of function experiments.

value: OreR;  Gender:female; Age:6 to 8 days;  Tissue:Ovary


title: CMA-03_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line CMA-03

source_name: Human Myeloma Cell Line CMA-03

tag: Human Myeloma Cell Line CMA-03


title: Leishmania major acetylH3 ChIP replicate #2

description: (refer to manuscript)

tag: LmjF promastigotes


title: egg chamber wildtype repA3

description: We hand-dissected stage 9-10 egg chambers. Flies were transferred to a fresh cornmeal vial with yeast and incubated at 23C for 24h prior to dissection. Ovaries were hand-dissected in cold PBS and egg chambers at stages 9–10 (defined in Spradling, 1993) were separated from older and younger stages and divided into three groups of equal number egg chambers. To prevent RNA degradation, egg chambers were collected in groups of 20 in the RNA stabilizing buffer (RNeasy Mini Kit, Qiagen, Valencia, CA), over 5 rounds to accumulate a total of 100 egg chambers for each biological replicate (a total of 300 egg chambers from each genetic background). Wildtype replicates A1-A3 were used as the control for the EGFR gain and loss of function, and BMP gain of function experiments.


title: egg chamber EGFR gain of function rep1


title: egg chamber wildtype repB1


title: egg chamber wildtype repA2


title: egg chamber EGFR gain of function rep2


title: ada2delta vs. ADA2 (array3)

description: Experiment was performed to analyze the effects of deletion of ada2 on gene expression. This array is one of three dye-swapped replicates.

source_name: Cy3: BY4842 (ada2delta)

tag: Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.


title: egg chamber wildtype repB3


title: ADA2 vs. ada2delta (array2)

source_name: Cy5: BY4842 (ada2delta)


title: Leishmania major TBP ChIP replicate#1

description: (refer to manuscript)

tag: Frieldin strain promastigotes


title: CMA-01_GWP

description: Genome-wide profiling data from Human Myeloma Cell Line CMA-01

source_name: Human Myeloma Cell Line CMA-01

tag: Human Myeloma Cell Line CMA-01


title: egg chamber EGFR loss of function rep3

source_name: stage 9-10 egg chambers

tag: Genotype


title: egg chamber wildtype repA1


title: egg chamber EGFR loss of function rep1


title: Leishmania major SNAP50 ChIP replicate #1

description: (refer to manuscript)

source_name: SNAP50 immunoprecipitated chromatin

tag: Input chromatin put through immunoprecipitation without antiserum


title: Leishmania major SNAP50 ChIP replicate #3

description: (refer to manuscript)

source_name: SNAP50 antiserum precipitated input chromatin


title: Leishmania major acetylH3 ChIP - stationary promastigotes

description: (refer to manuscript)

tag: stationary phase promastigotes


title: ADA2 vs. ada2delta (array1)

description: Experiment was performed to analyze the effects of deletion of ada2 on gene expression.  This array is one of three dye-swapped replicates.

hyb_protocol: Hybridization was performed at MOgene LC (St. Louis, MO).  Labeled material was fragmented according to the protocol described in the Agilent processing manual and hybridized overnight with the array in a rotating oven at 60 degrees Celsius in an ozone-free environment.  Wash conditions used were as outlined in the Agilent processing manual.

data_processing: Data processing was performed at MOgene LC (St. Louis, MO).  Feature extraction, normalization and background subtraction of reported values were performed using Agilent software.

label_protocol: Labeling was performed at MOgene LC (St. Louis, MO).  Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies).  1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.).  The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.).  All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.


title: CS128_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS128

hyb_protocol: Following fragmentation, 40 micrograms of biotin-labeled DNA were hybridized for 16 hr at 48°C on GeneChip Human Mapping 50K XbaI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 50K XbaI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 1 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1.

source_name: Human B-cell chronic lymphocytic leukemia patient CS128

tag: Legend

tag: Sex


title: Leishmania major acetylH3 ChIP replicate#1

description: (refer to manuscript)

source_name: AcetylH3-Ab precipitated chromatin

tag: Input chromatin precipitated without antiserum


title: Leishmania major SNAP50 ChIP replicate #2

description: (refer to manuscript)


title: GE126_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE126

source_name: Human B-cell chronic lymphocytic leukemia patient GE126


title: CS89_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS89

source_name: Human B-cell chronic lymphocytic leukemia patient CS89


title: C100_W2_35

status: Public on Nov 10 2008

city: Wuerzburg

last: Stoll

address: Biozentrum am Hubland

department: Dpt. of Microbiology

institute: University of Wuerzburg

description: host developmental stage: fully melanized workers (35 midguts), 27 µg RNA

hyb_protocol: Macroarrays were prehybridized and hybridized with the labled cDNA in 5x SSPE, 2% SDS, 1x Denhardt’s solution, 100 µg/ml salmon sperm DNA for 20 hours at 55°C.

scan_protocol: Arrays were exposed to storage phosphor screens for 2 days and scanned on a Typhoon 9200 Phosphoimager at 50 microns.

data_processing: Typhoon scans were analyzed with ArrayVision 6.0. Background was subtracted from median based trimmed mean (MTM) values. Background-subtracted MTM values were corrected by gDNA derived individual spot factors and normalized to the median signal of each array.

organism: Candidatus Blochmanniella floridana

source_name: bacteria from ant colony C100, stage W2

label_protocol: Alpha-33P-labeled dATP was incorporated during cDNA synthesis with random hexamers (RevertAid First Strand cDNA Synthesis Kit, fermentas).

growth_protocol: Ants were fed a complex diet and kept under stable environmental conditions.

extract_protocol: Cell pellets were frozen at -80°C, resuspended in 100µl TE buffer (pH 8.0), and RNA was extracted with the RNeasy Mini Kit from Qiagen (Hilden, Germany).  Residual DNA was removed with the DNA-free Kit from Ambion (Austin, TX, USA).  RNA yield and purity was determined photometrically.

treatment_protocol: Midguts were dissected in isolation buffer (35 mM TrisHCl pH 7.6, 25 mM KCl, 250 mM sucrose), emptied, homogenized and bacteria pelleted by centrifugation.

tag: bacteria isolated from ant colony C100


title: C118_W2_49

description: host developmental stage: fully melanized workers (49 midguts), 15 µg RNA

source_name: bacteria from ant colony C118, stage W2

tag: bacteria isolated from ant colony C118


title: C254_W3_40

description: host developmental stage: old (> 4 months) workers from an isolated subcolony (40 midguts), 22 µg RNA

source_name: bacteria from ant colony C254, stage W3

tag: bacteria isolated from ant colony C254


title: C254_W3_55

description: host developmental stage: old (> 4 months) workers from an isolated subcolony (55 midguts), 20 µg RNA


title: CS71_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS71

source_name: Human B-cell chronic lymphocytic leukemia patient CS71


title: 6_noTx

city: Boston

first: Marc

last: Raab

state: MA

address: 44 Binney Street

institute: Dana Farber Cancer Institute

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs  washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using  phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner (Gene Array Scanner (Affymetrix)), and the positions and intensities of the fluorescent emissions are captured.

data_processing: CEL files were obtained using the Affymetrix Microarray Suite 5.0 software. The DNA Chip Analyzer (DChip) was used to normalize all CEL files to a baseline array with overall median intensity, and the model-based expression (perfect match minus mismatch) was used to compute the expression values.

source_name: cell line

label_protocol: Synthesis of double-stranded cDNA which then serves as a  template for the synthesis of biotinylated cRNA by in vitro transcription. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample. The purified cRNA is fragmented in order to facilitate the subsequent  hybridization step.

extract_protocol: Total RNA was isolated from enzastaurin-treated or untreated MM.1S cells  using TRIzol reagent (Invitrogen, Carlsbad, CA).

tag: Multiple Myeloma MM.1S cells, not treated, time 6 hours


title: RC81_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC81

source_name: Human B-cell chronic lymphocytic leukemia patient RC81


title: C79_W2_60

description: host developmental stage: fully melanized workers (60 midguts), 15 µg RNA

source_name: bacteria from ant colony C79, stage W2

tag: bacteria isolated from ant colony C79


title: C254_W3_50

description: host developmental stage: old (> 4 months) workers from an isolated subcolony (50 midguts), 21 µg RNA


title: C90_W2_35

description: host developmental stage: fully melanized workers (35 midguts), 31 µg RNA

source_name: bacteria from ant colony C90, stage W2

tag: bacteria isolated from ant colony C90


title: CS103_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS103

source_name: Human B-cell chronic lymphocytic leukemia patient CS103


title: 3_Enza

tag: Multiple Myeloma MM.1S cells, treated with enzastaurin, time 3 hours


title: 12_noTx

tag: Multiple Myeloma MM.1S cells, not treated, time 12 hours


title: 6_Enza

tag: Multiple Myeloma MM.1S cells, treated with enzastaurin,time 6 hours


title: RC14_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC14

source_name: Human B-cell chronic lymphocytic leukemia patient RC14


title: C254_W3_48

description: host developmental stage: old (> 4 months) workers from an isolated subcolony (48 midguts), 20 µg RNA


title: 3_noTx

tag: Multiple Myeloma MM.1S cells, not treated, time 3 hours


title: GE110_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE110

source_name: Human B-cell chronic lymphocytic leukemia patient GE110


title: GE87_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE87

source_name: Human B-cell chronic lymphocytic leukemia patient GE87


title: GE93_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE93

source_name: Human B-cell chronic lymphocytic leukemia patient GE93


title: CS115_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS115

source_name: Human B-cell chronic lymphocytic leukemia patient CS115


title: RC94_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC94

source_name: Human B-cell chronic lymphocytic leukemia patient RC94


title: C100_W2_112

description: host developmental stage: fully melanized workers (112 midguts), 20 µg RNA


title: Leishmania major TBP ChIP replicate #3

description: (refer to manuscript)

source_name: TBP antiserum immunoprecipitated input chromatin

tag: LmjF promastigotes

source_name: Input chromatin


title: C90_W1_30

description: host developmental stage: young callow workers (30 midguts), 40 µg RNA

source_name: bacteria from ant colony C90, stage W1


title: C79_W1_38

description: host developmental stage: young callow workers (38 midguts), 23 µg RNA

source_name: bacteria from ant colony C79, stage W1


title: C90_W1_100

description: host developmental stage: young callow workers (100 midguts), 28 µg RNA


title: C90_W1_72

description: host developmental stage: young callow workers (72 midguts), 20 µg RNA


title: C90_P3_120

description: host developmental stage: pupae shortly before eclosion (120 midguts), 20 µg RNA

source_name: bacteria from ant colony C90, stage P3


title: GE104_1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE104

source_name: Human B-cell chronic lymphocytic leukemia patient GE104


title: C118_P3_60

description: host developmental stage: pupae shortly before eclosion (60 midguts), 33 µg RNA

source_name: bacteria from ant colony C118, stage P3


title: C118_W1_40

description: host developmental stage: young callow workers (40 midguts), 33 µg RNA

source_name: bacteria from ant colony C118, stage W1


title: C90_P3_30

description: host developmental stage: pupae shortly before eclosion (30 midguts), 20 µg RNA


title: C79_P3_45

description: host developmental stage: pupae shortly before eclosion (45 midguts), 31 µg RNA

source_name: bacteria from ant colony C79, stage P3


title: C118_P2_59

description: host developmental stage: pupae shortly after metamorphosis (59 midguts), 25 µg RNA

source_name: bacteria from ant colony C118, stage P2


title: C79_P2_50

description: host developmental stage: pupae shortly after metamorphosis (50 midguts), 37 µg RNA

source_name: bacteria from ant colony C79, stage P2


title: C104_P2_140

description: host developmental stage: pupae shortly after metamorphosis (140 midguts), 27 µg RNA

source_name: bacteria from ant colony C104, stage P2

tag: bacteria isolated from ant colony C104


title: C331_P2_120

description: host developmental stage: pupae shortly after metamorphosis (120 midguts), 26 µg RNA

source_name: bacteria from ant colony C331, stage P2

tag: bacteria isolated from ant colony C331


title: C118_P1_50

description: host developmental stage: young pupae (50 midguts), 25 µg RNA

source_name: bacteria from ant colony C118, stage P1


title: C118_L2_80

description: host developmental stage: mid-aged larvae (80 midguts), 34 µg RNA

source_name: bacteria from ant colony C118, stage L2


title: 12_Enza

source_name: cell line

tag: Multiple Myeloma MM.1S cells, treated with enzastaurin, time 12 hours


title: C79_P1_60

description: host developmental stage: young pupae (60 midguts), 23 µg RNA

source_name: bacteria from ant colony C79, stage P1


title: C337_L2_300

description: host developmental stage: mid-aged larvae (300 midguts), 21 µg RNA

source_name: bacteria from ant colony C337, stage L2

tag: bacteria isolated from ant colony C337


title: C259_P1_50

description: host developmental stage: young pupae (50 midguts), 16 µg RNA

source_name: bacteria from ant colony C259, stage P1

tag: bacteria isolated from ant colony C259


title: C118_L1

description: host developmental stage: very young larvae (~300 whole animals), 25 µg RNA

source_name: bacteria from ant colony C118, stage L1


title: C79_L2_75

description: host developmental stage: mid-aged larvae (75 midguts), 30 µg RNA

source_name: bacteria from ant colony C79, stage L2


title: SQ 115 LuxA_2-3

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

description: Euprymna scolopes, age 18 hours, hatchling, genetic variation: pooled clutches rep2 same, source: Paiko HI, tissue: light organ

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 sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005 Triton X-102 before scanning. Slides were hybridized for 17 h 60 degrees c in a rotating oven, and washed.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1.0.0 analysis software.

data_processing: raw data as output from GenePix Pro 5.1.0.0 analysis software. VALUEs represent log2 (test/ref) ratios.

molecule: other

organism: Euprymna scolopes

source_name: Euprymna Scolopes run-off reference

label_protocol: Samples were labeled with Genisphere 3DNA Array 350 RNA labeling kit.

growth_protocol: 13,962 nonredundant E. coli clones were grown individually to stationary phase and then equal volumes were combined.  A plasmid prep was performed on 50ml of the combined samples.  Inserts were then amplified via PCR for 10 cycles then 1µl of the PCR product was then used for an additional 25 cycles of PCR amplification.

extract_protocol: Trizol procedure

tag: RNA transcribed from equal volumes of stationary culture of E. coli cDNA clones representing each unique spot on the microarray.

source_name: pool of 100 Euprymna scolopesi light organs

label_protocol: 1 µg Total RNA was labeled with Genisphere 3DNA Array 350 RNA labeling kit.

growth_protocol: 6hr innoculation with V.fischeri ES114 LuxA- mutant (Laura Sycuro)(5000 cells/ml), then transferred into OSW without V.fischeri without VAI. Dissected at 18hrs post-innoculation.

extract_protocol: Total RNA isolation was accomplished with Epicenter and Qiagen RNeasy Mini Kit reagents. Total RNA was cleaned up using Millipore Microcon 30

value: pooled clutches rep2 same, source:Paiko HI, tissue:light organ


title: C79_L1

description: host developmental stage: very young larvae (~300 whole animals), 35 µg RNA

source_name: bacteria from ant colony C79, stage L1


title: C259_L1

description: host developmental stage: very young larvae (~300 whole animals), 40 µg RNA

source_name: bacteria from ant colony C259, stage L1


title: SQ 113 LuxA_3-3

description: Euprymna scolopes, age 18 hours, hatchling, genetic variation: pooled clutches rep3 same, source: Paiko HI, tissue: light organ

source_name: pool of 100 Euprymna scolopes light organs

value: pooled clutches rep3 same, source:Paiko HI, tissue:light organ

source_name: Euprymna Scolopoes run-off reference


title: SQ 110 LuxI plus VAI_2-3

growth_protocol: 6hr innoculation with V.fischeri ES114 LuxI- mutant (Cheryl Whistler)(5000 cells/ml), then transferred into OSW without V.fischeri with VAI. Dissected at 18hrs post-innoculation.

tag: Euprymna scolopes, age 18 hours, hatchling, genetic variation


title: SQ 103 Symbiotic_3-7

growth_protocol: 6hr innoculation with V.fischeri ES114(5000 cells/ml), then transferred into OSW without V.fischeri without VAI. Dissected at 18hrs post-innoculation.


title: SQ 106 Aposymbiotic plus VAI_1-3

description: Euprymna scolopes, age 18 hours, hatchling, genetic variation: pooled clutches repl same, source: Paiko HI, tissue: light organ

growth_protocol: 6hr innoculation without V.fischeri, then transferred into OSW without V.fischeri with VAI. Dissected at 18hrs post-innoculation.

value: pooled clutches repl same, source:Paiko HI, tissue:light organ


title: SQ 112 LuxI plus VAI_3-3


title: C337_L1

source_name: bacteria from ant colony C337, stage L1


title: SQ 108 Aposymbiotic_2-8

growth_protocol: 6hr in HOSW, then transferred into HOSW without V.fischeri without VAI. Dissected 18hr post-innoculation


title: SQ 104 LuxI plus VAI_3-2


title: SQ 107 LuxI_1-3

description: Euprymna scolopes, age 18 hours, hatchling, genetic variation: pooled clutches rep1 same, source: Paiko HI, tissue: light organ

growth_protocol: 6hr innoculation with V.fischeri ES114 LuxI- mutant (Cheryl Whistler)(5000 cells/ml), then transferred into OSW without V.fischeri without VAI. Dissected at 18hrs post-innoculation.

value: pooled clutches rep1 same, source:Paiko HI, tissue:light organ


title: SQ 114 Aposymbiotic plus VAI_2-3


title: SQ 063 LuxI plus VAI_2-2


title: SQ 062 LuxI_2-2


title: SQ 105 LuxA_3-2


title: SQ 058 LuxA_1-2


title: SQ 109 Symbiotic_2-7


title: SQ 065 Aposymbiotic_3-6


title: 40 ug/mL rATG treated for 6h, biological rep3 (S6)

city: Bethesda

first: Xingmin

last: Feng

address: 9000 Rockville Pike

institute: National Institutes of Health

description: Gene expression data from rATG-treated PBMC.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was extracted with the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: rATG-treated for 6h


title: SQ 061 Symbiotic_2-6


title: SQ 066 Symbiotic_3-6


title: SQ 102 Aposymbiotic_3-7


title: SQ 057 LuxI plus VAI_1-2


title: YFP Control IP Replicate 2 hybridized to array 2 of 2

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

institute: Emory University

description: Biological replicate 2 of 2, hybridization 2 of 2

hyb_protocol: performed by Nimblegen Systems, Inc

scan_protocol: performed by Nimblegen Systems, Inc

data_processing: Z-score normalization

source_name: YFP LNCaP cells

label_protocol: performed by Nimblegen Systems, Inc

growth_protocol: LNCaP cells were grown to 95% confluency in the presence of T-medium (invitrogen)

extract_protocol: Chromatin IP performed as described in Odom et al., Science 303, 1378 (Feb 27, 2004)

tag: LNCaP cells stably infected with IRES-YFP

source_name: IP: YFP LNCaP cells


title: SQ 067 LuxI_3-2


title: SQ 064 LuxA_2-2


title: 40 ug/mL rATG treated for 6h, biological rep2 (S5)


title: SQ 056 LuxI_1-2


title: 40 ug/mL hATG treated for 6h, biological rep3 (S6)

description: Gene expression data from hATG-treated PBMC.

tag: hATG-treated for 6h


title: SQ 060 Aposymbiotic plus VAI_2-2


title: SQ 054 Aposymbiotic plus VAI_1-2


title: SQ 052 Symbiotic_2-5


title: 2.5 ug/mL rATG treated for 6h, biological rep3 (S6)


title: 2.5 ug/mL rATG treated for 6h, biological rep2 (S5)


title: 40 ug/mL rATG treated for 6h, biological rep1 (S4)


title: SQ 050 Aposymbiotic_2-6


title: 40 ug/mL hATG treated for 6h, biological rep2 (S5)


title: 2.5 ug/mL rATG treated for 6h, biological rep1 (S4)


title: HA-SOX4 IP Replicate 2 hybridized to array 2 of 2

description: Biological replicate 2 of 3, hybridization 2 of 2

source_name: HA-SOX4/YFP LNCaP cells

tag: LNCaP cells stably infected with HA-SOX4-IRES-YFP

source_name: IP: HA-SOX4/YFP LNCaP cells


title: SQ 051 Aposymbiotic plus VAI_2-1


title: YFP Control IP Replicate 1 hybridized to array 2 of 2

description: Biological replicate 1 of 2, hybridization 2 of 2


title: 2.5 ug/mL hATG treated for 6h, biological rep2 (S5)


title: SQ 049 LuxA_1-1


title: 2.5 ug/mL hATG treated for 6h, biological rep1 (S4)


title: SQ 047 LuxI_1


title: SQ 055 Symbiotic_1-6


title: SQ 048 LuxI plus VAI_1-1


title: Untreated for 6h, biological rep3 (S6)

description: Gene expression data from untreated PBMC.

tag: untreated for 6h


title: HA-SOX4 IP Replicate 3 hybridized to array 2 of 2

description: Biological replicate 3 of 3, hybridization 2 of 2


title: SQ 045 Aposymbiotic plus VAI_1-1


title: SQ 043 LuxA_3-1


title: Untreated for 6h, biological rep2 (S5)


title: SQ 044 Aposymbiotic_1-5


title: Untreated for 6h, biological rep1 (S4)


title: 10 ug/mL rATG treated for 6h, biological rep3 (S3)


title: SQ 059 Aposymbiotic_2-7


title: SQ 041 LuxI_3-1


title: SQ 042 LuxI plus VAI_3-1


title: SQ 046 Symbiotic_1-5


title: HA-SOX4 IP Replicate 1 hybridized to array 2 of 2

description: Biological replicate 1 of 3, hybridization 2 of 2


title: SQ 053 Aposymbiotic_1-6


title: 10 ug/mL hATG treated for 6h, biological rep3 (S3)


title: LNCaP - SOX4 siRNA, Day2, U133B

description: no additional information

hyb_protocol: as described by Affymetrix

scan_protocol: as described by Affymetrix

data_processing: GCRMA normalization

source_name: LNCaP - SOX4 siRNA D2

label_protocol: as described by Affymetrix

growth_protocol: LNCaP cells were grown in the presence of T-medium (invitrogen)

extract_protocol: total RNA was extracted using the Qiagen RNeasy Mini Kit

treatment_protocol: LNCaP cells were transfected with either a SOX4 cDNA, a pool of siRNAs against SOX4 or a GFP control cDNA using DMRIE-C (Invitrogen).  24 hours post-transfection total RNA was harvested and Affymetrix expression profiling performed

tag: LNCaP prostate cancer cells


title: 10 ug/mL hATG treated for 6h, biological rep2 (S2)


title: 10 ug/mL hATG treated for 6h, biological rep1 (S1)


title: SQ 039 Aposymbiotic_3-5


title: SQ 040 Symbiotic_3-5


title: SQ 036 LuxI_2-1


title: LNCaP - SOX4 siRNA, Day1, U133B

description: no additional information

source_name: LNCaP - SOX4 siRNA D1


title: LNCaP - SOX4 cDNA, Day1, U133B

description: no additional information

source_name: LNCaP - SOX4 cDNA D1


title: SQ 037 LuxI plus VAI_2-1


title: SQ 038 LuxA_2-1


title: 10 ug/mL rATG treated for 6h, biological rep1 (S1)