title: 5713384020_H

description: SAMPLE 229


title: 5713384020_G

status: Public on May 01 2013

type: RNA

city: Seoul

first: Yuyoung

last: Lee

address: 50 Irwon-Dong, Gangnam-Gu

country: South Korea

institute: SMC

description: SAMPLE 228

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software package to extract raw data was Genomestudio. The intensity of the probes was transformed by binary logarithm and then was normalized using the quantile normalization method.

molecule: total RNA

organism: Homo sapiens

source_name: cervical cancer

label_protocol: RNA was labelled using the WG-DASL kit from Illumina.

extract_protocol: RNA was extracted using a High Pure RNA Paraffin Kit protocol - Roche.

tag: Stage

tag: largest diameter


title: 5713384020_F

description: SAMPLE 227


title: 5713384020_E

description: SAMPLE 226


title: 5713384019_I

description: SAMPLE 221


title: 5713384019_H

description: SAMPLE 220


title: 5713384020_C

description: SAMPLE 224


title: PCL-030_miRNA_1

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-030

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55¡C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Agilent Feature Extraction Software version 10.7.3.1 (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as absent (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

source_name: Primary plasma cell leukemia patient PCL-030

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37¡C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: tissue

value: Primary plasma cell leukemia

tag: igh translocation


title: PCL-027_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-027

source_name: Primary plasma cell leukemia patient PCL-027


title: PCL-029_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-029

source_name: Primary plasma cell leukemia patient PCL-029


title: PCL-028_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-028

source_name: Primary plasma cell leukemia patient PCL-028


title: 5713384019_L

description: SAMPLE 222


title: 5713384020_A

description: SAMPLE 223


title: PCL-026_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-026

source_name: Primary plasma cell leukemia patient PCL-026


title: 5713384019_G

description: SAMPLE 219

value: IIA


title: 5713384019_C

description: SAMPLE 218


title: 5713384015_H

description: SAMPLE 215


title: 5713384019_B

description: SAMPLE 217


title: 5713384015_L

description: SAMPLE 216


title: 5713384015_A

description: SAMPLE 213


title: PCL-023_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-023

source_name: Primary plasma cell leukemia patient PCL-023


title: PCL-021_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-021

source_name: Primary plasma cell leukemia patient PCL-021


title: 5713384020_D

description: SAMPLE 225


title: 5713384013_L

description: SAMPLE 212


title: PCL-020_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-020

source_name: Primary plasma cell leukemia patient PCL-020


title: 5713384013_J

description: SAMPLE 210


title: 5713384013_I

description: SAMPLE 209


title: 5713384015_B

description: SAMPLE 214


title: PCL-019_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-019

source_name: Primary plasma cell leukemia patient PCL-019


title: 5713384013_K

description: SAMPLE 211


title: MM-253_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-253

source_name: Multiple myeloma patient MM-253

value: Multiple myeloma

tag: tc classification


title: MM-295_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-295

source_name: Multiple myeloma patient MM-295


title: PCL-017_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-017

source_name: Primary plasma cell leukemia patient PCL-017


title: PCL-016_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-016

source_name: Primary plasma cell leukemia patient PCL-016


title: MM-243_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-243

source_name: Multiple myeloma patient MM-243


title: 5713384013_D

description: SAMPLE 207


title: PCL-018_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-018

source_name: Primary plasma cell leukemia patient PCL-018


title: 5713384013_B

description: SAMPLE 205


title: MM-239_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-239

source_name: Multiple myeloma patient MM-239


title: MM-229_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-229

source_name: Multiple myeloma patient MM-229


title: MM-246_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-246

source_name: Multiple myeloma patient MM-246


title: 5713384013_C

description: SAMPLE 206

source_name: cervical cancer


title: 5713384057_J

description: SAMPLE 200


title: 5713384013_F

description: SAMPLE 208


title: 5713384057_K

description: SAMPLE 201


title: 5713384005_I

description: SAMPLE 203


title: MM-177_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-177

source_name: Multiple myeloma patient MM-177


title: MM-212_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-212

source_name: Multiple myeloma patient MM-212


title: MM-179_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-179

source_name: Multiple myeloma patient MM-179


title: 5713384057_G

description: SAMPLE 198


title: MM-206_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-206

source_name: Multiple myeloma patient MM-206


title: 5713384057_C

description: SAMPLE 197


title: MM-143_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-143

source_name: Multiple myeloma patient MM-143


title: MM-154_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-154

source_name: Multiple myeloma patient MM-154


title: MM-131_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-131

source_name: Multiple myeloma patient MM-131


title: 5713384047_J

description: SAMPLE 195


title: 5713384047_K

description: SAMPLE 196


title: 5713384047_H

description: SAMPLE 193


title: MM-123_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-123

source_name: Multiple myeloma patient MM-123


title: 5713384057_H

description: SAMPLE 199


title: MM-115_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-115

source_name: Multiple myeloma patient MM-115


title: 5713384047_I

description: SAMPLE 194


title: MM-104_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-104

source_name: Multiple myeloma patient MM-104


title: siPBX1 treated with EGF rep2

city: Lebanon

first: luca

last: magnani

state: NH

address: NCCC one medical drive

department: Genetics

country: USA

institute: Dartmouth College

description: replicate 2

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: siPBX1 treated with EGF

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

growth_protocol: Cells were grown in stripped media (DMEM w/o phenol, CDT treated serum 10%, glutamine and penicillin/streptomycin).

extract_protocol: RNA was extracted with  with QIAGEN RNeasy  kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Efficient knock down was validated with RT-qPCR.

treatment_protocol: 72h post transfection with the appropriate siRNA, cells were stimulated with 100ng/mL EGF or water for 3h prior RNA extraction

tag: cell line

tag: cell type

value: breast cancer

tag: er expression

value: postitive


title: 5713384047_C

description: SAMPLE 190


title: siPBX1 treated with DMSO rep2

description: replicate 2

source_name: siPBX1 treated with DMSO


title: siControl treated with DMSO rep2

description: replicate 2

source_name: siControl treated with DMSO


title: siControl treated with EGF rep2

description: replicate 2

source_name: siControl treated with EGF


title: siPBX1 treated with EGF rep1

description: replicate 1


title: 5713384047_F

description: SAMPLE 192


title: 5713384047_D

description: SAMPLE 191


title: PCL-022_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-022

source_name: Primary plasma cell leukemia patient PCL-022


title: MM-074_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-074

source_name: Multiple myeloma patient MM-074


title: siPBX1 treated with DMSO rep1

description: replicate 1


title: siControl treated with DMSO rep1

description: replicate 1


title: siControl treated with EGF rep1

description: replicate 1


title: 5713384047_B

description: SAMPLE 189

source_name: cervical cancer


title: MM-069_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-069

source_name: Multiple myeloma patient MM-069


title: PBX_C2

description: LTED treated with siCTRL rep2

source_name: LTED treated with siCTRL

growth_protocol: LTED are growth in DMEM +10% CDT treated FBS + glutamine + pen/strep.

extract_protocol: mRNA was extracted using RNAeasy (quiagen) according to manufacturer instruction.

treatment_protocol: Cells were treated with MRK003 or siPBX1 for 72h before mRNA was extracted. Controls were siCTRL or DMSO.

value: LTED

value: endocrine therapy resistant breast cancer


title: PBX_C1

description: LTED treated with siCTRL rep1


title: PBX_3

description: LTED treated with siPBX1 rep3

source_name: LTED treated with siPBX1


title: 5713384047_A

description: SAMPLE 188


title: 5713384046_L

description: SAMPLE 187


title: PBX_2

description: LTED treated with siPBX1 rep2


title: MM-052_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-052

source_name: Multiple myeloma patient MM-052


title: 5713384046_J

description: SAMPLE 186


title: 5713384046_H

description: SAMPLE 185


title: MRK_C2

description: LTED treated with DMSO rep2

source_name: LTED treated with DMSO


title: PBX_1

description: LTED treated with siPBX1 rep1


title: MRK_C1

description: LTED treated with DMSO rep1


title: 5713384046_G

description: SAMPLE 184


title: MRK_2

description: LTED treated with MRK003 rep2

source_name: LTED treated with MRK003


title: MM-087_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-087

source_name: Multiple myeloma patient MM-087


title: MRK_1

description: LTED treated with MRK003 rep1


title: MRK_C3

description: LTED treated with DMSO rep3


title: MRK_3

description: LTED treated with MRK003 rep3


title: MM-043_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-043

source_name: Multiple myeloma patient MM-043


title: MM-050_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-050

source_name: Multiple myeloma patient MM-050


title: MM-049_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-049

source_name: Multiple myeloma patient MM-049


title: PBX_C3

description: LTED treated with siCTRL rep3


title: MM-067_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-067

source_name: Multiple myeloma patient MM-067


title: 5713384046_F

description: SAMPLE 183


title: Female E18 A-2

city: Boston

first: Sana

last: Mujahid

state: MA

address: 800 Washington St.

department: Pedatrics

institute: Tufts Medical Center

description: Test

data_processing:
MammU6 housekeeping gene was used for the normalization.
Target gene signals normalized to housekeeping genes to give deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
All biological and technical replicates were averaged.
DeltadeltaCt was calculated by normalizing all other conditions to Male E15 time point.
Fold change was then calculated using  2^-deltadeltaCt formula.

label: Taqman Non-Fluorescent Quencher (3'), MGB (Minor Groove Binder) (3'), FAM (5')

organism: Mus musculus

source_name: Lung isolated from swiss webster mice

extract_protocol: Total RNA was extracted with miRVana miRNA isolation Kit (Ambion)

value: lung

tag: strain

value: Swiss Webster

tag: gender

value: female

tag: development stage


title: 5713384046_E

description: SAMPLE 182


title: Female E18 B-2

description: Test


title: MM-042_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-042

source_name: Multiple myeloma patient MM-042


title: Female E17 B-1

description: Test


title: Female E17 B-2

description: Test


title: 5713384005_A

description: SAMPLE 202


title: 5713384046_C

description: SAMPLE 181


title: 5713384043_L

description: SAMPLE 180


title: 5713384005_L

description: SAMPLE 204


title: FemaleE18 B-1

description: Test


title: Female E18 A-1

description: Test


title: Female E17 A-1

description: Test


title: Female E17 A-2

description: Test


title: Female E16 A-2

description: Test


title: 5713384043_K

description: SAMPLE 179


title: 5713384043_J

description: SAMPLE 178


title: Male E18 B-2

description: Test

value: male


title: Female E15 A-1

description: Test


title: Male E18 A-2

description: Test


title: MM-034_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-034

source_name: Multiple myeloma patient MM-034


title: MM-040_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-040

source_name: Multiple myeloma patient MM-040


title: MM-039_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-039

source_name: Multiple myeloma patient MM-039


title: Female E16 B-2

description: Test


title: MM-032_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-032

source_name: Multiple myeloma patient MM-032


title: 5713384043_E

description: SAMPLE 174

source_name: cervical cancer


title: Male E17 B-2

description: Test


title: Male E17 B-1

description: Test


title: Female E16 B-1

description: Test


title: 5713384043_D

description: SAMPLE 173


title: MM-038_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-038

source_name: Multiple myeloma patient MM-038


title: MM-037_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-037

source_name: Multiple myeloma patient MM-037


title: Female E15 B-2

description: Test


title: Female E15 B-1

description: Test


title: Male E17 A-1

description: Test


title: MM-036_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-036

source_name: Multiple myeloma patient MM-036


title: MM-035_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-035

source_name: Multiple myeloma patient MM-035


title: Female E16 A-1

description: Test


title: Male E16 A-2

description: Test


title: MM-025_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-025

source_name: Multiple myeloma patient MM-025


title: Male E18 B-1

description: Test


title: 5713384043_I

description: SAMPLE 177


title: Male E16 A-1

description: Test


title: Male E18 A-1

description: Test


title: Female E15 A-2

description: Test


title: Male E17 A-2

description: Test


title: MM-030_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-030

source_name: Multiple myeloma patient MM-030


title: 5713384036_L

description: SAMPLE 171


title: 5713384043_G

description: SAMPLE 175


title: 5713384043_H

description: SAMPLE 176


title: 5713384036_K

description: SAMPLE 170


title: Male E16 B-2

description: Test


title: Male E16 B-1

description: Test


title: MM-026_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-026

source_name: Multiple myeloma patient MM-026


title: MM-027_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-027

source_name: Multiple myeloma patient MM-027


title: Male E15 B-2

description: Control


title: 5713384036_I

description: SAMPLE 168


title: MM-016_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-016

source_name: Multiple myeloma patient MM-016


title: MM-015_miRNA_1

description: MicroRNA profiling data from multiple myeloma patient MM-015

source_name: Multiple myeloma patient MM-015


title: Male E15 A-2

description: Control

source_name: Lung isolated from swiss webster mice


title: 5713384043_C

description: SAMPLE 172


title: 5713384036_H

description: SAMPLE 167


title: 5713384036_J

description: SAMPLE 169


title: Male E15 B-1

description: Control


title: HC-toxin rep1

city: Heidelberg

first: Marco

last: Lodrini

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation in Chipster (v.1.4.7).

label_protocol: 200 ng of total RNA was labelled using standard Illumina protocols

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: BE(2)-C cells were treated with the pan-HDACi HC-toxin (20 nM) or solvent control (methanol) for 24 h.

value: BE(2)-C neuroblastoma cells

tag: treated with

value: pan-HDACi HC-toxin (20 nM) for 24h


title: HC-toxin rep2

description: SAMPLE 5


title: 75_post

type: other

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

hyb_protocol: We blocked printed peptide arrays with 0.1 mg ml-1 biotin (Sigma) in PBS for 10 min at RT with 500 rpm orbital agitation. After rinsing the arrays six times in peptide binding buffer (PBB): [50 mM Tris (Mallinckrodt Baker, Phillipsburg, NJ) pH 7.5, 150 mM NaCl (Mallinckrodt AR, Phillipsburg NJ), 0.05% NP-40 (Sigma) + 2.5% FCS), we applied mAb and pAb antibodies diluted to 1.0 μg ml–1 or patient serum diluted 1:80 in PBB. Following primary incubation for 3 h at RT with 500 rpm orbital agitation, we rinsed the arrays six times with PBB then six times in PBST before applying secondary antibody reagents (goat anti-mouse IgG, goat anti-rabbit IgG or goat anti-human IgG conjugated to Cy3, Jackson ImmunoResearch) diluted to 0.375 μg ml–1 in PBST plus 20% FCS for 30 min at RT with 500 rpm orbital agitation. We then rinsed arrays six times in PBST, three times in PBS and three times in diH20 and dried arrays in microscope slide racks centrifuged at 300 g for 5 min at RT.

scan_protocol: We immediately scanned processed peptide arrays with an Axon digital scanner and analyzed scanned images with Genepix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

label: Goat anti-Human IgG/IgM conjugated to Cy3 (Jackson Immunoresearch, West Grove, PA)

molecule: other

source_name: serum

extract_protocol: All individuals were ambulatory and generally healthy as determined by clinical history. Females of childbearing potential were tested for pregnancy by a urine sample. Volunteers at initial enrollment had no active systemic or serious concurrent illness, no history of immunodeficiency, nor any known or suspected impairment of immunologic function, including clinically significant liver disease, diabetes mellitus treated with insulin, moderate to severe renal disease, blood pressure >150/95 at screening, chronic hepatitis B or C, recent or current use of systemic immunosuppressive medication. In addition, none of the volunteers were recipients of blood or blood products within the past 6 months or blood donors within 6 weeks prior to immunization. Volunteers were screened to assure that they did not have signs of febrile illness on day of enrollment and baseline blood draw. A total of ~120 ml peripheral blood was obtained in three visits (~40 ml/visit): at day 0 (pre-vaccine), 5-7 and 28 7 days after receiving a single intramuscular dose of trivalent seasonal influenza vaccine Fluzone (Sanofi Pasteur, Swiftwater, PA). Each dose of the vaccine contained a total of 45  g of antigen corresponding to 15  g HA each of H1N1, H3N2 and B strains of the seasonal viruses included for that year. Serum was separated by centrifugation of clotted blood, and stored at -80 C before use. Serum samples from visit 1 (day 0) and 3 (day 28   7) were used for array experiments and microneutralization titer determination.

tag: age

tag: h1n1 cpost

tag: h3n2 cpost

tag: b cpost

tag: molecule

value: IgG/IgM


title: HC-toxin rep3

description: SAMPLE 6


title: 76_pre


title: 76_post


title: Male E15 A-1

description: Control


title: 74_pre


title: MeOH rep3

description: SAMPLE 3

value: methanol (solvent control) for 24 h


title: 73_pre


title: 5713384036_G

description: SAMPLE 166

tag: Stage


title: MeOH rep2

description: SAMPLE 2


title: 74_post


title: MeOH rep1

description: SAMPLE 1


title: 75_pre


title: 71_pre


title: 71_post


title: 72_pre


title: 73_post


title: 5713384036_F

description: SAMPLE 165

tag: largest diameter


title: 70_post


title: 5713384036_D

description: SAMPLE 163


title: 70_pre


title: 5713384036_B

description: SAMPLE 161


title: 69_pre


title: 5713384036_E

description: SAMPLE 164


title: 69_post


title: 5713384036_C

description: SAMPLE 162


title: 5713384036_A

description: SAMPLE 160


title: 72_post


title: 68_pre


title: 5713384034_L

description: SAMPLE 159


title: 5713384034_J

description: SAMPLE 157


title: 5713384034_K

description: SAMPLE 158


title: 68_post


title: AT89

first: Alan

last: Branco

address: 665 Huntington Ave.

department: Environmental Health

institute: Harvard School of Public Health

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 400B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

source_name: Total RNA from D melanogaster mutant genotypes with variable Y chromosomes.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

tag: genotype

tag: Sex

value: male (XY)

value: 2 days old, unmated


title: AT91

description: Biological replicate


title: AT90

description: Biological replicate


title: 5713384034_F

description: SAMPLE 155


title: AT88

description: Biological replicate


title: 67_post


title: 65_post


title: 5713384034_I

description: SAMPLE 156


title: 66_pre


title: 67_pre


title: 66_post


title: 63_post


title: 64_pre


title: 64_post


title: 65_pre


title: 5713384034_D

description: SAMPLE 154


title: AT86

description: Biological replicate


title: 5713384034_C

description: SAMPLE 153


title: AT85

description: Biological replicate


title: 62_pre


title: 62_post


title: 63_pre


title: AT84

description: Biological replicate


title: AT87

description: Biological replicate


title: 5713384034_A

description: SAMPLE 151


title: 61_post


title: 61_pre


title: AT112

description: Biological replicate

value: +/+;Yohio (background 2)

value: +/+;Ycongo (background 2)


title: 5713317111_K

description: SAMPLE 150


title: 5713384034_B

description: SAMPLE 152


type: genomic

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

description: SbIII1000.3 vs. SbIII1000.4 SbIII1000.3 vs. LmjFSbIII1000.4 x2_252168110006_S01_CGH_105_Dec08_2_2

hyb_protocol: Hybridizationwas performed at 65°C with Leishmania Agilent arrays.

scan_protocol: Detection of CY3 and CY5 signals were performed on a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA USA) at 5 µm resolution.

data_processing: The signal intensity data were extracted from the primary scanned images using GenePix Pro 6.0 software (Axon Instruments, Union City, CA, USA). Normalization and statistical analyses were performed in R 2.2.1 software using the LIMMA (Linear Models for Microarray Data) 2.7.3 package. Background correction was performed using the “edwards” method; within-array normalization was done by loess and between array normalization by the Aquantile method. Multiple testing corrections were done using the false discovery rate method with a threshold p value of 0.05. Only genes statistically significant with an absolute ratio greater than 2 were considered.

molecule: genomic DNA

organism: Leishmania major

label_protocol: Four microgram of digested DNA was labeled   using Cy5- or Cy3- dCTP (Amersham), random hexamers (Roche) and exo- Klenow DNA polymerase (NEB). Fluorescent probes were then purified with ArrayIt columns (telechem) and quantified.

growth_protocol: Promastigotes  were grown till mid-log phase

extract_protocol: Genomic DNA was isolated from mid log phase promastigotes by DNAzol, followed by shearing the DNA through 22 G1’’ and 27 G ½’’ needles (Becton Dickinson). Sheared DNA was digested with PvuII and MseI, purified by phenol, chloroform extraction and ethanol precipitation.

treatment_protocol: There is no treatment protocol.

label: Cy 5


description: SbIII1000.4 vs. SbIII1000.5 SbIII1000.4 vs. LmjFSbIII1000.5 x2_252168110006_S01_CGH_105_Dec08_2_1


title: 60_post


title: 60_pre


title: AT110

description: Biological replicate


title: 5713317111_J

description: SAMPLE 149


title: AT109

description: Biological replicate


title: 59_post


title: 59_pre


description: WT vs. SbIII1000.4 WT vs. LmjFSbIII1000.4 x2_252168110006_S01_CGH_105_Dec08_1_2

source_name: LmjF WT

value: WT


title: 5713317111_G

description: SAMPLE 147


description: SbIII1000.5 vs.  WT SbIII1000.5 vs. LmjF WT x2_252168110006_S01_CGH_105_Dec08_1_3


title: AT108

description: Biological replicate


title: 5713317111_F

description: SAMPLE 146

value: IIA


description: WT vs. SbIII1000.3 WT vs. LmjFSbIII1000.3 x2_252168110006_S01_CGH_105_Dec08_1_1


title: 58_post


title: AT106

description: Biological replicate


title: 5713317111_I

description: SAMPLE 148


title: 58_pre


title: AT105

description: Biological replicate


title: AT111

description: Biological replicate


title: AT107

description: Biological replicate


title: 5713317111_E

description: SAMPLE 145


description: SbIII1000.5 vs. SbIII1000.3 SbIII1000.5 vs. LmjFSbIII1000.3 x2_252168110006_S01_CGH_105_Dec08_1_4


title: 5713317111_C

description: SAMPLE 143


title: AT103

description: Biological replicate


title: 5713317111_D

description: SAMPLE 144


title: 57_pre


title: AT104

description: Biological replicate


title: 5713317111_B

description: SAMPLE 142


title: 5713317044_L

description: SAMPLE 141


title: 56_post


title: 5713317044_K

description: SAMPLE 140


title: AT101

description: Biological replicate


title: 56_pre


title: A86

description: Biological replicate


title: 55_post


title: 5713317044_J

description: SAMPLE 139


title: AT102

description: Biological replicate


title: 55_pre


title: 5713317044_I

description: SAMPLE 138


title: A83

description: Biological replicate


title: 54_post


title: 57_post


title: F

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

hyb_protocol: Hybridization was performed for 16-18h in a 42C waterbath (sample was loaded under a glass coverslip and array was placed in a water-tight hybridization chamber).

scan_protocol: Arrays were scanned using an Axon GenePix 4000B at 5uM resolution according to the NimbleGen Users Guide v 8.0.

data_processing: Qspline normalization and SegMNT CGH analysis were performed using NimbleScan v2.6 and plotted for figures using GraphPad PRISM.

organism: Plasmodium falciparum

source_name: F clone

label_protocol: Genomic DNA was labeled with Cy3 and Cy5 random nanomers per the NimbleGen Users Guide v 8.0.

growth_protocol: Parasites were grown in RPMI 1640 plus 20% human plasma, human erythrocytes (A+), and DSM1 at 37C and 5% oxygen and 5% CO2.

extract_protocol: Clonal asynchronous P. falciparum blood-stage parasites were lysed with saponin, and genomic DNA was extracted using the Qiagen DNeasy kit.

treatment_protocol: Dd2 parasites were selected in 0.3uM DSM1 and cloned by limiting dilution.

tag: tissue

value: whole body

tag: parasite stage

value: erythrocytic

tag: round of selection

tag: array identifier

source_name: Clonal Dd2 P. falciparum

growth_protocol: Parasites were grown in RPMI 1640 plus 20% human plasma, human erythrocytes (A+) at 37C and 5% oxygen and 5% CO2.

treatment_protocol: Cloned by limiting dilution.

tag: sample type

value: reference


title: Fis non-aerated 24hr replicate 3

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: Biological replicate 3 of 3.

hyb_protocol: Hybridizations  The entire volume of each labelled DNA sample was carefully pipetted over each of the four gaskets in a glass slide (Oxford Gene Technology, Agilent). The order of samples from top to bottom, were as follows: aerated mid-log, aerated late-stationary phase, non-aerated mid-log, and non-aerated late-stationary phase. For orientation reference, the slide barcode was always at bottom. Subsequently, the microarray slide (Oxford Gene Technology, Agilent) was placed carefully on top of the loaded gaskets slide, avoiding any bubble formation and with its reference barcode in the same orientation.  Both slides were kept against each other for adequate hybridization in a tight metallic holder.  Slides were incubated in the hybridization oven (Shel Lab, Hybridizer) at 55ºC overnight (24 hrs).

scan_protocol: Genome-wide chip microarray scanning   The hybridized microarray slide was separated from the gasket slide and washed twice in buffer 1 (20X SSPE (SIGMA), 10% Tween and sterile ddH2O), and twice again in buffer 2 (20X SSPE (SIGMA), 100% Polyethylene Glycol (PEG) (Fluka)). The microarray slide was blot dried from the corners with a regular paper towel prior to scan reading.  The slide was inserted into a microarray scanner (Axon) array side up (barcode side facing down). In order to view the microarray, each oligonucleotide on an OGT services array is assigned a unique feature number. The identity of the feature number is given by a CD-ROM with GenePix Array List (GAL) files.

data_processing: From the scan output the F532/F635 Median values were selected for foreground intensities and B532/B635 Median values for background intensities. Background was subtracted from foreground. Any spot with background-corrected intensity below 1 was discharded. Spots that were flagged manually ('Flag' column), automatically ('Autoflag' column) or considered a control spot ('ControlType' column) were also skipped. For the remaining spots the log2-ratios (log2(test/control)) were calculated. The final values for the matrix were generated by subtracting the median log2-ratio of each slide from the log2-ratios of each spot on that slide. These values were then read into ChiPOTle (Buck et al., 2005) for peak detection.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Fis ChIP DNA from SL1344 cells

label_protocol: Labelling by random priming of DNA samples:  The DNA was labelled using BioPrime Random Labelling Kit (Invitrogen) as described below. Labelling method used for array hybridization as follows: reagents, 2.5 X Random primer solution; ChIP Flagged IP DNA or Input DNA; and sterile H2O were mixed on ice in a microfuge tube.  The DNA amount labelled was different for Input and Flag-tagged IP DNA samples. DNA quantity labelled was 40 μl of unamplified Flag-tagged IP DNA and approximately 200 ng of Input DNA.  This mixture was heated at 100°C for 10 min to denature the DNA and then chilled briefly on ice. The following reagents were added to the tubes on ice:  10 X dNTP mix, 1 mM Cy3/Cy5 labelled dCTP (1 mM Cy3-dCTP, 1 mM Cy5-dCTP, GE Healthcare). Input IP mock DNA samples were labelled with Cy5 (blue) dCTP, and ChIP Flagged IP DNA samples were labelled with Cy3 (red) dCTP) and 40 U/μl of  Klenow fragment. The final volume per labelling reaction was 150 μl.  The reagents were mixed gently but thoroughly and incubated at 37°C overnight.  Stop buffer (10 mM EDTA) was added to the reaction mix to terminate the reaction.  Purification of labelled DNA samples:  Labelled DNA samples were purified as follows. Micro-spin G50 columns (GE Healthcare) were used to remove the unlabelled nucleotides from the labelled DNA samples. Three columns were used for each of the labelling reactions.  The resin was resuspended in the columns by vortexing gently. The caps were loosened and the bottom of the tubes snapped off. The columns were placed in 2 ml microfuge tubes and centrifuged at 4000 rpm for 1 min.  A volume of 50 μl of sterile filtered HPLC water was applied to the resin-bed and the columns were centrifuged at 4000 rpm for 1 min.  The columns were placed in fresh 1 ml microfuge tubes and the labelled DNA samples were carefully applied to the resin-bed. The columns were then centrifuged at 13000 rpm for 1 min.  The purified DNA samples were collected in the 1.5 ml microfuge tubes and the samples (Input + ChIP) from the same labelled reaction were pooled together. The final volume for the labelled DNA samples was approximately 180 μl. A volume of 5 μl of each labelled DNA was analyzed on a 1% agarose 1 X TBE gel and stained with ethidium bromide for visualization of smeared DNA. One tenth of the sample volume of 3M sodium acetate was added to precipitate DNA. Two and a half volumes of 100% ETOH were added to each sample. Samples were subsequently incubated at –80ºC in the dark for 1-3 hrs or, at –20ºC overnight.  DNA was pelleted after spinning in the dark for 20 min at RT and at 13000 rpm.  Alcohol was drained and pellet resuspended in 80% ETOH. The tubes were allowed to air-dry for 15-30 min in a dark place.  Pellet was resuspended in 100 μl Hybridization buffer (1M Sodium chloride, 50 mM MES (Sodium salt SIGMA) (pH 6.5), 20 mM EDTA, 20% formamide (SIGMA), and 1% Triton X100). Labelled DNA was subsequently heated at 70ºC for 10 min and denatured at 100ºC for another 10 min.  It was briefly placed on ice prior to hybridization.

growth_protocol: Constructed strain SG07 fis::3XFlag was used for this set of experiments to identify peaks of Fis-binding on gene regions that are occupied by Fis. Bacterial cells were grown in Luria Bertani medium, under non-aerated conditions, and harvested from late-stationary phase (24 hr).  All culture samples were normalized at a total OD A600 of 10, as culture samples replicates from each growth phase and condition were combined to result in that total OD.

extract_protocol: Immunoprecipitated DNA Chromatin (ChIP DNA) and input or mock immunoprecipitated (IP) DNA from culture samples were extracted using phenol (Sigma) and chloroform, and concentrated by ethanol precipitation.  A volume of 2 μl of yeast tRNA (5 mg/ml, Invitrogen) was added to each sample (except input IP) just before adding 250 μl of phenol (Sigma) and 250 μl of chloroform. Samples were vortexed and centrifuged at 13000 rpm for 5 min at room temperature. The aqueous layer (top layer) was carefully removed and placed in a fresh tube. A volume of 500 μl of chloroform was added to each sample. The samples were vortexed and centrifuged at 13000 rpm for 5 min at room temperature. The aqueous layer was again transferred to a fresh microfuge tube.  At this point, 5 μg of glycogen (5 mg/ml, Roche), 1 μl of yeast tRNA (5 mg/ml, Invitrogen) (except input IP), and 50 μl (20 μl for input IP) of 3M NaAc (pH 5.2) was added to each sample and mixed well. The DNA was precipitated with 1375 μl (550 μl for input IP) of 100% ethanol and incubated at -70ºC from 30 min to 1 to 2 hours maximum (or -20°C overnight).  The samples were centrifuged at 13000 rpm for 20 min at 4ºC. The DNA pellets were washed with 500 μl of ice-cold 70% ethanol and air-dried for 10-15 minutes. The DNA pellets of the IP samples were resuspended in 50 μl of sterile distilled water and 100 μl for the Input DNA samples. Samples were stored at -20°C.

treatment_protocol: Subsequently, cells were fixed, lysed and sonicated. At this point, sheared chromatin (Ch) DNA from all culture samples was immunoprecipitated (IP), in which case it was either added IgG  or FLAG-tag antibody, and both named IP test samples.  DNA carrying FLAG-tag antibody was named ChIP Flagged DNA, and DNA carrying IgG was named ChIP IgG DNA. The DNA without either antibody, but subsequently frozen at -80ºC, was used later for the chip microarray portion as an internal DNA control, which was labeled input or mock IP DNA.  In order to determine the Fis enrichment in either ChIP DNA samples, real-time quantitative PCR was done in their respective extracted DNA to measure the relative levels of promoter and gene regions of known Fis-binding sites. ChIP Flagged DNA was compared to ChIP IgG DNA, which was used as a control.

tag: strain

tag: chip antibody

value: Fis

tag: growth condition

value: grown for 24 hours under non-aerated conditions

source_name: Input DNA from SL1344

value: None, Input DNA


title: 5713317044_F

description: SAMPLE 136

source_name: cervical cancer


title: 54_pre

tag: age


title: E

source_name: E clone


title: A79

description: Biological replicate


title: A263

description: Biological replicate


title: 5713317044_D

description: SAMPLE 134


title: Fis aerated 24hr replicate 3

description: Biological replicate 3 of 3.

growth_protocol: Constructed strain SG07 fis::3XFlag was used for this set of experiments to identify peaks of Fis-binding on gene regions that are occupied by Fis. Bacterial cells were grown in Luria Bertani medium, under aerated conditions, and harvested from late-stationary phase (24 hr).  All culture samples were normalized at a total OD A600 of 10, as culture samples replicates from each growth phase and condition were combined to result in that total OD.

value: grown for 24 hours under aerated conditions


title: Fis aerated 2hr replicate 3

description: Biological replicate 3 of 3.

growth_protocol: Constructed strain SG07 fis::3XFlag was used for this set of experiments to identify peaks of Fis-binding on gene regions that are occupied by Fis. Bacterial cells were grown in Luria Bertani medium, under aerated conditions, and harvested from mid-log (2 hr) phase.  All culture samples were normalized at a total OD A600 of 10, as culture samples replicates from each growth phase and condition were combined to result in that total OD.

value: grown for 2 hours under aerated conditions


title: Fis non-aerated 2hr replicate 2

description: Biological replicate 2 of 3.

growth_protocol: Constructed strain SG07 fis::3XFlag was used for this set of experiments to identify peaks of Fis-binding on gene regions that are occupied by Fis. Bacterial cells were grown in Luria Bertani medium, under non-aerated conditions, and harvested from mid-log (2 hr) phase.  All culture samples were normalized at a total OD A600 of 10, as culture samples replicates from each growth phase and condition were combined to result in that total OD.

value: grown for 2 hours under non-aerated conditions


title: A261

description: Biological replicate


title: 5713317044_G

description: SAMPLE 137


title: Fis non-aerated 2hr replicate 3

description: Biological replicate 3 of 3.

growth_protocol: grown for 2 hours under non-aerated conditions


title: 53_post

tag: h1n1 cpost

value: IgG/IgM


title: A76

description: Biological replicate


title: C

source_name: C clone


title: 53_pre

tag: h3n2 cpost


title: 5713317044_C

description: SAMPLE 133


title: A260

description: Biological replicate


title: Fis aerated 24hr replicate 2

description: Biological replicate 2 of 3.

growth_protocol: grown for 24 hours under aerated conditions


title: D

source_name: D clone


title: Fis non-aerated 24hr replicate 2

description: Biological replicate 2 of 3.

growth_protocol: grown for 24 hours under non-aerated conditions


title: 5713317044_E

description: SAMPLE 135


title: Fis aerated 2hr replicate 2

description: Biological replicate 2 of 3.

growth_protocol: grown for 2 hours under aerated conditions


title: 5713317044_B

description: SAMPLE 132


title: 52_post

tag: b cpost


title: 51_post

tag: molecule


title: 51_pre


title: 5713384056_K

description: SAMPLE 131

tag: Stage


title: A259

description: Biological replicate


title: 5713384056_I

description: SAMPLE 129

tag: largest diameter


title: A258

description: Biological replicate

tag: genotype


title: 5713384056_J

description: SAMPLE 130


title: 52_pre


title: Fis non-aerated 24hr replicate 1

description: Biological replicate 1 of 3.


title: A139

description: Biological replicate

tag: Sex


title: A262

description: Biological replicate


title: Fis non-aerated 2hr replicate 1

description: Biological replicate 1 of 3.


title: A137

description: Biological replicate


title: 50_pre


title: 50_post


title: 5713384056_H

description: SAMPLE 128


title: 49_post


title: 5713384056_G

description: SAMPLE 127


title: 49_pre


title: 48_post


title: 5713384056_F

description: SAMPLE 126


title: Peritoneal  Macrophage Cells, treated with 70nmole Cr(VI)

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: Indian Institute of Toxicology Research

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent-Whole Genome Mouse 4x44k (AMADID: 14868). 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX V 11 75th Percentile Normalization.

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Briefly, 125µg lipopolysaccharide (Sigma Aldrich) in 1ml PBS was administered i.p. to each mouse on day 0. Lipopolysaccharides are known to activate recruitment of macrophages. On day 4, Potassium dichromate (purity ≥ 99.8%, Qualigens India) was administered ip. LA was co-administered i.p in equimolar doses together with Chromate for evaluation of its preventive effect. Dose-1 (35nmol K2Cr2O7) or Dose-2 (70nmol K2Cr2O7) was prepared fresh in 0.5 ml PBS containing 100ng 12-o-tetradecanoyl phorbol 13-acetate (TPA, Sigma) immediately before use. Control group of animals received only 100ng TPA in 0.5 ml PBS. After 4 days of K2Cr2O7 administration, macrophages were harvested by repeated peritoneal lavage using chilled collection medium.

extract_protocol: RNA was prepared using using Qiagen Rneasy Minikit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Eight week old male Swiss albino mice (20-25g b wt) were procured from quality accredited Animal House Facility at our institute. Institutional Animal Ethics Committee had approved the use of mice for these experiments. Animals were provided water & pellet diet ad libitum during experiment. Mice were randomized in three groups of ten animals in each and housed at 25oC with 12h light dark cycle. Animals were provided pellet diet and water ad libitum. Cell transformation potential of test concentrations was determined using the procedure of Massa et al., 1990.This method is in use in literature for detection of cell transforming potential of chemical carcinogens (Esmaeili et al., 2007). Briefly, 125µg lipopolysaccharide (Sigma Aldrich) in 1ml PBS was administered i.p. to each mouse on day 0. Lipopolysaccharides are known to activate recruitment of macrophages. On day 4, Potassium dichromate (purity ≥ 99.8%, Qualigens India) was administered ip. LA was co-administered i.p in equimolar doses together with Chromate for evaluation of its preventive effect. Dose-1 (35nmol K2Cr2O7) or Dose-2 (70nmol K2Cr2O7) with or without LA was prepared fresh in 0.5 ml PBS containing 100ng 12-o-tetradecanoyl phorbol 13-acetate (TPA, Sigma) immediately before use. Control group of animals received only 100ng TPA in 0.5 ml PBS. After 4 days of K2Cr2O7 (Cr6+) or LA+ K2Cr2O7 (Cr6+) administration, macrophages were harvested by repeated peritoneal lavage using chilled collection medium 90%Hanks199 (Sigma) - NaHCO3 - 10% FBS (Gibco) - 1% Antibiotic (Gibco) -1ng/ml GM - CSF (Sigma); chilled condition saved macrophages from sticking to glass surface. The approximate yield of macrophages per mouse was 2-4x106 cells. Harvested cells were centrifuged and pelleted at 1000xg, resuspended in culture medium containing DMEM (sigma) with 10% fetal bovine serum and 1% Antibiotic (Gibco) -1ng/ml GM - CSF (Sigma). Cell density was determined using haemocytometer after decontaminating the RBCs. RNA was isolated from the samples and microarray was proceeded using 4X44K array.

tag: cell type

value: Macrophage cell

value: Swiss albino

tag: agent

value: 70nmole Cr(VI)

tag: gender

value: male


title: 48_pre


title: 5713384056_D

description: SAMPLE 125


title: A138

description: Biological replicate

value: male (XY)

value: 2 days old, unmated


title: Fis aerated 24hr replicate 1

description: Biological replicate 1 of 3.


title: Peritoneal  Macrophage Cells

source_name: Peritoneal  Macrophage Cells


title: 0.7mm-anther-meiocytes-vs-tapetum-Rep-2-Cy3-0.7mm-meiocyte

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
Cy3-254_4
compare 0.7mm anther meiocytes to 0.7mm anther tapetum
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing:
After removal of spots flagged by Feature Extraction as below background or saturated or outliers, intensities for each channel from Feature Extraction were normalized using lowess.  Average intensities were then calculated for each sample type for comparison.
The limma package of R was used to normalize the median intensities for each channel as follows: within each array using loess and between arrays using quantile method.

organism: Zea mays

source_name: 0.7mm anther meiocytes 1171-5 Me

label_protocol: Total RNA (50 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol:
For whole anthers, total RNA was extracted from 30 - 60 mg of frozen tissues with TRIzol, digested with DNase I, and cleaned up with Qiagen RNeasy Mini kit. For laser microdissection, a PALM microbeam LCM was
used for dissection, and RNA was extracted and cleaned up with a PicoPure column (Arcturus), treated with Dnase I, and resuspended in dH2O.

tag: tissue

value: 0.7mm anther meiocytes


title: 5713384055_L

description: SAMPLE 122


title: A136

description: Biological replicate


title: 5713384056_C

description: SAMPLE 124


title: 47_post


title: Fis aerated 2hr replicate 1

description: Biological replicate 1 of 3.


title: 0.7mm-anther-meiocytes-vs-tapetum-Rep-1-Cy3-0.7mm-tapetum

description:
Cy3-254_3
compare 0.7mm anther tapetum to 0.7mm anther meiocytes
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

data_processing:
After removal of spots flagged by Feature Extraction as below background or saturated or outliers, intensities for each channel from Feature Extraction were normalized using lowess.  Average intensities were then calculated for each sample type for comparison.
The limma package of R was used to normalize the median intensities for each channel as follows: within each array using loess and between arrays using method.

source_name: 0.7mm anther tapetum 1171-5 tapetum

value: 0.7mm anther tapetum


title: 0.2mm-anther-msca1-vs-mac1-Rep-2-Cy3-0.2mm-msca1

description:
Cy3-254_2
compare 0.2mm anther msca1 to 0.2mm anther mac1
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.2mm anther msca1 0.20 msca1-51 WA

value: 0.2mm anther msca1


title: 47_pre


title: 5713384056_A

description: SAMPLE 123


title: blood monocytes_normal_rep 4

city: San Francisco

first: Christine

middle: L.

last: Hsieh

address: 4150 Clement St. 111R

department: Immunology

institute: UC San Francisco/ San Francisco VA Medical Center

description:
MonoNrm_4
Normal blood monocytes.

hyb_protocol: The products were hybridized to Agilent Whole Mouse Genome 4x44K microarrays according to the manufacturer's protocol.

scan_protocol: Arrays were scanned with an Agilent microarray scanner, and raw signal intensities were extracted with Feature Extraction v10.5 software.

data_processing: Data were normalized by using the quantile normalization method (Bolstad et al., 2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. A one-way ANOVA linear model was fit to the comparison to estimate the mean M values and calculated moderated t-statistic, B statistic, false discovery rate and p-value for each gene for the comparison of interest. Adjusted p-values were produced by the method proposed by Holm (1979). All procedures were carried out using functions in the R package limma in Bioconductor [Smyth (2004), Gentleman (2004)].

source_name: blood monocytes, normal

label_protocol: Further sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF SABRE Functional Genomics Facility. RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies), and RNA was amplified by use of a whole transcriptome amplification kit (Sigma-Aldrich). Subsequent Cy3-CTP labeling was performed by using a NimbleGen one-color labeling kit (Roche-NimbleGen Inc). The quality of the amplified products was assessed using an Agilent 2100 Bioanalyzer and Nanodrop ND-8000 (Nanodrop Technologies, Inc.).

extract_protocol: Total RNA was isolated using an RNAqueous-Micro kit (Ambion) according to the manufacturer's instructions. Samples were eluted in water.

treatment_protocol:
Surgery: Controlled cortical impact (CCI) surgery or sham surgery was performed on anesthetized animals under a protocol approved by the San Francisco VA Medical Center Animal Care Committee. Briefly, bupivacaine was administered subcutaneously above the skull, and an incision was made followed by a 2.5mm circular craniectomy. TBI was inflicted by a 2 mm circular, flat pneumatic piston traveling at 3 m/s, penetrating 1.5 mm, for 150 ms (Amscien Instruments, Richmond, VA with extensive modifications by H&R Machine, Capay, CA). Target brain coordinates for the center of injury were 1.5 mm lateral, 2.3 mm posterior to the bregma point. After minor bleeding had ceased, the skin was clipped together and animals were monitored for recovery. Sham animals received all surgical procedures without piston impact. As needed, animals were given rehydration therapy and liquid diet for the first three days.
Brain and blood leukocyte isolation: Brain leukocytes were harvested according to previously published methods (Sedgwick et al., 1991). Briefly, peripheral blood was collected through the inferior vena cava, and then total body perfusion was performed through the heart. Brains were obtained and mechanically disassociated through a 100 μm cell strainer. Washed cells were treated with 400 U/ml DNase I (Sigma-Aldrich) and 0.5 mg/ml collagenase type I (Worthington) at 37°C for 30 min. Leukocytes were isolated by separation on a Percoll gradient (Amersham Biosciences). For PBL isolation, mononuclear cells were separated from peripheral blood using ficoll-hypaque (GE Healthcare).
Flow cytometry and antibodies: Fc receptors were blocked with 10% rat serum (Sigma) and cells were stained with fluorescent antibodies. Leukocyte analysis used a combination of the following antibodies: anti-CD45 (clone Ly5) APC (eBioscience), anti-CD11b (clone M1/70) PE (Invitrogen), anti-Ly6G (clone 1A8) PE-Cy7 (BD Biosciences), F4/80 (clone BM8) PE-Cy5 (eBioscience). Sytox blue (Invitrogen) was used to gate out dead cells. Cells were sorted on a FACSAria (BD Biosciences) directly into cell lysis buffer (Ambion). Sorted samples were frozen at -80C°.

value: YARG

value: blood

value: monocytes

tag: treatment

value: 12-16 weeks


title: blood monocytes_post-TBI day 1_rep 4

description:
MonoInj_4
Blood monocytes 1d post-TBI.

source_name: blood monocytes, post-TBI d1

tag: strain

value: traumatic brain injury (TBI)


title: blood monocytes_post-TBI day 1_rep 1

description:
MonoInj_1
Blood monocytes 1d post-TBI.


title: blood monocytes_post-TBI day 1_rep 3

description:
MonoInj_3
Blood monocytes 1d post-TBI.


title: 0.2mm-anther-msca1-vs-fertilesib-Rep-2-Cy3-0.2mm-mac1

description:
Cy3-253_4
compare 0.2mm anther msca1 to 0.2mm anther fertile sib
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_4.txt


title: 0.2mm-anther-msca1-vs-mac1-Rep-1-Cy3-0.2mm-mac1

description:
Cy3-254_1
compare 0.2mm anther mac1 to 0.2mm anther msca1
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.2mm anther mac1 0.20 mac1-39 WA

value: 0.2mm anther mac1


title: Peritoneal  Macrophage Cells, treated with 35nmole Cr(VI)

value: 35nmole Cr(VI)


title: 46_post

source_name: serum

value: IgG/IgM


title: 5713384055_K

description: SAMPLE 121


title: 45_post


title: 0.2mm-anther-msca1-vs-fertilesib-Rep-1-Cy3-0.2mm-fertilesib

description:
Cy3-253_3
compare 0.2mm anther fertile sib to 0.2mm anther msca1
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.2mm anther fertile sib 0.20 WT-58 WA

value: 0.2mm anther fertile sib


title: blood monocytes_normal_rep 3

description:
MonoNrm_3
Normal blood monocytes.


title: 5713384055_H

description: SAMPLE 119


title: 0.2mm-anther-mac1-vs-fertilesib-Rep-2-Cy3-0.2mm-mac1

description:
Cy3-253_2
compare 0.2mm anther mac1 to 0.2mm anther fertile sib
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.2mm anther mac1 0.20 mac1-59 WA


title: blood monocytes_normal_rep 2

description:
MonoNrm_2
Normal blood monocytes.


title: Arg1+ brain macrophages_post-TBI day 1_rep 4

description:
MacPos_4
Arginase-1+ TBI brain macrophages 1d post-TBI.

source_name: Arg1+ brain macrophages, post-TBI d1

value: brain

value: Arg1+ macrophages


title: 5713384055_J

description: SAMPLE 120


title: 0.15mm-anther-fertilesib-vs-0.4mm-mac1-Rep-1-Cy3-0.15mm-mac1

description:
Cy3-248_3
compare 0.4mm anther mac1 to 0.15mm anther fertile sib
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.4mm anther mac1 0.4 mac1 -16

value: 0.4mm anther mac1


title: 5713384055_F

description: SAMPLE 117


title: 46_pre


title: 0.2mm-anther-mac1-vs-fertilesib-Rep-1-Cy3-0.2mm-fertilesib

description:
Cy3-253_1
compare 0.2mm anther fertile sib to 0.2mm anther mac1
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.2mm anther fertile sib 0.20 WT-6 WA


title: 0.15mm-anther-fertilesib-vs-0.4mm-mac1-Rep-2-Cy3-0.4mm-fertilesib

description:
Cy3-248_4
compare 0.15mm anther fertile sib to 0.4mm anther mac1
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.15mm anther fertile sib 0.15-3

value: 0.15mm anther fertile sib


title: 5713384055_C

description: SAMPLE 115

source_name: cervical cancer


title: 5713384055_G

description: SAMPLE 118


title: 0.4mm-anther-mac1-vs-fertilesib-Rep-2-Cy3-0.4mm-mac1

description:
Cy3-248_2
compare 0.4mm anther mac1 to 0.4mm anther fertile sib
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.4mm anther mac1 0.4 mac1-13


title: Arg1+ brain macrophages_post-TBI day 1_rep 3

description:
MacPos_3
Arginase-1+ TBI brain macrophages 1d post-TBI.

value: male


title: Arg1+ brain macrophages_post-TBI day 1_rep 1

description:
MacPos_1
Arginase-1+ TBI brain macrophages 1d post-TBI.


title: 44_pre


title: Arg1+ brain macrophages_post-TBI day 1_rep 2

description:
MacPos_2
Arginase-1+ TBI brain macrophages 1d post-TBI.


title: 43_post


title: 45_pre


title: 5713384055_D

description: SAMPLE 116

value: IIA


title: 43_pre


title: 44_post


title: Arg1- brain macrophages_post-TBI day 1_rep 4

description:
MacNeg_4
Arginase-1- TBI brain macrophages 1d post-TBI.

source_name: Arg1- brain macrophages, post-TBI d1

value: Arg1- macrophages


title: Arg1- brain macrophages_post-TBI day 1_rep 3

description:
MacNeg_3
Arginase-1- TBI brain macrophages 1d post-TBI.


title: 5713384033_G

description: SAMPLE 114


title: 42_post


title: 0.4mm-anther-wt-vs-0.25mm-Rep-2-Cy3-0.4mm

description:
Cy3-247_4
compare 0.4mm anther wt to 0.25mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.4mm anther wt 0.4 wt-9

value: 0.4mm anther wt


title: 5713384033_F

description: SAMPLE 113


title: 5713384033_C

description: SAMPLE 111


title: Arg1- brain macrophages_post-TBI day 1_rep 2

description:
MacNeg_2
Arginase-1- TBI brain macrophages 1d post-TBI.

value: YARG


title: 41_post


title: 42_pre


title: 5713384033_D

description: SAMPLE 112


title: 0.4mm-anther-mac1-vs-fertilesib-Rep-1-Cy3-0.4mm-fertilesib

description:
Cy3-248_1
compare 0.4mm anther fertile sib to 0.4mm anther mac1
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.4mm anther fertile sib 0.4 wt-11

value: 0.4mm anther fertile sib


title: 0.25mm-anther-wt-vs-0.15mm-Rep-1-Cy3-0.15mm

description:
Cy3-247_1
compare 0.15mm anther wt to 0.25mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.15mm anther wt 0.15-3

value: 0.15mm anther wt


title: Arg1- brain macrophages_post-TBI day 1_rep 1

description:
MacNeg_1
Arginase-1- TBI brain macrophages 1d post-TBI.

value: 12-16 weeks


title: 41_pre


title: 40_post


title: 0.7mm-anther-whole-vs-endo/epi-Rep-4-Cy3-endo/epi

description:
Cy3-97_4
compare 0.7mm anther endothecium/epidermis to 0.7mm anther whole
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.7mm anther endothecium/epidermis 1171-8 E/E

value: 0.7mm anther endothecium/epidermis


title: 0.25mm-anther-wt-vs-0.15mm-Rep-2-Cy3-0.25mm

description:
Cy3-247_2
compare 0.25mm anther wt to 0.15mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.25mm anther wt 0.25-6

value: 0.25mm anther wt


title: 40_pre


title: 0.7mm-anther-whole-vs-endo/epi-Rep-3-Cy3-whole

description:
Cy3-97_3
compare 0.7mm anther whole  to 0.7mm anther endothecium/epidermis
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.7mm anther whole 1171-1.2 WA

value: 0.7mm anther whole


title: 39_post

value: IgG/IgM


title: S63del/CHOP null sciatic nerve at 4 months, biological rep1

city: Milano

first: Maurizio

last: D'Antonio

address: via Olgettina 58

department: DIBIT

institute: San Raffaele Scientific Institute

description: Gene expression from 4-months S63del/CHOP null (neuropathic, rescued) scatic nerve

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analysed with GeneChip Operating Software v1.4 (GCOS1.4).

source_name: Sciatic nerves from 4 months old S63del/CHOP null mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Sciatic nerves were dissected from WT, CHOP null, S63del amd S63del/CHOP null mice at the indicated timepoints (P5, P28 and 4-months)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was then purified with Rneasy kit (Qiagen) following manufacturer's instruction.

treatment_protocol: Sciatic nerves were dissected, the perineureal sheath was removed, and the nerve were snap-frozen with liquid nitrogen. Prior to RNA extraction, the nerves were pulverized with mortar and pestle, and transferred in the Trizol reagent (Invitrogen).

value: Sciatic nerve

value: P0S63del/CHOP null

value: 4 months


title: 5713384031_I

description: SAMPLE 108


title: 5713384031_K

description: SAMPLE 110


title: 39_pre

source_name: serum


title: 5713384031_G

description: SAMPLE 107


title: S63del sciatic nerve at 4 months, biological rep1

description: Gene expression from 4-months S63del (neuropathic) scatic nerve

source_name: Sciatic nerves from 4 months old S63del mice


title: 5713384031_F

description: SAMPLE 106


title: 0.7mm-anther-whole-vs-endo/epi-Rep-2-Cy3-endo/epi

description:
Cy3-97_2
compare 0.7mm anther endothecium/epidermis to 0.7mm anther whole
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.7mm anther endothecium/epidermis 1171 -5  E/E


title: 0.7mm-anther-whole-vs-endo/epi-Rep-1-Cy3-whole

description:
Cy3-97_1
compare 0.7mm anther whole  to 0.7mm anther endothecium/epidermis
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.7mm anther whole 1171-1.1 WA


title: CHOP null sciatic nerve at 4 months, biological rep2

description: Gene expression from 4-months CHOP null scatic nerve

source_name: Sciatic nerves from 4 months old CHOP null mice

value: CHOP null


title: CHOP null sciatic nerve at 4 months, biological rep1


title: 38_post


title: 0.7mm-anther-whole-vs-meiocytes-Rep-2-Cy3-whole

description:
Cy3-103_4
compare 0.7mm anther whole  to 0.7mm anther meiocytes
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.7mm anther whole 1171-8.2 WA


title: WT sciatic nerve at 4 months, biological rep2

description: Gene expression from 4-months WT scatic nerve

source_name: Sciatic nerves from 4 months old WT mice

value: WT


title: 5713384031_C

description: SAMPLE 103

source_name: cervical cancer


title: 5713384031_E

description: SAMPLE 105


title: 5713384031_D

description: SAMPLE 104


title: 0.7mm-anther-whole-vs-tapetum-Rep-2-Cy3-whole

description:
Cy3-103_2
compare 0.7mm anther whole  to 0.7mm anther tapetum
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.7mm anther whole 1171-8.1 WA


title: WT sciatic nerve at 4 months, biological rep1


title: 38_pre


title: 0.7mm-anther-whole-vs-meiocytes-Rep-1-Cy3-meiocytes

description:
Cy3-103_3
compare 0.7mm anther meiocytes to 0.7mm anther whole
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.7mm anther meiocytes 1171-7.2.2 Me

value: 0.7mm anther meiocytes


title: 37_pre


title: 0.7mm-anther-whole-vs-tapetum-Rep-1-Cy3-tapetum

description:
Cy3-103_1
compare 0.7mm anther tapetum to 0.7mm anther whole
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.7mm anther tapetum 1171-7.2.2 T

value: 0.7mm anther tapetum


title: S63del/CHOP null sciatic nerve at P28, biological rep2

description: Gene expression from P28 S63del/CHOP null (neuropathic, rescued) scatic nerve

source_name: Sciatic nerves from P28 S63del/CHOP null mice

value: Postnatal day 28


title: 36_post


title: 35_post


title: 0.7mm-anther-meiocytes-vs-tapetum-Rep-2-Cy5-0.7mm-tapetum

description:
Cy5-254_4
compare 0.7mm anther meiocytes to 0.7mm anther tapetum
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.7mm anther tapetum 1171-1 tapetum


title: 37_post


title: 36_pre


title: 0.2mm-anther-msca1-vs-mac1-Rep-2-Cy5-0.2mm-mac1

description:
Cy5-254_2
compare 0.2mm anther msca1 to 0.2mm anther mac1
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.2mm anther mac1 0.20 mac1-59 WA

value: 0.2mm anther mac1


title: S63del/CHOP null sciatic nerve at P28, biological rep1


title: 5713384031_A

description: SAMPLE 102

value: IIA


title: S63del sciatic nerve at P28, biological rep2

description: Gene expression from P28 S63del (neuropathic) scatic nerve

source_name: Sciatic nerves from P28 S63del mice


title: 0.7mm-anther-meiocytes-vs-tapetum-Rep-1-Cy5-0.7mm-meiocyte

description:
Cy5-254_3
compare 0.7mm anther tapetum to 0.7mm anther meiocytes
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.7mm anther meiocytes 1171-1 Me


title: 5713384011_K

description: SAMPLE 100


title: 5713384011_L

description: SAMPLE 101


title: S63del sciatic nerve at P28, biological rep1


title: CHOP null sciatic nerve at P28, biological rep1

description: Gene expression from P28 CHOP null scatic nerve

source_name: Sciatic nerves from P28 CHOP null mice


title: 0.2mm-anther-msca1-vs-fertilesib-Rep-2-Cy5-0.2mm-fertilesib

description:
Cy5-253_4
compare 0.2mm anther msca1 to 0.2mm anther fertile sib
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.2mm anther fertile sib 0.20 WT-75 WA

value: 0.2mm anther fertile sib


title: 0.2mm-anther-msca1-vs-mac1-Rep-1-Cy5-0.2mm-msca1

description:
Cy5-254_1
compare 0.2mm anther mac1 to 0.2mm anther msca1
raw data file:
US84703594_251604710254_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.2mm anther msca1 0.20 msca1-35 WA

value: 0.2mm anther msca1


title: 5713384011_J

description: SAMPLE 99


title: WT sciatic nerve at P28, biological rep2

description: Gene expression from P28 WT scatic nerve

source_name: Sciatic nerves from P28 WT mice


title: 5713384011_H

description: SAMPLE 97


title: 0.2mm-anther-msca1-vs-fertilesib-Rep-1-Cy5-0.2mm-msca1

description:
Cy5-253_3
compare 0.2mm anther fertile sib to 0.2mm anther msca1
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_3.txt


title: 5713384011_F

description: SAMPLE 96


title: 35_pre

source_name: serum


title: CHOP null sciatic nerve at P28, biological rep2


title: 5713384011_I

description: SAMPLE 98


title: WT sciatic nerve at P28, biological rep1


title: 0.2mm-anther-mac1-vs-fertilesib-Rep-2-Cy5-0.2mm-fertilesib

description:
Cy5-253_2
compare 0.2mm anther mac1 to 0.2mm anther fertile sib
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.2mm anther fertile sib 0.20 wt-33 WA


title: 34_pre


title: 34_post


title: 5713384011_E

description: SAMPLE 95


title: 33_post


title: 33_pre


title: S63del/CHOP null sciatic nerve at P5, biological rep2

description: Gene expression from P5 S63del/CHOP null (neuropathic, rescued) scatic nerve

source_name: Sciatic nerves from P5 S63del/CHOP null mice

value: Postnatal day 5


title: 5713384011_D

description: SAMPLE 94


title: 5713384011_A

description: SAMPLE 92


title: 0.15mm-anther-fertilesib-vs-0.4mm-mac1-Rep-2-Cy5-0.4mm-mac1

description:
Cy5-248_4
compare 0.15mm anther fertile sib to 0.4mm anther mac1
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.4mm anther mac1 0.4 mac1-18

value: 0.4mm anther mac1


title: S63del/CHOP null sciatic nerve at P5, biological rep1


title: S63del/CHOP null sciatic nerve at 4 months, biological rep2

description: Gene expression from 4-months S63del/CHOP null (neuropathic, rescued) scatic nerve

source_name: Sciatic nerves from 4 months old S63del/CHOP null mice


title: 0.4mm-anther-mac1-vs-fertilesib-Rep-2-Cy5-0.4mm-fertilesib

description:
Cy5-248_2
compare 0.4mm anther mac1 to 0.4mm anther fertile sib
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.4mm anther fertile sib 0.4 wt-12

value: 0.4mm anther fertile sib


title: S63del sciatic nerve at P5, biological rep2

description: Gene expression from P5 S63del (neuropathic) scatic nerve

source_name: Sciatic nerves from P5 S63del mice


title: 0.15mm-anther-fertilesib-vs-0.4mm-mac1-Rep-1-Cy5-0.15mm-fertilesib

description:
Cy5-248_3
compare 0.4mm anther mac1 to 0.15mm anther fertile sib
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.15mm anther fertile sib 0.15-12

value: 0.15mm anther fertile sib


title: CHOP null sciatic nerve at P5, biological rep2

description: Gene expression from P5 CHOP null scatic nerve

source_name: Sciatic nerves from P5 CHOP null mice


title: 5713384010_L

description: SAMPLE 91

source_name: cervical cancer


title: 32_pre

value: IgG/IgM


title: 5713384011_C

description: SAMPLE 93


title: 31_pre


title: 31_post


title: 32_post


title: 0.2mm-anther-mac1-vs-fertilesib-Rep-1-Cy5-0.2mm-mac1

description:
Cy5-253_1
compare 0.2mm anther fertile sib to 0.2mm anther mac1
raw data file:
US84703594_251604710253_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.2mm anther mac1 0.20 mac1-39 WA


title: 0.4mm-anther-mac1-vs-fertilesib-Rep-1-Cy5-0.4mm-mac1

description:
Cy5-248_1
compare 0.4mm anther fertile sib to 0.4mm anther mac1
raw data file:
US84703594_251604710248_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.4mm anther mac1 0.4 mac1-4


title: 5713384010_K

description: SAMPLE 90


title: CHOP null sciatic nerve at P5, biological rep1

value: Sciatic nerve


title: 30_post


title: 30_pre


title: S63del sciatic nerve at P5, biological rep1


title: 0.4mm-anther-wt-vs-0.25mm-Rep-1-Cy5-0.4mm

description:
Cy5-247_3
compare 0.25mm anther wt to 0.4mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.4mm anther wt 0.4 wt-6

value: 0.4mm anther wt


title: 29_post


title: 0.4mm-anther-wt-vs-0.25mm-Rep-2-Cy5-0.25mm

description:
Cy5-247_4
compare 0.4mm anther wt to 0.25mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.25mm anther wt 0.25-3

value: 0.25mm anther wt


title: 29_pre


title: WT sciatic nerve at P5, biological rep1

description: Gene expression from P5 WT scatic nerve

source_name: Sciatic nerves from P5 WT mice


title: 5713384010_J

description: SAMPLE 89


title: 0.25mm-anther-wt-vs-0.15mm-Rep-2-Cy5-0.15mm

description:
Cy5-247_2
compare 0.25mm anther wt to 0.15mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.15mm anther wt 0.15-6

value: 0.15mm anther wt


title: 28_post


title: 5713384010_H

description: SAMPLE 87


title: 0.4mm-anther-wt-vs-0.25mm-Rep-1-Cy3-0.25mm

description:
Cy3-247_3
compare 0.25mm anther wt to 0.4mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_3.txt


title: 0.7mm-anther-whole-vs-endo/epi-Rep-3-Cy5-endo/epi

description:
Cy5-97_3
compare 0.7mm anther whole  to 0.7mm anther endothecium/epidermis
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.7mm anther endothecium/epidermis 1171-7 E/E

value: 0.7mm anther endothecium/epidermis


title: WT sciatic nerve at P5, biological rep2

description: Gene expression from P5 WT scatic nerve

value: WT


title: 0.25mm-anther-wt-vs-0.15mm-Rep-1-Cy5-0.25mm

description:
Cy5-247_1
compare 0.15mm anther wt to 0.25mm anther wt
raw data file:
US84703594_251604710247_S01_GE2-v5_95_Feb07_2_JF_1_1.txt


title: 5713384010_I

description: SAMPLE 88


title: 5713317118_H

description: SAMPLE 82


title: 28_pre

source_name: serum


title: 5713384010_G

description: SAMPLE 86


title: 27_post


title: 0.7mm-anther-whole-vs-endo/epi-Rep-4-Cy5-whole

description:
Cy5-97_4
compare 0.7mm anther endothecium/epidermis to 0.7mm anther whole
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.7mm anther whole 1171-5.2 WA

value: 0.7mm anther whole


title: 27_pre


title: 0.7mm-anther-whole-vs-endo/epi-Rep-2-Cy5-whole

description:
Cy5-97_2
compare 0.7mm anther endothecium/epidermis to 0.7mm anther whole
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.7mm anther whole 1171-5.1 WA


title: 5713384031_J

description: SAMPLE 109


title: 5713384010_E

description: SAMPLE 85


title: 5713384010_D

description: SAMPLE 84


title: Brain_Schizophrenia_Subject11

city: Belmont

first: Sarah

last: Mauney

address: 115 Mill St.

institute: McLean Hospital

description: Gene expression data from parvalbumin neurons in layer 3 of the STG

hyb_protocol: Labeled aRNA underwent hybridization as explained in the TURBO Biotin labeling™ kit (end-labeling; Life Technologies Corporation). Gene expression profiling was performed using the Affymetrix Human X3P GeneChip®, which possesses an extreme 3' bias in its probe design and hence is particularly suitable for samples that are prone to RNA degradation, such as postmortem human brain tissue. The hybridization and scanning procedures were performed at the Partners HealthCare Center for Personalized Genetic Medicine (Cambridge, MA).

scan_protocol: The scanning procedures were performed at the Partners HealthCare Center for Personalized Genetic Medicine (Cambridge, MA) with a GeneChip® Model 3000 7G scanner using the Affymetrix GCOS v1.3 operating system.

data_processing: GCOS v1.3

molecule: polyA RNA

source_name: Parvalbumin neurons layer 3 STG, schizophrenia

label_protocol: The TURBO Biotin labeling™ kit (end-labeling; Life Technologies Corporation) was used to label the aRNA obtained from amplified samples (15 μg).

extract_protocol: RNA extraction and isolation was performed using the Picopure™ RNA Isolation kit (Life Technologies Corporation), with a DNase step (Qiagen Inc., CA). The RNA underwent two rounds of linear amplification using the RiboAmp® kit (Life Technologies, CA). A dilution of the resulting aRNA (approximately 250 ng/µl) was used to determine transcript lengths with the Experion StdSens Labchip (Bio-Rad, CA). The concentration and purity of RNA were determined by absorbance measurements at the optical density of A260 and A280, using a NanoDrop spectrophotometer (Thermo Scientific, DE).

treatment_protocol: Liquid nitrogen vapor fresh-frozen blocks containing the superior temporal gyrus (STG) from subjects were cut on a cryostat at 8μm. PV neurons were identified with a rapid immunohistochemistry procedure. Briefly, mounted sections were incubated in an anti-PV antibody (1:10 dilution; mouse, Sigma-Aldrich, MO) for 7 minutes and in peroxidase AffiniPure donkey anti-mouse IgG secondary antibody (1:10 dilution; Jackson ImmunoResearch Laboratories, PA) for 7 minutes, together with an RNase Inhibitor (40U/µl; Roche, Basel). Neurons were ultimately visualized with the NovaRED™ substrate-chromogen (12 minutes; Vector, CA). Approximately 300 PV-immunolabeled neurons per subject were captured onto a CapSure HS™ LCM cap (Life Technologies, NY).

value: brain

value: Male

tag: post mortem interval (pmi)

tag: phenotype

value: Schizophrenia


title: 26_post

tag: age


title: 26_pre

tag: h1n1 cpost


title: 0.7mm-anther-whole-vs-endo/epi-Rep-1-Cy5-endo/epi

description:
Cy5-97_1
compare 0.7mm anther whole  to 0.7mm anther endothecium/epidermis
raw data file:
US84703594_251604710097_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.7mm anther endothecium/epidermis 1171-1 E/E


title: 25_post

tag: h3n2 cpost


title: 5713317110_H

description: SAMPLE 79


title: 0.7mm-anther-whole-vs-meiocytes-Rep-2-Cy5-meiocytes

description:
Cy5-103_4
compare 0.7mm anther whole  to 0.7mm anther meiocytes
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: 0.7mm anther meiocytes 1171-8.2.1/2 Me

value: 0.7mm anther meiocytes


title: Brain_Schizophrenia_Subject8

value: Female

value: parvalbumin neurons in layer 3 of the STG


title: Brain_Schizophrenia_Subject12


title: Brain_Schizophrenia_Subject6


title: Brain_Schizophrenia_Subject4


title: 5713317110_K

description: SAMPLE 80


title: Brain_Schizophrenia_Subject5


title: 5713317118_K

description: SAMPLE 83


title: 5713317118_C

description: SAMPLE 81


title: 0.7mm-anther-whole-vs-tapetum-Rep-1-Cy5-whole

description:
Cy5-103_1
compare 0.7mm anther tapetum to 0.7mm anther whole
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_1.txt

source_name: 0.7mm anther whole 1171-7.1 WA


title: 5713317110_G

description: SAMPLE 78


title: 5713317110_D

description: SAMPLE 77


title: Brain_Schizophrenia_Subject2


title: 0.7mm-anther-whole-vs-tapetum-Rep-2-Cy5-tapetum

description:
Cy5-103_2
compare 0.7mm anther whole  to 0.7mm anther tapetum
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_2.txt

source_name: 0.7mm anther tapetum 1171-8.2.1/2 T

value: 0.7mm anther tapetum


title: Brain_Schizophrenia_Subject1


title: Brain_Control_Subject11

source_name: Parvalbumin neurons layer 3 STG, control

value: control


title: 0.7mm-anther-whole-vs-meiocytes-Rep-1-Cy5-whole

description:
Cy5-103_3
compare 0.7mm anther meiocytes to 0.7mm anther whole
raw data file:
US84703594_251604710103_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

source_name: 0.7mm anther whole 1171-7.2 WA


title: Brain_Control_Subject10


title: 25_pre

tag: b cpost


title: 24_post

tag: molecule


title: 5713317110_C

description: SAMPLE 76

source_name: cervical cancer

tag: Stage


title: 23_post


title: 24_pre


title: Brain_Control_Subject8


title: 23_pre


title: 5713317110_A

description: SAMPLE 75

value: IIA

tag: largest diameter


title: Liver_Fasted_vs_Fed_rep4

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Comparison of total RNA from paired fasted and re-fed mouse livers

hyb_protocol: Labeled samples were purified using the RNeasy Kit (Qiagen) and hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.

scan_protocol: After hybridization the arrays were washed and scanned with the Agilent DNA Microarray Scanner G2565B. Median intensities of each array element were captured with Agilent Feature Extraction v10.5.1.1.

data_processing: Median feature intensities were normalized by the print tip loess method in LIMMA (Smyth GK, et al. Bioinformatics 2005). Differentially expressed gene calls were performed by SAM (Tusher VG, et al. PNAS 2001) at 10% FDR and absolute fold-change cutoff of 1.5.

source_name: mouse liver, refed 2hr

label_protocol: 200ng of total RNA from each fasted and re-fed mouse livers (n = 4 per group) were amplified and labeled with Cy3 or Cy5 using Low Input Quick Amp Labeling Kit, two-color (Agilent, #5190-2306) with a dye swap experimental design.

growth_protocol: All mice used in this study were 8-12 week-old male C57BL/6J mice.

extract_protocol: Total RNA was extracted from livers collected from fasted and re-fed mice using the RNeasy Kit (Qiagen), then assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Fasted mice had food removed from their cages for 24h prior to liver harvest. Re-fed mice had food removed from their cages for 24h, and then were given access to food for 2h prior to liver harvest.

value: liver

tag: condition

value: Fasted 24h, Re-fed 2h

source_name: mouse liver, fasted 24hr

value: Fasted 24h


title: 22_post

value: IgG/IgM


title: S63del sciatic nerve at 4 months, biological rep2

description: Gene expression from 4-months S63del (neuropathic) scatic nerve

source_name: Sciatic nerves from 4 months old S63del mice

value: Sciatic nerve

tag: genotype

value: 4 months


title: 5713384061_L

description: SAMPLE 74

data_processing: The software package to extract raw data was Genomestudio. The intensity of the probes was transformed by binary logarithm and then was normalized using the quantile normalization method.

extract_protocol: RNA was extracted using a High Pure RNA Paraffin Kit protocol - Roche.


title: Brain_Control_Subject6

tag: Sex

tag: cell type


title: 5713384061_K

description: SAMPLE 73


title: Liver_Fasted_vs_Fed_rep3


title: 5713384061_H

description: SAMPLE 71


title: 5713384061_I

description: SAMPLE 72


title: 5713384061_G

description: SAMPLE 70


title: Brain_Control_Subject5


title: Liver_Fasted_vs_Fed_rep2


title: 21_post


title: Brain_Control_Subject1


title: 22_pre


title: Liver_Fasted_vs_Fed_rep1


title: Brain_Control_Subject4


title: CD4_miR155_KO_RFP_plus_rep2

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

hyb_protocol: Micrarrays were hybridized using the standard Agilent One-color heterologous gene expression hybridization and wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing:
Images from scanner processed using Agilent Feature Extraction software version 10.5.1.1
Array data filtered to remove control features and features flagged as nonuniform or population outliers.
Remaining values for each unique probe were averaged to yield a single value per probe sequence.
Intensities were median centered and log-base 2 transformed.

source_name: CD4 cells, miR155 knockout, RFP plus

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

extract_protocol: Total RNA extracted with Qiagen RNEasy mini kit

treatment_protocol: FACS sort CD4+IL17F RFP+ cells

tag: genotype/variation

value: miR155 knockout


title: CD4_WT_RFP_plus_rep1

source_name: CD4 cells, WT, RFP plus

value: WT


title: nbp35-3/-  rep2

city: Nara

first: Miyuki

last: Nakamura

address: 8916-5 Takayama

country: Japan

institute: Nara Institute of Science and Technology

hyb_protocol: Following fragmentation, 10 ug (5 ug for sample '2EA1021_10', '4EA1021_11', '6EA1021_12') of cRNA were hybridized for 16 hr at 45 degrees on GeneChip Arabidpsis ATH1 Gemome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA processing using R/Bioconductor

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana of  2 weeks  nbp35-4/- seedlings

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit  （Affymetrix) from 250 ng (200 ng for sample '2EA1021_10', '4EA1021_11', '6EA1021_12') total RNA according to the manufacturer's instructions.  Biotinylated cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: Plants were grown on MS plates for 2 weeks under 16 h light/8 h dark at 22˚C.

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 2-week-old whole plants were collected and frozen by liquid nitrogen.

tag: tissue

value: whole seedling

value: 2 weeks after imbibition

tag: genetic background


title: 5713384061_F

city: Seoul

first: Yuyoung

last: Lee

address: 50 Irwon-Dong, Gangnam-Gu

institute: SMC

description: SAMPLE 69


title: CD4_WT_RFP_plus_rep2


title: CD4_miR155_KO_RFP_plus_rep1


title: Brain_Control_Subject2

value: brain

value: Male


title: nbp35-3/-  rep1


title: 20_pre

source_name: serum


title: 20_post


title: 21_pre


title: 19_post


title: 19_pre


title: 18_post


title: Ovcar_silencedRNASET2_rep2_mouse

city: Varese (VA)

last: Fabbri

address: via dunant 5

institute: Università dell'Insubria

description:
Ovcar_silencedRNASET2_rep2
Gene expression of RNASET2-silenced OVCAR3 injected into mice

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.5.1.1).

source_name: RNASET2-silenced OVCAR3

label_protocol: standard Agilent protocol

growth_protocol: 6-weeks-old male nude mice were challenged subcutaneously in the left flank with parental or RNASET2-silenced OVCAR3 cells. Animals were monitored twice a week for weight and tumor growth (measuring three perpendicular diameters), and killed at day 39. Separate experiments were performed with three different clones of both control (parental cells) and RNASET2-silenced cells.

extract_protocol: Mice were killed at day 39 and tumors were frozen for RNA extraction.Total RNA extracted using RNeasy Plus kit (Qiagen) according to the manufacturer's instructions

tag: strain

value: nude mice

tag: transfection

value: silnced RNASET2


title: Ovcar_silencedRNASET2_rep3_mouse

description:
Ovcar_silencedRNASET2_rep3
Gene expression of RNASET2-silenced OVCAR3 injected into mice


title: 18_pre


title: nar1-4/-  rep2

source_name: Arabidopsis thaliana of  2 weeks  nar1-4/- seedlings


title: 5713384061_E

description: SAMPLE 68

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label_protocol: RNA was labelled using the WG-DASL kit from Illumina.


title: Ovcar_silencedRNASET2_rep1_mouse

description:
Ovcar_silencedRNASET2_rep1
Gene expression of RNASET2-silenced OVCAR3 injected into mice


title: 5713384051_I

description: SAMPLE 63


title: Wild type rep2

source_name: Arabidopsis thaliana of  2 weeks  wild type seedlings

value: Wild type


title: 5713384051_L

description: SAMPLE 64


title: Wild type rep1


title: Ovcar_control_rep2_mouse

description:
Ovcar_control_rep2
Gene expression of OVCAR3 injected into mice

source_name: Control OVCAR3

value: empty vector


title: Ovcar_control_rep3_mouse

description:
Ovcar_control_rep3
Gene expression of OVCAR3 injected into mice


title: Ovcar_control_rep1_mouse

description:
Ovcar_control_rep1
Gene expression of OVCAR3 injected into mice


title: 5713384051_H

description: SAMPLE 62


title: T6

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Biology

country: United Kingdom

institute: Nottingham University

description: gene expression data from conidia germinated for 6h in liquid ACM media

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: GeneSpring GX 11 (Agilent Technologies, Inc), Data were normalized using the RMA algorithm. Raw intensity signal values were normalized per chip to the 75th percentile and baseline transformation to the median of all samples (time points) was used.

organism: Aspergillus niger

source_name: conidia germinated for 6h

label_protocol: GeneChip® IVT Express Kit

growth_protocol: A. niger strain N402, a cpsA1 derivative of A. niger N400 (Bos et al. 1988) was grown on Aspergillus complete medium (ACM) (containing per litre: NaNO3 6g, KCl, 0.52 g; MgSO4.7H2O, 0.52 g; KH2PO4, 1.52 g; Na2B4O7.10H2O, 0.008 mg; CuSO4.5H2O, 0.16 mg; FePO4.H2O, 0.16 mg; MnSO4.4H2O, 0.16 mg; NaMoO4.2H2O, 0.16 mg; ZnSO4, 1.6 mg, Bacto casamino acids, 1g, yeast extract, 1g, Bacto peptone, 2g, glucose, 10g, vitamins: p-aminobenzoic acid, 4mg, thiamine HCl, 0.5mg, D-biotin, 0.02mg, nicotinic acid, 1mg,  pyridoxine hydrochloride, 2.5mg, choline chloride, 0.014g, riboflavin, 1mg, agar 20g where applicable  ) for 6 days at 28oC to develop mature conidia. Conidia were harvested by washing the agar slopes with a 0.01% (w/v) Tween 80 solution. The conidial suspension was filtered through sterile synthetic wool and conidia were counted using a haemocytometer. Conidia (104/ml) were germinated in liquid ACM media for 1, 2, 4 and 6 hours at 28˚C, in 2L conical flasks containing 1000 ml of medium, shaken at 150rpm.  Germinated conidia were recovered by filtration into 0.5 ml RNA extraction buffer (0.6M NaCl, 0.2M sodium acetate, 0.1M EDTA, 4% w/v SDS) and snap frozen in liquid nitrogen. Frozen dormant or germinated conidia were mixed with 0.5ml glass beads and disintegrated in a Sartorius dismembranator (4 min, 2000rpm).

extract_protocol: RNA was extracted using the TRIzol reagent protocol (Invitrogen) according to manufacturer’s instructions, followed by an additional clean-up using RNeasy columns (Qiagen) including the on-column DNAase treatment step.

tag: developmental stage

value: conidia germinated for 6h


title: 5713384061_C

description: SAMPLE 66


title: 17_post

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

tag: age


title: 17_pre

tag: h1n1 cpost


title: 16_post

tag: h3n2 cpost


title: 16_pre

tag: b cpost


title: 15_post

tag: molecule


title: 15_pre


title: 14_post


title: MPM Epithelioid_87

city: Boston

first: Assunta

last: De Rienzo

state: Massachusetts

address: 75 Francis Street

department: Surgery

institute: Brigham and Women's Hospi

description: SAMPLE 87

hyb_protocol: 0.75 ug of total RNA was amplified using Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA, USA).  cRNA was hybridized to Illumina Human-6 Expression BeadChip (Illumina, San Diego, CA, USA) as recommended by the manufacturer

scan_protocol: The arrys were scanned by the Bead Station (Illumina, San Diego, CA, USA) as recommended by the manufacturer

data_processing: Array data processing was performed with Illumina BeadStudio software.

source_name: Tumor

label_protocol: Cy3-streptavidin (Amersham Biosciences, Little Chalfont, United Kingdom) as recommended by the manufacturer

extract_protocol: RNA was extracted using Triazol reagent (Invitrogen Corporation, Carlsbad, CA, USA) according to the manufacturer’s instructions.  DNase I (Invitrogen Corporation, Carlsbad, CA, USA) treatment was performed according to the manufacturer’s instructions

value: MPM Epithelioid


title: 14_pre

last: Price

institute: Oberlin College

hyb_protocol: We blocked printed peptide arrays with 0.1 mg ml-1 biotin (Sigma) in PBS for 10 min at RT with 500 rpm orbital agitation. After rinsing the arrays six times in peptide binding buffer (PBB): [50 mM Tris (Mallinckrodt Baker, Phillipsburg, NJ) pH 7.5, 150 mM NaCl (Mallinckrodt AR, Phillipsburg NJ), 0.05% NP-40 (Sigma) + 2.5% FCS), we applied mAb and pAb antibodies diluted to 1.0 μg ml–1 or patient serum diluted 1:80 in PBB. Following primary incubation for 3 h at RT with 500 rpm orbital agitation, we rinsed the arrays six times with PBB then six times in PBST before applying secondary antibody reagents (goat anti-mouse IgG, goat anti-rabbit IgG or goat anti-human IgG conjugated to Cy3, Jackson ImmunoResearch) diluted to 0.375 μg ml–1 in PBST plus 20% FCS for 30 min at RT with 500 rpm orbital agitation. We then rinsed arrays six times in PBST, three times in PBS and three times in diH20 and dried arrays in microscope slide racks centrifuged at 300 g for 5 min at RT.

scan_protocol: We immediately scanned processed peptide arrays with an Axon digital scanner and analyzed scanned images with Genepix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).

extract_protocol: All individuals were ambulatory and generally healthy as determined by clinical history. Females of childbearing potential were tested for pregnancy by a urine sample. Volunteers at initial enrollment had no active systemic or serious concurrent illness, no history of immunodeficiency, nor any known or suspected impairment of immunologic function, including clinically significant liver disease, diabetes mellitus treated with insulin, moderate to severe renal disease, blood pressure >150/95 at screening, chronic hepatitis B or C, recent or current use of systemic immunosuppressive medication. In addition, none of the volunteers were recipients of blood or blood products within the past 6 months or blood donors within 6 weeks prior to immunization. Volunteers were screened to assure that they did not have signs of febrile illness on day of enrollment and baseline blood draw. A total of ~120 ml peripheral blood was obtained in three visits (~40 ml/visit): at day 0 (pre-vaccine), 5-7 and 28 7 days after receiving a single intramuscular dose of trivalent seasonal influenza vaccine Fluzone (Sanofi Pasteur, Swiftwater, PA). Each dose of the vaccine contained a total of 45  g of antigen corresponding to 15  g HA each of H1N1, H3N2 and B strains of the seasonal viruses included for that year. Serum was separated by centrifugation of clotted blood, and stored at -80 C before use. Serum samples from visit 1 (day 0) and 3 (day 28   7) were used for array experiments and microneutralization titer determination.


title: 5713384049_E

description: SAMPLE 53

tag: Stage


title: HH14 right sinus venosus slide 1 rep 1

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: HH14_Right sinus  venosus _ slide 1 _ rep1

hyb_protocol: Slides were pre-hybridized (5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 1% (w/v) bovine serum albumin, fraction V (Sigma)) for 45 minutes at 42°C to block the remaining reactive epoxide groups and reduce background signal. Cy3 and Cy5 labelled RNA samples were combined as described in the experimental design and mixed with 2x hybridization mixture to a final concentration of 5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 0.2 \mug/\muL herring sperm DNA (Invitrogen). Target-RNA mix was denatured for 5 minutes at 70°C and incubated at 42°C for 30 minutes. Hybridization was done in a GeneTAC hybridization station (Genomic Solutions) for 16 hours at 42°C with agitation. The arrays were washed at room temperature in 5 successive buffers, i.e., 1x SSC + 0.2% SDS, 0.1x SSC + 0.2% SDS, 1x SSC, 0.1x SSC and 0.001x SSC, each step lasting 4 minutes. The slides were finally pressure-air dried and stored in the dark.

scan_protocol: Slides were scanned using an Agilent G2565BA microarray scanner on a 10 micro m resolution. The resulting images were split into the red and green channels prior to feature extraction with the GenePix Pro 6.1.0.2 (Axon Instruments Inc.) software.

data_processing: Median spot intensities were imported from the genepix results files using the Limma package. Flagged spots were assigned a weight of 0.1, control spots were removed and the remaining data were normalized with lowess (parameters: span = 0.25, iterations = 2) and aquantile transformations using the R/Limma package in Bioconductor

organism: Gallus gallus

source_name: Right sinus

label_protocol: 1500 ng amplified RNA ( Ambion MessageAmp-II ) wasd labelled with either Cy3 or Cy5 as decribed by 't Hoen PA ( Nucleic Acids Res. 2003 Mar 1;31(5):e20 )

growth_protocol: Embryonic chicken were staged according to Hamburger and Hamilton. HH14 Left and Right sinus horns were isolated.

extract_protocol: Total RNA was isolated using Macherey-Nagel nucleospin columns and DnaseI treated. Quantified with the Nanodrop ND1000 and QC with an Agilent nanoChip.

value: right sinus venosus


title: MPM Epithelioid_86

description: SAMPLE 86


title: 13_post

city: Oberlin

first: Jordan

address: 119 Woodland St


title: nar1-4/-  rep1


title: 5713384061_D

description: SAMPLE 67

tag: largest diameter


title: MPM Epithelioid_90

description: SAMPLE 90


title: 5713384051_D

description: SAMPLE 60


title: 13_pre


title: 5713384049_C

description: SAMPLE 52


title: T0

description: gene expression data from dormant conidia

source_name: dormant conidia

value: dormant conidia


title: MPM Sarcomatoid_85

description: SAMPLE 85

value: MPM Sarcomatoid


title: 5713384049_A

description: SAMPLE 51