title: 6157-2852-Cy5

status: Public on Sep 21 2010

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

description: log2 ratio Cy5/Cy3

hyb_protocol: Array platform: 70 mer oligonucleotides (Human Oligo Set 4.0; Operon, Cologne, Germany). Pretreatment of slides: 2 min in 0.2perc SDS; 2 min in ddH2O at RT; 2 min in ddH2O at 95C, followed by 1 min centrifugation at 1000 rpm. Application of preheated (60 min 60C, 10 min 70C), dye-labeled cDNA in Ultra-Hyb hybridization buffer on microarrays in a GeneTAC Hybridization Station. Hybridization for 40h at 42C with gentle agitation. Wash steps: 36C; 5 min 0.5xSSC, 0.1perc SDS; 3 min 0.05xSSC, 0.1perc SDS; 20s 0.05xSSC; 20s 0.05xSSC, 0.1perc Tween20.

scan_protocol: Scanning of hybridized microarrays at 5 μm resolution and variable PMT voltage to obtain maximal signal intensities with < 0.1perc probe saturation, a count ratio of 0.8-1.2 (Cy5/Cy3) and maximal congruence of histogram curves using a GenePix 4000B microarray scanner (Axon Instruments, Union City, USA).

data_processing: Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).

source_name: culture type: control

label_protocol: Sample labelling by Klenow reaction using Cy3- or Cy5-labeld dUTP. Purification of labelled samples on Microcon YM-30 filter columns. Addition of blocking reagents: 25 μg Cot-1 DNA, 25 μg poly-A RNA, and 75 μg yeast tRNA.

extract_protocol: Total RNA isolation by Trizol extraction and purification on RNeasy Mini spin columns. Amplification of RNA by first- and second-strand cDNA synthesis. In vitro transcription of extracted cDNA by RiboMAX Large Scale RNA Production System T7.

tag: sex

value: M

value: in old annotation control was named 'co'

tag: time point (days)

source_name: culture_type: control


title: 6478-3175-Cy3

type: RNA

country: Germany

description: log2 ratio Cy5/Cy3

molecule: total RNA

organism: Homo sapiens

value: F

value: control

value: sample


title: 6153-2848-Cy3

description: log2 ratio Cy5/Cy3


title: 6153-2848-Cy5

description: log2 ratio Cy5/Cy3


title: 6478-3175-Cy5

description: log2 ratio Cy5/Cy3


title: 12615-12617-Cy3

description: log2 ratio Cy5/Cy3

source_name: culture type: CM

value: B-CLL 45

value: CM


title: 12621-12623-Cy3

description: log2 ratio Cy5/Cy3

value: B-CLL 47


title: 12618-12620-Cy5

description: log2 ratio Cy5/Cy3

value: B-CLL 46

source_name: culture_type: CM


title: 12615-12617-Cy5

description: log2 ratio Cy5/Cy3


title: HSMM-DS14430

status: Public on Jan 07 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
Normal Human Skeletal Muscle Myoblasts
X_Hs_HSMM_E_101115_09_RS17245_W.CEL

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymterix Gene Chip Scanner 3000

data_processing:
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf

label: biotin

source_name: Normal Human Skeletal Muscle Myoblasts

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

treatment_protocol: For WI-38 cell type, Tamoxifen treated replicates only: induce senescence, cells at 50-80% confluency are treated for 72 hours with 20nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis is inhibited and the cells have an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci

tag: cell type

value: Normal Human Skeletal Muscle Myoblasts

tag: term


title: WI-38-DS14323

description:
Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, treated with Tamoxifen
X_Hs_WI38_E_101115_16_RS17252_W.CEL


title: 12621-12623-Cy5

description: log2 ratio Cy5/Cy3


title: WI-38-DS14315

description:
Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER
X_Hs_WI38_E_101115_14_RS17250_W.CEL


title: HEK293-DS13681

description:
embryonic kidney
X_Hs_HEK293_E_101115_05_RS17241_W.CEL

source_name: embryonic kidney

value: embryonic kidney


title: LNCaP-DS14680

description:
prostate adenocarcinoma
X_Hs_LNCAP_E_101115_12_RS17248_W.CEL

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma


title: LNCaP-DS14684

description:
prostate adenocarcinoma
X_Hs_LNCAP_E_101115_13_RS17249_W.CEL


title: HSMM-DS14426

description:
Normal Human Skeletal Muscle Myoblasts
X_Hs_HSMM_E_101115_08_RS17244_W.CEL


title: HSMMtube-DS15542

description:
Normal Human Skeletal Muscle Myoblasts, differentiated
X_Hs_HSMM_E_101115_10_RS17246_W.CEL


title: HA-c-DS14765

description:
Human astrocytes, cerebellar
X_Hs_HAc_E_101115_03_RS17239_W.CEL

source_name: Human astrocytes, cerebellar

value: Human astrocytes, cerebellar


title: HRGEC-DS13716

description:
Human Renal Glomerular Endothelial Cells
X_Hs_HRGEC_E_101115_07_RS17243_W.CEL


title: BE2_C-DS14635

description:
Human neuroblastoma
X_Hs_BE2c_E_101115_02_RS17238_W.CEL

source_name: Human neuroblastoma

value: Human neuroblastoma


title: HUVEC-DS13475

description:
Human Umbilical Vein Endothelial Cell
X_Hs_HUVEC_E_101115_11_RS17247_W.CEL

source_name: Human Umbilical Vein Endothelial Cell

value: Human Umbilical Vein Endothelial Cell


title: 12611-12613-Cy3

description: log2 ratio Cy5/Cy3

value: B-CLL 44


title: WI-38-DS14328

description:
Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, treated with Tamoxifen
X_Hs_WI38_E_101115_17_RS17253_W.CEL


title: HRGEC-DS13705

description:
Human Renal Glomerular Endothelial Cells
X_Hs_HRGEC_E_101115_06_RS17242_W.CEL


title: Wild-type unstimulated

status: Public on Aug 22 2010

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Gene CHIP scanner 3000.

data_processing: The data were analyzed with RMA using R program.

organism: Mus musculus

source_name: Wild-type macrophages unstimulated

label_protocol: Biotinylated cRNA were prepared by NuGEN Ovation system according to the manufactuerer's inscrution.

growth_protocol: Mouse bone marrow cells were cultured with M-CSF for 5 days.

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

treatment_protocol: stimulated with 100 ng/ml LPS for 4 hours

tag: genotype/variation

value: Wild-type unstimulated

tag: treatment

value: unstimulated


title: RPTEC-DS14061

description:
Renal Proximal Tubule Epithelial Cells
X_Hs_RPTEC_E_100901_12_RS16428_W.CEL

source_name: Renal Proximal Tubule Epithelial Cells

value: Renal Proximal Tubule Epithelial Cells


title: A549-DS14285

description:
epithelial cell line derived from a lung carcinoma tissue
X_Hs_A549_E_100901_07_RS16423_W.CEL


title: HA-c-DS14770

description:
Human astrocytes, cerebellar
X_Hs_HAc_E_101115_04_RS17240_W.CEL


title: RPTEC-DS14065

description:
Renal Proximal Tubule Epithelial Cells
X_Hs_RPTEC_E_100901_13_RS16429_W.CEL


title: HA-sp-DS14794

description:
Human astrocytes, spinal cord
X_Hs_HAsp_E_100901_10_RS16426_W.CEL

source_name: Human astrocytes, spinal cord

value: Human astrocytes, spinal cord


title: HBMEC-DS13806

description:
Human Brain Microvascular Endothelial Cells
X_Hs_HBMEC_E_100901_11_RS16427_W.CEL


title: BE2_C-DS14625

description:
Human neuroblastoma
X_Hs_BE2c_E_101115_01_RS17237_W.CEL


title: HA-sp-DS14790

description:
Human astrocytes, spinal cord
X_Hs_HAsp_E_100901_09_RS16425_W.CEL


title: Wild-type LPS

source_name: Wild-type macrophages stimulated with LPS for 4 h

value: Wild-type LPS

value: stimulated with LPS for 4 h


title: A549-DS14289

description:
epithelial cell line derived from a lung carcinoma tissue
X_Hs_A549_E_100901_08_RS16424_W.CEL


title: WI-38-DS14320

description:
Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER
X_Hs_WI38_E_101115_15_RS17251_W.CEL


title: NHA-DS12805

status: Public on Aug 16 2010

source_name: Normal Human Astrocytes

value: Normal Human Astrocytes


title: NHA-DS12800


title: HCT-116-DS13547

source_name: colorectal carcinoma

value: colorectal carcinoma


title: HCT-116-DS13551


title: HMF-DS13363

source_name: Human Mammary Fibroblast

value: Human Mammary Fibroblast


title: HPF-DS13380

source_name: Human Pulmonary Fibroblasts

value: Human Pulmonary Fibroblasts


title: HEK293-DS13696


title: HMF-DS13368


title: HPAF-DS13416

source_name: Human Pulmonary Artery Fibroblasts

value: Human Pulmonary Artery Fibroblasts


title: HBMEC-DS13817

source_name: Human Brain Microvascular Endothelial Cells


title: HCFaa-DS13480

source_name: Human Cardiac Fibroblasts-Adult Atrial

value: Human Cardiac Fibroblasts-Adult Atrial


title: HVMF-DS13981

source_name: Human Villous Mesenchymal Fibroblast Cells


title: HPAF-DS13411


title: AoAF-DS13523

source_name: Normal Human Aortic Adventitial Fibroblast Cells


title: HMVEC-dBl-Ad-DS13337

description: X_Hs_HMVECdBlAd_E_100603_19_DS13337_W_2.CEL

source_name: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: AoAF-DS13513

value: Normal Human Aortic Adventitial Fibroblast Cells


title: HMVEC-dBl-Ad-DS13329

description: X_Hs_HMVECdBlAd_E_100603_18_DS13329_W.CEL

value: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: HMVEC-dBl-Neo-DS13233

description: X_Hs_HMVECdBlNeo_E_100603_14_DS13233_W_2.CEL

source_name: Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: HMVEC-dBl-Neo-DS13242

description: X_Hs_HMVECdBlNeo_E_100603_15_DS13242_W_2.CEL

value: Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: HPF-DS13390


status: Public on Aug 05 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: Antibody information listed below: official name: EZview Red ANTI-FLAG® M2 Affinity Gel;target name: FLAG;host: Mouse;antigen: DYKDDDDK;clonal: Monoclonal;purified: Affinity;company: Sigma;catalog: F-2426;reference: http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&N5=Product No.|BRAND KEY&N4=F2426|SIGMA&N25=0&QS=ON&F=SPEC;short description: Binds to the FLAG epitope wherever it is located in the fusion protein: amino-terminal Met-amino-terminal carboxy-terminal or internal. Binding is not Ca2+-dependent.sSuitable for purifying N-terminal Met-N-terminal C-terminal FLAG fusion proteins 3xFLAG fusion proteins.

hyb_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

data_processing: Tiling_Array_Signal_Extraction protocol. Mismatch (MM) probe values are subtracted from their corresponding perfect match (PM) probes.  Processed data are obtained using following parameters: BPMap is BPmap:GPL5634:RW:1&oldid=22907   Tiling_Array_Normalization_and_Smoothing protocol. Biological replicates (usually 3 but sometimes 2) are normalized using quantile normalization.  The normalized signal from multiple replicates are then smoothed to produce a composite signal. Each probe's value is replaced by the psuedomedian of all probes in a window around it from all replicates. This is done in a sliding window fashion shifted one probe at a time. The window size is set to 110bp, which corresponds to about 4 probes.  Processed data are obtained using following parameters: window size is 110

label: Biotin

organism: Caenorhabditis elegans

source_name: L3-L4 hypodermal cells tiling array extraction1_array1 channel_1

label_protocol: The NuGEN WT Pico RNA amplification kit was used to generate amplified single stranded cDNA from RNA samples. Starting material is 10 ng of RNA for mRNA tagging experiments and 1-5 ng of RNA for embryonic cells isolated by FACS.  The NuGEN WT-Ovation Exon Module was used to synthesize double stranded cDNA from the amplified single stranded cDNA template.   This was followed by fragmentation and labeling with the NuGEN FL-Ovation cDNA Biotin Module.

growth_protocol:
Animals were synchronized by treating a mixed stage hermaphrodite population with bleach to collect embryos.   The embryos surviving bleach treatment were incubated without food, causing the larvae to arrest at the L1 stage upon hatching.  Starved L1 larvae were plated in the presence of food and raised at 20 degrees Celsius (or indicated temperature) to desired stage.
For embryonic assays, embryonic cells were obtained using methods previously described [Christensen et al, 2002). Briefly, embryos were isolated from gravid adults following lysis in a hypochlorite solution. Intact embryos were separated from debris by flotation on 30% sucrose. For later stages, the embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated on standard NGM plates in the presence of food (OP50) and raised at 20 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for postdeirid, vulval and germline development. Animals were collected at the mid-L2, late L3-mid L4 and young adult (pre-gravid) stages and washed in M9 buffer. mid-L2 worms were collected when postdeirid divisions complete. L3/L4 animals were collected when a majority of animals diplayed a bilaterally symmetrical "christmas tree" vulval anatomy (See view at 40 hr, Fig 18, Sulston and Horvitz, Dev. Biol. 56, 110-156, 1977) Young Adult  were collected when vulvae fully formed and oocytes present in gonad, but no embryos. The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of M9 buffer.

extract_protocol: Briefly, staged worms were treated with formaldehyde to cross link RNAs to FLAG-PAB-1, lysed with in a French pressure cell (3x for L2, 4x for L3/L4/YA), followed by glass homogenizer (30x) on ice.  The lysate is cleared by centrifugation and RNA purified (trizol) from a 100 ul sample  to estimate RNA (A260) in the total lysate.    Homogenate (200ug total RNA) was incubated with anti-FLAG beads at 4°C for two hours and washed. The Low salt wash reduces non-specific RNA bound to the beads (see Von Stetina, Watson et al. Genome Biology 8:R135, 2007). Formaldehyde cross-linking was reversed and bound RNAs eluted by incubation at 65 C for 30 min. RNAs were extracted using Trizol/chloroform followed by isopropanol precipitation, and DNAse treatment (Column RNA cleanup from April 2006 Qiagen RNeasy Mini Handbook.  RNAs were resuspended in RNase-free H2O, and stored at 20°C. The samples are polyA enriched, but there is a significant quantity of rRNA that comes down non-specifically in the prep.  Note:  Animals used for cell/tissue-specific profiling carry a promoter::3XFLAG::PAB-1 construct.  Animals used for control samples are N2 without an 3XFLAG-tagged PAB-1, and a mockIP is performed.  Therefore, the protocol is the same for cell/tissue-specific profiling and control samples, and reference samples represent background signals from the IP technique.

tag: strain

value: NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1)

tag: tissue

value: hypodermis (L3-L4)

tag: developmental stage

value: L3-L4 larva 20dC 22h 23dC 24hr post-L1

tag: genotype

value: Hermaphrodite


title: NHDF-Ad-DS12863

source_name: Adult Normal Human Dermal Fibroblasts

value: Adult Normal Human Dermal Fibroblasts


title: HVMF-DS13977

value: Human Villous Mesenchymal Fibroblast Cells


scan_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

source_name: L3-L4 hypodermal cells tiling array extraction2_array1 channel_1


source_name: L3-L4 reference (mockIP) tiling array extraction1_array1 channel_1

value: reference (L3-L4)

value: wild type


source_name: Young Adult Cephalic sheath (CEPsh) tiling array extraction1_array1 channel_1

value: OS3991 (engineered, target gene hlh-17 tagged by 3xFlag::PAB-1)

value: CEPsh (YA)

value: Young Adult 20dC 72hr post-L1


title: HMVEC-LBl-DS13372

description: X_Hs_HMVECLBl_E_100603_22_DS13372_W_2.CEL

source_name: Normal Human Blood Microvascular Endothelial Cells, Lung-Derived


source_name: L2 glutamate receptor expressing neurons tiling array extraction3_array1 channel_1

value: NC1842 (engineered, target gene glr-1 tagged by 3xFlag::PAB-1)

value: Glutamate receptor expressing neurons (L2)

value: larva mid-L2 20dC 22h post-L1

value: mixed Male and Hermaphrodite population


title: HPdLF-DS13569

source_name: Normal Human Periodontal Ligament Fibroblast Cells


source_name: L3-L4 reference (mockIP) tiling array extraction2_array1 channel_1


title: HMVEC-dNeo-DS12929

description: X_Hs_HMVECdNeo_E_100603_07_DS12929_W.CEL

source_name: Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived


source_name: Young Adult Cephalic sheath (CEPsh) tiling array extraction2_array1 channel_1


source_name: Young Adult Cephalic sheath (CEPsh) tiling array extraction3_array1 channel_1


source_name: L3-L4 hypodermal cells tiling array extraction3_array1 channel_1


title: HMVEC-dNeo-DS12937

description: X_Hs_HMVECdNeo_E_100603_08_DS12937_W.CEL

value: Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived


source_name: Young Adult reference (mockIP) tiling array extraction3_array1 channel_1

value: reference (YA)


title: HCFaa-DS13484

source_name: Human Cardiac Fibroblasts-Adult Atrial

value: Human Cardiac Fibroblasts-Adult Atrial


source_name: Young Adult reference (mockIP) tiling array extraction2_array1 channel_1


source_name: L2 coelomocytes tiling array extraction1_array1 channel_1

value: NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1)

value: Coelomocytes (L2)


source_name: Young Adult reference (mockIP) tiling array extraction1_array1 channel_1

value: Hermaphrodite


source_name: L3-L4 dopaminergic neuron tiling array extraction3_array1 channel_1

value: NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1)

value: Dopaminergic neurons (L3-L4)

value: L3-L4 larva 20dC 22h 23dC 24hr post-L1


title: HMVEC-LBl-DS13375

description: X_Hs_HMVECLBl_E_100603_23_DS13375_W_2.CEL

value: Normal Human Blood Microvascular Endothelial Cells, Lung-Derived


source_name: L3-L4 dopaminergic neuron tiling array extraction2_array1 channel_1


source_name: L3-L4 dopaminergic neuron tiling array extraction1_array1 channel_1


source_name: L2 glutamate receptor expressing neurons tiling array extraction1_array1 channel_1


source_name: L2 coelomocytes tiling array extraction3_array1 channel_1


source_name: L2 coelomocytes tiling array extraction2_array1 channel_1


source_name: L2 A-class neuron tiling array extraction3_array1 channel_1

value: NC694 (engineered, target gene unc-119 tagged by 3xFlag::PAB-1)

value: unc-119(ed1) III; wdEx257.


source_name: L2 A-class neuron tiling array extraction2_array1 channel_1


source_name: L2 A-class neuron tiling array extraction1_array1 channel_1


title: HPdLF-DS13573

source_name: Normal Human Periodontal Ligament Fibroblast Cells


source_name: L2 glutamate receptor expressing neurons tiling array extraction2_array1 channel_1


source_name: L3-L4 reference (mockIP) tiling array extraction3_array1 channel_1

value: reference (L3-L4)

value: wild type


source_name: L2 GABA neurons tiling array extraction3_array1 channel_1

value: NC1627 (engineered, target gene C04G2.1 tagged by 3xFlag::PAB-1)

value: GABA neurons (L2)


title: NHDF-Ad-DS12855

source_name: Adult Normal Human Dermal Fibroblasts

value: Adult Normal Human Dermal Fibroblasts


source_name: L2 GABA neurons tiling array extraction1_array1 channel_1

value: larva mid-L2 20dC 22h post-L1

value: mixed Male and Hermaphrodite population


source_name: L2 body wall muscle tiling array extraction3_array1 channel_1

value: SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1)

value: body wall muscle


source_name: L2 body wall muscle tiling array extraction1_array1 channel_1


source_name: L2 excretory cell tiling array extraction3_array1 channel_1

value: NC1598 (engineered, target gene clh-4 tagged by 3xFlag::PAB-1)

value: Excretory cell (L2)


source_name: L2 excretory cell tiling array extraction1_array1 channel_1


source_name: L2 intestine tiling array extraction3_array1 channel_1

value: SD1084 (engineered, target gene ges-1 tagged by 3xFlag::PAB-1)

value: Intestine (L2)


source_name: L2 intestine tiling array extraction2_array1 channel_1


source_name: L2 body wall muscle tiling array extraction2_array1 channel_1


source_name: L2 panneural tiling array extraction2_array1 channel_1

value: SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1)

value: Pan-neural (L2)


source_name: L2 intestine tiling array extraction1_array1 channel_1


source_name: L2 reference (mockIP) tiling array extraction3_array1 channel_1

value: reference (L2)


source_name: L3-L4 PVD & OLL neurons tiling array extraction2_array1 channel_1

value: NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1)

value: PVD OLLs (L3-L4)

value: L3-L4 larva 20dC 22h 23dC 24hr post-L1

value: Hermaphrodite


source_name: L3-L4 PVD & OLL neurons tiling array extraction1_array1 channel_1


title: HMVEC-dLy-Neo-DS13146

description: X_Hs_HMVECdLyNeo_E_100603_10_DS13146_W.CEL

source_name: Normal Neonatal Human Lymphatic Microvascular Endothelial Cells, Dermal-Derived


title: HMVEC-dLy-Ad-DS13256

description: X_Hs_HMVECdLyAd_E_100603_16_DS13256_W_3.CEL

source_name: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


source_name: L3-L4 PVD & OLL neurons tiling array extraction3_array1 channel_1


source_name: L2 reference (mockIP) tiling array extraction2_array1 channel_1

value: wild type


source_name: L2 reference (mockIP) tiling array extraction1_array1 channel_1


source_name: L2 panneural tiling array extraction3_array1 channel_1


source_name: L2 excretory cell tiling array extraction2_array1 channel_1


title: HConF-DS11642

source_name: Human Conjunctival Fibroblast

value: Human Conjunctival Fibroblast


title: 14R/13S - repeat 2 - mAdbID:56828

status: Public on Jul 07 2010

city: Bethesda

first: Huei-Fung

last: Tsai

state: MD

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

description: mAdb experiment ID: 56828

hyb_protocol: Hybridization Protocol Other: Microarray hybridization was done at the NIH/NIAID/RTB core facility. The 70-mer oligo arrays were prehybridized at 42°C in prehybridization buffer (5X SSC, 1% BSA, 0.1% SDS) for 30-60 min and then hybridized to the labelled cDNA in 50 ul of hybridization buffer (25% formamide, 5X SSC, 0.2% SDS, 20 ug/ml Poly (dA40-60), 200 ug/ml Cot-1 DNA, 80 ug/ml yeast t-RNA) overnight at 42°C. The microarrays were washed three times in wash buffer A (1X SSC, 0.05% SDS) and washing buffer B (0.1X SSC).

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 3.2;; 3.58 Temperature: 28.68

data_processing:
mAdb Data Processing
Calculation Method: Background correction was done using median intensity minus median background. Calculations were based on signals greater than 100 in both channels and excluding features designated as controls or flagged as bad or not found. Ratios were normalized using the 50th percentile (median).

organism: Nakaseomyces glabratus

source_name: Sensitive Isolate - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Thirty micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated from log phase culture of C. glabrata grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).

value: log-phase culture

value: WT

source_name: Resistant Isolate - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Thirty micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care).

value: CgPDR1 gain-of-function mutation


title: 4R/3S - repeat 4 - mAdbID:83792

description: mAdb experiment ID: 83792

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.73;; 3.74 Temperature: 30.66


title: 14R/13S - repeat 1 - mAdbID:56799

description: mAdb experiment ID: 56799

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 3.22;; 3.62 Temperature: 28.04


title: 4R/3S - repeat 2 - mAdbID:83790

description: mAdb experiment ID: 83790

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.74;; 3.71 Temperature: 30.81


title: 4R/3S - repeat 3 - rev. label - mAdbID:83791

description: mAdb experiment ID: 83791

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.74;; 3.75 Temperature: 30.75

source_name: Sensitive Isolate - Cy5

source_name: Resistant Isolate - Cy3


source_name: L2 panneural tiling array extraction1_array1 channel_1

value: larva mid-L2 20dC 22h post-L1

value: mixed Male and Hermaphrodite population


title: CD8+CX3CR1- DC

status: Public on Jul 28 2010

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

hyb_protocol: According to Affymetrix manual

scan_protocol: According to Affymetrix manual

source_name: spleens

label_protocol: According to Affymetrix manual

growth_protocol: After collagenase D digestion, spleens from Cx3cr1gfp/+ C57BL/6 mice were enriched for CD11c+ cells by magnetic separation according to the manufacturer’s protocol (MiltenyiBiotec GmbH). Splenic CD11chi cells were isolated using the FACS ARIA high-speed sorter (Becton-Dickinson).

extract_protocol: QIAGEN miniRNA extraction kit was used.

value: Cx3cr1gfp/+ C57BL/6

tag: bmp4 treated

tag: dendritic cell


title: 6R/5S - repeat 3 - rev. label - mAdbID:80542

description: mAdb experiment ID: 80542

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.76;; 3.72 Temperature: 30.14


title: HMVEC-dLy-Neo-DS13150

description: X_Hs_HMVECdLyNeo_E_100603_11_DS13150_W.CEL

value: Normal Neonatal Human Lymphatic Microvascular Endothelial Cells, Dermal-Derived


title: CD8+CX3CR1+ DC


title: 6R/5S - repeat 5 - mAdbID:80578

description: mAdb experiment ID: 80578

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.76;; 3.73 Temperature: 30.26


title: 4R/3S - repeat 5 - mAdbID:83800

description: mAdb experiment ID: 83800

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.73;; 3.74 Temperature: 30.54


title: HMVEC-LLy-DS13193

description: X_Hs_HMVECLly_E_100603_13_DS13193_W_2.CEL

source_name: Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived


title: 6R/5S - repeat 1 - mAdbID:80539

description: mAdb experiment ID: 80539

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.76;; 3.85 Temperature: 30.63


title: 6R/5S - repeat 2 - mAdbID:80540

description: mAdb experiment ID: 80540

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.79;; 3.83 Temperature: 30.84


title: 22R/21S - repeat 4 - mAdbID:75030

description: mAdb experiment ID: 75030

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.14;; 2.95 Temperature: 31.94


title: HMEC-DS13921

source_name: Human Mammary Epithelial Cells

value: Human Mammary Epithelial Cells


title: 22R/21S - repeat 5 - rev. label - mAdbID:75032

description: mAdb experiment ID: 75032

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.12;; 2.9 Temperature: 32.09


title: 6R/5S - repeat 4 - rev. label - mAdbID:80541

description: mAdb experiment ID: 80541

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.77;; 3.72 Temperature: 30.17


title: 18R/17S - repeat 3 - mAdbID:65119

description: mAdb experiment ID: 65119

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.22;; 3.53 Temperature: 31


title: 16R/15S - repeat 5 - mAdbID:71142

description: mAdb experiment ID: 71142

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.3;; 3.28 Temperature: 31.3


title: HMVEC-LLy-DS13185

scan_protocol: Affymterix Gene Chip Scanner 3000

value: Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived


title: 12R/11S - repeat 3 - mAdbID:65122

description: mAdb experiment ID: 65122

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.21;; 2.89 Temperature: 31.12


title: 12R/11S - repeat 2 - mAdbID:65120

description: mAdb experiment ID: 65120

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.12;; 3.33 Temperature: 32.03


title: 18R/17S - repeat 4 - mAdbID:64105

description: mAdb experiment ID: 64105

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.1;; 3.37 Temperature: 31


scan_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

source_name: L2 GABA neurons tiling array extraction2_array1 channel_1

value: NC1627 (engineered, target gene C04G2.1 tagged by 3xFlag::PAB-1)

value: GABA neurons (L2)


title: 18R/17S - repeat 5 - rev. label - mAdbID:64106

description: mAdb experiment ID: 64106

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.19;; 3.42 Temperature: 31.06


title: 18R/17S - repeat 2 - mAdbID:65118

description: mAdb experiment ID: 65118

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.06;; 3.46 Temperature: 30.87


title: 12R/11S - repeat 5 - rev. label - mAdbID:64104

description: mAdb experiment ID: 64104

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.02;; 3.34 Temperature: 31


title: 18R/17S - repeat 1 - mAdbID:65117

description: mAdb experiment ID: 65117

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.26;; 2.87 Temperature: 31.36


title: HMVEC-dLy-Ad-DS13261

description: X_Hs_HMVECdLyAd_E_100603_17_DS13261_W.CEL

value: Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived


title: DN DC

scan_protocol: According to Affymetrix manual


title: CD4+ DC


title: 4R/3S - repeat 1 - rev. label - mAdbID:84013

description: mAdb experiment ID: 84013

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.68;; 3.73 Temperature: 30.72


title: 12R/11S - repeat 4 - mAdbID:64103

description: mAdb experiment ID: 64103

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.17;; 3.35 Temperature: 31.09


title: 14R/13S - repeat 3 - mAdbID:57026

description: mAdb experiment ID: 57026

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.05;; 3.11 Temperature: 30.69


title: 14R/13S - repeat 4 - mAdbID:57027

description: mAdb experiment ID: 57027

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.29;; 3.19 Temperature: 30.75


title: 16R/15S - repeat 1 - mAdbID:57720

description: mAdb experiment ID: 57720

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.17;; 3 Temperature: 30.08


title: 16R/15S - repeat 4 - mAdbID:58136

description: mAdb experiment ID: 58136

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.1;; 3.3 Temperature: 30.81


title: 16R/15S - repeat 2 - mAdbID:57722

description: mAdb experiment ID: 57722

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.1;; 3.03 Temperature: 30.57


title: 16R/15S - repeat 3 - rev. label - mAdbID:58135

description: mAdb experiment ID: 58135

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.29;; 2.89 Temperature: 31.39


title: HConF-DS11637

scan_protocol: Affymterix Gene Chip Scanner 3000


title: 22R/21S - repeat 3 - mAdbID:62896

description: mAdb experiment ID: 62896

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.23;; 3.7 Temperature: 31.39


title: 22R/21S - repeat 1 - mAdbID:58800

description: mAdb experiment ID: 58800

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.14;; 3.41;; n/a;; n/a Temperature: 32.31


title: 14R/13S - repeat 5 - rev. label - mAdbID:57029

description: mAdb experiment ID: 57029

scan_protocol: Creator: GenePix Pro 5.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.3;; 3.18 Temperature: 30.87


title: 12R/11S - repeat 1 - mAdbID:58798

description: mAdb experiment ID: 58798

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.27;; 3.28;; n/a;; n/a Temperature: 31.82


title: H7-hESC-DS13133

source_name: Undifferentiated human embryonic stem cells


title: 22R/21S - repeat 2 - mAdbID:62890

description: mAdb experiment ID: 62890

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.14;; 3.56 Temperature: 31.09


title: ex vivo TNP-pLN FDC-1

status: Public on Jul 05 2010

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

description: freshly prepared FDCs from pLN immunized with TNP-KLH

hyb_protocol: The labeled cRNA was hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The image was quantified by using GCOS software.

source_name: mouse FDC from immunized pLNs

label_protocol: RNA was subjected to biotinilated cRNA synthesis by using Target Labeling lit (Affymetrix).

growth_protocol: Balb/cAnNCrlCrlj wild type mice were maintained in specific pathogen-free conditions (SPF) at the animal facility of the Research Center for Allergy and Immunology. To culture FDCs, purified FDCs were cultured in D-MEM with 10% fetal calf serum (FCS), 0.02M HEPES, 0.2mM non-essential amino acids (NEAA), TNFα (5ng/ml) and anti-LTβR (1μg/ml).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen).

treatment_protocol: To stimulate FDCs in vitro, the cells were were cultured without of with the following stimuli: Pam2CSK4 (100ng/ml), LPS (20µg/ml), all-trans-retinoic acid (RA, 40nM).

value: from Balb/cAnNCrlCrlj wild type mice, immunized with TNP-KLH with incomplete Freund's adjuvant

value: Adult mouse lymph nodes


title: ex vivo TNP-pLN FDC-2

department: Research Center for Allergy and Immunology


title: HBEs infected with PR8 pre trypsin PR8pre1.5_E12_1

status: Public on Mar 30 2010

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station

scan_protocol: GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner

data_processing: Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes

source_name: Human bronchial epithelial cells (HBE)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).

growth_protocol: HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).

extract_protocol: Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.

tag: final order

value: Human bronchial epithelial cells (HBE)

tag: sample type

value: HBEs infected with PR8 pre trypsin

tag: agent

value: PR8 pre trypsin

tag: moi

tag: time


title: ex vivo PP FDC-3

description: freshly prepared FDCs from PP

source_name: mouse FDC from PPs

value: from Balb/cAnNCrlCrlj wild type mice, without immunization

value: Adult mouse Peyer's patches


title: ex vivo PP FDC-1

description: freshly prepared FDCs from PP


title: HBEs infected with PR8 pre trypsin PR8pre4_G9_1

value: 4 h


title: HBEs infected with PR8 pre trypsin PR8pre6_B11_1

value: 6 h


title: ex vivo naive pLN FDC-1

description: freshly prepared FDCs from naïve pLN

source_name: mouse FDC from naïve pLNs


title: HBEs infected with PR8 post trypsin PR8post8_D5_2

value: HBEs infected with PR8 post trypsin

value: PR8 post trypsin

value: 8 h


title: HBEs infected with PR8 post trypsin PR8post8_D4_1


title: HBEs infected with PR8 post trypsin PR8post2_A8_a

value: 2 h


title: HBEs infected with PR8 post trypsin PR8post2_A9_b


title: ex vivo PP FDC-2

description: freshly prepared FDCs from PP


title: HBEs infected with PR8 post trypsin PR8post4_G10_a


title: HBEs infected with PR8 post trypsin PR8post4_G11_b


title: ex vivo naive pLN FDC-2

description: freshly prepared FDCs from naïve pLN


title: HBEs infected with PR8 pre trypsin PR8pre8_D3_1


title: ex vivo naive pLN FDC-3

description: freshly prepared FDCs from naïve pLN


title: HBEs infected with PR8 post trypsin PR8post6_B12_a


title: HBEs infected with PR8 post trypsin PR8post18_G6_2


title: HBEs infected with PR8 post trypsin PR8post12_F1_1


title: HBEs infected with PR8 pre trypsin PR8pre2_A7_1


title: HBEs infected with PR8 post trypsin PR8post12_F2_2


title: HBEs infected with PR8 pre trypsin PR8pre1_D8_1

value: 1 h


title: HBEs infected with PR8 post trypsin PR8post6_C1_b


title: HBEs infected with PR8 post trypsin PR8post18_G5_1


title: HBEs infected with PR8 pre trypsin PR8pre18_G4_1


title: HBEs infected with PR8 pre trypsin PR8pre0.5_B11_1


title: HBEs infected with PR8 pre trypsin PR8pre12_E12_1


title: HBEs infected with PR8 pre trypsin PR8pre0.25_A9_1


title: HBEs infected with PR8 post trypsin PR8post1_D9_1


title: HBEs infected with PR8 post trypsin PR8post1_D10_2


title: HBEs treated with media alone MockIFN4_G7_1

description:
HBEs treated with media alone
MockIFN4

value: HBEs treated with media alone

value: media alone


title: HBEs infected with PR8 post trypsin PR8post0.25_H8_1


title: HBEs treated with media alone MockIFN8_D1_1

description:
HBEs treated with media alone
MockIFN8


title: HBEs treated with media alone MockIFN6_B9_1

description:
HBEs treated with media alone
MockIFN6


title: HBEs infected with PR8 post trypsin PR8post1.5_F1_1


title: HBEs treated with media alone MockIFN1.5_E10_1


title: HBEs treated with media alone MockIFN18_G2_1

description:
HBEs treated with media alone
MockIFN18


title: HBEs treated with media alone MockIFN1_D6_a

description:
HBEs treated with media alone
MockIFN1


title: HBEs treated with media alone MockIFN18_G3_2

description:
HBEs treated with media alone
MockIFN18


title: HBEs infected with PR8 post trypsin PR8post1.5_F2_2


title: HBEs treated with LTX transfection reagent LTX8_C7_1

value: LTX transfection reagent


title: HBEs treated with media alone MockIFN4_G8_2

description:
HBEs treated with media alone
MockIFN4


title: HBEs treated with media alone MockIFN0.25_A7_1


title: HBEs infected with PR8 post trypsin PR8post0.5_B12_1


title: HBEs infected with PR8 post trypsin PR8post0.25_H9_2


title: HBEs treated with media alone MockIFN12_E11_2

description:
HBEs treated with media alone
MockIFN12


title: HBEs treated with media alone MockIFN0.5_B9_1


title: HBEs treated with media alone MockIFN1_D7_b

description:
HBEs treated with media alone
MockIFN1


title: HBEs treated with media alone MockIFN6_B10_2

description:
HBEs treated with media alone
MockIFN6


title: HBEs treated with media alone MockIFN2_A6_b

description:
HBEs treated with media alone
MockIFN2


title: HBEs treated with media alone MockIFN0.25_A8_2


title: HBEs treated with media alone MockIFN8_D2_2

description:
HBEs treated with media alone
MockIFN8


title: HBEs treated with media alone MockIFN1.5_E11_2


title: HBEs treated with LTX transfection reagent LTX8_C8_2


title: HBEs treated with media alone MockIFN0.5_B10_2


title: HBEs infected with PR8 post trypsin PR8post0.5_C1_2


title: HBEs treated with media alone MockIFN12_E10_1

description:
HBEs treated with media alone
MockIFN12


title: HBEs treated with media alone MockIFN2_A5_a

description:
HBEs treated with media alone
MockIFN2


title: HBEs treated with LTX transfection reagent LTX6_B4_2


title: HBEs treated with LTX transfection reagent LTX6_B3_1


title: HBEs treated with LTX transfection reagent LTX4_G1_1


title: HBEs treated with LTX transfection reagent LTX1.5_E5_2


title: HBEs treated with LTX transfection reagent LTX12_E4_1


title: HBEs treated with LTX transfection reagent LTX1_C12_1


title: HBEs treated with LTX transfection reagent LTX0.25_A2_2


title: HBEs transfected with vRNA LTX+RNA12_E7_2

description:
HBEs transfected with vRNA
LTX+RNA12

value: HBEs transfected with vRNA

value: vRNA


title: HBEs treated with LTX transfection reagent LTX18_F8_1

value: Human bronchial epithelial cells (HBE)


title: HBEs treated with LTX transfection reagent LTX18_F9_2


title: HBEs treated with LTX transfection reagent LTX1_D1_2


title: HBEs treated with LTX transfection reagent LTX12_E5_2


title: HBEs transfected with vRNA LTX+RNA2_A1_a

description:
HBEs transfected with vRNA
LTX+RNA2


title: HBEs treated with LTX transfection reagent LTX0.5_B3_1


title: HBEs transfected with vRNA LTX+RNA8_C10_2

description:
HBEs transfected with vRNA
LTX+RNA8


title: HBEs transfected with vRNA LTX+RNA18_F11_2

description:
HBEs transfected with vRNA
LTX+RNA18


title: HBEs treated with LTX transfection reagent LTX0.5_B4_2


title: HBEs treated with LTX transfection reagent LTX1.5_E4_1


title: HBEs transfected with vRNA LTX+RNA4_G4_b

description:
HBEs transfected with vRNA
LTX+RNA4


title: HBEs transfected with vRNA LTX+RNA4_G3_a

description:
HBEs transfected with vRNA
LTX+RNA4


title: HBEs transfected with vRNA LTX+RNA1_D2_1

description:
HBEs transfected with vRNA
LTX+RNA1


title: HBEs treated with LTX transfection reagent LTX4_G2_2


title: HBEs transfected with vRNA LTX+RNA1_D3_2

description:
HBEs transfected with vRNA
LTX+RNA1


title: HBEs transfected with vRNA LTX+RNA6_B6_b

description:
HBEs transfected with vRNA
LTX+RNA6


title: HBEs transfected with vRNA LTX+RNA8_C9_1

description:
HBEs transfected with vRNA
LTX+RNA8


title: HBEs transfected with vRNA LTX+RNA1.5_E7_2

description:
HBEs transfected with vRNA
LTX+RNA1.5


title: HBEs transfected with vRNA LTX+RNA18_F10_1

description:
HBEs transfected with vRNA
LTX+RNA18


title: HBEs transfected with vRNA LTX+RNA6_B5_a

description:
HBEs transfected with vRNA
LTX+RNA6


title: HBEs treated with LTX transfection reagent LTX0.25_A1_1


title: HBEs transfected with vRNA LTX+RNA2_A2_b

description:
HBEs transfected with vRNA
LTX+RNA2


title: HBEs transfected with vRNA LTX+RNA12_E6_1

description:
HBEs transfected with vRNA
LTX+RNA12


title: HBEs transfected with vRNA LTX+RNA1.5_E6_1

description:
HBEs transfected with vRNA
LTX+RNA1.5


title: HBEs transfected with vRNA LTX+RNA0.5_B6_2

description:
HBEs transfected with vRNA
LTX+RNA0.5


title: HBEs transfected with vRNA LTX+RNA0.5_B5_1

description:
HBEs transfected with vRNA
LTX+RNA0.5


title: HBEs transfected with vRNA LTX+RNA0.25_A4_2

description:
HBEs transfected with vRNA
LTX+RNA0.25


title: HBEs treated with IFNb IFN6_C5_a

description:
HBEs treated with IFNb
IFN6

value: HBEs treated with IFNb

value: IFNb

tag: dose


title: HBEs treated with IFNb IFN2_B2_b

description:
HBEs treated with IFNb
IFN2


title: HBEs treated with IFNb IFN8_D9_1

description:
HBEs treated with IFNb
IFN8


title: HBEs treated with IFNb IFN6_C6_b

description:
HBEs treated with IFNb
IFN6


title: HBEs treated with IFNb IFN0.25_B2_b

description:
HBEs treated with IFNb
IFN0.25


title: HBEs treated with IFNb IFN1.5_F6_a

description:
HBEs treated with IFNb
IFN1.5


title: HBEs treated with IFNb IFN1_E3_2

description:
HBEs treated with IFNb
IFN1


title: HBEs treated with IFNb IFN12_F7_2

description:
HBEs treated with IFNb
IFN12


title: HBEs treated with IFNb IFN18_G11_2

description:
HBEs treated with IFNb
IFN18


title: HBEs treated with IFNb IFN4_H4_2

description:
HBEs treated with IFNb
IFN4


title: HBEs treated with IFNb IFN1_E2_1

description:
HBEs treated with IFNb
IFN1


title: HBEs treated with IFNb IFN2_B1_a

description:
HBEs treated with IFNb
IFN2


title: HBEs treated with IFNb IFN0.25_B1_a

description:
HBEs treated with IFNb
IFN0.25


title: HBEs treated with IFNb IFN1.5_F7_b

description:
HBEs treated with IFNb
IFN1.5


title: HBEs infected with delNS1 pre trypsin delNS1pre4_G12_1

value: HBEs infected with delNS1 pre trypsin

value: delNS1 pre trypsin


title: HBEs infected with delNS1 pre trypsin delNS1pre2_A10_1


title: HBEs infected with delNS1 pre trypsin delNS1pre12_F3_1


title: HBEs infected with delNS1 pre trypsin delNS1pre8_D6_1


title: HBEs infected with delNS1 pre trypsin delNS1pre18_G7_1


title: HBEs infected with delNS1 pre trypsin delNS1pre6_C2_1


title: HBEs infected with delNS1 pre trypsin delNS1pre1_D11_1


title: HBEs treated with IFNb IFN12_F6_1

description:
HBEs treated with IFNb
IFN12


title: HBEs transfected with vRNA LTX+RNA0.25_A3_1

description:
HBEs transfected with vRNA
LTX+RNA0.25


title: HBEs treated with IFNb IFN4_H3_1

description:
HBEs treated with IFNb
IFN4

value: 4 h


title: HBEs treated with IFNb IFN18_G10_1

description:
HBEs treated with IFNb
IFN18


title: HBEs infected with delNS1 pre trypsin delNS1pre1.5_F3_1


title: HBEs treated with IFNb IFN0.5_C6_2

description:
HBEs treated with IFNb
IFN0.5


title: HBEs treated with IFNb IFN8_D10_2

description:
HBEs treated with IFNb
IFN8


title: HBEs infected with delNS1 post trypsin delNS1post8_D8_2

value: HBEs infected with delNS1 post trypsin

value: delNS1 post trypsin


title: HBEs treated with IFNb IFN0.5_C5_1

description:
HBEs treated with IFNb
IFN0.5


title: HBEs infected with delNS1 post trypsin delNS1post8_D7_1


title: HBEs infected with delNS1 pre trypsin delNS1pre0.25_A10_1


title: HBEs infected with delNS1 post trypsin delNS1post6_C4_b

value: 6 h


title: HBEs infected with delNS1 pre trypsin delNS1pre0.5_C2_1


title: HBEs infected with delNS1 post trypsin delNS1post4_H2_2


title: HBEs infected with delNS1 post trypsin delNS1post1.5_F5_2


title: HBEs infected with delNS1 post trypsin delNS1post6_C3_a


title: HBEs infected with delNS1 post trypsin delNS1post12_F5_2


title: HBEs infected with delNS1 post trypsin delNS1post1_E1_2


title: HBEs infected with delNS1 post trypsin delNS1post2_A12_b


title: pooling of multiple samples to control for plate affects control-poolingAll_H6_5


title: HBEs infected with delNS1 post trypsin delNS1post18_G8_1


title: HBEs infected with delNS1 post trypsin delNS1post0.5_C4_2


title: pooling of multiple samples to control for plate affects control-poolingAll_H5_4


title: HBEs infected with delNS1 post trypsin delNS1post18_G9_2


title: HBEs infected with delNS1 post trypsin delNS1post2_A11_a


title: pooling of multiple samples to control for plate affects control-poolingAll_H10_1


title: HBEs infected with delNS1 post trypsin delNS1post0.25_A11_1


title: pooling of multiple samples to control for plate affects control-poolingAll_H12_3


title: HBEs treated with 6ul of pre trypsin media 6pre8_D11_1

value: pre trypsin media

value: 6ul 1 ug/ml TPCK trypsin

value: 8 h


title: pooling of multiple samples to control for plate affects control-poolingAll_H7_6


title: HBEs infected with delNS1 post trypsin delNS1post4_H1_1


title: HBEs infected with delNS1 post trypsin delNS1post0.5_C3_1


title: HBEs infected with delNS1 post trypsin delNS1post1_D12_1

value: 1 h


title: HBEs treated with 6ul of pre trypsin media 6pre4_H5_1


title: HBEs infected with delNS1 post trypsin delNS1post0.25_A12_2


title: HBEs treated with 6ul of pre trypsin media 6pre18_G12_1


title: HBEs treated with 6ul of pre trypsin media 6pre0.5_C7_1


title: pooling of multiple samples to control for plate affects control-poolingAll_H11_2


title: HBEs infected with delNS1 post trypsin delNS1post12_F4_1


title: HBEs infected with delNS1 post trypsin delNS1post1.5_F4_1


title: HBEs treated with 500ul of post trypsin media 500post1.5_F10_1

value: post trypsin media

value: 500ul 1 ug/ml TPCK trypsin


title: HBEs treated with 500ul of post trypsin media 500post1.5_F11_2


title: HBEs treated with 500ul of post trypsin media 500post4_H8_2


title: HBEs treated with 500ul of post trypsin media 500post8_E2_2


title: HBEs treated with 500ul of post trypsin media 500post18_H3_2


title: HBEs treated with 500ul of post trypsin media 500post8_E1_1


title: HBEs treated with 6ul of pre trypsin media 6pre1.5_F8_1


title: HBEs treated with 500ul of post trypsin media 500post0.5_C10_2


title: HBEs treated with 500ul of post trypsin media 500post4_H7_1


title: HBEs treated with 500ul of post trypsin media 500post0.5_C9_1


title: HBEs treated with 25ul of post trypsin media 25post8_D12_1

value: 25ul 1 ug/ml TPCK trypsin


title: HBEs treated with 25ul of post trypsin media 25post4_H6_1


title: HBEs treated with 25ul of post trypsin media 25post18_H1_1


title: HBEs treated with 25ul of post trypsin media 25post0.5_C8_1


title: HBEs treated with 25ul of post trypsin media 25post1.5_F9_1


title: HBEs treated with 500ul of post trypsin media 500post18_H2_1


title: 0 Dis XIII-UBP6del; (A22034)

status: Public on Feb 25 2010

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIII-UBP6∆ (A22034)

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-08 Scan Time : 13:17:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file
Normalizaton: Default settings of Agilent Feature Extractor

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wt

extract_protocol:
Extraction method: Hoffman-Winston prep:
http://dunham.gs.washington.edu/MDyeastDNAprep.pdf

tag: strain name

value: wt

source_name: Dis XIII-UBP6del (A22034)

value: Dis XIII-UBP6del (A22034)


title: HBEs treated with 100ul of pre trypsin media 100pre8_E3_1

tag: cell type

value: Human bronchial epithelial cells (HBE)

value: 100ul 1 ug/ml TPCK trypsin


title: HBEs treated with 100ul of pre trypsin media 100pre18_H4_1


title: HBEs treated with 100ul of pre trypsin media 100pre0.5_C11_1


title: HBEs treated with 100ul of pre trypsin media 100pre4_H9_1


title: 0 Dis XII-UBP6del; (A22033)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XII-UBP6∆ (A22033)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-07 Scan Time : 14:03:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XII-UBP6del (A22033)

value: Dis XII-UBP6del (A22033)


title: 0 Dis XV-UBP6del; (A22036)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XV-UBP6∆ (A22036)

source_name: Dis XV-UBP6del (A22036)

value: Dis XV-UBP6del (A22036)


title: 0 Dis XVI-UBP6del; (A22037)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XVI-UBP6∆ (A22037)

source_name: Dis XVI-UBP6del (A22037)

value: Dis XVI-UBP6del (A22037)


title: 0 Dis XI-UBP6del; (A22032)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-UBP6∆ (A22032)

source_name: Dis XI-UBP6del (A22032)

value: Dis XI-UBP6del (A22032)


title: 0 Dis XI-del;ubp6-cup1-UBI4 (A25101)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XI-∆ubp6-cup1-UBI4 (A25101)

scan_protocol: Pixel Size : 5 Scan Date : 2009-09-16 Scan Time : 09:05:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis XI-delubp6-cup1-UBI4 (A25101)

value: Dis XI-delubp6-cup1-UBI4 (A25101)


title: 0 Dis V-UBP6del;-lys2 (A23499)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-UBP6∆-lys2 (A23499)

scan_protocol: Pixel Size : 5 Scan Date : 2009-02-09 Scan Time : 15:49:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis V-UBP6del-lys2 (A23499)

value: Dis V-UBP6del-lys2 (A23499)


title: 0 Dis V-del;ubp6-cup1-UBI4 (A25098)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-∆ubp6-cup1-UBI4 (A25098)

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-09 Scan Time : 11:02:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file
Normalizaton: Default settings of Agilent Feature Extractor

source_name: Dis V-delubp6-cup1-UBI4 (A25098)

value: Dis V-delubp6-cup1-UBI4 (A25098)


title: 0 Dis XIV-UBP6del; (A22035)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis XIV-UBP6∆ (A22035)

source_name: Dis XIV-UBP6del (A22035)

value: Dis XIV-UBP6del (A22035)


title: 0 Dis VIII-UBP6del; (A22029)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis VIII-UBP6∆ (A22029)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-02 Scan Time : 13:29:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis VIII-UBP6del (A22029)

value: Dis VIII-UBP6del (A22029)


title: 0 Dis I-UBP6del; (A22025)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis I-UBP6∆ (A22025)

scan_protocol: Pixel Size : 5 Scan Date : 2008-10-02 Scan Time : 16:30:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis I-UBP6del (A22025)

value: Dis I-UBP6del (A22025)


title: 0 Dis V-UBP6del; (A22028)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis V-UBP6∆ (A22028)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-02 Scan Time : 13:27:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis V-UBP6del (A22028)

value: Dis V-UBP6del (A22028)


title: 0 Dis IX-UBP6del; (A22030)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IX-UBP6∆ (A22030)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-02 Scan Time : 13:28:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Dis IX-UBP6del (A22030)

value: Dis IX-UBP6del (A22030)


title: 0 Dis IV-UBP6del; (A22027)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis IV-UBP6∆ (A22027)

scan_protocol: Pixel Size : 5 Scan Date : 2008-11-21 Scan Time : 14:47:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Dis IV-UBP6del (A22027)

value: Dis IV-UBP6del (A22027)


title: 0 Dis II-UBP6del; (A22026)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 Dis II-UBP6∆ (A22026)

scan_protocol: Pixel Size : 5 Scan Date : 2008-09-18 Scan Time : 08:53:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: wt

source_name: Dis II-UBP6del (A22026)

value: Dis II-UBP6del (A22026)


title: 0 WT-UBP6del; (A22024)

description:
Detailed protocols are available in 'GSE20464_protocols.zip', which is linked to the Series GSE20464 record as a supplementary file.
0 WT-UBP6∆ (A22024)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-02 Scan Time : 13:27:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: WT-UBP6del (A22024)

value: WT-UBP6del (A22024)


title: HBEs treated with 100ul of pre trypsin media 100pre1.5_F12_1

source_name: Human bronchial epithelial cells (HBE)

value: Human bronchial epithelial cells (HBE)

value: pre trypsin media

value: 100ul 1 ug/ml TPCK trypsin


title: HEEpiC-DS12763

status: Public on Feb 17 2010

description:
Human Esophageal Epithelial Cells
X_Hs_HEEpiC_E_091214_08_DS12763_W.CEL

scan_protocol: Affymterix Gene Chip Scanner 3000

source_name: Human Esophageal Epithelial Cells

value: Human Esophageal Epithelial Cells


title: NHLF-DS12829

description:
Normal Human Lung Fibroblasts
X_Hs_NHLF_E_091214_10_DS12829_W.CEL

source_name: Normal Human Lung Fibroblasts

value: Normal Human Lung Fibroblasts

tag: term


title: CMK-DS12393

description:
Human Acute Megakaryocytic Leukemia Cells
X_Hs_CMK_E_091118_04_DS12393_W.CEL


title: HCM-DS12592

description:
Human Cardiac Myocytes
X_Hs_HCM_E_091214_04_DS12592_W.CEL

source_name: Human Cardiac Myocytes

value: Human Cardiac Myocytes


title: H7-hESC-DS11909

description:
Undifferentiated human embryonic stem cells
X_Hs_hESCT0_E_091028_02_DS11909_W.CEL


title: HEEpiC-DS12768

description:
Human Esophageal Epithelial Cells
X_Hs_HEEpiC_E_091214_09_DS12768_W.CEL


title: NHLF-DS12834

description:
Normal Human Lung Fibroblasts
X_Hs_NHLF_E_091214_11_DS12834_W.CEL


title: HCF-DS12491

description:
Human Cardiac Fibroblasts
X_Hs_HCF_E_091208_09_DS12491_W.CEL

source_name: Human Cardiac Fibroblasts

value: Human Cardiac Fibroblasts


title: HCF-DS12501

description:
Human Cardiac Fibroblasts
X_Hs_HCF_E_091208_10_DS12501_W.CEL


title: NHDF-neo-DS11923

description:
Neonatal Human Dermal Fibroblasts
X_Hs_NHDFneo_E_091028_04_DS11923_W.CEL

source_name: Neonatal Human Dermal Fibroblasts

value: Neonatal Human Dermal Fibroblasts


title: HNPCEpiC-DS12467

description:
Human Non-Pigment Ciliary Epithelial Cells
X_Hs_HNPCEpiC_E_091208_08_DS12467_W.CEL


title: NHDF-neo-DS11918

description:
Neonatal Human Dermal Fibroblasts
X_Hs_NHDFneo_E_091028_03_DS11918_W.CEL


title: HCPEpiC-DS12447

description:
Human Choroid Plexus Epithelial Cells
X_Hs_HCPEpiC_E_091118_08_DS12447_W.CEL

source_name: Human Choroid Plexus Epithelial Cells

value: Human Choroid Plexus Epithelial Cells


title: AG04449-DS12329

description:
Fetal buttock/thigh fibroblast
X_Hs_AG04449_E_091208_05_DS12329_W.CEL

source_name: Fetal buttock/thigh fibroblast

value: Fetal buttock/thigh fibroblast


title: AG04449-DS12319

description:
Fetal buttock/thigh fibroblast
X_Hs_AG04449_E_091118_01_DS12319_W.CEL


title: HNPCEpiC-DS12471

description:
Human Non-Pigment Ciliary Epithelial Cells
X_Hs_HNPCEpiC_E_091211_02_DS12471_W.CEL


title: AG10803-DS12374

description:
Adult human abdominal skin fibroblasts
X_Hs_AG10803_E_091118_03_DS12374_W.CEL

source_name: Adult human abdominal skin fibroblasts

value: Adult human abdominal skin fibroblasts


title: AG09309-DS12352

description:
Adult human toe fibroblast
X_Hs_AG09309_E_091118_02_DS12352_W.CEL

source_name: Adult human toe fibroblast

value: Adult human toe fibroblast


title: HCPEpiC-DS12457

description:
Human Choroid Plexus Epithelial Cells
X_Hs_HCPEpiC_E_091208_07_DS12457_W.CEL


title: HIPEpiC-DS12694

description:
Human Iris Pigment Epithelial Cells
X_Hs_HIPEpiC_E_091211_07_DS12694_W.CEL

source_name: Human Iris Pigment Epithelial Cells

value: Human Iris Pigment Epithelial Cells


title: AG09319-DS12291

description:
Adult human gum tissue fibroblasts
X_Hs_AG09319_E_091208_04_DS12291_W.CEL

source_name: Adult human gum tissue fibroblasts

value: Adult human gum tissue fibroblasts


title: HCM-DS12599

description:
Human Cardiac Myocytes
X_Hs_HCM_E_091214_05_DS12599_W.CEL


title: AG04450-DS12255

description:
Fetal lung fibroblast
X_Hs_AG04450_E_091208_01_DS12255_W.CEL

source_name: Fetal lung fibroblast

value: Fetal lung fibroblast


title: AG04450-DS12270

description:
Fetal lung fibroblast
X_Hs_AG04450_E_091208_02_DS12270_W.CEL


title: HAEpiC-DS12673

description:
Human Amniotic Epithelial Cells
X_Hs_HAEpiC_E_091211_06_DS12673_W.CEL

source_name: Human Amniotic Epithelial Cells

value: Human Amniotic Epithelial Cells


title: AG10803-DS12384

description:
Adult human abdominal skin fibroblasts
X_Hs_AG10803_E_091208_06_DS12384_W.CEL


title: AG09319-DS12286

description:
Adult human gum tissue fibroblasts
X_Hs_AG09319_E_091208_03_DS12286_W.CEL


title: AG09309-DS12357

description:
Adult human toe fibroblast
X_Hs_AG09309_E_091211_01_DS12357_W.CEL


title: HRPEpiC-DS12568

description:
Human Retinal Pigment Epithelial Cells
X_Hs_HRPEpiC_E_091211_03_DS12568_W.CEL

source_name: Human Retinal Pigment Epithelial Cells

value: Human Retinal Pigment Epithelial Cells


title: HIPEpiC-DS12699

description:
Human Iris Pigment Epithelial Cells
X_Hs_HIPEpiC_E_091214_07_DS12699_W.CEL


title: Gsc+Sox17+Endoderm

status: Public on Nov 25 2009

city: Tallahassee

first: David

middle: M.

last: Gilbert

state: Florida

address: 319 Stadium Drive

institute: Florida State University

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 labeled DNA samples (6 ug) were hybridized to a Nimblegen mouse expression microarray representing 42,586 transcripts (Roche NimbleGen Inc., 2006-08-03_MM8_60mer_expr).

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw data (i.e. from .pair files) were converted to gene-by-gene data of 42,586 transcripts using RMA algorithm in NimbleScan.

source_name: Total RNA extracted from Gsc+Sox17+Endoderm

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, RNA specimens were converted to double-stranded cDNA according to NimbleGen's instructions, and cDNA samples (1 ug each) were Cy3-labeled by Klenow reaction using end-labeled Cy3-random 9-mers.

extract_protocol: Total RNA was prepared using RNeasy Kit (QIAGEN) for most samples, following the manufacturer's instructions. Alternatively, RNAqueous-  Micro kit (Ambion) was used to isolate total RNA for low yield samples derived  from cells collected by flow cytometry (Gsc+Sox17- Mesoderm and Gsc+Sox17+ Endoderm RNA).

tag: cell line


title: Gsc+Sox17-Mesoderm

source_name: Total RNA extracted from Gsc+Sox17-Mesoderm


title: HRPEpiC-DS12583

description:
Human Retinal Pigment Epithelial Cells
X_Hs_HRPEpiC_E_091208_11_DS12583_W.CEL


title: D3 EBM6R, replicate 2

source_name: Total RNA extracted from D3 EBM6R


title: EpiSC7, replicate 1

source_name: Total RNA extracted from EpiSC7


title: NB4-DS12543

description:
acute promyelocytic leukemia cell line
X_Hs_NB4_E_091214_03_DS12543_W.CEL

source_name: acute promyelocytic leukemia cell line

value: acute promyelocytic leukemia cell line


title: HAEpiC-DS12663

description:
Human Amniotic Epithelial Cells
X_Hs_HAEpiC_E_091211_05_DS12663_W.CEL


title: NB4-DS12538

description:
acute promyelocytic leukemia cell line
X_Hs_NB4_E_091214_02_DS12538_W.CEL


title: EpiSC7, replicate 2


title: D3 NPC/EBM9, replicate 1

source_name: Total RNA extracted from D3 NPC/EBM9


title: D3 NPC/EBM9, replicate 2


title: D3 EBM6R, replicate 1


title: Replication timing of Gsc+Sox17+Endoderm

description: merge replicates 1 and 2

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (6 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of Gsc+Sox17+ Endoderm

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

value: Gsc+Sox17+ Endoderm (day6 differentiated ESCs)

source_name: Late-replicating DNA of Gsc+Sox17+ Endoderm


title: Jurkat-DS12659

description:
T lymphoblastoid cell line derived from an acute T cell leukemia
X_Hs_JURKAT_E_091211_04_DS12659_W.CEL


title: D3 EBM6, replicate 2

source_name: Total RNA extracted from D3 EBM6


title: D3 EBM6, replicate 1


title: Replication timing of 46C NPC/ASd6

source_name: Early-replicating DNA of 46C NPC/ASd6

value: NPC, ASd6

source_name: Late-replicating DNA of 46C NPC/ASd6


title: D3 EBM3, replicate 2

source_name: Total RNA extracted from D3 EBM3


title: Replication timing of partially-reprogrammed iPSC, 1A2

source_name: Early-replicating DNA of partially-reprogrammed iPSC, 1A2

value: piPSC, 1A2

value: partially reprogrammed iPSC (induced pluripotent stem cells), female

source_name: Late-replicating DNA of partially-reprogrammed iPSC, 1A2


title: Replication timing of Gsc+Sox17-Mesoderm

description: merge replicates 1 and 2

source_name: Early-replicating DNA of Gsc+Sox17- Mesoderm

value: Gsc+Sox17- Mesoderm (day6 differentiated ESCs)

source_name: Late-replicating DNA of Gsc+Sox17- Mesoderm


title: Replication timing of J185a myoblast

description: merge replicates 1 and 2

source_name: Early-replicating DNA of J185a Myoblast

value: Fetal myoblast

source_name: Late-replicating DNA of J185a Myoblast


title: Replication timing of D3 NPC/EBM9

description: merge replicates 1 and 2

source_name: Early-replicating DNA of D3 NPC/EBM9

value: EBM9/NPC (day9 differentiated ESCs)

source_name: Late-replicating DNA of D3 NPC/EBM9


title: Replication timing of partially-reprogrammed iPSC, 1B3

source_name: Early-replicating DNA of partially-reprogrammed iPSC, 1B3

value: piPSC, 1B3

source_name: Late-replicating DNA of partially-reprogrammed iPSC, 1B3


title: Replication timing of MEF (male)

source_name: Early-replicating DNA of MEF (male)

value: MEF

value: MEF (embryonic fibroblasts), male

source_name: Late-replicating DNA of MEF (male)


title: Replication timing of D3 EBM6

description: merge replicates 1 and 2

source_name: Early-replicating DNA of EBM6

value: EBM6 (day6 differentiated ESCs)

source_name: Late-replicating DNA of EBM6


title: MCF-7-DS12619

description:
mammary gland, adenocarcinoma
X_Hs_MCF7_E_091214_06_DS12619_W.CEL

source_name: mammary gland, adenocarcinoma

value: mammary gland, adenocarcinoma


title: Replication timing of MEF (female)

source_name: Early-replicating DNA of MEF (female)

value: MEF (embryonic fibroblasts), female

source_name: Late-replicating DNA of MEF (female)


title: D3 EBM3, replicate 1

source_name: Total RNA extracted from D3 EBM3


title: D3 ESC, replicate 2

source_name: Total RNA extracted from D3 ESC


title: SKMC-DS11949

description:
Human skeletal muscle cells
X_Hs_SKMC_E_091028_05_DS11949_W.CEL

source_name: Human skeletal muscle cells

value: Human skeletal muscle cells


title: D3 ESC, replicate 1


title: Replication timing of D3 EBM3

description: merge replicates 1 and 2

source_name: Early-replicating DNA of EBM3

value: EBM3 (day3 differentiated ESCs)

source_name: Late-replicating DNA of EBM3


title: Replication timing of EpiSC7

description: merge replicates 1 and 2

source_name: Early-replicating DNA of EpiSC7

value: Epiblast-derived stem cells, female

source_name: Late-replicating DNA of EpiSC7


title: Replication timing of iPSC, 1D4

source_name: Early-replicating DNA of iPSC, 1D4

value: iPSC, 1D4

value: iPSC (induced pluripotent stem cells), female

source_name: Late-replicating DNA of iPSC, 1D4


title: Replication timing of iPSC

description: merge replicates 1 and 2

source_name: Early-replicating DNA of iPSC

value: iPSC

value: iPSC (induced pluripotent stem cells)

source_name: Late-replicating DNA of iPSC


title: Replication timing of D3 EPL

description: merge replicates 1 and 2

source_name: Early-replicating DNA of EPL cells

value: EPL (early primitive ectoderm-like) cells

source_name: Late-replicating DNA of EPL cells


title: Replication timing of partially-reprogrammed iPSC, V3

source_name: Early-replicating DNA of partially-reprogrammed iPSC, V3

value: piPSC, V3

value: partially reprogrammed iPSC (induced pluripotent stem cells), female

source_name: Late-replicating DNA of partially-reprogrammed iPSC, V3


title: Replication timing of EpiSC5, clone O

description: merge replicates 1 and 2

source_name: Early-replicating DNA of EpiSC5, clone O

value: EpiSC5, clone O

value: Epiblast-derived stem cells

source_name: Late-replicating DNA of EpiSC5, clone O


title: Replication timing of TT2 ESC

description: merge replicates 1 and 2

source_name: Early-replicating DNA of TT2 ESC

value: ESC

source_name: Late-replicating DNA of TT2 ESC


title: Replication timing of 46C ESC

description: merge replicates 1 and 2

source_name: Early-replicating DNA of 46C ESC

source_name: Late-replicating DNA of 46C ESC


title: Replication timing of D3 ESC

description: merge replicates 1 and 2

source_name: Early-replicating DNA of D3 ESC

source_name: Late-replicating DNA of D3 ESC


title: Replication timing of TT2 NPC/ASd9

description: merge replicates 1 and 2

source_name: Early-replicating DNA of TT2 NPC/ASd9

value: NPC, ASd9

source_name: Late-replicating DNA of TT2 NPC/ASd9


title: Replication timing of iPSC, 2D4

source_name: Early-replicating DNA of iPSC, 2D4

value: iPSC, 2D4

source_name: Late-replicating DNA of iPSC, 2D4


title: SKMC-DS11939

status: Public on Nov 19 2009

source_name: human skeletal muscle cells

treatment_protocol: not applicable

value: human skeletal muscle cells


title: BG02ES-SH01

source_name: human embryonic stem cell (hESC) BG02

value: human embryonic stem cell (hESC) BG02


title: HGF-DS11752

source_name: human gingaval fibroblast

value: human gingaval fibroblast


title: PANC-1-DS9955

source_name: pancreatic carcinoma

value: pancreatic carcinoma


title: MCF-7-DS9445

source_name: mammary gland, adenocarcinoma

value: mammary gland, adenocarcinoma


title: H0287-SH02

source_name: human lymphoblastoid cell line derived from peripheral blood (male)


title: HMEC-DS8680

source_name: human mammary epithelial cells

value: human mammary epithelial cells


title: HL-60-DS11733

source_name: human promyelocytic leukemia cells

value: human promyelocytic leukemia cells


title: HGF-DS11738


title: PANC-1-DS9873


title: SAEC-DS10514

source_name: small airway epithelial cells

value: small airway epithelial cells


title: NHEK-DS11474

source_name: adult normal human epidermal keratinocytes


title: BJ-DS11522

source_name: skin fibroblast

value: skin fibroblast


title: HeLa-S3-DS11528

source_name: cervical carcinoma

value: cervical carcinoma


title: HRCE-DS10662

source_name: human renal cortical epithelial cells

value: human renal cortical epithelial cells


title: K562-DS11524

source_name: chronic myeloid leukemia

value: chronic myeloid leukemia


title: SK-N-SH_RA-DS10153

source_name: neuroblastoma cell line differentiated w/ retinoic acid


title: HeLa-S3-DS8200


title: Th2-DS7842

source_name: primary human Th2 T cells

value: primary human Th2 T cells


title: GM12878-DS11526

source_name: lymphoblastoid

value: lymphoblastoid


title: HUVEC-DS10060

source_name: umbilical vein endothelial cells

value: umbilical vein endothelial cells


title: NB4-DS10683

source_name: acute promyelocytic leukemia cell line

value: acute promyelocytic leukemia cell line


title: K562-DS11525


title: Jurkat-DS10681

source_name: T lymphoblastoid cell line derived from an acute T cell leukemia


title: SAEC-DS10518


title: E coli LY180_rep1

status: Public on Aug 25 2009

city: Gainesville

first: Peter

middle: Christopher

last: Turner

state: FL

address: Bldg 981, Museum Road

department: Micro and Cell Science

institute: University of Florida

description: This data is the first of 2 replicates (OID 8641)

hyb_protocol: Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

organism: Escherichia coli

label_protocol: Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown in AM1 medium with 10% xylose to OD 550 = 1.5 (0.66 g dcw/liter). 4 replicate 350 ml fermentors per strain.

extract_protocol: Cells were chilled in dry ice/ethanol, centrifuged, and the pellet resuspended in RNA Later (Qiagen) before storing at –80 C. Total RNA was extracted using the RNeasy Mini kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.

treatment_protocol: Samples were taken at OD = 1.5, then furfural added to 0.5 g/L. Samples were taken at 15 min after furfural addition.

value: wild-type (ethanologenic)


title: HRE-DS10641

source_name: human renal epithelial cells

value: human renal epithelial cells


title: Th1-DS7840

source_name: primary human Th1 T cells

value: primary human Th1 T cells


title: E coli EMFR9_w 0.5g/L Furfural_rep1

source_name: EMFR9 + furfural

value: furfural resistant mutant


title: SK-N-SH_RA-DS8482

value: neuroblastoma cell line differentiated w/ retinoic acid


title: E coli LY180_w 0.5g/L Furfural_rep1

source_name: LY180 + furfural


title: HRE-DS10631


title: E coli EMFR9_rep1


title: K562-DS7664


title: SKMC-DS7911

source_name: human skeletal muscle cells

value: human skeletal muscle cells


title: SF268_PI103_Brepeat_1hr

status: Public on Apr 21 2009

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 5ug of Cy5 labelled sample was mixed with Cy5 labelled control totalRNA,concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 μl hybridisation mix (19 μl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150μl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000B-2. Voltage: 510, 400. Resolution (micrometers): 10.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: SF268_PI103_B_1hr(Brain Cancer Cell Line Treated with PI103  )

label_protocol: Total RNA (5 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (GE, UK) using the Cyscribe Indirect cDNA Labelling Kit protocol (GE, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Total RNA was extracted from cells with the ABI PRISM™ 6100 Nucleic Acid PrepStation, using the RNA Cell method according to instructions from the manufacturer

tag: Cell Line

tag: Time Course

value: 1 hour

source_name: SF268_Control(Untreated tumour cell line SF268)


title: mouse dendritic cells from Peyer's patch

status: Public on Apr 28 2009

city: Wuhan

first: quan

last: xing

address: Luoyu Road 237

country: China

institute: wuhan university

description: Used CD11c microbeads to select the dendritic cells from mice Peyer's patches, then utilized FACS sorting to sort cd11c+ dendritic cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression levels of probe sets were normalized using GCOS. As selection criteria we used: fold change > 2 or < -2 and raw p value < 0.05

source_name: dendritic cells from Peyer's patch

label_protocol: 15ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

extract_protocol: Total RNA was extracted from tissues by a phenol-chloroform method (TRIZOL reagent) and performed a cleanup using QIAGEN RNeasy Total RNA Isolation kit according to manufacturer’s protocol

tag: strain

value: Balb/c

tag: gender

value: female

tag: age

value: 4 weeks

tag: tissue

value: Peyer's patch

value: dendritic cells


title: mouse epidermal Langerhans cells

description: Used MHC class II microbeads to select the Langerhans cells from mice epidermis, then utilized FACS sorting to sort MHC class II Langerhans cells.

source_name: Langerhans cells from epidermis

value: skin


title: U87MG_PI103_C_6hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 530, 430. Resolution (micrometers): 10.

source_name: U87MG_PI103_C_6hr(Brain Cancer Cell Line Treated with PI103)

value: 6 hour

source_name: U87MG_Control(Untreated tumour cell line to be used as control.)


title: SF268_PI103_Arepeat_1hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 390. Resolution (micrometers): 10.

source_name: SF268_PI103_A_1hr(Brain Cancer Cell Line Treated with PI103)


title: U87MG_PI103_C_24hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 510, 430. Resolution (micrometers): 10.

source_name: U87MG_PI103_C_24hr(Brain Cancer Cell Line Treated with PI103)

value: 24 hour


title: U87MG_PI103_C_12hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 400, 350. Resolution (micrometers):10.

source_name: U87MG_PI103_C_12hr(Brain Cancer Cell Line Treated with PI103)

value: 12 hour


title: GM06990-DS7748

source_name: lymphoblastoid

value: lymphoblastoid


title: U87MG_PI103_C_2hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 400. Resolution (micrometers): 10.

source_name: U87MG_PI103_C_2hr(Brain Cancer Cell Line Treated with PI103)

value: 2 hour


title: U87MG_PI103_B_24hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 410. Resolution (micrometers): 10.

source_name: U87MG_PI103_B_24hr(Brain Cancer Cell Line Treated with PI103)


title: HepG2-DS7764

source_name: liver carcinoma

value: liver carcinoma


title: HepG2-DS7768


title: GM12878-DS8626


title: HMEC-DS8683

source_name: human mammary epithelial cells

value: human mammary epithelial cells


title: U87MG_PI103_B_12hr

source_name: U87MG_PI103_B_12hr(Brain Cancer Cell Line Treated with PI103)


title: SK-N-SH_RA-DS8476

source_name: neuroblastoma cell line differentiated w/ retinoic acid


title: U87MG_PI103_B_1hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 430. Resolution (micrometers): 10.

source_name: U87MG_PI103_B_1hr(Brain Cancer Cell Line Treated with PI103  )


title: U87MG_PI103_B_30min

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 450. Resolution (micrometers): 10.

source_name: U87MG_PI103_B_30min(Brain Cancer Cell Line Treated with PI103)

value: 30 minute


title: U87MG_PI103_A_2hr

source_name: U87MG_PI103_A_2hr(Brain Cancer Cell Line Treated with PI103)


title: U87MG_PI103_A_12hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 430. Resolution (micrometers): 10.

source_name: U87MG_PI103_A_12hr(Brain Cancer Cell Line Treated with PI103)


title: U87MG_PI103_A_24hr

source_name: U87MG_PI103_A_24hr(Brain Cancer Cell Line Treated with PI103)


title: U87MG_PI103_A_1hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 450. Resolution (micrometers): 10.

source_name: U87MG_PI103_A_1hr(Brain Cancer Cell Line Treated with PI103)


title: GM06990-DS7784


title: HL-60-DS7830

source_name: human promyelocytic leukemia cells

value: human promyelocytic leukemia cells


title: U87MG_PI103_A_6hr

scan_protocol: Scanner: Axon4000B-2. Voltage:500, 440. Resolution (micrometers):10.

source_name: U87MG_PI103_A_6hr(Brain Cancer Cell Line Treated with PI103)

source_name: U87MG_Control(Untreated tumour cell line to be used as control.)


title: U87MG_PI103_C_1hr

source_name: U87MG_PI103_C_1hr(Brain Cancer Cell Line Treated with PI103  )


title: SF268_PI103_C_24hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 390. Resolution (micrometers): 10.

source_name: SF268_PI103_C_24hr(Brain Cancer Cell Line Treated with PI103)

source_name: SF268_Control(Untreated tumour cell line SF268)


title: SF268_PI103_C_30min

source_name: SF268_PI103_C_30min(Brain Cancer Cell Line Treated with PI103)


title: U87MG_PI103_B_6hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 410. Resolution (micrometers): 10.

source_name: U87MG_PI103_B_6hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_B_24hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 400, 320. Resolution (micrometers): 10.

source_name: SF268_PI103_B_24hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_C_6hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 420. Resolution (micrometers): 10?.

source_name: SF268_PI103_C_6hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_Brepeat_2hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 510, 400. Resolution (micrometers): 10.

source_name: SF268_PI103_B_2hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_C_12hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 400. Resolution (micrometers): 10.

source_name: SF268_PI103_C_12hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_B_6hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 440, 340. Resolution (micrometers): 10.

source_name: SF268_PI103_B_6hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_C_2hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 390. Resolution (micrometers):10.

source_name: SF268_PI103_C_2hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_C_1hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 400. Resolution (micrometers): 10.

source_name: SF268_PI103_C_1hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_B_12hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 390, 340. Resolution (micrometers): 10.

source_name: SF268_PI103_B_12hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_B_1hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 380. Resolution (micrometers): 10.

source_name: SF268_PI103_B_1hr(Brain Cancer Cell Line Treated with PI103  )


title: SF268_PI103_B_30min

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 400. Resolution (micrometers): 10.

source_name: SF268_PI103_B_30min(Brain Cancer Cell Line Treated with PI103)


title: BJ-DS7708

scan_protocol: Affymterix Gene Chip Scanner 3000

source_name: skin fibroblast

value: skin fibroblast


title: U87MG_PI103_A_30min

scan_protocol: Scanner: Axon4000B-2. Voltage: 520, 450. Resolution (micrometers): 10.

source_name: U87MG_PI103_A_30min(Brain Cancer Cell Line Treated with PI103)

source_name: U87MG_Control(Untreated tumour cell line to be used as control.)


title: SF268_PI103_A_12hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 540, 460. Resolution (micrometers): 10.

source_name: SF268_PI103_A_12hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_A_2hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 370, 310. Resolution (micrometers): 10.

source_name: SF268_PI103_A_2hr(Brain Cancer Cell Line Treated with PI103  )

source_name: SF268_Control(Untreated tumour cell line SF268)


title: GM12878-DS8623

source_name: lymphoblastoid


title: SF268_PI103_A_6hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 530, 460. Resolution (micrometers): 10.

source_name: SF268_PI103_A_6hr(Brain Cancer Cell Line Treated with PI103)


title: BJ-DS11523


title: U87MG_PI103_B_2hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 420. Resolution (micrometers): 10.

source_name: U87MG_PI103_B_2hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_B_2hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 390. Resolution (micrometers): 10.

source_name: SF268_PI103_B_2hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_A_24hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 540, 440. Resolution (micrometers): 10.

source_name: SF268_PI103_A_24hr(Brain Cancer Cell Line Treated with PI103)


title: SF268_PI103_A_1hr

scan_protocol: Scanner: Axon4000B-2. Voltage: 550, 460. Resolution (micrometers): 10.

source_name: SF268_PI103_A_1hr(Brain Cancer Cell Line Treated with PI103)

value: 1 hour


title: 26_skin_pre__

status: Public on Apr 01 2009

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days

scan_protocol: Scanner: Axon4000B-2. Voltage: 480,370. Resolution (micrometers): 10.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

source_name: 26_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 256mg/2.)

extract_protocol: Total RNA was isolated and purified from the Trizol fraction with the RNeasy Mini Kit (Qiagen Westburg bv., Leusden, The Netherlands).

tag: treatment

value: pre treatment

tag: sample tissue type

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)

extract_protocol: Universal Human total RNA Supplied By Stratagene    Centrifuge @ 12000g for 20min at 4C, Pipette out supernatant, add 200ul of 70% Ethanol, vortex and centrifuge @ 12000g for 20min. Pipette out supernatant and leave to air dry for 30 min. Add 200ul of RNAse free water.

value: Mixed Pool of Human Cell Lines


title: Caco-2-DS11539

source_name: colorectal adenocarcinoma

value: colorectal adenocarcinoma


title: 22_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 350. Resolution (micrometers): 10.

source_name: 22_blood_post(Blood taken post treatment, ES-285 dose 256mg/2.)

extract_protocol: RNA was extracted from whole blood using the PreAnalytiX PAXGene system according to the manufacturers instructions. The total RNA samples were then further purified using Qiagen RNeasy Cleanup, as manufacturers instructions.

value: post treatment

value: blood


title: 25_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 475,350. Resolution (micrometers): 10.

source_name: 25_skin_post(  Skin Biopsy taken post treatment, ES-285 dose 256mg/2.)

value: skin


title: 01_blood_post

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were left at 42C for 3 days.

scan_protocol: Scanner: Axon4000B-2. Voltage: 510, 360. Resolution (micrometers): 10.

source_name: 01_blood_post(Blood taken post treatment, ES-285 dose 4mg/2.)


title: 12_blood_post

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days.

scan_protocol: Scanner: Axon4000B-2. Voltage: 520, 452. Resolution (micrometers): 10.

source_name: 12_blood_post(Blood taken post treatment, ES-285 dose 32mg/2.)


title: 10_blood_pre

scan_protocol: Scanner: Axon4000B-2. Voltage: 555,438. Resolution (micrometers): 10.

source_name: 10_blood_pre(Blood taken pre treatment, ES-285 dose 16mg/2.)


title: 26_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 530,390. Resolution (micrometers): 10.

source_name: 26_skin_post(skin biopsy taken post treatment, ES-285 dose 256mg/2.)


title: 10_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 520, 425. Resolution (micrometers): 10.

source_name: 10_blood_post(Blood taken post treatment, ES-285 dose 16mg/2.)


title: 26_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 440,320. Resolution (micrometers): 10.

source_name: 26_blood_pre(Blood taken pre treatment, ES-285 dose 256mg/2.)


title: 25_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 600,325. Resolution (micrometers): 10.

source_name: 25_skin_pre(  Skin Biopsy taken pre treatment, ES-285 dose 256mg/2.)