title: EJM_STY

description:
Hybridized to 250K_Sty
EJM

source_name: Blood/Lymph cell line EJM

value: EJM


title: HT-1197_STY

status: Public on Nov 03 2011

type: genomic

city: Charlestown

first: Stephen

middle: Michael

last: Rothenberg

state: MA

address: 13th Street, Bldg. 149, 7th Floor

department: Cancer Center

country: USA

institute: Massachusetts General Hospital

description:
Hybridized to 250K_Sty
HT-1197

hyb_protocol: Hybridization was performed as described in the 500k assay manual (P/N 701930 Rev. 2).

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000 with autoloader and 7G upgrade and images were acquired using GenChip operating software version 1.4.

data_processing:
CEL files and TXT files (generated by Affymetrix GTYPE using the Dynamic Model Mapping algorithm) were processed by dCHIP version 2008 using Model-based expression. The following parameters were used: Background subtraction--Mismatch probe (PM/MM difference); Normalization--Invariant set probe selection method and Running median smoothing method (baseline array NA06990); Raw copy number determination--Signal / (mean signal of normal samples at this SNP) * 2; log2 ratio--log2(Signal / mean signal of normal samples at this SNP); Inferred copy number method-- Median smoothing with window size of 3.

The SNP calls are available in the supplementary .txt file that is linked to this record. The data table containing the Signal values (analgous to the expression value in expression array analysis) for each SNP probe produced by dCHIP is available in the supplementary .txt file that is linked to the Series GSE20306 record.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Bladder cell line HT-1197

label_protocol: Labeling was performed as described in the 500k assay manual (P/N 701930 Rev. 2).

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted with the Qiagen Blood Amp kit (P/N 51161).

treatment_protocol: None.

tag: cell line


title: LC4-1_STY

description:
Hybridized to 250K_Sty
LC4-1

source_name: Blood/Lymph cell line LC4-1


title: HPAF-II_STY

description:
Hybridized to 250K_Sty
HPAF-II

source_name: Pancreas cell line HPAF-II

value: HPAF-II


title: HCC-56_STY

description:
Hybridized to 250K_Sty
HCC-56

source_name: Intestine cell line HCC-56


title: HEC-1_STY

description:
Hybridized to 250K_Sty
HEC-1

source_name: Uterus cell line HEC-1


title: CoCM-1_STY

description:
Hybridized to 250K_Sty
CoCM-1

source_name: Intestine cell line CoCM-1


title: KYM-1_STY

description:
Hybridized to 250K_Sty
KYM-1

source_name: Muscle cell line KYM-1


title: TCCSUP_STY

description:
Hybridized to 250K_Sty
TCCSUP

source_name: Bladder cell line TCCSUP

value: TCCSUP


title: 1A6_STY

description:
Hybridized to 250K_Sty
1A6

source_name: Bladder cell line 1A6


title: A-427_STY

description:
Hybridized to 250K_Sty
A-427

source_name: Lung:NSCLC cell line A-427


title: SW837_STY

description:
Hybridized to 250K_Sty
SW837

source_name: Intestine cell line SW837


title: HDQ-P1_STY

description:
Hybridized to 250K_Sty
HDQ-P1

source_name: Breast cell line HDQ-P1


title: Panc 08.13_STY

description:
Hybridized to 250K_Sty
Panc 08.13

source_name: Pancreas cell line Panc 08.13


title: MDA-MB-361_STY

description:
Hybridized to 250K_Sty
MDA-MB-361

source_name: Breast cell line MDA-MB-361


title: HCC1428_STY

description:
Hybridized to 250K_Sty
HCC1428

source_name: Breast cell line HCC1428


title: NOMO-1/ADM_STY

description:
Hybridized to 250K_Sty
NOMO-1/ADM

source_name: Blood/Lymph cell line NOMO-1/ADM


title: NY_STY

description:
Hybridized to 250K_Sty
NY

source_name: Bone cell line NY

value: NY


title: TK_STY

description:
Hybridized to 250K_Sty
TK

source_name: Blood/Lymph cell line TK

value: TK


title: KMS-12-PE_STY

description:
Hybridized to 250K_Sty
KMS-12-PE

source_name: Blood/Lymph cell line KMS-12-PE


title: GOTO_STY

description:
Hybridized to 250K_Sty
GOTO

source_name: Kidney cell line GOTO

value: GOTO


title: T1-73_STY

description:
Hybridized to 250K_Sty
T1-73

source_name: Bone cell line T1-73


title: SW 156_STY

description:
Hybridized to 250K_Sty
SW 156

source_name: Kidney cell line SW 156


title: MLMA_STY

description:
Hybridized to 250K_Sty
MLMA

source_name: Blood/Lymph cell line MLMA

value: MLMA


title: JAR_STY

description:
Hybridized to 250K_Sty
JAR

source_name: Miscellaneous cell line JAR

value: JAR


title: KY821_STY

description:
Hybridized to 250K_Sty
KY821

source_name: Blood/Lymph cell line KY821


title: KMRC-2_STY

description:
Hybridized to 250K_Sty
KMRC-2

source_name: Kidney cell line KMRC-2


title: MY_STY

description:
Hybridized to 250K_Sty
MY

source_name: Blood/Lymph cell line MY

value: MY


title: PWR-1E_STY

description:
Hybridized to 250K_Sty
PWR-1E

source_name: Prostate cell line PWR-1E


title: Hs 738.St/Int_STY

description:
Hybridized to 250K_Sty
Hs 738.St/Int

source_name: Stomach cell line Hs 738.St/Int

value: Hs 738.St/Int


title: SCH_STY

description:
Hybridized to 250K_Sty
SCH

source_name: Stomach cell line SCH

value: SCH


title: LI90_STY

description:
Hybridized to 250K_Sty
LI90

source_name: Liver cell line LI90


title: HCC38_STY

description:
Hybridized to 250K_Sty
HCC38

source_name: Breast cell line HCC38


title: P30/OHK_STY

description:
Hybridized to 250K_Sty
P30/OHK

source_name: Blood/Lymph cell line P30/OHK


title: Hs 707(A).T_STY

description:
Hybridized to 250K_Sty
Hs 707(A).T

source_name: Bone cell line Hs 707(A).T


title: 769-P_STY

description:
Hybridized to 250K_Sty
769-P

source_name: Kidney cell line 769-P


title: SNG-M_STY

description:
Hybridized to 250K_Sty
SNG-M

source_name: Uterus cell line SNG-M

value: SNG-M


title: HK-2_STY

description:
Hybridized to 250K_Sty
HK-2

source_name: Kidney cell line HK-2


title: CCD 1103 KIDTr_STY

description:
Hybridized to 250K_Sty
CCD 1103 KIDTr

source_name: Kidney cell line CCD 1103 KIDTr

value: CCD 1103 KIDTr


title: KMH-2_STY

description:
Hybridized to 250K_Sty
KMH-2

source_name: Thyroid cell line KMH-2


title: DG-75_STY

description:
Hybridized to 250K_Sty
DG-75

source_name: Blood/Lymph cell line DG-75


title: NB(TU)1-10_STY

description:
Hybridized to 250K_Sty
NB(TU)1-10

source_name: Kidney cell line NB(TU)1-10


title: VMRC-RCZ_STY

description:
Hybridized to 250K_Sty
VMRC-RCZ

source_name: Kidney cell line VMRC-RCZ

value: VMRC-RCZ


title: MRK-nu-1_STY

description:
Hybridized to 250K_Sty
MRK-nu-1

source_name: Breast cell line MRK-nu-1


title: KO52_STY

description:
Hybridized to 250K_Sty
KO52

source_name: Blood/Lymph cell line KO52


title: JHH-2_STY

description:
Hybridized to 250K_Sty
JHH-2

source_name: Liver cell line JHH-2


title: CCK-81_STY

description:
Hybridized to 250K_Sty
CCK-81

source_name: Intestine cell line CCK-81


title: OVTOKO_STY

description:
Hybridized to 250K_Sty
OVTOKO

source_name: Ovary cell line OVTOKO

value: OVTOKO


title: NEC8_STY

description:
Hybridized to 250K_Sty
NEC8

source_name: Testes cell line NEC8


title: COLO 320DM_STY

description:
Hybridized to 250K_Sty
COLO 320DM

source_name: Intestine cell line COLO 320DM

value: COLO 320DM


title: YMB-1_STY

description:
Hybridized to 250K_Sty
YMB-1

source_name: Breast cell line YMB-1


title: UE6E7T-2_STY

description:
Hybridized to 250K_Sty
UE6E7T-2

source_name: Blood/Lymph cell line UE6E7T-2


title: SLVL_STY

description:
Hybridized to 250K_Sty
SLVL

source_name: Blood/Lymph cell line SLVL

value: SLVL


title: SCC-3_STY

description:
Hybridized to 250K_Sty
SCC-3

source_name: Blood/Lymph cell line SCC-3


title: BEAS-2B_STY

description:
Hybridized to 250K_Sty
BEAS-2B

source_name: Lung cell line BEAS-2B


title: Ca9-22_STY

description:
Hybridized to 250K_Sty
Ca9-22

source_name: Head & Neck cell line Ca9-22


title: CCD 1105 KIDTr_STY

description:
Hybridized to 250K_Sty
CCD 1105 KIDTr

source_name: Kidney cell line CCD 1105 KIDTr

value: CCD 1105 KIDTr


title: CAL-12T_STY

description:
Hybridized to 250K_Sty
CAL-12T

source_name: Lung:NSCLC cell line CAL-12T


title: HSC-2_STY

description:
Hybridized to 250K_Sty
HSC-2

source_name: Head & Neck cell line HSC-2


title: OVMIU_STY

description:
Hybridized to 250K_Sty
OVMIU

source_name: Ovary cell line OVMIU

value: OVMIU


title: VMRC-RCW_STY

description:
Hybridized to 250K_Sty
VMRC-RCW

source_name: Kidney cell line VMRC-RCW

value: VMRC-RCW


title: SAS_STY

description:
Hybridized to 250K_Sty
SAS

source_name: Head & Neck cell line SAS

value: SAS


title: MOLT-4F_STY

description:
Hybridized to 250K_Sty
MOLT-4F

source_name: Blood/Lymph cell line MOLT-4F


title: OVISE_STY

description:
Hybridized to 250K_Sty
OVISE

source_name: Ovary cell line OVISE

value: OVISE


title: RCM-1_STY

description:
Hybridized to 250K_Sty
RCM-1

source_name: Intestine cell line RCM-1


title: MCAS_STY

description:
Hybridized to 250K_Sty
MCAS

source_name: Ovary cell line MCAS

value: MCAS


title: YKG-1_STY

description:
Hybridized to 250K_Sty
YKG-1

source_name: Brain:Glioblastoma cell line YKG-1


title: Lu-134-B_STY

description:
Hybridized to 250K_Sty
Lu-134-B

source_name: Lung cell line Lu-134-B


title: HO-1-u-1_STY

description:
Hybridized to 250K_Sty
HO-1-u-1

source_name: Head & Neck cell line HO-1-u-1


title: MS-1-L_STY

description:
Hybridized to 250K_Sty
MS-1-L

source_name: Lung cell line MS-1-L


title: RMG-I_STY

description:
Hybridized to 250K_Sty
RMG-I

source_name: Ovary cell line RMG-I

value: RMG-I


title: K562/ADM_STY

description:
Hybridized to 250K_Sty
K562/ADM

source_name: Blood/Lymph cell line K562/ADM


title: HSC-3_STY

description:
Hybridized to 250K_Sty
HSC-3

source_name: Head & Neck cell line HSC-3


title: SUIT-2_STY

description:
Hybridized to 250K_Sty
SUIT-2

source_name: Pancreas cell line SUIT-2


title: huH-1_STY

description:
Hybridized to 250K_Sty
huH-1

source_name: Liver cell line huH-1


title: BALL-1_STY

description:
Hybridized to 250K_Sty
BALL-1

source_name: Blood/Lymph cell line BALL-1


title: OSC-20_STY

description:
Hybridized to 250K_Sty
OSC-20

source_name: Head & Neck cell line OSC-20


title: CaR-1_STY

description:
Hybridized to 250K_Sty
CaR-1

source_name: Intestine cell line CaR-1


title: JHH-4_STY

description:
Hybridized to 250K_Sty
JHH-4

source_name: Liver cell line JHH-4


title: HuCCT1_STY

description:
Hybridized to 250K_Sty
HuCCT1

source_name: Liver cell line HuCCT1


title: P32/ISH_STY

description:
Hybridized to 250K_Sty
P32/ISH

source_name: Blood/Lymph cell line P32/ISH


title: RKN_STY

description:
Hybridized to 250K_Sty
RKN

source_name: Ovary cell line RKN

value: RKN


title: HCC-827_STY

description:
Hybridized to 250K_Sty
HCC-827

source_name: Lung:NSCLC cell line HCC-827


title: P31/FUJ_STY

description:
Hybridized to 250K_Sty
P31/FUJ

source_name: Blood/Lymph cell line P31/FUJ


title: KP-4_STY

description:
Hybridized to 250K_Sty
KP-4

source_name: Pancreas cell line KP-4


title: HUP-T3_STY

description:
Hybridized to 250K_Sty
HUP-T3

source_name: Pancreas cell line HUP-T3


title: J82_STY

description:
Hybridized to 250K_Sty
J82

source_name: Bladder cell line J82


title: SKG-IIIb_STY

description:
Hybridized to 250K_Sty
SKG-IIIb

source_name: Cervix cell line SKG-IIIb

value: SKG-IIIb


title: KP-1N_STY

description:
Hybridized to 250K_Sty
KP-1N

source_name: Pancreas cell line KP-1N


title: SKN_STY

description:
Hybridized to 250K_Sty
SKN

source_name: Uterus cell line SKN

value: SKN


title: ME-180_STY

description:
Hybridized to 250K_Sty
ME-180

source_name: Cervix cell line ME-180


title: LC-1 sq_STY

description:
Hybridized to 250K_Sty
LC-1 sq

source_name: Lung:NSCLC cell line LC-1 sq

value: LC-1 sq


title: HSC-4_STY

description:
Hybridized to 250K_Sty
HSC-4

source_name: Head & Neck cell line HSC-4


title: JHH-6_STY

description:
Hybridized to 250K_Sty
JHH-6

source_name: Liver cell line JHH-6


title: KOSC-2 cl3-43_STY

description:
Hybridized to 250K_Sty
KOSC-2 cl3-43

source_name: Head & Neck cell line KOSC-2 cl3-43

value: KOSC-2 cl3-43


title: KHM-3S_STY

description:
Hybridized to 250K_Sty
KHM-3S

source_name: Lung cell line KHM-3S


title: IMR-90_STY

description:
Hybridized to 250K_Sty
IMR-90

source_name: Lung cell line IMR-90


title: TASK1_STY

description:
Hybridized to 250K_Sty
TASK1

source_name: Miscellaneous cell line TASK1


title: KON_STY

description:
Hybridized to 250K_Sty
KON

source_name: Head & Neck cell line KON

value: KON


title: MB 157_STY

description:
Hybridized to 250K_Sty
MB 157

source_name: Breast cell line MB 157


title: EPLC-272H_STY

description:
Hybridized to 250K_Sty
EPLC-272H

source_name: Lung:NSCLC cell line EPLC-272H


title: SW 1573_STY

description:
Hybridized to 250K_Sty
SW 1573

source_name: Lung:NSCLC cell line SW 1573


title: ASH-3_STY

description:
Hybridized to 250K_Sty
ASH-3

source_name: Thyroid cell line ASH-3


title: SCC-4_STY

description:
Hybridized to 250K_Sty
SCC-4

source_name: Head & Neck cell line SCC-4


title: HO-1-N-1_STY

description:
Hybridized to 250K_Sty
HO-1-N-1

source_name: Head & Neck cell line HO-1-N-1


title: CAL-148_STY

description:
Hybridized to 250K_Sty
CAL-148

source_name: Breast cell line CAL-148


title: VMRC-LCP_STY

description:
Hybridized to 250K_Sty
VMRC-LCP

source_name: Lung:NSCLC cell line VMRC-LCP

value: VMRC-LCP


title: HUP-T4_STY

description:
Hybridized to 250K_Sty
HUP-T4

source_name: Pancreas cell line HUP-T4


title: h7858_PLSDAvPL_rep4

type: RNA

city: Ithaca

first: Matthew

last: Stasiewicz

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

description: Biological replicate 4 of 4.

hyb_protocol: Before hybridization, microarray slides were first incubated for 1 h in a blocking solution at 42°C containing 1% bovine serum albumin (Sigma), 5X SSC (where 1X SSC contains 0.15 M NaCl and 15 mM sodium citrate) and 0.1% sodium dodecyl sulfate (SDS), then washed twice for 5 min in 0.1X SSC, 30 s in sterile water, and dried by centrigugation (1800 RPM, 3 min).  The combined cDNA samples were hydrated in 65 μl of a filter sterilized hydration hybridization buffer (500 ul formamide, 250 μl 20X SSC, 239 μl water, 10 μl 10% SDS, 1μl 0.1 M dithiothreitol, and 60 μl 10 mg/ml Salmon Sperm DNA [Invitrogen, Carlsbad, CA]) and denatured by a 5 min incubation at 95°C.  Denatured samples were then applied to arrays overlaid with LifterSlips (24mm x 60mm; Thermo Scientific, Portsmouth, NH), and hybridized for 16 h at 42°C.  Post-hybridization, slides were washed in 2X SSC and 0.1% SDS for 5 min at 42°C, in 2X SSC for 5 min at room-temperature, twice in 0.2S SSC for 2.5 min at room-temperature, dipped in water, then dried by centrifugation

scan_protocol: Slides were scanned with a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) and images quantified using GenePix Pro software (v6.0)

data_processing: Fluorescence of Cy3 and Cy5 channels were extracted as median intensity values, with no background correction, and imported in the statistical platform R (v2.2.1). The software package MAANOVA (v0.98-7, [http://www.bioconductor.org/packages/bioc/1.7/src/contrib/html/maanova.html]) was used to spatially normalize the intensity values of each array by printing block using LOWESS normalization and normalized values were averaged for each of three replicates per probe.

molecule: total RNA

organism: Listeria monocytogenes

source_name: h7858_PL treated

label_protocol: The SuperScript Plus indirect cDNA labeling system (Invitrogen, Carlsbad, CA) was used to prepare cDNA which was labeled with Cy3/Cy5 dyes (Amersham mono-reactive CyDye packs; GE Healthcare, Uppsala, Sweden).  First-strand cDNA was synthesized by first incubating 6 μg total RNA with 3 μg random hexamers primers in a total volume of 17.4 μl RNase-free water for 10 min at 70°C followed by a 10 min chill on ice.  Then Superscript III reverse-transcriptase, an aa-dUTP/dNTP mix (amino-allyl deoxyuridine triphosphate (Sigma) with deoxynucleoside triphosphates), dithiothreitol, and buffer were added and incubated at 42°C for 17 h.  The reaction was stopped by hydrolyzing RNA with 10 μl each 1 N NaOH and 0.5 M EDTA and incubation at 65°C for 15 min, followed by neutralization in 10 μl 1 N HCl.  cDNA was purified using a Qiagen PCR purification kit, dried in a Vacufuge Plus (Eppendorf, Hauppauge, NY)  and labeled with Cy3/5 fluorescent dyes by adding 4.5 μl of 1M sodium-carbonate at pH 9.3 and the appropriate dye at 0.55 M in DMSO and incubating at room-temperature for 2 h.  The reaction was stopped with 35μl of 100 mM sodium acetate at pH 5.2 and the labeled cDNA re-purified with another Qiagen PCR purification kit.  Labeled cDNA was quantified with the UV spectrophotometer to determine the frequency of incorporation, the number of labeled nucleotides per thousand nucleotides of cDNA, and all samples had frequencies of incorporation between 20 and 70.  Appropriate Cy3 and Cy5 labeled samples for competitive hybridization were combined, dried in the Vacufuge Plus, and stored at -80°C until hybridization.

growth_protocol: Pregrowth to stationary phase in chemically defined media followed by treatment with organic acids for 8h.

extract_protocol: After 8h incubation in treatment media the 100 ml treatment cultures were added to 10 ml of chilled 10% phenol:ethanol solution in 250ml polypropelene centrifuge bottles (Nalgene) to stop RNA transcription.  Cells were then pelleted by centrifugation (10,000 rpm, 10 min) at 4°C, suspended in 5 ml TRI reagent (Ambion, Austin, TX) for mechanical lysis by bead beating (in screw cap tubes with 3ml of 0.1 mm acid-washed zirconium beads, 5 min homogenization in a Mini-Beadbeater-8, BioSpec Products, Inc., Barlesville, OK),  and RNA extracted according to the TRI reagent manufacturer’s recommendations.  RNA samples were treated with RQ1 DNase (70U/100μl RNA; Promega, Madison, WI), followed by cleanup in a Qiagen RNeasy mini kit (QIAGEN, Valencia, CA).  RNA was quantified using a Nanodrop ND-1000 UV spectrophotometer (Nanodrop Technologies, Wilmingon, DE) and any samples with A260/A280 or A260/A230 < 1.8 were precipitated in 3-volumes ethanol and 1/10 volume sodium acetate at - 80°C, washed with ethanol, and hydrated in nuclease free water.   The RNA integrity of all samples was measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA) and only samples with an RNA Integrity Number > 8.0 were used.

treatment_protocol: PL treated cells adapted 8h

tag: strain

source_name: h7858_PLSDA treated


title: h7858_PLSDAvSDA_rep4

description: Biological replicate 4 of 4.

source_name: h7858_SDA treated

treatment_protocol: SDA treated cells adapted 8h


title: Hs 839.T_STY

description:
Hybridized to 250K_Sty
Hs 839.T

source_name: Skin cell line Hs 839.T


title: TE7_STY

description:
Hybridized to 250K_Sty
TE7

source_name: Esophagus cell line TE7


title: h7858_PLvCTRL_rep4

description: Biological replicate 4 of 4.

source_name: h7858_CTRL treated

treatment_protocol: CTRL treated cells adapted 8h


title: h7858_PLSDAvSDA_rep3

description: Biological replicate 3 of 4.


title: SAT_STY

description:
Hybridized to 250K_Sty
SAT

source_name: Head & Neck cell line SAT

value: SAT


title: SKN-3_STY

description:
Hybridized to 250K_Sty
SKN-3

source_name: Head & Neck cell line SKN-3


title: SK-NEP-1_STY

description:
Hybridized to 250K_Sty
SK-NEP-1

source_name: Kidney cell line SK-NEP-1


title: SW-1710_STY

description:
Hybridized to 250K_Sty
SW-1710

source_name: Bladder cell line SW-1710


title: h7858_PLSDAvPL_rep3

description: Biological replicate 3 of 4.


title: h7858_PLvCTRL_rep3

description: Biological replicate 3 of 4.


title: PA-TU-8988T_STY

description:
Hybridized to 250K_Sty
PA-TU-8988T

source_name: Pancreas cell line PA-TU-8988T


title: OUMS-23_STY

description:
Hybridized to 250K_Sty
OUMS-23

source_name: Intestine cell line OUMS-23


title: h7858_SDAvCTRL_rep3

description: Biological replicate 3 of 4.


title: h7858_PLvCTRL_rep2

description: Biological replicate 2 of 4.


title: h7858_SDAvCTRL_rep2

description: Biological replicate 2 of 4.


title: h7858_SDAvCTRL_rep4

description: Biological replicate 4 of 4.


title: OCUG-1_STY

description:
Hybridized to 250K_Sty
OCUG-1

source_name: Liver cell line OCUG-1


title: h7858_PLSDAvPL_rep2

description: Biological replicate 2 of 4.


title: h7858_PLSDAvPL_rep1

description: Biological replicate 1 of 4.


title: KMRC-20_STY

description:
Hybridized to 250K_Sty
KMRC-20

source_name: Kidney cell line KMRC-20


title: h7858_SDAvCTRL_rep1

description: Biological replicate 1 of 4.


title: h7858_PLvCTRL_rep1

description: Biological replicate 1 of 4.


title: f6854_SDAvCTRL_rep3

description: Biological replicate 3 of 4.

source_name: f6854_CTRL treated

source_name: f6854_SDA treated


title: f6854_PLSDAvPL_rep3

description: Biological replicate 3 of 4.

source_name: f6854_PL treated

source_name: f6854_PLSDA treated


title: KMRC-1_STY

description:
Hybridized to 250K_Sty
KMRC-1

source_name: Kidney cell line KMRC-1


title: TCO-1_STY

description:
Hybridized to 250K_Sty
TCO-1

source_name: Thyroid cell line TCO-1


title: h7858_PLSDAvSDA_rep1

description: Biological replicate 1 of 4.

source_name: h7858_SDA treated

source_name: h7858_PLSDA treated


title: f6854_PLvCTRL_rep3

description: Biological replicate 3 of 4.


title: h7858_PLSDAvSDA_rep2

description: Biological replicate 2 of 4.


title: IHH-4_STY

description:
Hybridized to 250K_Sty
IHH-4

source_name: Thyroid cell line IHH-4


title: f6854_PLSDAvSDA_rep3

description: Biological replicate 3 of 4.


title: HuH-7_STY

description:
Hybridized to 250K_Sty
HuH-7

source_name: Liver cell line HuH-7


title: f6854_PLSDAvPL_rep4

description: Biological replicate 4 of 4.


title: HLE_STY

description:
Hybridized to 250K_Sty
HLE

source_name: Liver cell line HLE

value: HLE


title: f6854_PLvCTRL_rep4

description: Biological replicate 4 of 4.


title: HCE7_STY

description:
Hybridized to 250K_Sty
HCE7

source_name: Esophagus cell line HCE7


title: HBE4-E6/E7_STY

description:
Hybridized to 250K_Sty
HBE4-E6/E7

source_name: Lung cell line HBE4-E6/E7


title: f6854_PLSDAvSDA_rep2

description: Biological replicate 2 of 4.


title: f6854_PLvCTRL_rep1

description: Biological replicate 1 of 4.


title: f6854_SDAvCTRL_rep4

description: Biological replicate 4 of 4.


title: f6854_PLSDAvPL_rep1

description: Biological replicate 1 of 4.


title: f6854_PLSDAvSDA_rep4

description: Biological replicate 4 of 4.


title: f6854_PLSDAvSDA_rep1

description: Biological replicate 1 of 4.


title: f6854_SDAvCTRL_rep1

description: Biological replicate 1 of 4.


title: G-402_STY

description:
Hybridized to 250K_Sty
G-402

source_name: Kidney cell line G-402


title: GRANTA-519_STY

description:
Hybridized to 250K_Sty
GRANTA-519

source_name: Blood/Lymph cell line GRANTA-519


title: wt-media-78-weeks-4

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 450 Protocol: Midi-euk2v3_450

hyb_protocol: 60rpm, 18h, 45 centigrade in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

organism: Mus musculus

source_name: media of abdominal aorta

label_protocol: T7-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY) with an IVT of 68h

growth_protocol: ApoE-/- and wild-type mice on the C57BL/6J background were from The Jackson Laboratories (Bar Harbor, Maine). Mice were housed in SPF conditions with standard chow diet and were euthanized by carbon dioxide inhalation.

extract_protocol: RNA was extracted using a phenol/chloroform extraction according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Micro-kit (Qiagen, Hilden, Germany).

treatment_protocol: The abdominal aorta was exposed, perfused in situ with ice-cold PBS/2mM EDTA and was removed inclusive of paraaortal lymph nodes, adipose and connective tissue. The isolated abdominal aorta was cut in half and embedded in Tissue Tec (Sakura Finetek, Zoeterwoude, NL) and was frozen at -80 centigrade. 200 unstained 10 micrometer cryo-sections of aorta abdominalis were microdissected with a Palm MicroBeam laser system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) and pooled in Trizol (Invitrogen, Carlsbad, CA).

tag: tissue

value: media of abdominal aorta

tag: gender

value: male

tag: age

value: 78 weeks


title: G-401_STY

description:
Hybridized to 250K_Sty
G-401

source_name: Kidney cell line G-401


title: f6854_PLSDAvPL_rep2

description: Biological replicate 2 of 4.


title: f6854_PLvCTRL_rep2

description: Biological replicate 2 of 4.

source_name: f6854_CTRL treated


title: f6854_SDAvCTRL_rep2

description: Biological replicate 2 of 4.

source_name: f6854_SDA treated


title: FU97_STY

description:
Hybridized to 250K_Sty
FU97

source_name: Stomach cell line FU97


title: CAL-85-1_STY

description:
Hybridized to 250K_Sty
CAL-85-1

source_name: Breast cell line CAL-85-1


title: wt-media-78-weeks-5


title: CAL-29_STY

description:
Hybridized to 250K_Sty
CAL-29

source_name: Bladder cell line CAL-29


title: 6 hr- SA + Silwet

city: Berkeley

first: Mary

middle: C

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene Expression Data

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1 at Functional Genomics Laboratory, UC Berkeley.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G at the Univeristy of California, Berkeley, Functional Genomics lab.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy. Background correction was performed by correcting PM (perfect match) only, to reduce noise from signal intensity. Quantile normalization was performed to make the distributions of signal intensities uniform across chips.

organism: Arabidopsis thaliana

source_name: Col-0, 6 hr post SA + Silwet

label_protocol: Target labeling was performed according to the protocols given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1 at the Functional Genomics Laboratory, UC Berkeley.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds were equally distributed in each box using a template, with 12 plants per box.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 2-1/2 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 70% RH, 12 h photoperiod with photosynthetically active radiation=180 µE m-2 s-1.

extract_protocol: Total RNA was extracted using the RNAEasy kit from Qiagen according to the manufacturer's instructions.  Optional treatment with DNAse I was performed. RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At 3.5 weeks, a subset of boxes was treated with 0.5 mM SA + 0.02% Silwet or 0.02% Silwet alone.  A fine spray of the solution was sprayed on the plant leaves in a given box.  For each sample, 0.2 g of fully expanded mature leaves of similar age were excised from 2-4 plants and immediately frozen in liquid nitrogen.  Samples were collected at 3, 6, 12, 24, and 48 hours post treatment. An untreated sample was also collected just prior to treatment. Biological replicates were collected but not processed.

tag: ecotype

value: mature leaf

tag: treatment

value: 6 hr post SA + Silwet


title: 24 hr- SA + Silwet

description: Gene Expression Data

source_name: Col-0, 24 hr post SA + Silwet

value: 24 hr post SA + Silwet


title: 12 hr- SA + Silwet

description: Gene Expression Data

source_name: Col-0, 12 hr post SA + Silwet

value: 12 hr post SA + Silwet


title: 3 hr- SA + Silwet

description: Gene Expression Data

source_name: Col-0, 3 hr post SA + Silwet

value: 3 hr post SA + Silwet


title: wt-adventitia-78-weeks-5

source_name: adventitia of abdominal aorta

value: adventitia of abdominal aorta


title: wt-adventitia-78-weeks-4


title: CAL-120_STY

description:
Hybridized to 250K_Sty
CAL-120

source_name: Breast cell line CAL-120


title: CAL-51_STY

description:
Hybridized to 250K_Sty
CAL-51

source_name: Breast cell line CAL-51


title: BFTC-905_STY

description:
Hybridized to 250K_Sty
BFTC-905

source_name: Bladder cell line BFTC-905


title: 6 hr- Silwet

description: Gene Expression Data

source_name: Col-0, 6 hr post Silwet

value: 6 hr post Silwet


title: A-375_STY

description:
Hybridized to 250K_Sty
A-375

source_name: Skin cell line A-375


title: A2058_STY

description:
Hybridized to 250K_Sty
A2058

source_name: Skin cell line A2058


title: Untreated

description: Gene Expression Data

source_name: Col-0, untreated


title: 639-V_STY

description:
Hybridized to 250K_Sty
639-V

source_name: Bladder cell line 639-V


title: 12 hr -Silwet

description: Gene Expression Data

source_name: Col-0, 12 hr post Silwet

value: 12 hr post Silwet


title: JIMT-1_STY

description:
Hybridized to 250K_Sty
JIMT-1

source_name: Breast cell line JIMT-1


title: maize-4 leaf stage-rep2

city: Macomb

first: Richard

middle: Oliver

last: Musser

state: IL

department: Biological Sciences

institute: Western Illinois University

hyb_protocol: 40 picomoles of Cy5 labeled reference cDNA and 40 pmol of Cy3 labeled seedling, 4-leaf, or 6-leaf cDNA was completely evaporated in a speedvac and suspended in 38 μL of sterile water and 2 μL of poly DNA (20 μg/μL). Pre-hybridization of the microarray slide and hybridization of probes to the slide in a sealed hybridization chamber were carried out according to an established protocol (Hedge et al. 2000) except for an additional high stringency wash at room temperature.

scan_protocol: Microarray hybridizations were scanned on a GenePix 4000B scanner (Molecular Devices, Inc., Sunnyvale, CA). Full resolution scanning was  analyzed and the scatter plot was used to check for the signal of the mRNA spikes. When necessary, the photomultiplier tube levels were adjusted, and the slide scanned again until the controls had equal signal intensity for both channels.

data_processing: Mean background subtracted, and ratio (Cy3/Cy5) representing test/reference for each microarray chip. Each of the Cy3 labeled seedling, 4-leaf shoot, or 6-leaf shoot treatments were divided by the reference sample labeled Cy5 for each chip.

organism: Zea mays

source_name: maize-4 leaf stage-rep2

label_protocol: Total RNA was converted to amino allyl modified cDNA followed by chemical coupling of Cy5 or Cy3 (GE Healthcare Biosciences, Piscataway, NJ) using the FairPlay III microarray labeling kit (Stratagene, La Jolla, CA). Five different mRNA spikes (SpotReport® Alien® mRNA spikes 1, 3, 5, 7, and 10, Stratagene) were added at varying concentrations to the labeling reaction for scanner normalization. Labeled cDNA was quantified with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and checked for uniform labeling by gel electrophoresis (Liu and Slininger 2007).

growth_protocol: The plants were grown in a controlled environment chamber set for 25°C, 50 ± 10% relative humidity and 16 hr light/8 hr dark. Lighting was provided by a combination of florescent and incandescent bulbs.

extract_protocol: Tissue was ground in a mortar and pestle using liquid nitrogen and RNA was extracted from the powdered tissue using Trizol (Invitrogen, Carlsbad, CA). Extracted RNA was treated with DNase (Qiagen, Valencia, CA) and purified with the RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Three different life stages were sampled: a) seedlings, which had grown just above the  soil line, also served as reference tissue; b) leaf shoots from plants with four leaves; and c) leaf  shoots from plants with six leaves.

tag: developmental stage

value: 4 leaf stage

source_name: maize-seedling ref

value: seedling


title: PLC/PRF/5_STY

description:
Hybridized to 250K_Sty
PLC/PRF/5

source_name: Liver cell line PLC/PRF/5


title: BICR 22_STY

description:
Hybridized to 250K_Sty
BICR 22

source_name: Head & Neck cell line BICR 22

value: BICR 22


title: maize-6 leaf stage-rep1

source_name: maize-6 leaf stage-rep1

value: 6 leaf stage


title: 647-V_STY

description:
Hybridized to 250K_Sty
647-V

source_name: Bladder cell line 647-V


title: maize-6 leaf stage-rep3

source_name: maize-6 leaf stage-rep3


title: P116_STY

description:
Hybridized to 250K_Sty
P116 T

source_name: Blood/Lymph cell line P116


title: maize-seedling-rep2


title: maize-seedling-rep3


title: MMH-D3, 54 hours post-serum shock

city: La Jolla

first: Susanna

middle: S

last: Wang

address: 9500 Gilman Dr.

institute: UCSD

hyb_protocol: Standard Affymetrix methods.

scan_protocol: GeneChip scanner 7.0G.

data_processing: Normalized by GCRMA in the R/Bioconductor environment.

source_name: differentiated MMH-D3 hepatocyte cell line, 54 hours post synchronization

label_protocol: Affymetrix Single Amplification Protocol from GeneChip Manual Rev.5.

growth_protocol: MMH-D3 hepatocytes were grown to confluency in complete growth medium according to the methods of Amicone et al. 1997 at 37C with 5% carbon dioxide. Upon confluency, they were differentiated for 14 days in complete growth medium + 2% DMSO, changed every other day.

extract_protocol: RNA was isolated using the Qiagen RNeasy MiniPrep Kit. Lysate was homogenized using Qiagen Qiashredder.

treatment_protocol: Differentiated MMH-D3 hepatocytes were synchronized by serum shock and incubated for 12 hours before beginning time course collection.

tag: cell type

value: hepatocytes

tag: time (hours) post-synchronization


title: maize-6 leaf stage-rep2

source_name: maize-6 leaf stage-rep2


title: maize-4 leaf stage-rep3

source_name: maize-4 leaf stage-rep3


title: maize-4 leaf stage-rep1

source_name: maize-4 leaf stage-rep1


title: maize-seedling-rep1


title: MMH-D3, 56 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 56 hours post synchronization


title: MMH-D3, 52 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 52 hours post synchronization


title: MMH-D3, 58 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 58 hours post synchronization


title: HT-29_STY

description:
Hybridized to 250K_Sty
HT-29

source_name: Intestine cell line HT-29


title: THP1_DMSO

city: Beijing

first: jianqin

last: li

address: No. 151 Malianwa North Road, Haidian District

country: China

institute: The Institute of Medicinal Plant Development

description: Gene expression data from THP1 treated with DMSO

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA).

data_processing: The data were analyzed with Affymetrix Expression Console Version 1.1 according to Affymetrix's guidelines. RMA was used for normalization.

label: Biotin

source_name: THP1 cells treated with DMSO

label_protocol: Biotinylated cRNA was generated using standard Affymetrix protocols.

growth_protocol: Each cell line (2.5 × 105 cells/well) was cultured in the recommended medium in 96-well plates for 24 h.

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

treatment_protocol: The U937 cells were maintained in DMEM medium plus 10% fetal bovine serum. Tan IIA (3 µg/mL) was added and the cells were cultured for 12 and 24 h, respectively.The vehicle control groups were treated with 0.1% DMSO.

value: Human acute monocytic leukemia cell line


title: MMH-D3, 44 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 44 hours post synchronization


title: MMH-D3, 42 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 42 hours post synchronization


title: U937_treated_Tan IIA_12

description: Gene expression data from U937 treated with Tan IIA for 12h

source_name: U937 cells treated with Tan IIA for 12h

value: Human leukemic monocyte lymphoma cell line


title: MMH-D3, 46 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 46 hours post synchronization


title: MOLT_DMSO

description: Gene expression data from MOLT treated with DMSO

source_name: MOLT cells treated with DMSO

value: Human acute lymphoblastic leukemia cell line


title: D1.1_STY

description:
Hybridized to 250K_Sty
D1.1

source_name: Blood/Lymph cell line D1.1


title: Jurkat, Clone E6-1_STY

description:
Hybridized to 250K_Sty
JURKAT EC-1

source_name: Blood/Lymph cell line Jurkat, Clone E6-1

value: Jurkat, Clone E6-1


title: J.γ1_STY

description:
Hybridized to 250K_Sty
J GAMMA 1

source_name: Blood/Lymph cell line J.γ1


title: MMH-D3, 50 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 50 hours post synchronization


title: MEGO1_DMSO

description: Gene expression data from MEG01 treated with DMSO

source_name: MEG01 cells treated with DMSO

value: megakaryoblastic leukemia cell line


title: U937_DMSO

description: Gene expression data from U937 treated with DMSO

source_name: U937 cells treated with DMSO


title: U937_treated_Tan IIA_24

description: Gene expression data from U937 treated with Tan IIA for 24h

source_name: U937 cells treated with Tan IIA for 24h


title: MMH-D3, 48 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 48 hours post synchronization


title: VM-CUB1_STY

description:
Hybridized to 250K_Sty
VM-CUB1

source_name: Bladder cell line VM-CUB1


title: PCI-4B_STY

description:
Hybridized to 250K_Sty
PCI-4B

source_name: Head & Neck cell line PCI-4B


title: Patient WRA Stromal Cell+CD154+IL-4

city: Leicester

first: Simon

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

country: United Kingdom

institute: University of Leicester

description: Human MicroRNA Array (A) plates (containing assays for 377 miRNA) were used (Applied Biosystems, #4398965).

scan_protocol: Reactions were carried out on a 7900 HT Real Time PCR System (Applied Biosystems)

data_processing: Results were normalized to the internal control RNU44.  Data analysis was performed using Multiple Experiment Viewer (MeV v10.2).

label: FAM

source_name: Chronic lymphocytic leukaemia B-cells

label_protocol: MicroRNA extracts were made using a miRvana miRNA isolation kit (Applied Biosystems), and reverse transcribed using MegaPlex RT Primers and a TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems).

growth_protocol: Chronic lymphocytic leukaemia cells from patients with peripheral blood white cell counts >100x109/l were isolated by Ficoll density gradient separation of heparinised venous whole blood. 3x106 cells/ml were cultured in RPMI1640 medium (Invitrogen) supplemented with FBS (Invitrogen) and penicillin/streptomycin in a 37C and 5% CO2 incubator. CLL cells were co-cultured with 80-90% confluent and 35 Gy irradiated non-transfected mouse fibroblasts (NT culture) or mouse fibroblasts transfected with human CD40 ligand (CD154) with IL-4 (R&D Systems) at 10 ng/ml in the medium. Culture was for 24 hours before harvesting.

value: Stromal Cell+CD154+IL-4


title: Patient BRP Stromal Cell+CD154+IL-4

extract_protocol: MicroRNA extracts were made using a miRvana miRNA isolation kit (Applied Biosystems), and reverse transcribed using MegaPlex RT Primers and a TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems).


title: Patient BJA Stromal Cell+CD154+IL-4


title: Patient GP Stromal Cell+CD154+IL-4


title: Patient WRA Stromal Cell

value: Stromal Cell


title: Patient GP Stromal Cell


title: Patient BRP Stromal Cell


title: MMH-D3, 36 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 36 hours post synchronization


title: Patient BJA Stromal Cell


title: MMH-D3, 30 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 30 hours post synchronization


title: HL60_DMSO

description: Gene expression data from HL60 treated with DMSO

source_name: HL60 cells treated with DMSO

value: Human promyelocytic leukemia cell line


title: MMH-D3, 34 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 34 hours post synchronization


title: MMH-D3, 40 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 40 hours post synchronization


title: Patient WRA Peripheral Blood

value: Peripheral Blood


title: Patient BRP Peripheral Blood


title: Patient BJA Peripheral Blood


title: Patient GP Peripheral Blood


title: MMH-D3, 28 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 28 hours post synchronization


title: WT STATIONARY Cy5 PA3880 DEL STATIONARY Cy3 14228561

status: Public on Nov 02 2011

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Pseudomonas aeruginosa

source_name: Total RNA extracted from cells grown aerobically

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

tag: genotype/variation

value: wild type

value: grown aerobically

value: mutant


title: MMH-D3, 38 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 38 hours post synchronization


title: MMH-D3, 22 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 22 hours post synchronization


title: MMH-D3, 26 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 26 hours post synchronization


title: WT STATIONARY Cy3 PA3880 DEL STATIONARY Cy5 14228557


title: WT ANAEROBIC Cy3 PA3880 DEL ANAEROBIC Cy5 14228556

source_name: Total RNA extracted from cells grown anaerobically

value: grown anaerobically


title: MMH-D3, 14 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 14 hours post synchronization


title: MMH-D3, 32 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 32 hours post synchronization


title: MMH-D3, 24 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 24 hours post synchronization


title: TLR3-/- B Poly(I:C) 2h PBMC

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: Labeled cRNA (750ng) were hyb O/N on Illumina HT12v4 bead arrays, washed and stained following manufacturer's protocol.

scan_protocol: Arrays were scanned on Illumina iScan following manufacturer's specifications.  GenomeScan 2.3.0.13

data_processing:
The data were generated using Illumina iScan and the GenomeScan 2.3.0.13 specifications.  Data were background subtracted and normalized using Illumina GenomeStudio version 1.5.1.3 using the average chip normalization method.
Illumina GenomeStudio V1.5.1.3 computed scaled and background subtracted signal intensity values.

label_protocol: Illumina TotalPrep96 was used following manufacturer's instructions.

growth_protocol: The fibroblast cells were cultured in DMEM medium supplemented with 10% fetal calf serum (FCS).  The PBMCs were cultured in RPMI medium complemented with 10% FCS.

extract_protocol: RNEasyMini Kit (Qiagen,Valencia, CA, USA) was used for RNA purification following manufacturer's instructions.

treatment_protocol: Cell lysis and RNA stabilization was carried out using RLT buffer (Qiagen, Valencia, CA, USA) supplemented with 1% Betamercapto ethanol

value: PBMC

tag: disease state

value: TLR3-/- Patient

value: Poly(I:C) 2h


title: WT ANAEROBIC Cy5 PA3880.DEL ANAEROBIC Cy3 14228555


title: CTL4 IL1b 2h PBMC

value: Healthy

value: IL1b 2h


title: TLR3-/- B IL1b 8h PBMC

value: IL1b 8h


title: TLR3-/- B Poly(I:C) 8h PBMC

value: Poly(I:C) 8h


title: MMH-D3, 20 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 20 hours post synchronization

value: hepatocytes


title: MMH-D3, 16 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 16 hours post synchronization


title: MMH-D3, 12 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 12 hours post synchronization


title: CTL4 Poly(I:C) 8h PBMC


title: CTL4 IL1b 8h PBMC


title: MMH-D3, 18 hours post-serum shock

source_name: differentiated MMH-D3 hepatocyte cell line, 18 hours post synchronization


title: TLR3-/- B IL1b 2h PBMC


title: CTL4 Poly(I:C) 2h PBMC


title: CTL3 IL1b 2h PBMC


title: CTL3 Poly(I:C) 2h PBMC


title: MyD88-/- IL1b 2h skin fibroblast

value: skin fibroblast

value: MyD88-/- Patient


title: CTL3 IL1b 8h PBMC


title: CTL2 IL1b 2h PBMC


title: UNC93B-/- IL1b 8h skin fibroblast

value: UNC93B-/- Patient


title: CTL2 Poly(I:C) 2h PBMC


title: CTL3 Poly(I:C) 8h PBMC


title: UNC93B-/- Poly(I:C) 8h skin fibroblast


title: UNC93B-/- IL1b 2h skin fibroblast


title: MyD88-/- Poly(I:C) 2h skin fibroblast


title: CTL2 IL1b 8h PBMC


title: TLR3-/- IL1b 2h skin fibroblast


title: TLR3-/- IL1b 8h skin fibroblast


title: TLR3-/- Poly(I:C) 8h skin fibroblast


title: CTL2 Poly(I:C) 8h PBMC


title: UNC93B-/- Poly(I:C) 2h skin fibroblast


title: TLR3-/- Poly(I:C) 2h skin fibroblast


title: TLR3+/- Poly(I:C) 8h skin fibroblast

value: TLR3+/- Patient


title: C12 IL1b 8h skin fibroblast


title: C12 IL1b 2h skin fibroblast


title: MyD88-/- Poly(I:C) 8h skin fibroblast


title: C12 Poly(I:C) 2h skin fibroblast


title: TLR3+/- Poly(I:C) 2h skin fibroblast


title: MyD88-/- IL1b 8h skin fibroblast


title: TLR3+/- IL1b 8h skin fibroblast


title: TLR3+/- IL1b 2h skin fibroblast


title: C12 Poly(I:C) 8h skin fibroblast


title: C5 Poly(I:C) 8h skin fibroblast


title: C5 IL1b 8h skin fibroblast


title: C5 Poly(I:C) 2h skin fibroblast


title: C5 IL1b 2h skin fibroblast


title: C1 Poly(I:C) 8h skin fibroblast


title: MD69-T180

city: Woburn

first: Christos

last: Hatzis

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).

source_name: breast cancer tissue, patient MD69, RNAlater, 180 min ischemic time

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Fresh tissue surgical excision specimens from breast cancer collected at time of surgery.  The tissue was then cut into pieces of 1-2 mm in a petri dish using a sterile blade, mixed, and divided into 8 equal portions.  A portion was placed into 1.5 ml RNAlater RNA stabilization reagent (Ambion, Inc., Austin TX) at baseline and 20, 40, 60, 120, and 180 minutes thereafter, or snap frozen in dry ice in a pre-chilled sample vial at baseline and 40 minutes thereafter. The time that each tissue portion was placed into contact with RNAlater solution or in the pre-chilled vial was recorded. Samples were stored at -70°C until RNA extraction.

tag: patient id

tag: stabilization

value: RNAlater

tag: passedqc

value: Y

tag: rna_integrity_number (as reported by the agillent bioanalyzer)


title: MD71-T60

source_name: breast cancer tissue, patient MD71, RNAlater, 60 min ischemic time


title: C1 IL1b 8h skin fibroblast


title: MD71-T40

source_name: breast cancer tissue, patient MD71, RNAlater, 40 min ischemic time


title: C1 IL1b 2h skin fibroblast


title: MD69-T60

source_name: breast cancer tissue, patient MD69, RNAlater, 60 min ischemic time


title: MD71-T20

source_name: breast cancer tissue, patient MD71, RNAlater, 20 min ischemic time


title: MD67-T180

source_name: breast cancer tissue, patient MD67, RNAlater, 180 min ischemic time


title: MD69-T120

source_name: breast cancer tissue, patient MD69, RNAlater, 120 min ischemic time


title: MD71-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD71, flash frozen, 40 min ischemic time

value: FlashFrozen


title: MD69-T40

source_name: breast cancer tissue, patient MD69, RNAlater, 40 min ischemic time


title: MD71-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD71, flash frozen, 0 min ischemic time


title: MD71-T0

source_name: breast cancer tissue, patient MD71, RNAlater, 0 min ischemic time


title: MD67-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD67, flash frozen, 0 min ischemic time


title: MD69-T20

source_name: breast cancer tissue, patient MD69, RNAlater, 20 min ischemic time


title: MD67-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD67, flash frozen, 40 min ischemic time


title: C1 Poly(I:C) 2h skin fibroblast


title: MD67-T120

source_name: breast cancer tissue, patient MD67, RNAlater, 120 min ischemic time


title: MD69-T0

source_name: breast cancer tissue, patient MD69, RNAlater, 0 min ischemic time


title: MD69-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD69, flash frozen, 0 min ischemic time


title: MD67-T40

source_name: breast cancer tissue, patient MD67, RNAlater, 40 min ischemic time


title: MD71-T120

source_name: breast cancer tissue, patient MD71, RNAlater, 120 min ischemic time


title: MD71-T180

source_name: breast cancer tissue, patient MD71, RNAlater, 180 min ischemic time


title: MD67-T60

source_name: breast cancer tissue, patient MD67, RNAlater, 60 min ischemic time


title: MD69-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD69, flash frozen, 40 min ischemic time


title: MD66-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD66, flash frozen, 40 min ischemic time

value: N


title: MD67-T20

source_name: breast cancer tissue, patient MD67, RNAlater, 20 min ischemic time


title: MD66-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD66, flash frozen, 0 min ischemic time


title: MD66-T20

source_name: breast cancer tissue, patient MD66, RNAlater, 20 min ischemic time


title: MD66-T180

source_name: breast cancer tissue, patient MD66, RNAlater, 180 min ischemic time


title: MD52-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD52, flash frozen, 40 min ischemic time


title: MD52-T120

source_name: breast cancer tissue, patient MD52, RNAlater, 120 min ischemic time


title: MD66-T40

source_name: breast cancer tissue, patient MD66, RNAlater, 40 min ischemic time


title: MD67-T0

source_name: breast cancer tissue, patient MD67, RNAlater, 0 min ischemic time


title: MD52-T60

source_name: breast cancer tissue, patient MD52, RNAlater, 60 min ischemic time


title: MD66-T120

source_name: breast cancer tissue, patient MD66, RNAlater, 120 min ischemic time


title: MD52-T20

source_name: breast cancer tissue, patient MD52, RNAlater, 20 min ischemic time


title: MD52-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD52, flash frozen, 0 min ischemic time


title: MD52-T40

source_name: breast cancer tissue, patient MD52, RNAlater, 40 min ischemic time


title: MD52-T0

source_name: breast cancer tissue, patient MD52, RNAlater, 0 min ischemic time


title: MD66-T0

source_name: breast cancer tissue, patient MD66, RNAlater, 0 min ischemic time


title: MD50-T180

source_name: breast cancer tissue, patient MD50, RNAlater, 180 min ischemic time


title: MD50-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD50, flash frozen, 40 min ischemic time


title: MD50-T60

source_name: breast cancer tissue, patient MD50, RNAlater, 60 min ischemic time


title: MD66-T60

source_name: breast cancer tissue, patient MD66, RNAlater, 60 min ischemic time


title: MD52-T180

source_name: breast cancer tissue, patient MD52, RNAlater, 180 min ischemic time


title: MD50-T40

source_name: breast cancer tissue, patient MD50, RNAlater, 40 min ischemic time


title: MD50-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD50, flash frozen, 0 min ischemic time


title: MD49-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD49, flash frozen, 0 min ischemic time


title: MD50-T120

source_name: breast cancer tissue, patient MD50, RNAlater, 120 min ischemic time


title: MD50-T0

source_name: breast cancer tissue, patient MD50, RNAlater, 0 min ischemic time


title: MD49-T120

source_name: breast cancer tissue, patient MD49, RNAlater, 120 min ischemic time


title: MD49-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD49, flash frozen, 40 min ischemic time


title: MD49-T40

source_name: breast cancer tissue, patient MD49, RNAlater, 40 min ischemic time


title: MD49-T60

source_name: breast cancer tissue, patient MD49, RNAlater, 60 min ischemic time


title: T-2 toxin/LPS-IFNγ Activated Macrophage, replicate 4

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

description:
TAM-rep4
Biological replicate 4 of 5. Activated monocytes-derived macrophage, treated 1 hour with 1,4ng/ml OF T-2 toxin followed by 3 hours with 10 µg/ml LPS + 1ng/ml INFγ.

hyb_protocol: Hybridizations were carried out for 16 hours at 42°C in a Ventana Discovery XT System. The slides were washed according to the recommended protocol (Corning, Product #40026) and dried by centrifugation at 1000 rpm for 1 min.

scan_protocol: Slides were scanned using a GenePix™ 4000B array scanner. Array images were processed with the GenePix™ Pro software V6.0.

data_processing:
Data were analyzed under R (www.r-project.org) using the limma package of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function with the following weight function (assigning a weight of 1 or 0 to each spot):

myfunw<-function(x) {
okflag<-x$Flags>-50
okFPix<-x[,F Pixels]>=50
okred1<-((x[,F635 Median]-x[,B635 Median])/x[,B635 SD])>=2
okred2<-x[F635 Median]/x[,B635 Median]>=2
okgreen1<-((x[,F532 Median]-x[,B532 Median])/x[,B532 SD])>=2
okgreen2<-x[F532 Median]/x[,B532 Median]>=2
oksatred1<-x[,F635 Median]<65500
oksatred2<-x[,F635 % Sat.]<=20
oksatgreen1<- x[,F532 Median]<65500
oksatgreen2<- x[,F532 % Sat.]<=20
okR2<-x[,Rgn R2 (635/532)]>0.5
okCirc<-x$Circularity==100
as.numeric(okflag&okFPix&okred1&okred2&okgreen1&okgreen2
&oksatred1&oksatgreen1&oksatred2&oksatgreen2&okR2&okCirc) }.

Only the spots that had a weight of 1 on at least 80% (12 out of 15) of the microarrays were further analyzed (11124 spots selected). Local background was subtracted on Cy3 and Cy5 data. A lowess normalization was applied to the log(Cy5/Cy3) data using the normalizeWithinArrays function. A quantile normalization was applied to both channels but based on the assumption that only the red channel (Cy5, common reference) had the same emprirical distribution accross arrays. The normalizeBetweenArrays function was used with the argument method=Rquantile to perform this step. Data were finally expressed as log(Green channel/Red channel) = log(Cy3/Cy5) = log (test/common reference).

organism: Sus scrofa

source_name: Total RNA from T-2 toxin-treated and LPS-IFNγ-activated monocyte-derived macrophages

label_protocol: Each pig/condition RNA was labeled with Cy3, and the common reference, created by mixing all samples, was labeled with Cy5. Total RNA (5µg) were reverse-transcribed and directly labeled using the ChipShot™ Direct Labeling System (Promega, Charbonniere, France). The CyDye-labelled cDNAs were purified using the ChipShot™ Membrane Clean-Up System (Promega, Charbonniere, France).

growth_protocol: Monocytes were isolated from jugular venous blood of young female pigs collected aseptically and were isolated by density gradient centrifugation and submitted to a lysis solution to eliminate red cells. For the generation of monocyte-derived macrophages, the cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum (FBS, Eurobio, Les Ulis, France) completed with 1% L-Glutamin (Invitrogen, Cergy Pontoise, France), 1% non-essential amino acids (Sigma,France), 100 IU/ml penicillin, 100 µg/ml streptomycin (Invitrogen, Cergy Pontoise, France) and CSF-1 growth factor. The culture was conduced at 39ºC with 5% CO2 during 4 days.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: The macrophage samples were incubated in culture medium (control batch), in culture medium supplemented with LPS (10 μg/ml) and IFNγ (1ng/mL), or in culture medium supplemented with T-2 toxin (1.4ng/ml), LPS (10 μg/ml) and IFNγ (1ng/mL), both at 37°C.

tag: genotype

value: wild type

value: female

value: 9 to 11 weeks

value: blood

value: monocyte-derived macrophages

value: 1.4ng/ml T-2 toxin + 10 µg/ml LPS + 1ng/ml INFγ in culture medium

tag: treatment duration

value: 1 hour with T-2 toxin followed by 3 hours under LPS-IFNγ treatment

tag: breed

value: cross breed without defined genomic background

source_name: Total RNA from pooled macrophages including control, LPS-IFNγ activated and T-2 toxin/LPS-IFNγ activated

tag: sample type

value: reference


title: MD49-T20

source_name: breast cancer tissue, patient MD49, RNAlater, 20 min ischemic time


title: T-2 toxin/LPS-IFNγ Activated Macrophage, replicate 2

description:
TAM-rep2
Biological replicate 2 of 5. Activated monocytes-derived macrophage, treated 1 hour with 1,4ng/ml OF T-2 toxin followed by 3 hours with 10 µg/ml LPS + 1ng/ml INFγ.

tag: gender

tag: tissue


title: T-2 toxin/LPS-IFNγ Activated Macrophage, replicate 3

description:
TAM-rep3
Biological replicate 3 of 5. Activated monocytes-derived macrophage, treated 1 hour with 1,4ng/ml OF T-2 toxin followed by 3 hours with 10 µg/ml LPS + 1ng/ml INFγ.

tag: age


title: T-2 toxin/LPS-IFNγ Activated Macrophage, replicate 1

description:
TAM-rep1
Biological replicate 1 of 5. Activated monocytes-derived macrophage, treated 1 hour with 1,4ng/ml OF T-2 toxin followed by 3 hours with 10 µg/ml LPS + 1ng/ml INFγ.

tag: treatment


title: MD49-T0

source_name: breast cancer tissue, patient MD49, RNAlater, 0 min ischemic time


title: MD40-T60

source_name: breast cancer tissue, patient MD40, RNAlater, 60 min ischemic time


title: LPS-IFNγ Activated Macrophage, replicate 4

description:
AM-rep4
Biological replicate 4 of 5. Activated monocytes-derived macrophage, treated 3 hours with10 µg/ml LPS + 1ng/ml INFγ.

source_name: Total RNA from LPS-IFNγ-activated monocyte-derived macrophages

value: 10 µg/ml LPS + 1ng/ml INFγ in culture medium

value: 1 hour culture medium followed by 3 hours under LPS-IFNγ treatment


title: MD40-T40

source_name: breast cancer tissue, patient MD40, RNAlater, 40 min ischemic time


title: T-2 toxin/LPS-IFNγ Activated Macrophage, replicate 5

description:
TAM-rep5
Biological replicate 5 of 5. Activated monocytes-derived macrophage, treated 1 hour with 1,4ng/ml OF T-2 toxin followed by 3 hours with 10 µg/ml LPS + 1ng/ml INFγ.


title: 342749_10mMCy3-0.05mMCy5

city: Groningen

first: Tomas

last: Kloosterman

address: Nijenborgh 7

department: Natural Sciences

country: Netherlands

institute: University of Groningen

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman TG et al., 2006b

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of 0.05 mM Arg wild-type strain over 10mM Arg wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Net intensity (tr.mean) {A}

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

growth_protocol: Cells were grown to MID-log phase in CDM with either 0.05 mM arginine or 10 mM arginine.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from Four replicate cultures.

value: Wild type

tag: condition

value: 10 mM arginine

source_name: Net intensity (tr.mean) {B}

value: 0.05 mM arginine


title: MD40-T180

source_name: breast cancer tissue, patient MD40, RNAlater, 180 min ischemic time

value: RNAlater

value: Y


title: Control Macrophage, replicate 5

description:
CM-rep5
Biological replicate 5 of 5. Control monocytes-derived macrophage, untreated.

source_name: Total RNA from monocyte-derived macrophages

tag: cell type

value: culture medium

value: 4 hours


title: LPS-IFNγ Activated Macrophage, replicate 2

description:
AM-rep2
Biological replicate 2 of 5. Activated monocytes-derived macrophage, treated 3 hours with10 µg/ml LPS + 1ng/ml INFγ.

value: wild type

value: female


title: LPS-IFNγ Activated Macrophage, replicate 3

description:
AM-rep3
Biological replicate 3 of 5. Activated monocytes-derived macrophage, treated 3 hours with10 µg/ml LPS + 1ng/ml INFγ.

value: 9 to 11 weeks

value: blood


title: MD64-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD64, flash frozen, 40 min ischemic time

value: FlashFrozen


title: LPS-IFNγ Activated Macrophage, replicate 1

description:
AM-rep1
Biological replicate 1 of 5. Activated monocytes-derived macrophage, treated 3 hours with10 µg/ml LPS + 1ng/ml INFγ.

value: monocyte-derived macrophages


title: MD40-T20

source_name: breast cancer tissue, patient MD40, RNAlater, 20 min ischemic time


title: MD40-T120

source_name: breast cancer tissue, patient MD40, RNAlater, 120 min ischemic time


title: MD40-T0

source_name: breast cancer tissue, patient MD40, RNAlater, 0 min ischemic time


title: LPS-IFNγ Activated Macrophage, replicate 5

description:
AM-rep5
Biological replicate 5 of 5. Activated monocytes-derived macrophage, treated 3 hours with10 µg/ml LPS + 1ng/ml INFγ.

value: cross breed without defined genomic background


title: MD49-T180

source_name: breast cancer tissue, patient MD49, RNAlater, 180 min ischemic time


title: MD50-T20

source_name: breast cancer tissue, patient MD50, RNAlater, 20 min ischemic time


title: 342748_10mMCy3-0.05mMCy5

description: Sample 1


title: 343735_wtCy3-argR1-ahrCCy5

description: Sample 2

data_processing: Dual-channel array images were analyzed with Genepix Pro software. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of argR1-ahrC mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

source_name: F532 Mean

growth_protocol: Cells were grown to MID-log phase in CDM with 10 mM arginine.

source_name: F635 Mean

value: argR1-ahrC mutant


title: 185508_wtCy3-argR1Cy5

description: Sample 2

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of argR1mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

value: argR1 mutant


title: 343734_wtCy5-argR1-ahrCCy3

description: Sample 1


title: 343733_wtCy5-ahrCCy3

description: Sample 3

data_processing: Dual-channel array images were analyzed with Genepix Pro software. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of ahrC mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

value: ahrC mutant


title: MD64-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD64, flash frozen, 0 min ischemic time


title: 185512_wtCy5-argR1Cy3

description: Sample 3

value: Wild type


title: 343731_wtCy3-ahrCCy5

description: Sample 1

value: 10 mM arginine


title: 343732_wtCy3-ahrCCy5

description: Sample 2


title: Control Macrophage, replicate 4

description:
CM-rep4
Biological replicate 4 of 5. Control monocytes-derived macrophage, untreated.

source_name: Total RNA from pooled macrophages including control, LPS-IFNγ activated and T-2 toxin/LPS-IFNγ activated

value: reference


title: CD11c uninfected

city: Fort Worth

first: Jerry

last: Simecka

address: 3500 Camp Bowie Blvd

department: Molecular Biology & Immunology

institute: UNT Health Science Center

description: Oligonucleotide probes are spotted on a membrane with 128 spots. Positive and negative probes are included. SuperArray GEArray cat. Num. OM-011 used.

hyb_protocol: per manufacturers' standard protocol (SuperArray)

data_processing:
online analysis and data processing, at SuperArray's website
signal intensities were normalized with respect to Gapdh and Ppia genes. AP threshold was set at 1.5 and comparison between groups was a ratio between averaged normalized spot intensities of infected and uninfected mice

source_name: CD11c uninfected

label_protocol: True-labeling AMP (SuperArray)

extract_protocol: Total RNA extracted from pulmonary CD11c+ or F4/80+ cells, collected from broth inoculated (control) mice or M. pulmonis, using Trizol (Invitrogen)

treatment_protocol: Wild-type (C3H/HeN) mice were either infected with Mycoplasma pulmonis or inoculated with Mycoplasma broth (uninfected)

value: pooled RNA (15 mice from 2 experiments)

value: Age:6-12 weeks

tag: Sex

value: Female

tag: infection

value: pulmonary CDC11c+ cells

tag: genetic background


title: CD11c infected

scan_protocol: per manufacturers' standard protocol (SuperArray)

source_name: CD11c infected

value: pooled RNA (5 mice per expt)

value: Mycoplasma pulmonis


title: 185504_wtCy3-argR1Cy5

description: Sample 1

tag: genotype/variation


title: Control Macrophage, replicate 3

description:
CM-rep3
Biological replicate 3 of 5. Control monocytes-derived macrophage, untreated.

value: wild type

value: female

value: 9 to 11 weeks

value: culture medium

value: 4 hours


title: F4/80 uninfected

source_name: F480 uninfected

value: pulmonary F4/80+ cells


title: F4/80 infected

source_name: F480 infected


title: Control Macrophage, replicate 2

description:
CM-rep2
Biological replicate 2 of 5. Control monocytes-derived macrophage, untreated.

value: blood

value: monocyte-derived macrophages

value: cross breed without defined genomic background


title: S06 AA 21-Af3

city: Jefferson

first: Fanxue

last: Meng

state: AR

address: 3900 NCTR Road, HFT-130

institute: National Center for Toxicological Research

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Raw intensities experienced the adjustments of data-filtering, log 2 transformation, gene centering and normalization with a cyclic LOWESS (locally weighted regression). MiRNAs with all 6 samples intensities larger than the intensity threshold of 32 were considered detectable.

organism: Rattus norvegicus

source_name: treated with aristolochic acid (AA)

label_protocol: To perform the miRNA array experiment, total RNA (2 to 5 µg) was first size fractionated using a YM-100 Microcon centrifugal filter (Millipore). The small RNAs (< 300 nt) were then 3’-extended with a poly(A) tail using poly(A) polymerase.  Thereafter, an oligonucleotide tags was ligated to the poly(A) tail for later staining with fluorescent dye Cy3.

growth_protocol: All animal procedures followed the recommendations of the NCTR Institutional Animal Care and Use Committee for the handling, maintenance, treatment, and sacrifice of the rats.

extract_protocol: RNAs were isolated from about 40-50 mg rat kidney tissue suspended in RNA-Later ICE (Ambion Inc., Austin, TX) using mirVanaTM miRNA isolation kit (Ambion). This kit combines the advantages of acid-phenol:chloroform extraction and glass solid-phase extraction and can yield high quality of microRNA-retaining total RNAs. RNA concentrations were determined on NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, Delaware) and the qualities were checked on on an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) using an RNA6000 Nano LabChip (Agilent).

treatment_protocol: Male, 6-week-old Big Blue rats were treated with Aristolochic Acid as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 12 weeks. The animals were sacrificed 1 day after the last treatment. The kidneys were isolated, flash frozen in liquid nitrogen, and stored at - 80°C.

tag: strain

value: Fisher 344

value: Big Blue Transgenic

value: male

value: 6 weeks

value: kidney


title: S05 AA 20-Af3


title: Control Macrophage, replicate 1

description:
CM-rep1
Biological replicate 1 of 5. Control monocytes-derived macrophage, untreated.

value: reference


title: S04 AA 19-Af3


title: MD64-T60

source_name: breast cancer tissue, patient MD64, RNAlater, 60 min ischemic time

tag: patient id

tag: stabilization

value: RNAlater

tag: passedqc

value: Y


title: MD64-T20

source_name: breast cancer tissue, patient MD64, RNAlater, 20 min ischemic time

tag: rna_integrity_number (as reported by the agillent bioanalyzer)


title: S03 Control 15-Af3

source_name: untreated control


title: MD64-T180

source_name: breast cancer tissue, patient MD64, RNAlater, 180 min ischemic time


title: MD64-T120

source_name: breast cancer tissue, patient MD64, RNAlater, 120 min ischemic time


title: 39E 10mM xylose vs. 39E 50mM xylose

city: Norman

first: Christopher

middle: L

last: Hemme

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

description:
total RNA/ genomic DNA
Cy5 dUTP for RNA, Cy3 dUTP for genomic DNA
Each oligonucleotide probe had two replicates on a single slide. Additionally, six different concentrations (11, 22, 45, 90, 180 and 360 ng/ul) of genomic DNA were spotted (eight duplicates for each of the six concentrations on a single slide) as positive controls.

hyb_protocol: The Cy3 labeled genomic DNA was used as a common reference to co-hybridize the Cy5 labeled RNA samples on each slide. Hybridization was carried out using a TECAN HS4800 Pro Hybridization Station (Tecan, NC) by following the manufacturer’s instructions. This system automatically performs hybridization, washing and drying of arrays.

scan_protocol: slides were scanned using a ProScanArrayTM microarray analysis system (Perkin Elmer®, MA).

data_processing: To determine signal intensity of fluorescence for each spot, the 16-bit TIFF scanned images were analyzed by the software ImaGene 6.1 (Biodiscovery Inc., EI Segundo, CA). Microarray data were analyzed as previously described by Mukhopadhyay et al. (Mukhopadhyay et al., 2006; He et al., 2009b). Briefly, it includes the following major steps. (i) Empty spots with SNR <2.0 (SNR, signal-to-noise ratio), and bad spots were flagged and removed before normalization. (ii) The net signal of each spot was calculated by subtracting the background signal and adding a pseudo signal of 100 to obtain a positive value. For resulting net signals of <50, a value of 50 was used. (iii) The total signal intensity of all microarray (slides) in this experiment was normalized with the genomic DNA signal (Cy3 signal), and a normalization factor was calculated for each slide. (iv) Both Cy3 and Cy5 signal intensity of each spot were adjusted by multiplying the normalization factor calculated above. Therefore, the resultant Cy5 signal of each probe presents the normalized signal intensity for each gene. (v) A ratio R of Cy5/Cy3 signal was calculated for each spot on each array. (vi) To compare genomic analysis, the control and treatment conditions were defined respectively so as to identify the control (Rc) and treatment (Rt) ratios. And then log2 R value was calculated for each gene. (vii) Finally, to access the significant change between treatment and control, a Z score was calculated via following equation: , where 0.25 is a pseudovariance term. Typically, a cutoff |Log2R|?1.0 and |Z|? 2.0 was used to determine changes with significance.

label: Cy5, Cy3

organism: Thermoanaerobacter pseudethanolicus ATCC 33223

source_name: 39E samples grown on 10mM

label_protocol: Ten microgram of total RNA was reverse-transcribed using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 1 mM Cy5 dUTP (Invitrogen) according to previous  description (He et al., 2006). The purified 500 ng genomic DNA was fluorescently labeled by random priming using Klenow fragment of DNA polymerase  in the presence of 1mM Cy3 dUTP as described elsewhere (He et al., 2005).

growth_protocol: Thermoanaerobacter pseudethanolicus 39E was grown anaerobically in defined medium supplemented with 10mM or 50 mM xylose as the sole carbon source.

extract_protocol: Total cellular RNA was isolated using Trizol Reagent (Invitrogen). RNA samples were treated with Rnase-free DNaseI and purifed using the total RNA Isolation Kit (NucleoSpin RNAII, Macherey-Nagel Inc. Genomic DNA was isolated and purified from Thermoanaerobacter pseudethanolicus 39E by CTAB (hexadecyltrimethylammonium bromide)-NaCl method (Zhou et al., 1995).

value: 10mM xylose

tag: growth phase

value: mid-log

source_name: 39E samples grown on 50mM xylose

value: 50 mM xylose


title: malignant transformed oral leukoplakia Ca5

city: Shanghai

first: Weiwen

last: Jiang

address: Room305,building1,No.639 Zhizaoju Road

institute: Shanghai Ninth People’s Hospital

hyb_protocol: The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: The ratio of red signal to green signal was calculated after background subtraction and normalization using the global Lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System)

source_name: malignant transformed oral leukoplakia tissues

label_protocol: After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.11.0).

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions

value: malignant transformed oral leukoplakia

source_name: equal mixture of all samples

value: mixture of normal mucosa, oral leukoplakia, malignant transformed oral leukoplakia


title: 39E 50mM xylose vs. 39E 200mM xylose

source_name: 39E samples grown on 50mM

growth_protocol: Thermoanaerobacter pseudethanolicus 39E was grown anaerobically in defined medium supplemented with 50mM or 200mM xylose as the sole carbon source.

value: 50mM xylose

source_name: 39E samples grown on 200mM xylose

value: 200 mM xylose


title: malignant transformed oral leukoplakia Ca4


title: S02 Control 14-Af3


title: malignant transformed oral leukoplakia Ca3


title: S01 Control 13-Af3


title: malignant transformed oral leukoplakia Ca2


title: malignant transformed oral leukoplakia Ca1


title: oral leukoplakia OLK19

source_name: oral leukoplakia tissues

value: oral leukoplakia


title: oral leukoplakia OLK20


title: oral leukoplakia OLK18


title: MD64-T40

source_name: breast cancer tissue, patient MD64, RNAlater, 40 min ischemic time


title: MD57-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD57, flash frozen, 0 min ischemic time

value: FlashFrozen


title: MD64-T0

source_name: breast cancer tissue, patient MD64, RNAlater, 0 min ischemic time


title: MD57-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD57, flash frozen, 40 min ischemic time


title: 39E 10mM xylose vs. 39E 200mM xylose

growth_protocol: Thermoanaerobacter pseudethanolicus 39E was grown anaerobically in defined medium supplemented with 10mM or 200mM xylose as the sole carbon source.


title: MD57-T60

source_name: breast cancer tissue, patient MD57, RNAlater, 60 min ischemic time


title: oral leukoplakia OLK16


title: MD57-T120

source_name: breast cancer tissue, patient MD57, RNAlater, 120 min ischemic time


title: oral leukoplakia OLK15


title: oral leukoplakia OLK12


title: MD57-T40

source_name: breast cancer tissue, patient MD57, RNAlater, 40 min ischemic time


title: oral leukoplakia OLK14


title: oral leukoplakia OLK13


title: oral leukoplakia OLK17


title: MD57-T20

source_name: breast cancer tissue, patient MD57, RNAlater, 20 min ischemic time


title: MD57-T180

source_name: breast cancer tissue, patient MD57, RNAlater, 180 min ischemic time


title: oral leukoplakia OLK9


title: oral leukoplakia OLK11


title: MD57-T0

source_name: breast cancer tissue, patient MD57, RNAlater, 0 min ischemic time


title: E2_acetate_b

city: Stanford

first: Jared

last: Wenger

address: 300 Pasteur Drive

institute: Stanford University Medical School

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88661.gif

hyb_protocol: not provided

scan_protocol: Agilent Feature Extraction

data_processing: Agilent Feature Extraction software

organism: Saccharomyces cerevisiae

source_name: pooled reference

label_protocol: LRILAK labeling

extract_protocol: not provided

tag: reference

value: pool of 6 parental strains

growth_protocol: Wenger 2010 chemostat; Strains for chemostat cell cultures were grown 1% YPD cultures and 1mL aliquots were frozen in 15% glycerol at -80 oC. The entire contents of a single1mL frozen aliquot of evolved (E1-E5) or ancestral (CP1AB or simply P) isolates were used to inoculate an individual chemostat (ATR SixFors fermentation apparatus, ATR Biotechnologies) with working volume set to 400mL of minimal (SC) media defined by [1]. Batch cultures were then grown for 24 hours to achieve saturation. After saturation was achieved, chemostat pumps were turned on to the desired dilution rate and 2-3 vessel volumes of turnover were allowed so cultures could reach steady state. The dilution rate was set to 0.17hr-1 for aerobic (0.08% glucose) and anaerobic glucose limitation (0.08% glucose + 420mg mL-1 Tween 80 + 10mg L-1 ergosterol) and 0.05hr-1 for aerobic acetate limitation (10.9g/L sodium acetate). Aerobic conditions were achieved by sparging with 25 L h-1 of sterile air and anaerobic conditions by sparging cultures with 25 L hr-1 sterile-filtered, humidified N2 (g).

extract_protocol: To isolate total RNA, 100mL of sample was quickly filtered through 0.45 mm Nylon filters (Whatman) and flash frozen in liquid nitrogen. RNA for gene-expression measurements was isolated using the hot acid-phenol method described by [2].1. Adams J, Hansche PE (1974) Population studies in microorganisms. I.Evolution of diploidy in Saccharomyces cerevisiae. Genetics 76: 327-338.2. Ferea TL, Botstein D, Brown PO, Rosenzweig RF (1999) Systematicchanges in gene expression patterns following adaptive evolution in yeast.Proceedings of the National Academy of Sciences 96: 9721-9726

tag: strain name

tag: media

value: aerobic


title: E3_anaerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79789.gif

source_name: pooled reference (all 6 parental)

value: anaerobic


title: oral leukoplakia OLK7

tag: tissue


title: oral leukoplakia OLK6


title: E3_aerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79808.gif


title: E4_anaerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79799.gif


title: oral leukoplakia OLK10


title: oral leukoplakia OLK2


title: oral leukoplakia OLK3


title: oral leukoplakia OLK4


title: oral leukoplakia OLK5


title: MD53-T180

source_name: breast cancer tissue, patient MD53, RNAlater, 180 min ischemic time


title: MD53-T120

source_name: breast cancer tissue, patient MD53, RNAlater, 120 min ischemic time

value: N


title: oral leukoplakia OLK8

source_name: equal mixture of all samples


title: E3_acetate_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88656.gif


title: E4_acetate_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88657.gif


title: oral leukoplakia OLK1


title: MD53-T40

source_name: breast cancer tissue, patient MD53, RNAlater, 40 min ischemic time


title: MD53-T60

source_name: breast cancer tissue, patient MD53, RNAlater, 60 min ischemic time


title: MD53-T0-F (no RNAlater)

source_name: breast cancer tissue, patient MD53, flash frozen, 0 min ischemic time


title: MD53-T40-F (no RNAlater)

source_name: breast cancer tissue, patient MD53, flash frozen, 40 min ischemic time


title: normal mucosa N4

source_name: normal mucousal tissues

value: normal mucosa


title: normal mucosa N5


title: E3_acetate_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88662.gif


title: P_anaerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79811.gif


title: E2_aerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79807.gif


title: normal mucosa N3


title: normal mucosa N1


title: E2_acetate_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88655.gif


title: E4_anaerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79790.gif


title: normal mucosa N2


title: MD53-T0

source_name: breast cancer tissue, patient MD53, RNAlater, 0 min ischemic time


title: MD53-T20

source_name: breast cancer tissue, patient MD53, RNAlater, 20 min ischemic time


title: WFS1 KO USHT_08_316_ko

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description: Gene expression data from hypothalamus of wfs1 deficient mice

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to standard protocols

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with RMA and further analyzed using Bioconductir software based on R language

source_name: hypothalamus

label_protocol: 100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay

growth_protocol: Frozen in liquid nitrogen

treatment_protocol: Hypothalami were dissected under dissection microscope

tag: genotype

value: WFS1 KO

value: hypothalamus


title: P_aerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79813.gif


title: WFS1 WT USHT_05_318_ko

value: WFS1 WT


title: WFS1 WT USHT_09_332_wt


title: WFS1 WT USHT_07_314_ko


title: WFS1 KO USHT_04_319_ko


title: WFS1 WT USHT_03_335_wt


title: WFS1 KO USHT_06_333_wt


title: P_anaerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79836.gif


title: P_acetate_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88653.gif


title: WFS1 KO USHT_02_323_ko


title: E1_aerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79824.gif


title: E1_acetate_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88654.gif


title: E1_anaerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79796.gif


title: WFS1 WT USHT_20_331_wt


title: WFS1 WT USHT_19_320_ko


title: WFS1 KO USHT_01_337_wt


title: WFS1 KO USHT_18_330_wt


title: WFS1 WT USHT_17_315_ko


title: E5_acetate_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88664.gif


title: E3_aerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79828.gif


title: E4_aerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79830.gif


title: E5_anaerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79791.gif


title: WFS1 WT USHT_14_317_ko


title: E1_anaerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79787.gif


title: WFS1 KO USHT_15_329_wt


title: WFS1 KO USHT_13_312_ko


title: E5_anaerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79800.gif


title: WFS1 WT USHT_11_326_wt


title: E3_anaerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79798.gif


title: 0DPA inner ovule cells vs. 7DPA cotton fiber cells

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Gossypium hirsutum L. cv. TM-1

hyb_protocol: One Cy3-dCTP reaction is mixed with one Cy5-dCTP reaction to make one probe. Therefore, two “identical” probes each containing an equal amount of Cy3- and Cy5-labeled cDNAs were hybridized with two slides, which constituted one dye-swap experiment. The dye-swap was repeated once as a technical replication. The large dye-swap (four slides) was repeated using another biological sample (e.g., RNAs isolated from different pools of 3-DPA ovules). Therefore, each experiment consists of four technical replications and two biological replications in a total of eight slides (Chen et al. 2004). Hybridization was performed overnight (∼14 h) at 65°C. After hybridization, the slides were washed twice for 4 min each in 2X SSC, 0.2% SDS, again twice for 2 min each in 0.2XSSC, and twice for 2 min each in 0.05X SSC.

scan_protocol: The slides were scanned using GenePix 4000B (Axon, Foster City, CA), and the images were captured by GenePix Pro 4.1 software.

data_processing: After the data were processed using log2 ratios of green and red hybridization signals, a robust and locally weighted linear regression (lowess) (Cleveland 1979) was used to remove non-linear components (e.g. dye and pin effects) (Quackenbush 2002). For the duplicate spots in each feature, we used an average value for data analysis. No additional steps for data normalization and background subtraction are needed for the AVONA model (Lee et al. 2004). The data were then subjected to the analysis of variance (ANOVA) test in a linear model to estimate the significant changes in gene expression caused by the two treatments (genotypes) (Black and Doerge 2002; Lee et al. 2004). A standard t-test statistic was used for this comparison based on the normality assumption for the residuals. The standard false discovery rate (FDR) (Hochberg and Tamhane 1987) was applied to control multiple testing errors using a significance level α= 0.05.

organism: Gossypium hirsutum

source_name: 0DPA inner ovule cells

label_protocol: RNA was amplified with a Amino Allyl MessageAmp™ aRNA amplification Kit (Ambion, Austin, TX). Two rounds of amplication were performed to get sufficient quantities of aRNA. Amplified RNA was coupled with Cy5 dyes (Amersham Biosciences, Piscataway, NJ) and purified using Qiagen RNeasy mini column (Qiagen, Germantown, MD). About 1 µg of fragmented Cy5-labeled aRNA probes was used for hybridization.

extract_protocol: Captured cells were homogenized in 500 µl of RNA extraction buffer (200 mM sodium borate decahydrate (pH 9), 30 mM ethylene glycol bis-N,N’-tetraacetic acid (EGTA), 1% (w/v) sodium dodecyl sulfate (SDS), 1% (w/v) sodium deoxycholate, 2% (w/v) polyvinylpyrrolidone (PVP), 0.5% (v/v) Nonidet-40 (NP-40), 10 mM dithiothreitol (DTT)). After 250 µl of ethanol was added to the captured cells, the sample was loaded onto a Qiagen RNeasy mini column (Qiagen, Valencia, CA) and washed as per the manufacturer’s recommendation.

tag: cultivar

value: inner ovule cells

tag: developmental stage

value: 0 DPA

tag: capture technique

value: laser capture microdissection (LCM)

source_name: 7DPA cotton fiber cells

label_protocol: RNA was amplified with a Amino Allyl MessageAmp™ aRNA amplification Kit (Ambion, Austin, TX). Two rounds of amplication were performed to get sufficient quantities of aRNA. Amplified RNA was coupled with Cy3 dyes (Amersham Biosciences, Piscataway, NJ) and purified using Qiagen RNeasy mini column (Qiagen, Germantown, MD). About 1 µg of fragmented Cy3-labeled aRNA probes was used for hybridization.

value: cotton fiber cells

value: 7 DPA


title: E4_aerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79809.gif


title: 0DPA ovule epidermal cells vs. 2DPA ovule epidermal cells

description: Gossypium hirsutum L. cv. TM-1

source_name: 0DPA ovule epidermal cells

value: ovule epidermal cells

source_name: 2DPA ovule epidermal cells

value: 2 DPA


title: 0DPA ovule epidermal cells vs. -2DPA ovule epidermal cells

description: Gossypium hirsutum L. cv. TM-1

source_name: -2DPA ovule epidermal cells

value: -2 DPA


title: 0DPA inner ovule cells vs. 2DPA inner ovule cells

description: Gossypium hirsutum L. cv. TM-1

source_name: 2DPA inner ovule cells


title: 0DPA inner ovule cells vs. -2DPA inner ovule cells

description: Gossypium hirsutum L. cv. TM-1

source_name: -2DPA inner ovule cells


title: E4_acetate_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88663.gif

source_name: pooled reference


title: 0DPA ovule epidermal cells vs. 7DPA cotton fiber cells

description: Gossypium hirsutum L. cv. TM-1


title: E2_aerobic_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79826.gif

source_name: pooled reference (all 6 parental)


title: P_acetate_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88659.gif


title: E5_acetate_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88658.gif


title: E2_anaerobic_a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-05/79788.gif


title: 7DPA inner ovule cells vs. 7DPA cotton fiber cells

description: Gossypium hirsutum L. cv. TM-1

source_name: 7DPA inner ovule cells


title: 2DPA inner ovule cells vs. 2DPA ovule epidermal cells

description: Gossypium hirsutum L. cv. TM-1


title: E1_acetate_b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88660.gif


title: C1 EB 14 days

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

description: dual color Nimblegen data

hyb_protocol: According to the Nimblegen hybridization user guide

scan_protocol: Slides were scanned using the Agilent 2505B with upgrade to C  High-Resolution Microarray  Scanner and Agilent Scan Control software (Version A.8.4.1) and intensities were extracted using Nimblegen NimbleScan software (Version 2.6.0.0)

data_processing: Calculations performed in R using bioconductor packages: 1) poor quality probes were flagged and removed, 2) the common reference was used for within slide loess normalization, 3) RMA (background subtraction, between slide quantile normalization and median polish). SIGNAL_MEAN#1 contains Cy3 data and SIGNAL_MEAN#2 contain Cy5 data in the raw data files.

source_name: embryoid bodies derived from B at 14 days of suspension culture

label_protocol: RNA T7 amplification procedure

growth_protocol: Human testis derived ES-like cells were maintained in sulture conditions A (bFGF/Matrigel) (Mizrak S.C.et al.Hum Reprod. 2010 Jan;25(1):158-67),  B (bFGF/Mitomycine C inactivated MEFs feeder) and C (bFGF/CHIR99021/Matrigel)

extract_protocol: Total RNA extraction was performed using MagNa pure LC RNA isolation kit and MagNA Pure LC Instrument (Roche, The Netherlands).

treatment_protocol: Maintanance in medium A, B or C at 37C 5% CO2 and EB formation in ultra low attachment dishes in basic medium without bFGF

tag: cell type

value: embryoid bodies

tag: pluripotency

value: under study

tag: days of suspension culture

source_name: pooled from all samples, plus additional human ES cell lines, human dermal fibroblasts and testis derived ES-like cells from preburtal individuals and embryoid bodies derived from them at 4, 7, 10, 14 and 18 days of suspension culture.

tag: sample type

value: reference


title: 0DPA inner ovule cells vs. 0DPA ovule epidermal cells

description: Gossypium hirsutum L. cv. TM-1


title: C1 EB 7 days

description: dual color Nimblegen data

source_name: embryoid bodies derived from B at 7 days of suspension culture